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Not a living fossil: How the Coelacanth recently evolved dozens of new genes

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Not a living fossil: How the Coelacanth recently evolved dozens of new genes

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Coelacanths have an undeserved reputation as living fossils and the study adds to the growing body of research showing widespread evolution at the genome level. Credit: Alberto Fernandez Fernandez via Wikimedia Commons

The capture of the first living Coelacanth, a mighty ocean predator, off the coast of South Africa caused quite a stir in 1938, 65 million years after its supposed extinction. It became known as a "living fossil" owing to its anatomy looking almost identical to the fossil record. But while the Coelacanth's body may have changed little, its genome tells another story.

Toronto scientists have now revealed that the African Coelacanth, Latimeria chalumnae, gained 62 new genes through encounters with other species 10 million years ago. Their findings are reported in the journal Molecular Biology and Evolution.

What's even more fascinating is how these genes came about. Their sequences suggest they arose from transposons, also known as " selfish genes". These are parasitic DNA elements whose sole purpose is to make more copies of themselves, which they sometimes achieve by moving between species.

The findings show the dramatic effect traveling transposon DNA can have on the creation of genes and provide a glimpse into some of the forces that shaped the genome of one of the most ancient and mysterious organisms.

"Our findings provide a rather striking example of this phenomenon of transposons contributing to the host genome," says Tim Hughes, senior study author and a professor of molecular genetics in the Donnelly Centre for Cellular and Biomolecular Research at the University of Toronto.

"We don't know what these 62 genes are doing, but many of them encode DNA binding proteins and probably have a role in gene regulation, where even subtle changes are important in evolution," says Hughes, who is Canada Research Chair in Decoding Gene Regulation and John W. Billes Chair of Medical Research at the Temerty Faculty of Medicine at U of T.

Transposons are sometimes also called "jumping genes" because they switch location in the genome, thanks to a self-encoded enzyme that recognises and move its own DNA code via "cut and paste" mechanism. New copies can arise through serendipitous jumps during cell division when the whole genome is replicated.

Over time, the enzyme's code drifts into disrepair and the jumping ceases. But if the altered sequence confers even subtle selective advantage to the host, it can begin new life as a bona fide host gene.

There are myriad examples of transposon-derived genes across species, but the Coelacanth stands out for the sheer scale of it.

"It was surprising to see coelacanths pop out among vertebrates as having a really large number of these transposon-derived genes because they have an undeserved reputation of being a living fossil," says graduate student Isaac Yellan who spearheaded the study.

"The Coelacanth may have evolved a bit more slowly but it is certainly not a fossil," he says.

Yellan made the discovery while looking for counterparts in other species of a human gene he was studying. He knew that the gene, CGGBP1, had arisen from a particular type of transposon in the common ancestor of mammals, birds and reptiles. It was named after the protein it encodes, which binds CGG-containing DNA sequences, but it was difficult to study partly because it has no counterpart in other commonly researched species, such as fruitfly.

After scanning all available genomes, Yellan was able to find related genes, but their distribution across species was patchy and not what you'd expect from common ancestry. In addition to the single CGGBP-like gene in all mammals, birds and reptiles, Yellan found copies in some, but not all, fish he looked at, as well as in lamprey, a primitive vertebrate, and a type of fungus. Worms, molluscs, and most insects had none. And then there were 62 in the Coelacanth, whose genome became available in 2013.

With common ancestry ruled out, it appears instead that the transposons came into various lineages at different times by being carried between species through what is known as horizontal gene transfer.

"Horizontal gene transfer fuzzies up the picture of where the transposons came from but we know from other species that it can occur via parasitism," says Yellan. "The most likely explanation is that they were introduced multiple times throughout evolutionary history."

It remains unclear what the genes are doing but several lines of evidence point to a finely-tuned role in gene regulation. Computational modeling and test tube experiments established that the genes' products are proteins which bind unique sequence signatures on the DNA, suggests a role in gene expression, similar to the human counterpart. Furthermore, the genes are varyingly switched on across dozen or so Coelacanth organs for which data exist, suggesting finely-tuned roles that are tissue-specific.

Where the genes originally came from and what they're doing in the Coelacanth may well remain a mystery. Research specimens are only occasionally pulled up by fishing boats and it took until 1998 to discover the other known living species, Latimeria menadoensis, in an Indonesian fish market.

The species split before the new genes appeared, ruling them out from driving speciation. Still, they might have shaped the African Coelacanth we know today whose majestic armor of royal blue scales throws shade on its brownish-coloured relative, said Yellan noting that this is pure speculation.

Alas, we may never find out.

"The Coelacanths are extremely rare," says Yellan. "And they're very good at hiding."

# data[].attributes.attachment_link.title
Not a living fossil: How the Coelacanth recently evolved dozens of new genes

# data[].attributes.attachment_link.description
The capture of the first living Coelacanth, a mighty ocean predator, off the coast of South Africa caused quite a stir in 1938, 65 million years after its supposed extinction. It became known as a "living fossil" owing to its anatomy looking almost identical to the fossil record.

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Catalytic Synthesis of Polyribonucleic Acid on Prebiotic Rock Glasses | Astrobiology

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Catalytic Synthesis of Polyribonucleic Acid on Prebiotic Rock Glasses | Astrobiology

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If the address matches an existing account you will receive an email with instructions to reset your password.

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On the origin and evolution of the asteroid Ryugu: A comprehensive geochemical perspective

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On the origin and evolution of the asteroid Ryugu: A comprehensive geochemical perspective

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Presented here are the observations and interpretations from a comprehensive analysis of 16 representative particles returned from the C-type asteroid Ryugu by the Hayabusa2 mission. On average Ryugu particles consist of 50% phyllosilicate matrix, 41% porosity and 9% minor phases, including organic matter. The abundances of 70 elements from the particles are in close agreement with those of CI chondrites. Bulk Ryugu particles show higher δ ¹⁸O, Δ ¹⁷O, and ε ⁵⁴ Cr values than CI chondrites. As such, Ryugu sampled the most primitive and least-thermally processed protosolar nebula reservoirs. Such a finding is consistent with multi-scale H-C-N isotopic compositions that are compatible with an origin for Ryugu organic matter within both the protosolar nebula and the interstellar medium. The analytical data obtained here, suggests that complex soluble organic matter formed during aqueous alteration on the Ryugu progenitor planetesimal (several 10's of km), <2.6 Myr after CAI formation. Subsequently, the Ryugu progenitor planetesimal was fragmented and evolved into the current asteroid Ryugu through sublimation.

Related papers from these authors

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On the origin and evolution of the asteroid Ryugu: A comprehensive geochemical perspective

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Presented here are the observations and interpretations from a comprehensive analysis of 16 representative particles returned from the C-type asteroid Ryugu by the Hayabusa2 mission. On average Ryugu particles consist of 50% phyllosilicate matrix, 41% porosity and 9% minor phases, including organic matter.

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Identifying the wide diversity of extraterrestrial purine and pyrimidine nucleobases in carbonaceous meteorites | Nature Communications

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Identifying the wide diversity of extraterrestrial purine and pyrimidine nucleobases in carbonaceous meteorites | Nature Communications

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Identifying the wide diversity of extraterrestrial purine and pyrimidine nucleobases in carbonaceous meteorites - Nature Communications

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All DNA/RNA nucleobases were identified in carbonaceous meteorites. Having been provided to the early Earth as a component in carbonaceous meteorites, these molecules might have played a role for the emergence of genetic functions in early life.

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L’explosion cambrienne s’explique naturellement | Pour la Science

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L’explosion cambrienne s’explique naturellement | Pour la Science

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Trois écologues britanniques viennent de mettre en évidence la complexification de l’écosystème marin expliquant l’explosion de biodiversité du début du Cambrien, il y a quelque 540 millions d’années.

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Découverte d'un ancêtre des étoiles de mers - Sciences et Avenir

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Découverte d'un ancêtre des étoiles de mers - Sciences et Avenir

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Le fossile de Cantabrigiaster fezouataensis a été découvert dans les montagnes de l'Anti-Atlas, au Maroc. C'est un drôle d'animal qui y a été extirpé : vieux de 480 millions d'années, il possède des caractéristiques communes aux étoiles de mers et aux crinoïdes (lys de mer) modernes. Sa découverte pourrait permettre de mieux comprendre l'évolution et la diversification des échinodermes, groupe qui comprend également les oursins et les ophiures.

Un fossile extrêmement bien préservé

Les argiles de Feouzata sont célèbres et précieux pour les paléontologues : ils abritent des milliers de fossiles d'animaux à corps mous qui vivaient dans un environnement marin ouvert au début de l'Ordovicien (-485 à -443 millions d'années). La plupart des espèces qu'on y retrouve n'ont rien de commun avec celles vivant actuellement, elles constituent des expériences de l'évolution qui, pour la plupart, se sont éteintes sans laisser de descendance comme celles de la faune de Burgess, au Canada. À l'exception de quelques animaux comme Cantabrigiaster fezouataensis qui rappelle les étoiles de mers. Toutefois ce dernier doit plutôt être vu comme un hybride puisqu'il lui manque environ 60% du plan corporel des étoiles de mer modernes. Ce qui s'avère très précieux pour les scientifiques qui s'attellent à l'étude de l'évolution de ce groupe. Ils disposent dorénavant d'un "modèle" primitif qui leur permettra de comprendre comment sa forme basique a pu se transformer pour donner naissance à des architectures corporelles plus modernes.
Le fossile de Cantabrigiaster fezouataensis. Crédit : Collections de l'Université Claude Bernard Lyon 1.
Pourquoi cinq bras ?

Le fossile a été étudié par une équipe de l'Université de Cambridge et sa description fait l'objet d'une publication dans la revue Biology Letters. Il a notamment été comparé avec une centaine d'espèces proches des vraies étoiles de mers ou astéries. Avec ce matériel, les chercheurs ont pu reconstituer les liens de parenté existant avec d'autres échinodermes. Ils en concluent que Cantabrigiaster fezouataensi est bien, même s'il n'en possède pas toutes les caractéristiques, le plus ancien représentant des astéries, ce qui repousse ce titre de près de 50 millions d'années ! Cette étoile de mer, donc, est notamment dotée d'une symétrie d'ordre 5 avec 5 bras qui ne sont pas entièrement détachés du reste du corps. Pour le reste du corps si la partie axiale correspond aux modèles modernes, les autres parties semblent être absentes et ont dû se rajouter plus tard au cours de l'évolution.

Les auteurs prévoient d'élargir leurs travaux à la recherche d'échinodermes précoces. " Une chose à laquelle nous espérons répondre à l'avenir est la raison pour laquelle les étoiles de mer ont développé leurs cinq bras", a déclaré Aaron Hunter, principal auteur de l'étude, dans un communiqué. " Cela semble être une forme stable à adopter pour elles mais nous ne savons pas encore pourquoi. Nous devons continuer à chercher le fossile qui nous donne cette connexion particulière en revenant directement aux premiers ancêtres comme Cantabrigiaster qui nous rapprochent de cette réponse".

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Découverte d'un ancêtre des étoiles de mers - Sciences et Avenir

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Le fossile de Cantabrigiaster fezouataensis a été découvert dans les montagnes de l'Anti-Atlas, au Maroc. C'est un drôle d'animal qui y a été extirpé : vieux de 480 millions d'années, il possède des caractéristiques communes aux étoiles de mers et aux crinoïdes (lys de mer) modernes.

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Origine de la vie : une nouvelle piste dans les océans il y a 4 milliards d'années, les Misos

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Origine de la vie : une nouvelle piste dans les océans il y a 4 milliards d'années, les Misos

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Dans une lettre adressée à son ami, le grand et explorateur britannique Joseph Dalton Hooker, évoque brièvement en 1871 un lieu et un scénario possible pour cette origine : " Q uelque petite mare chaude, en présence de toutes sortes de sels d' et d' phosphorique, de , de , d'électricité, etc. ", où " un composé de fut chimiquement formé, prêt à subir des changements encore plus complexes ".

Une variante de ce scénario sera considérée au XX e siècle tout d'abord avec la théorie de la soupe chaude primitive proposée par les biochimistes Alexandre Oparine (1894-1980) et John Haldane (1892-1964) dans les années 1920, puis avec la fameuse expérience de Miller en 1953.

L'expérience Miller met en évidence les origines chimiques de l'apparition de la vie comme l'explique cet extrait de la neuvième émission du magazine Cassiopée, Sommes-nous seuls dans l'univers ? (France Supervision, 1996) avec un texte et la voix off de Jean-Pierre Luminet. Il est possible de trouver d'autres vidéos similaires sur le site du projet multiplateforme francophone sur la cosmologie contemporaine " Du Big Bang au vivant ". © Jean-Pierre Luminet

Métabolisme, système génétique et membrane en coévolution

Le système génétique repose, lui, sur l' qui contient l'information permettant la synthèse des protéines du vivant. Problème : certaines de ces protéines, des , sont nécessaires à la duplication de l' par leur propriété de catalyseurs .

Les scientifiques restent confrontés depuis lors à un véritable gordien faisant intervenir l'origine du métabolisme, celle du système génétique et enfin celle de la compartimentation de la vie. Dans quel ordre ces trois composants sont-ils apparus et comment ? On tente de trancher ce nœud en partant de l'hypothèse qu'ils ont dû coévoluer tout en se complexifiant. Mais comment cette coévolution s'est-elle mise en place ?

Quel contexte géochimique pour l'apparition de la vie ?

Toujours est-il que pour tenter d'y voir plus clair, les recherches doivent avancer sur plusieurs fronts et des rebondissements concernant des hypothèses un temps favorisées ou défavorisées sont inévitables. Un dernier avatar de cette dialectique peut se trouver en consultant une publication dans le numéro de décembre de la revue Physics of Life Reviews . Il s'agit du fruit d'une vaste étude dans laquelle trois chercheurs de l'université de , de l'Institut de du globe de Paris (Université de Paris, IPGP, CNRS) et de l'université de Brême, proposent un nouveau scénario concernant les conditions géochimiques régnant à la surface de la primitive de l', il y a donc au moins 4 milliards d'années.

Rappelons que l' ère géologique de l'Hadéen a de bonnes raisons de porter son nom puisque Hadès est le dieu grec des Enfers. Juste après la collision à l'origine de la , très probablement moins de 100 millions d'années après la naissance il y a environ 4,56 milliards d'années de la Terre primitive, celle-ci était recouverte d'un océan de et l' atmosphère devait largement être composée de carbonique avec un peu d' et de vapeur d'eau, atteignant des de l'ordre de 70 atmosphères. Autant dire que notre future Planète bleue ressemblait à l'enfer vénusien actuel. Toutefois, on a des indications en faveur d'un refroidissement assez rapide et même de l'existence d'océans déjà il y a plus de 4 milliards d'années.

Mais les débats sont loin d'être terminés en ce qui concerne l'état de l'atmosphère et des océans à la fin de l'Hadéen. La mémoire géologique de la Terre datant de cette période a été largement détruite par la tectonique des plaques , ouvrant et fermant des océans, déchirant et collant des continents. Il est donc difficile de trouver des roches datant de l'Hadéen, d'autant plus que les informations qu'elles peuvent contenir ont été brouillées, dégradées, voire effacées, par le métamorphisme et la géodynamique terrestre.

Le travail publié par les chercheurs avance toutefois des arguments laissant penser qu'il y a 4 milliards d'années, une atmosphère riche en méthane et des océans basiques et riches en existaient. On tendait plutôt à penser avant ce travail, en se basant sur des roches plus jeunes datant de l', l'ère géologique qui suit l'Hadéen et se termine il y a environ 2,5 milliards d'années (avant la Grande Oxydation ), que les océans de la fin de l'Hadéen étaient principalement composés d' acide carbonique de formule H ₂CO ₃.

Si ces cinquante dernières années ont vu une grande quantité d'avancées scientifiques sur la question de l'apparition de la vie sur Terre, la question passionne toujours autant les scientifiques. De quels outils disposent-ils ? Sommes-nous réellement issus de poussières d'étoiles ? Que reste-t-il à découvrir ? © CNRS

Mais, d'après les géochimistes, comme les roches ignées , volcaniques, de l'Hadéen étaient probablement et surtout des roches appelées ultramafiques propres à cette période (un exemple très connu étant celui des que l'on appelle des Komatiites ), les réactions chimiques avec l'eau des océans auraient en fait rendu celle-ci plutôt , produisant de l' et synthétisant des composés carbonés comme l'explique un communiqué de l'IPGP. Ces réactions sont connues comme celles menant à la serpentinisation et à celles dites de Fischer-Tropsch . Très rapidement, ces réactions auraient contribué à pomper le CO ₂ de l'atmosphère de la jeune Terre et à la synthèse de méthane.

Tout cela est parfaitement compatible avec l'idée, avancée par les chercheurs, d'océans devenus alcalins et producteurs de silice rapidement pendant l'Hadéen. Or, selon eux, ces conditions étaient alors idéales pour une nouvelle synthèse, celle de structures minérales auto-organisées (ou Misos pour mineral self-organized structures) à base de silice, d'éléments carbonés et d'oxydes métalliques.

Une variante de l'hypothèse AHV ?

On ne peut s'empêcher de penser, avec cette nouvelle théorie, à celle de Michael Russell, connue en anglais sous le titre de Alkaline Hydrothermal Vent/serpentinization (AHV) hypothesis .

Faisons-en un exposé rapide déjà présenté par Futura. Sous la croûte océanique , on trouve des roches cousines des roches ultramafiques appelées péridotites . Au niveau des dorsales, là où le est à faible profondeur, ces roches sont infiltrées par l'eau de mer, ce qui les conduit à devenir une autre roche appelée serpentinite . Les réactions chimiques à l'œuvre sont justement celles dont on a parlé précédemment, c'est-à-dire avec le terme de serpentinisation. Elles produisent alors notamment du dihydrogène (H ₂), source d' énergie potentielle pour d'autres réactions chimiques, et du méthane (CH ₄) que l'on va retrouver dans l'eau des sources hydrothermales appelées fumeurs blancs. Cette eau est fortement basique (pH de 13) et, généralement, à 100 °C lorsqu'elle finit par ressortir dans un océan bien plus froid et plus acide. La production de méthane est là aussi abiogénique et s'explique par la réduction du CO ₂ par l'hydrogène selon une réaction catalytique de type Fischer-Tropsh.

Les Misos auraient pu avoir un rôle similaire en devenant l'équivalent de ces réacteurs chimiques naturels. Les premières cellules pourraient donc être des dérivées de ce type d'environnement.

Origine de la vie : une nouvelle piste, celle des pierres ponces
Article de Laurent Sacco publié le 07/09/2011
Des chercheurs des universités d'Oxford et de Western Australia viennent de publier une intéressante proposition dans le journal Astrobiology. Les pierres ponces flottant sur la soupe chaude primitive des océans de la jeune Terre pourraient avoir été le lieu de l'apparition de la vie.

Les trois grandes questions scientifiques fondamentales que nous a léguées le XX e sont certainement celles de l'origine de l', du rapport entre l'esprit et la et enfin de l' origine de la vie . Si l'on devait faire des pronostics sur la possibilité de répondre à ces trois énigmes au cours du XXI e siècle, la dernière aurait certainement des chances non négligeables d'être enfin résolue.

Les expériences de Stanley Miller ont montré par la suite que l'on pouvait synthétiser de cette façon des acides aminés mais à partir d'un mélange gazeux soumis à des décharges électriques, supposé reproduire l'atmosphère primitive soumise à des d'.

Le biochimiste russe Alexander Oparine, à l'origine d'une hypothèse sur la formation des premières molécules organiques sur Terre, parle (en russe, traduit ensuite par son interlocuteur) de la possibilité, dans un avenir pas très éloigné, de synthétiser la matière vivante, en choisissant judicieusement les différentes étapes à suivre. © Ina

Des réacteurs chimiques naturels ?

Un autre lien possible avec l' activité volcanique vient aujourd'hui d'être proposé par Martin Brasier, de l'université d'Oxford, et David Wacey de l' University of Western Australia. Dans un article publié dans Astrobiology (donné en lien ci-dessous), les deux chercheurs font remarquer que les pierres ponces qui flottent sur l'eau en formant de véritables tapis de roches présentent des caractéristiques prometteuses pour comprendre l'apparition des premières formes vivantes.

La pierre ponce possède le plus haut rapport surface/volume de toutes les roches connues et elle est la seule roche volcanique à flotter sur la mer. Les , les composés organiques et phosphatés s'adsorbent remarquablement bien sur sa surface. La roche elle-même est accueillante pour des catalyseurs organiques comme la . Produites lors de certaines éruptions volcaniques , on sait que les pierres ponces peuvent flotter un bon moment sur la surface de la mer avant de s'échouer sur des plages pendant de longues périodes.

Ainsi, comme le fait remarquer Brasier : " Une pierre ponce est potentiellement exposée à, entre autres choses, la associée à des éruptions volcaniques, les hydrocarbures et les métaux produits par les sources hydrothermales et les rayons ultraviolets du Soleil. Toutes ces conditions ont le potentiel d'accueillir, ou même de générer, les genres de processus chimiques que nous pensons avoir créé les premières cellules vivantes ".

Les chercheurs pensent que leur hypothèse peut être testée en examinant les restes de tapis flottant de pierres ponces, et en menant des expériences en laboratoire pour voir si ces roches ignées peuvent créer des composés organiques lorsqu'elles sont périodiquement chauffées et exposées à des rayonnements ultraviolets.

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Origine de la vie : une nouvelle piste dans les océans il y a 4 milliards d'années, les Misos

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Dans une lettre adressée à son ami, le grand et explorateur britannique Joseph Dalton Hooker, évoque brièvement en 1871 un lieu et un scénario possible pour cette origine : " Q uelque petite mare chaude, en présence de toutes sortes de sels d' et d' phosphorique, de , de , d'électricité, etc.

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Peut-on penser l’ADN comme un code informatique ?

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Peut-on penser l’ADN comme un code informatique ?

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Peut-on penser l’ADN comme un code informatique ?

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Dans une série documentaire récemment diffusée sur les écrans, l’ADN est présenté comme un texte où il suffit de copier-couper-coller pour agir sur les gènes. La réalité n’est-elle pas plus complexe ?

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D’où vient le cancer, et pourquoi n’a-t-il pas été éliminé par l’évolution ?

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D’où vient le cancer, et pourquoi n’a-t-il pas été éliminé par l’évolution ?

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Le cancer soulève pour les biologistes une myriade de questions fascinantes, pour la plupart non encore entièrement résolues. Comment expliquer les origines de cette maladie ? Pourquoi est-elle si difficile à soigner ? Pourquoi les vulnérabilités au cancer persistent-elles chez la plupart des organismes multicellulaires ?

Face à ces interrogations, les approches basées sur l'élucidation des mécanismes de cette maladie et les recherches cliniques ne suffisent pas. Nous devons observer le cancer selon une nouvelle perspective, en adoptant une vision évolutive ; en d'autres termes, nous devons poser sur le cancer le regard de Charles Darwin, père de la théorie de l'évolution.

Depuis quelques années, les réflexions émergeant de la concertation mutuelle des biologistes de l'évolution et des oncologues débouchent sur des avancées transversales profitables aux deux disciplines. Elles changent aussi notre appréhension de la maladie.

Comment l'évolution de la multicellularité prépare le terrain pour le cancer

Le cancer touche l'ensemble du règne animal multicellulaire. Et pour cause : il s'agit d'une maladie ancestrale liée à l'apparition des métazoaires (animaux composés de plusieurs cellules, contrairement aux protozoaires constitués d'une seule cellule), voici plus d'un demi-milliard d'années.

L'émergence de tels organismes complexes a nécessité la mise en place de hauts niveaux de coopération entre les nombreuses cellules qui les composent. Cette coopération est en effet sous-tendue par des comportements complémentaires et altruistes, en particulier l'apoptose, autrement dit le suicide cellulaire (par lequel une cellule déclenche son autodestruction en réponse à un signal donné) et le renoncement à la reproduction directe pour les cellules autres que les cellules sexuelles. L'évolution d'une multicellularité stable s'est donc faite par la sélection d'adaptations facilitant le fonctionnement collectif d'une part, et réprimant les réflexes unicellulaires ancestraux d'autre part.

Le cancer représente une rupture de cette coopération multicellulaire, suivie de l'acquisition d'adaptations permettant aux cellules " rénégates " de se perfectionner dans leur propre mode de vie. Autrement dit, les cellules malignes commencent à " tricher ". Elles peuvent le faire car elles ont subi des mutations génétiques (modification de la séquence des gènes) ou épigénétiques (modifications qui changent l'expression des gènes, transmissibles mais réversibles contrairement aux mutations génétiques), voire les deux, qui leur conférent une plus grande valeur sélective par rapport aux cellules au comportement coopératif. Il peut s'agir par exemple d'avantages de croissance, de multiplication, etc. Il est également impératif que les cellules porteuses de ces modifications se situent dans un micro-environnement favorable à leur prolifération.

Si ces " rébellions cellulaires " ne sont pas correctement réprimées par les systèmes de défenses de l'organisme (comme le système immunitaire), l'abondance des cellules cancéreuses peut augmenter localement. Conséquences : les ressources s'épuisent, et ces cellules peuvent alors enclencher des comportements individuels ou collectifs de dispersion et de colonisation vers de nouveaux organes, les tristement célèbres métastases responsables de la majorité des décès liés au cancer.

Alex Ritter, Jennifer Lippincott Schwartz and Gillian Griffiths, National Institutes of Health

En quelques mois ou années, une seule cellule cancéreuse peut ainsi produire un (éco)système complexe et structuré, la tumeur solide, comparable à un organe fonctionnel, ainsi que des métastases plus ou moins disséminées dans l'organisme.

Un aspect intrigant de cette maladie repose sur le nombre important de similitudes entre les attributs des cellules cancéreuses provenant de différents organes, individus et même espèces, ce qui suggère que des processus similaires opèrent à chaque fois. Cependant, chaque cancer évolue comme une entité nouvelle, car en dehors des cancers transmissibles évoqués précédemment, les tumeurs disparaissent à chaque fois avec leurs hôtes, sans transmettre leurs innovations génétiques et phénotypiques.

Comment, alors, expliquer ces similitudes ?

Persistance du cancer à travers les temps évolutifs

D'un point de vue évolutif, deux hypothèses peuvent expliquer l'apparition des cancers et la similitude de leurs attributs.

La théorie de l'atavisme explique le cancer par un retour aux capacités cellulaires antérieures, à savoir la libération d'un programme de survie hautement conservé, qui serait toujours présent dans chaque cellule eucaryote, et donc dans chaque organisme multicellulaire. Ce programme ancestral aurait été sélectionné pendant la période précambrienne, qui a débuté voici 4,55 milliards d'années et s'est achevée il y a 540 millions d'années. Durant cette période, qui a vu émerger la vie sur notre planète, les conditions environnementales étaient très différentes des conditions actuelles, et souvent défavorables. Les forces sélectives qui agissaient sur les organismes unicellulaires favorisaient les adaptations pour la prolifération cellulaire.

Certaines de ces adaptations, sélectionnées au cours de la vie unicellulaire, seraient toujours présentes, plus ou moins enfouies dans nos génomes. Lorsque leur expression échappe aux mécanismes de contrôle, une lutte entre les caractères unicellulaires ancestraux et les caractères multicellulaires actuels s'ensuit, et un cancer peut alors émerger. Au passage, cette hypothèse expliquerait aussi pourquoi les cellules cancéreuses s'accommodent très bien des environnements acides et pauvres en oxygène (" anoxiques "), car ces conditions étaient fréquentes au Précambrien.

La seconde hypothèse implique un processus de sélection somatique (les cellules somatiques sont toutes les cellules autres que les cellules sexuelles) conduisant à une évolution convergente, autrement dit à l'émergence de caractères analogues. Cette hypothèse propose que l'émergence des caractéristiques cellulaires définissant les cellules " tricheuses " est soumise à une forte sélection à chaque fois qu'une nouvelle tumeur émerge, et ce quelles que soient les causes immédiates desdites caractéristiques. Ces processus de sélection somatique se produisant dans des environnements largement régis par les mêmes contraintes écologiques (telles que celles qui règnent dans le corps des organismes multicellulaires), ils donneraient lieu à une évolution convergente.

C'est ce qui expliquerait que l'on observe des similitudes à travers la diversité de cancer. N'oublions pas que nous voyons seulement les cancers qui réussissent à se développer : on ne sait pas combien de " candidats " échouent faute d'acquérir, les bonnes adaptations aux bons moments.

Ces deux hypothèses ne sont pas mutuellement exclusives : la réémergence d'un programme ancestral peut être suivie d'une sélection somatique aboutissant à une évolution convergente.

Quelle que soit la raison de l'origine du cancer, une question se pose : puisque cette maladie cause souvent la mort de l'hôte, pourquoi la sélection naturelle n'a-t-elle pas été plus efficace pour rendre les organismes multicellulaires entièrement résistants au cancer ?

Les grands animaux n'ont pas plus de cancer

Les mécanismes de suppression du cancer sont nombreux et complexes. Chaque division cellulaire peut provoquer des mutations somatiques touchant les voies génétiques contrôlant la prolifération cellulaire, la réparation de l'ADN et/ou l'apoptose, perturbant ainsi le contrôle du processus de formation du cancer (carcinogenèse).

Si chaque division cellulaire comporte une chance donnée qu'une mutation cancérigène se produise, alors le risque de développer un cancer devrait être fonction du nombre de divisions cellulaires au cours de la vie d'un organisme. Cependant, les espèces de grande taille et à durée de vie longue n'ont pas davantage de cancers que celles de petite taille vivant moins longtemps.

Dans les populations naturelles animales, la fréquence du cancer varie généralement de 0 % à 40 % pour toutes les espèces échantillonnées et n'est pas liée à la masse corporelle. Les éléphants et les souris peuvent connaître des niveaux assez similaires de prévalence du cancer, bien que les éléphants aient beaucoup plus de divisions cellulaires au cours de leur vie que les souris. Ce phénomène est appelé " le paradoxe de Peto ".

L'explication de ce paradoxe réside dans le fait que les forces évolutives ont sélectionné des mécanismes de défense plus efficaces chez les grands animaux que chez les petits, ce qui permet de réduire le fardeau lié au cancer quand la taille augmente. Par exemple, les éléphants ont vingt copies du gène suppresseur de tumeur TP53, tandis que les humains n'en ont que deux.

À côté de ces tendances générales existent des exceptions notables, avec par exemple des espèces de petite taille ayant une durée de vie exceptionnellement longue. Ces espèces ont également peu de cancers. Un très bon exemple est celui du rat-taupe nu ( Heterocephalus glaber), un espèce dont les individus ont une longue durée de vie ( espèce longévive) et ne développent pas de tumeurs spontanées, à l'exception de quelques cas de cancers détectés de façon anecdotique.

Une maladie qui survient tardivement

Retenons aussi que l'efficacité des défenses anti-cancers connaît une diminution lorsque les organismes ont réalisé l'essentiel de leur reproduction, car les pressions évolutives sont moins fortes à ce stade de la vie. Cette baisse d'efficacité, couplée à l'accumulation des mutations au cours du temps, explique que la plupart des cancers (sein, prostate, poumon, pancréas...) surviennent dans la seconde partie de la vie.

Une implication évolutive majeure est que si, en monnaie " darwinienne ", le cancer n'est pas un souci majeur lorsqu'il survient après la phase reproductive, cela signifie aussi que nos défenses auront été optimisées par la sélection naturelle non pas pour systématiquement éradiquer les processus oncogéniques, mais pour les contrôler tant que nous sommes reproducteurs...

Ces défenses " low cost ", qui conduisent à tolérer les tumeurs, s'avèrent in fine plus avantageuses pour le succès reproducteur que des stratégies d'éradication systématique, qui seraient sans doute beaucoup plus coûteuses. Le système immunitaire, par exemple, ne travaille pas gratuitement... D'une façon générale, le vivant est régi par des compromis, ou " trade-offs " en anglais, faisant que tout investissement dans une fonction correspond à autant de ressources et d'énergie qui ne seront plus disponibles pour d'autres fonctions. Nos défenses contre les maladies, dont le cancer, n'échappent pas à cette règle de fonctionnement.

Hélas, ces défenses " low cost " contre le cancer sont au final des bombes à retardement... La logique darwinienne ne conduit en effet pas toujours à des résultats en adéquation avec les attentes sociétales en termes de santé !

Bien que la plupart des mutations cancérigènes se produisent dans les cellules somatiques au cours de la vie, de rares cas de cancer sont causés par des mutations héréditaires dans la lignée germinale, qui produit les cellules sexuelles. Ces mutations congénitales sont parfois en fréquence supérieure à ce qui serait prédit par l'équilibre mutation-sélection.

Ce paradoxe peut s'expliquer par divers processus évolutifs. Par exemple, il a été suggéré que la sélection naturelle n'agira probablement pas sur ces mutations si là encore leurs effets négatifs sur la santé surviennent après la période de reproduction.

Par ailleurs, la théorie de la pléiotropie antagoniste pourrait aussi être invoquée. Celle-ci stipule que certains gènes ont des effets opposés sur la probabilité de survie/reproduction selon l'âge considéré : ces effets seraient positifs au début de la vie, et négatifs par la suite. Quand l'effet positif du début est élevé, la sélection pourra retenir ce variant génétique, même s'il cause une maladie mortelle plus tard.

Par exemple, les femmes présentant une mutation des gènes BRCA1/2 ont un risque significativement plus élevé de développer des cancers du sein ou de l'ovaire, mais ces mutations semblent être corrélées à une fécondité accrue.

Des implications en matière de traitements

Le cancer, véritable fardeau dans les populations humaines, est donc avant tout un phénomène régi par des processus évolutifs, depuis son origine dans l'histoire de la vie jusqu'à son développement en temps réel chez une personne malade. La séparation traditionnelle entre oncologie et biologie évolutive doit de ce fait être abolie, car elle limite notre compréhension de la complexité des processus qui aboutissent à la survenue de la maladie.

Cette nouvelle perspective du cancer pourrait s'avérer utile pour développer des solutions thérapeutiques innovantes qui limiteraient les problèmes liés aux stratégies de traitement actuellement disponibles. Ces thérapies à hautes doses, qui visent à tuer le maximum de cellules malignes, aboutissent souvent à la prolifération de cellules résistantes. À l'inverse, la thérapie adaptative, profondément enracinée dans la biologie évolutive, pourrait constituer une approche alternative.

Read more: Traitement du cancer : l'éradication à tout prix n'est pas forcément la bonne approche

Cette stratégie consiste à diminuer la pression liée aux thérapies à hautes doses afin d'éliminer une partie seulement des cellules cancéreuses sensibles. Ce faisant, l'objectif est de maintenir un niveau significatif de compétition entre les cellules cancéreuses sensibles et les cellules cancéreuses résistantes, afin d'éviter ou de limiter la prolifération sans contrainte des résistantes.

Une problématique qui ne se limite pas à l'être humain

Jusqu'à récemment, l'oncologie avait très rarement emprunté les concepts de la biologie évolutive pour améliorer la compréhension des processus malins. De même, les écologistes et les biologistes de l'évolution ont largement ignoré l'existence de ces phénomènes dans leurs explorations du vivant. Mais les choses changent, et la prise en compte du cancer, ou plutôt des processus oncogéniques dans leur ensemble, au sein de la faune sauvage suscite un engouement croissant au sein de la communauté des écologistes et des biologistes de l'évolution.

Il apparaît en effet aujourd'hui clairement que le cancer est à la fois un modèle biologique pertinent pour étudier l'évolution du vivant et un phénomène biologique important pour comprendre plusieurs facettes de l'écologie des espèces animales, et leurs conséquences sur le fonctionnement des écosystèmes.

Même s'ils n'évoluent pas toujours vers des formes invasives/métastatiques, les processus tumoraux sont omniprésents chez les métazoaires et des travaux théoriques suggèrent qu'ils influencent probablement chez ces derniers des variables fondamentales en écologie, comme les traits d'histoire de vie, les aptitudes compétitrices, la vulnérabilité aux parasites et aux prédateurs, ou encore la capacité à disperser. Ces effets proviennent à la fois des conséquences pathologiques des tumeurs, mais aussi des coûts liés au fonctionnement des mécanismes de défense chez les hôtes.

Comprendre les conséquences écologiques et évolutives des interactions hôtes-tumeurs est ainsi devenu au cours de ces dernières années un thème de recherche phare en écologie et en biologie évolutive.

Ces questionnements scientifiques sont d'autant plus légitimes que la quasi-totalité des écosystèmes de la planète, en particulier les milieux aquatiques, est à présent polluée par des substances d'origine anthropique, souvent mutagènes. Il s'avère alors primordial de mieux comprendre les interactions hôtes-tumeurs, et leurs effets en cascade dans les communautés, pour prédire et anticiper les conséquences des activités humaines sur le fonctionnement des écosystèmes et le maintien de la biodiversité.

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D'où vient le cancer, et pourquoi n'a-t-il pas été éliminé par l'évolution ?

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Le cancer soulève pour les biologistes une myriade de questions fascinantes, pour la plupart non encore entièrement résolues. Comment expliquer les origines de cette maladie ? Pourquoi est-elle si difficile à soigner ? Pourquoi les vulnérabilités au cancer persistent-elles chez la plupart des organismes multicellulaires ?

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Evolution : le sommeil serait apparu... avant le cerveau - Science et vie

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Evolution : le sommeil serait apparu... avant le cerveau - Science et vie

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Cela avait déjà été repéré dans des études préalables sur des nématodes et des arthropodes, notamment les méduses, mais cette fois l'étonnement va plus loin : non seulement Hydra vulgaris dort, mais elle réagit comme les animaux à système nerveux central ou cerveau à des substances induisant le sommeil.

Mieux : les chercheurs ont constaté que la déprivation de sommeil active chez les hydres les mêmes gènes que ceux des animaux en manque de sommeil... Pourtant ce petit animal, d'à peine 1 à 3 cm de long, ne possède qu'un réseau diffus de fibres nerveuses.

Il semblerait donc que dans les processus évolutifs, le sommeil - et ses vertus physiologiques - a précédé l'apparition d'un système nerveux centralisé et d'un cerveau, contrairement à ce que les évolutionnistes pensaient jusque-là.

4 heures de sommeil pour 4 heures de veille

Quatre heures. Tel serait le cycle du sommeil de l'hydre d'eau douce. Dans le cas présent néanmoins, la définition du sommeil est quelque peu élargie car en général on le caractérise par une activité particulière du cerveau. Ici, c'est le comportement qui est monitoré.

Les chercheurs considèrent ainsi que l'hydre tombe dans les bras de Morphée quand elle ralentit et réduit ses mouvements (suivies par vidéo), un état qui peut être interrompu avec un flash de lumière, par exemple.

Ces cycles alternant activité et ralentissement, qu'on ne peut appeler " circadiens " puisqu'ils ne suivent pas le cycle solaire de 24 heures, sont donc l'indice le plus visible de l'existence d'un état de sommeil. Mais sur cette base, les chercheurs ont réussi à mieux le caractériser, voire le valider.

Sommeil induit

En effet, ils ont exposé les hydres à des substances qui, chez les animaux à cerveau (ou système nerveux central), régulent le sommeil.

Ainsi, la mélatonine, une hormone secrétée par notre cerveau (glande pinéale) et qu'on administre artificiellement dans des traitements contre l'insomnie légère, tend à augmenter le temps et la fréquence des phases de sommeil chez l'hydre.

L'acide γ-aminobutyrique (ou GABA), un neurotransmetteur lié au sommeil présent chez les mammifères, les oiseaux et les insectes, augmente l'état de sommeil de l'hydre. Seul résultat paradoxal : la dopamine (neurotransmetteur), qui normalement provoque l'éveil chez les animaux à cerveau, induit le sommeil chez l'hydre.

Mais c'est à l'échelle des gènes que la similarité entre animaux à cerveau et hydres est la plus frappante.

Le réseau de gènes du sommeil

En effet, on sait que la déprivation de sommeil entraine chez les premiers l'activation d'un réseau de gènes particulier.

Or en privant les hydres de leur sommeil bien mérité - par modification de la température ou des vibrations mécaniques - les chercheurs ont découvert que les mêmes gènes (212 en tout) s'activent chez l'hydre, induisant un allongement du temps de sommeil le lendemain et en supprimant la prolifération cellulaire.

Les chercheurs en ont conclu que la solution " sommeil " se serait mise en place avant l'émergence du système nerveux central et du cerveau. Le cas de l'effet paradoxal de la dopamine serait le seul " saut " dans la continuité évolutionnaire.

Comme l'a déclaré à la presse Taichi Itoh, l'un des cosignataires de l'article, " tandis que certains mécanismes du sommeil semblent avoir été conservés, d'autres peuvent avoir changé de fonction au cours de l'évolution du cerveau " .

Reste une question qui intéressera surtout les plus rêveurs d'entre nous : les hydres rêvent-elles de moutons aquatiques ?
Source : Science Advances, octobre 2020.

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Evolution : le sommeil serait apparu... avant le cerveau

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Cela avait déjà été repéré dans des études préalables sur des nématodes et des arthropodes, notamment les méduses, mais cette fois l'étonnement va plus loin : non seulement Hydra vulgaris dort, mais elle réagit comme les animaux à système nerveux central ou cerveau à des substances induisant le sommeil.

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L' « abominable mystère » de l'origine des fleurs a été percé

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L' « abominable mystère » de l'origine des fleurs a été percé

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Alors que les plantes à fleur, ou angiospermes, constituent aujourd'hui (et à l'époque de Charles Darwin) la famille de plantes la plus nombreuse et diversifiée - et quasiment toutes celles cultivées par les humains -, elles semblent être apparues d'un coup dans l'histoire évolutive.

>> Lire aussi : Comment cultiver des plantes dans l'espace ?

En effet, selon les enregistrements fossiles, les fleurs font une apparition remarquée dans les couches stratigraphiques vieilles d'environ 100 millions d'années (+/- 20 millions). Et elles semblent apparaître " clé-en-main ", sans aucune trace d'ancêtres présentant une esquisse ou un stade précoce d'évolution vers cette forme si efficace pour la reproduction.

Or une équipe internationale vient de dater leur véritable apparition, c'est-à-dire l'apparition des premiers ancêtres avec des caractéristiques-clé de cette grande famille de végétaux, à environ 200 millions d'années (+/- 50 millions).

Origine des fleurs : une coïncidence de dates

Il ne s'agit pas d'une découverte sur le terrain, c'est un calcul statistique de grande ampleur. Les chercheurs ont appliqué une méthode d'analyse poussée sur une base de plus de 700 publications scientifiques préalables relevant les caractéristiques de 15 000 enregistrements fossiles de nombreuses plantes.

Comme en paléogénétique, l'analyse statistique et les modèles mathématiques utilisés en théorie de l'évolution sont très robustes et permettent d'anticiper des résultats là ou l'on manque forcément de données.

Les chercheurs ont créé une simulation d'après leur modèle mathématique qui a fait remonter l' ancêtre commun des plantes à fleur à l'époque du Jurassique. Or cette estimation coïncide avec celle déjà connue des biologistes moléculaires et généticiens, réalisée par analyse des gènes des espèces actuelles.

Une double validation théorique qui laisse penser que l'absence de fossiles (découverts) des plantes à fleurs les plus anciennes a été due à leur faible probabilité de pouvoir fossiliser et à leur rareté - éclipsées par la dominance des fougères et conifères. " Cela me rappelle comment les mammifères modernes ont longtemps vécu à l'ère des dinosaures, avant de devenir une composante dominante de la faune moderne " , a déclaré à la presse l'auteur principal, Daniele Silvestro de l'Université de Fribourg en Suisse.

La théorie de l'évolution semble donc en avoir fini avec son abominable mystère, bien que ce résultat ne comble pas le manque effectif de fossiles anciens. Désormais au moins on sait mieux dans quelles couches sédimentaires les chercher.

>> Lire aussi : Pourquoi les fleurs se referment-elles quand le soleil se couche ?
Source : Nature, janvier 2021.

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L' " abominable mystère " de l'origine des fleurs a été percé

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Alors que les plantes à fleur, ou angiospermes, constituent aujourd'hui (et à l'époque de Charles Darwin) la famille de plantes la plus nombreuse et diversifiée - et quasiment toutes celles cultivées par les humains -, elles semblent être apparues d'un coup dans l'histoire évolutive. >> Lire aussi : Comment cultiver des plantes dans l'espace ?

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Plantes à fleurs : « l'abominable mystère » de Darwin s... - Science & Vie

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Plantes à fleurs : « l'abominable mystère » de Darwin s... - Science & Vie

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Le 17 Jan 2021 à 14H00 Par Ophélie CHARLERY-ADELE

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Plantes à fleurs : « l’abominable mystère » de Darwin s’éclaircit

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Des chercheurs pourraient bien avoir percé l’un des secrets des plantes fleurs : une intrigante coévolution.

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L'hémoglobine provient d'un gène unique transmis aux animaux par un ancêtre commun

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L'hémoglobine provient d'un gène unique transmis aux animaux par un ancêtre commun

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L'hémoglobine (Hb) est une protéine présente dans le sang des vertébrés ayant pour fonction de transporter l'oxygène depuis le système respiratoire vers le reste de l'organisme. Cette protéine est présente chez plus d'un million d'espèces différentes de bilatériens, tant et si bien que les biologistes ont longtemps pensé que le gène codant pour l'hémoglobine était apparu plusieurs fois au cours de l'évolution. Cependant, des travaux récents ont montré que ce gène était en réalité un gène unique transmis aux animaux bilatériens par leur ancêtre commun.
En étudiant le ver marin Platynereis dumerilii (un animal dont les gènes ont évolué extrêmement lentement), des chercheurs ont montré que si l'hémoglobine est apparue indépendamment chez plusieurs espèces d'animaux, elle descend en fait d'un seul gène transmis à tous par leur dernier ancêtre commun. Ces résultats ont été publiés dans la revue BMC Evolutionary Biology.

La couleur rouge du sang provient de l'hémoglobine, une protéine complexe spécialisée dans le transport de l'oxygène présent dans le système circulatoire des vertébrés, mais aussi dans les annélides (une famille de vers dont les membres les plus connus sont les vers de terre), les mollusques (notamment les escargots d'étang) et les crustacés (comme les daphnies). On pensait que pour que l'hémoglobine soit apparue dans des espèces aussi diverses, elle devait avoir été " inventée " plusieurs fois au cours de l'évolution.

Hémoglobine chez les animaux : elle est issue d'un même gène ancestral

Mais des recherches récentes ont montré que toutes ces hémoglobines nées " indépendamment " dérivent en fait d'un seul gène ancestral. Platynereis d. est considéré comme un animal qui a évolué lentement, car ses caractéristiques génétiques sont proches de celles de l'ancêtre marin de la plupart des animaux, Urbilateria. L'étude de ces vers en les comparant à d'autres espèces à sang rouge a permis de remonter aux origines des hémoglobines.

La recherche s'est concentrée sur la grande famille à laquelle appartiennent les hémoglobines : les globines, des protéines présentes dans presque tous les êtres vivants qui " stockent " des gaz comme l'oxygène et l'oxyde nitrique. Mais les globines agissent généralement à l'intérieur des cellules car elles ne circulent pas dans le sang comme l'hémoglobine.

Ces travaux montrent que chez toutes les espèces à sang rouge, c'est le même gène qui produit une globine appelée " cytoglobine " qui a évolué indépendamment pour devenir un gène codant pour l'hémoglobine. Cette nouvelle molécule en circulation a rendu le transport de l'oxygène plus efficace chez leurs ancêtres, qui sont devenus plus gros et plus actifs. Les auteurs veulent maintenant changer d'échelle et poursuivre ce travail en étudiant quand et comment les différentes cellules spécialisées des systèmes vasculaires bilatéraux sont apparues.

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L'hémoglobine provient d'un gène unique transmis aux animaux par un ancêtre commun

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L'hémoglobine (Hb) est une protéine présente dans le sang des vertébrés ayant pour fonction de transporter l'oxygène depuis le système respiratoire vers le reste de l'organisme. Cette protéine est présente chez plus d'un million d'espèces différentes de bilatériens, tant et si bien que les biologistes ont longtemps pensé que le gène codant pour l'hémoglobine était apparu plusieurs fois au cours de l'évolution.

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Plus de religion égale moins de sciences – {Sciences²}

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Plus de religion égale moins de sciences – {Sciences²}

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Peut-on concilier la croyance religieuse et une attitude scientifique ? Les partisans de cette thèse mettent en avant quelques noms de grands scientifiques ayant affirmé que leurs recherches ne les empêchaient pas de croire en Dieu. Mais les sociologues - des scientifiques eux aussi - n'acceptent pas de se contenter de quelques exemples. Ils veulent vérifier si cette thèse tient toujours debout lorsqu'on la confronte à des données issues d'une pratique sociologique classique : l'enquête sur les opinions et attitudes des populations.

Spoil direct : non, la thèse ne tient pas debout, elle s'écroule. Du moins pour les populations des Etats-Unis d'Amérique et d'Europe, montre une étude publiée récemment (1). Le résumé de l'étude l'affirme sans vraiment prendre de précautions oratoires : " quel que soit le pays considéré, plus les individus s'identifient à une religion et la pratiquent fortement, moins ils ont de compétence scientifique. D'autre part, c'est l'ensemble des représentations des sciences qui est affecté par l'univers religieux des individus. Plus les individus adhèrent à une religion, moins ils ont des attitudes positives envers les sciences. Les Européens et les Américains les moins religieux sont ceux dont les représentations des sciences et de leurs répercussions sociales sont les plus positives. "
Effet cognitif de la croyance en Dieu
Yves Gingras et Kristoff Tallin, deux sociologues patentés du Centre interuniversitaire de recherche sur la science et la technologie (CIRST, Québec, Canada), le second étant chercheur au CNRS, ont utilisé des résultats d'enquêtes sur les croyances et pratiques religieuses (2) permettant de dépasser les " inévitables variations individuelles qui n'ont qu'une valeur anecdotique" afin d'accéder aux " tendances sociales lourdes". Chez les scientifiques eux-mêmes, la dite tendance est anciennement mesurée : la " croyance en un Dieu personnel" n'était en 1914 que de " 27% de l'élite scientifique américaine" (Leuba, 1916). Une part qui avait chuté à 15% en 1933 (Leuba, 1934). Un demi-siècle plus tard, une enquête similaire mesurait une accélération du déclin de cette croyance en milieu scientifique, limitant à " 7% la proportion de croyants en un Dieu personnel " (Larson et Witham, 1998)

L'effet cognitif de la pratique scientifique sur la croyance en Dieu semble donc massif, mais qu'en est-il de la population générale ? Comment, s'interrogent les deux sociologues, " les attitudes envers les sciences varient en fonction du type et du niveau de croyances religieuses " ?
+ de religion = - de sciences
Premier résultat, massif, des trois enquêtes, une corrélation d'airain : plus on connait de sciences et moins le niveau de croyances religieuses est élevé... et inversement. Un constat dont la régularité est impressionnante surtout lorsque l'on se penche sur l'intensité des pratiques religieuses. A l'exception des musulmans (mais c'est là un résultat jugé douteux par les deux sociologues en raison d'un trop faible effectif), on observe un gradient. Plus la fermeté de l'opinion des non religieux est élevée (l'athéisme revendiqué étant son degré le plus haut) et plus les compétences scientifiques sont affirmées.

A l'inverse, plus les pratiques religieuses sont intenses (fréquences des prières, etc) et moins les connaissances scientifiques sont partagées. La conclusion des deux auteurs s'exprime ainsi : " Les résultats présentent donc une logique très structurée par rapport à la compétence scientifique : plus les personnes sont intégrées à une religion, moins elles sont performantes sur le plan des connaissances scientifiques. Par ailleurs, les indicateurs du niveau de pratique religieuse, de la prière et de l'importance de la religion dans la vie quotidienne varient tous dans le même sens : plus l'individu est pratiquant, priant ou religieux, moins son score de compétence scientifique est élevé. "

L'étude américaine permet de cibler des groupes particuliers, comme celui des évangélistes (à 86% se déclarant protestants, et 12% catholiques). Ce groupe particulièrement pratiquant affiche les plus mauvais résultats en connaissances scientifiques.
l'athée plus compétent
Mais dans quel sens fonctionne la causalité ? Nos deux sociologues n'ont évidemment pas négligé les autres causes possibles des corrélations observées. Et ont donc creusé les variables d'âges, de genre et de niveau d'études.

Les résultats sont assez peu surprenants. Dans l'enquête américaine, les hommes affichent de meilleures connaissances que les femmes (3). En dessous de 55 ans, pas de différences notables... et au dessus de 55 ans il s'agit d'un effet de l'âge de fin de scolarité. Une relation linéaire apparaît entre niveau d'études et score moyen de compétences scientifiques. Mais... Mais si l'on croise avec les données sur les religions, l'effet de ces dernières réapparaît sans l'ombre d'un doute : quel que soit l'âge de fin d'études, les sans religions sont toujours plus compétents en science que les religieux à âge égal. Plus encore : un individu " agnostique ou athée" de niveau d'étude " secondaire ou moins" sera en moyenne plus compétent en science qu'un " protestant ou catholique" de niveau " baccalauréat ou plus " ! Un résultat qui ne peut s'expliquer que par un rapport plus positif aux sciences et à leurs utilisations par les sociétés, général chez les sans religions, agnostiques et athées, favorable à la mémorisation de savoirs. Un rapport plus positif qui se lit dans les questions portant non sur les connaissances mais sur l'appréciation de l'apport des sciences aux sociétés humaines.

Dans les enquêtes européennes, " seule l'appartenance au protestantisme n'affecte pas la compétence scientifique de manière notable ", notent les deux sociologues.

Exit, donc, le soit disant bénéfice d'un " dialogue sciences/religions " au service de la rationalité. Les convictions religieuses pèsent manifestement sur la capacité des populations à s'approprier les résultats d'une approche scientifique du monde. Elles pèsent donc négativement sur leurs capacités à discuter en démocratie des usages des technologies qui en sont issues. La vogue du " naturel " - au sens ancien d'un ordre divin puisque la Nature est création divine - opposé à l'artificiel, et cela sans aucune analyse des avantages et des risques des objets naturels et artificiels en débat, en témoigne abondamment. Ainsi, la péridurale proposée à la femme qui accouche devient une pratique artificielle, donc mauvaise par principe, opposée à la douleur " naturelle " de l'accouchement " naturel " qu'il faudrait donc accepter sans se rebeller. Exemple facile. En voici un moins aisé : tout organisme génétiquement modifié est nécessairement mauvais, sans analyse de ses avantages et inconvénient, parce qu'il n'est pas " naturel " (alors que les ravageurs des cultures ou les adventices, eux, sont naturels...).
Sylvestre Huet
(1) Note de recherche 2020-02, CIRST.

(2) Les deux enquêtes Eurobaromètres menées en 2005 et en 2010 auprès des pays membres de l'Union européenne dont les données incluent les variables concernant la religion d'appartenance, le niveau de pratique religieuse et la croyance en l'existence d'un Dieu. Cela permet de prendre en compte différentes dimensions du rapport aux religions. La représentation des sciences est abordée sous plusieurs angles différents (à partir des connaissances scientifiques, des explications scientifiques et des attitudes par rapport aux sciences). Et l'enquête menée par le Pew Research Center en 2018 aux États-Unis. Les données nous informent sur l'appartenance à une religion, l'intensité de la pratique religieuse, la fréquence de la prière et l'importance de la religion dans la vie quotidienne. Les connaissances scientifiques sont mesurées à partir d'une série de neuf variables permettant d'élaborer un score de connaissance scientifique.

(3) Les questionnaires ne permettaient pas de creuser avec précision l'effet " prudence féminine " qui conduit ces dernières à répondre plus souvent " je ne sais pas " lorsque c'est possible tandis que les hommes ont plus souvent tendance à répondre au pif plutôt que d'admettre leur ignorance ce qui gonfle équitablement les bonnes... et les mauvaises réponses aux questions de connaissances scientifiques. Un résultat connu par ailleurs. Cette " prudence féminine " peut d'ailleurs s'interpréter de manière positive : savoir qu'on ne sait pas est une attitude profondément scientifique puisqu'elle conduit à la recherche (lire Sciences, les Français sont-ils nuls ?).

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Plus de religion égale moins de sciences

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Peut-on concilier la croyance religieuse et une attitude scientifique ? Les partisans de cette thèse mettent en avant quelques noms de grands scientifiques ayant affirmé que leurs recherches ne les empêchaient pas de croire en Dieu. Mais les sociologues - des scientifiques eux aussi - n'acceptent pas de se contenter de quelques exemples.

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Church of England to Darwin: We're Sorry

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Church of England to Darwin: We're Sorry

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The Church of England, the Anglican denomination that dates to the 16th century, has issued an apology of sorts to Charles Darwin, the British naturalist famous for having advanced the theory of evolution.

In an essay published on the C of E's Web site, "Good Religion Needs Good Science," the Rev. Malcolm Brown, the church's director of mission and public affairs, says that the church, in opposing Darwin's ideas, has at times been guilty of distorting them and wrongly assuming that they contradict Christian beliefs. The idea that God created humans is consistent with evolution, Brown writes. Evolution simply provides a greater understanding of the exact processes through which humans came to be.

The church's new point of view, which has been greeted with a mixture of curiosity and derision by the British press, was published with a series of documents about Darwin on the church's Web site. The publications coincide with the approaching bicentenary of Charles Darwin's birth in 1809 and the 150th anniversary of the publication of On the Origin of Species in 1859.

In his essay, Brown traces his church's opposition to many of Darwin's principles and attempts to explain them. He also warns against the "social misapplication" of Darwin's theories about survival of the fittest, which he says have been used to justify racism, other forms of discrimination, and "material self-interest."

But the church official's main point seems to be that evolutionary theory and religion are compatible, and that accepting faith does not mean rejecting science-or vice versa.

"For the sake of human integrity-and thus for the sake of good Christian living-some rapprochement between Darwin and Christian faith is essential," Brown writes.

"Charles Darwin: 200 years from your birth, the Church of England owes you an apology for misunderstanding you and, by getting our first reaction wrong, encouraging others to misunderstand you still. We try to practice the old virtues of 'faith seeking understanding' and hope that makes some amends. But the struggle for your reputation is not over yet, and the problem is not just your religious opponents but those who falsely claim you in support of their own interests. Good religion needs to work constructively with good science-and I dare to suggest that the opposite may be true as well."

Many scientists who defend the teaching of evolution in public school science classes -and reject efforts to introduce religious alternatives to it in those settings-say evolutionary theory is completely consistent with Christian faith. But they also argue that faith and science should be discussed in different spheres. Whether the Church of England's views on this subject shape public thinking remains to be seen.

# data[].attributes.attachment_link.title
Church of England to Darwin: We're Sorry

# data[].attributes.attachment_link.description
The Church of England, the Anglican denomination that dates to the 16th century, has issued an apology of sorts to Charles Darwin, the British naturalist famous for having advanced the theory of evolution. In an essay published on the C of E's Web site, "Good Religion Needs Good Science," the Rev.

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Les « sans religion » : la nouvelle religion ?

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Les « sans religion » : la nouvelle religion ?

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Les « sans religion » : la nouvelle religion ?

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L’augmentation du nombre de personnes se déclarant sans religion et la diversité de ce groupe interrogent aujourd’hui les chercheurs. C’est en effet, disent-ils une nouvelle « majorité silencieuse ».

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Cerebellar nuclei evolved by repeatedly duplicating a conserved cell-type set

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Cerebellar nuclei evolved by repeatedly duplicating a conserved cell-type set

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© 2021 American Association for the Advancement of Science. All rights reserved. AAAS is a partner of HINARI, AGORA, OARE, CHORUS, CLOCKSS, CrossRef and COUNTER.

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Paleontologists Find Evolutionary Link between Ediacaran and Early Cambrian Multicellular Animals | Sci-News.com

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Paleontologists Find Evolutionary Link between Ediacaran and Early Cambrian Multicellular Animals | Sci-News.com

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A Surprisingly Simple Biochemistry Rule Drives the Evolution of Useless Complexity

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A Surprisingly Simple Biochemistry Rule Drives the Evolution of Useless Complexity

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A Surprisingly Simple Biochemistry Rule Drives the Evolution of Useless Complexity

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New study shows that proteins become biochemically addicted to complex interactions without adaptation. A new study at the University of Chicago has shown that elaborate protein structures accumulate over deep time even when they serve no purpose, because a universal biochemical property and the

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Discovery boosts theory that life on Earth arose from RNA-DNA mix

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Discovery boosts theory that life on Earth arose from RNA-DNA mix

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Discovery boosts theory that life on Earth arose from RNA-DNA mix

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Chemists at Scripps Research have made a discovery that supports a surprising new view of how life originated on our planet.

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Hasard : il façonne tout le vivant ! - Science-et-vie.com

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Non, un être ne se développe pas sous la seule et implacable dictée de ses gènes. Le hasard se manifeste à tous les étages du vivant

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Study reveals a surprising similarity between bonobos and humans

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A new study reveals that bonobos and humans may share one similar social behavior: joint committment.

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Why don’t wildebeest have wheels? Exploring the limits of evolution

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Evolution has produced a stupendous diversity of lifeforms, but there are some adaptations it never seems to produce, like flying plants or zebras with guns. Is there is a limit to its creativity?

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160 Years Later, Study Shows Charles Darwin Was Right About Why Insects Are Losing the Ability to Fly

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160 Years Later, Study Shows Charles Darwin Was Right About Why Insects Are Losing the Ability to Fly

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Most insects can fly.

Yet scores of species have lost that extraordinary ability, particularly on islands.

On the small islands that lie halfway between Antarctica and continents like Australia, almost all the insects have done so.

Flies walk, moths crawl.

"Of course, Charles Darwin knew about this wing loss habit of island insects," says PhD candidate Rachel Leihy, from the Monash University School of Biological Sciences.

"He and the famous botanist Joseph Hooker had a substantial argument about why this happens. Darwin's position was deceptively simple. If you fly, you get blown out to sea. Those left on land to produce the next generation are those most reluctant to fly, and eventually evolution does the rest. Voilà."

But since Hooker expressed his doubt, many other scientists have too.

In short, they have simply said Darwin got it wrong.

Yet almost all of these discussions have ignored the place that is the epitome of flight loss - those 'sub-Antarctic' islands. Lying in the 'roaring forties' and 'furious fifties', they're some of the windiest places on Earth.

"If Darwin really got it wrong, then wind would not in any way explain why so many insects have lost their ability to fly on these islands," said Rachel.

Using a large, new dataset on insects from sub-Antarctic and Arctic islands, Monash University researchers examined every idea proposed to account for flight loss in insects, including Darwin's wind idea.

Reported on December 9, 2020, in Proceedings of the Royal Society B, they show that Darwin was right for this 'most windy of places'. None of the usual ideas (such as those proposed by Hooker) explain the extent of flight loss in sub-Antarctic insects, but Darwin's idea does. Although in a slightly varied form, in keeping with modern ideas on how flight loss actually evolves.

Windy conditions make insect flight more difficult and energetically costly. Thus, insects stop investing in flight and its expensive underlying machinery (wings, wing muscles) and redirect the resources to reproduction.

"It's remarkable that after 160 years, Darwin's ideas continue to bring insight to ecology," said Rachel, the lead author of the paper.

Professor Steven Chown, also from the School of Biological Sciences, added that the Antarctic region is an extraordinary laboratory in which to resolve some of the world's most enduring mysteries and test some of its most important ideas.

Reference: "Wind plays a major but not exclusive role in the prevalence of insect flight loss on remote islands" by Rachel I. Leihy and Steven L. Chown, 9 December 2020, Proceedings of the Royal Society B.
DOI: 10.1098/rspb.2020.2121

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160 Years Later, Study Shows Charles Darwin Was Right About Why Insects Are Losing the Ability to Fly

# data[].attributes.attachment_link.description
Most insects can fly. Yet scores of species have lost that extraordinary ability, particularly on islands. On the small islands that lie halfway between Antarctica and continents like Australia, almost all the insects have done so. Flies walk, moths crawl. "Of course, Charles Darwin knew

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Orientation Preference Maps in Microcebus murinus Reveal Size-Invariant Design Principles in Primate Visual Cortex: Current Biology

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Orientation Preference Maps in Microcebus murinus Reveal Size-Invariant Design Principles in Primate Visual Cortex: Current Biology

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Orientation Preference Maps in Microcebus murinus Reveal Size-Invariant Design Principles in Primate Visual Cortex

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Orientation preference maps are a hallmark of V1 organization in all primates studied
thus far, yet they are absent in rodents. It is uncertain whether these structures
scale with body or brain size. Using intrinsic signal imaging, Ho et al. reveal the
presence of such maps in the V1 of the world’s…

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Rapid evolution of coordinated and collective movement in response to artificial selection

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Rapid evolution of coordinated and collective movement in response to artificial selection

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© 2021 American Association for the Advancement of Science. All rights reserved. AAAS is a partner of HINARI, AGORA, OARE, CHORUS, CLOCKSS, CrossRef and COUNTER.

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Les humains précipitent l'évolution - Sciences et Avenir

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Les humains précipitent l'évolution - Sciences et Avenir

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A priori condamnés à mourir de fail, des oiseaux de proie américains ont évité l'extinction en développant des becs plus longs... en dix ans seulement, selon des observations récentes publiées dans Nature Ecology and Evolution. On imagine les yeux grands comme des soucoupes qu'ouvrirait Charles Darwin (1809-1882) à cette nouvelle, lui qui a construit sa théorie de l'évolution en s'appuyant justement sur les variations - qu'il estimait plutôt lentes - des becs de pinson en fonction de leur alimentation dans les îles Galapagos. Dans L'Origine des espèces (1859), il écrivait : "La sélection naturelle agira toujours très lentement, souvent seulement à de longs intervalles de temps." Le savant n'avait pas imaginé qu'au cours des 20e et 21e siècles, les humains exerceraient des pressions telles sur la biodiversité qu'ils en deviendraient l'un des moteurs ! Pas uniquement par le biais de la chasse, de la domestication ou de la modification des paysages, mais aussi à travers leurs voyages mondialisés, l'introduction d'espèces exotiques, le changement climatique et l'abus de produits chimiques. Au point qu'une nouvelle discipline est en train de naître selon l'écologue Timothy Farkas, de l'université du Nouveau-Mexique, à Albuquerque (États-Unis) : " l'évologie, un mélange entre les études d'écologie et d'évolution." Les exemples se multiplient et permettent de mieux comprendre l'ampleur du phénomène.

L'exemple du milan des marais des Everglades

Ainsi, l'histoire racontée par Robert J. Fletcher Jr, un chercheur de l'université de Floride à Gainesville (États-Unis), au sujet des changements morphologiques rapides des rapaces locaux à la suite des bouleversements humains est passionnante : il y a vingt-cinq ans, comme tous ses collègues, les scientifiques ne donnaient pas cher de la peau du milan des marais des Everglades ( Rostrhamus sociabilis plumbeus) en Floride. L'espèce était menacée par la raréfaction de sa proie quasi exclusive : un mollusque d'eau douce présent depuis plus de 2 millions d'années, mais peu à peu laminé par le drainage des canaux, la disparition des zones humides et la pollution. En 2007, l'inquiétude monte d'un cran avec l'invasion d'escargots géants d'eau douce ( Pomacea maculata), relâchés dans la nature par des vendeurs d'animaux de compagnie tropicaux. Les envahisseurs - increvables face à l'assèchement, les inondations et les produits chimiques -sont deux à cinq fois plus gros que les indigènes, leur coquille atteignant jusqu'à 15 cm de diamètre. Les premières observations montrent que les jeunes milans ne parviennent pas à en extraire la chair, leur bec étant trop petit, ce qui semble sonner le glas de l'espèce... Mais c'est l'inverse qui se produit ! Partout où l'escargot exotique prospère, les populations de milans augmentent.

Au laboratoire de Gainesville, les chercheurs pensent que les jeunes rapaces ont appris à manier ces proies plus massives jusqu'à ce que Rob Fletcher Jr suggère que les milans ont pu s'y adapter... par de plus gros becs. Le scepticisme de ses collègues est général mais l'analyse de onze années de données morphologiques lui donne raison. Les oisillons grandissent et grossissent bel et bien plus vite chaque année, surtout du bec ! "Jusqu'à plus 2 mm pour un appendice de 23,4 mm en moyenne chez les jeunes à l'envol, soit une augmentation de 9 % !" détaille Rob Fletcher Jr (Chez les adultes, la taille du "claquoir" varie de 26 à 34 mm).

La régulation génétique de la croissance modifiée

Malheureusement, faute de temps et de moyens, les scientifiques n'ont pas pu pousser plus loin leurs investigations. " Cependant, nous soupçonnons qu'un changement dans la régulation génétique de la croissance de cet appendice peut s'être produit, ce qui pourrait présager un véritable changement évolutif", souligne Rob Fletcher Jr. Car un oiseau peut avoir le potentiel génétique de développer un très gros bec, à condition qu'il exerce les muscles de son appendice en mangeant de plus grosses proies dans sa jeunesse. Pour le spécialiste, " ce travail illustre très clairement que même de grands prédateurs vertébrés peuvent répondre aux invasions à un rythme beaucoup plus rapide que nous le supposions". Prouver une évolution n'est cependant pas aisé. Pour en avoir le cœur net, " il faut mener, en laboratoire, de savantes expériences de croisement ou explorer des génomes et des épigénomes , explique Anne Charmantier, spécialiste en génétique et écologie évolutive au CNRS, à Montpellier. Il faut en effet déterminer si les organismes étudiés bénéficient d'une évolution passée ou s'ils ont la capacité d'ajuster eux-mêmes leur comportement ou leur morphotype en fonction de l'environnement. Et comprendre si des modifications génétiques sont - ou non - à l'œuvre."

C'est ce que fait Yoel Stuart, biologiste à l'université du Texas, à Austin (États-Unis), qui a introduit en 1995 le lézard anole brun ( Anolis sagrei) cubain dans de petites îles où l'anole vert ( A. carolinensis) coulait des jours tranquilles. Le chercheur souhaitait mesurer dans " ces laboratoires confinés de plein air" l'impact de cet envahisseur, arrivé en Floride avec des plantes importées auxquelles ses œufs étaient restés accrochés. La rencontre est stressante. Soumis à une concurrence alimentaire et spatiale et à une voracité cannibale, les lézards verts se perchent plus haut dans les arbres, là où les branches sont plus minces et ploient. Mais ils évitent la dégringolade ! Car en 20 générations (quatorze ans), ils se dotent de doigts plus longs et de coussinets collants plus larges sur les orteils. À titre de comparaison, si la taille de l'être humain évoluait aussi vite, elle passerait d'environ 1,80 m à 2 mètres en cinq cents ans. " La vitesse de la réponse évolutive nous a surpris, mais elle a renforcé la notion grandissante selon laquelle l'évolution peut être observée en quelques générations lorsque la survie et la reproduction en dépendent", détaille Yoel Stuart.

Autre pression humainement induite, celle du changement climatique en cours. " Avec la fonte des neiges, la chouette hulotte de Finlande (Strix aluco) a vu quasi disparaître sa forme grise au profit de la forme brune", explique Patrik Karell, de l'université d'Helsinki (Finlande). Le phénomène s'est accéléré au cours des vingt-huit dernières années, a-t-il détaillé dans un article de Nature (2011). Or la coloration des chouettes est hautement héréditaire, indépendante de l'âge et du sexe. Les scientifiques ont ainsi pu apporter les preuves solides d'une réponse génétique au changement climatique. Une première chez des animaux vertébrés. Dans la foulée, des études probantes ont été faites chez les saumons roses d'Alaska, montrant que les individus au profil génétique de migrateurs précoces ont été sélectionnés au détriment des migrateurs tardifs. Car fuir le plus tôt possible la chaleur des eaux est devenu vital...

La notion de spéciation remise en question

Le milieu urbain peut aussi favoriser l'éclosion de nouvelles espèces, comme Culex molestus, alias le moustique vorace du métro de Londres, distinct génétiquement des autres Culex comme l'a montré Kate Byrne, de la Queen Mary University de Londres (Royaume-Uni) dès 1998. Piégé dans les tunnels, l'insecte a changé de cible alimentaire en piquant humains et rats, faute d'oiseaux ; de surcroît, il n'hiberne plus et a abandonné la formation de nuées pour se reproduire. Aujourd'hui, ce moustique s'est répandu dans de nombreuses villes du monde (New York, Paris, Shanghai, Moscou). Un large recours aux produits chimiques a aussi favorisé l'apparition de punaises et de moustiques insensibles à tous les insecticides.

Mais l'exemple le plus frappant est l'apparition, en Espagne et en Allemagne, de "super-souris" résistantes à la warfarine, un anticoagulant censé réduire leurs boyaux en bouillie. " Quelques rongeurs d'Europe (Mus musculus domesticus) ont pu s'accoupler avec succès avec des cousins lointains naturellement immunisés et venus d'Algérie (Mus spretus) en suivant les migrations humaines", raconte Michael Kohn, de l'université Rice, au Texas (États-Unis), qui a mis au jour ces hybridations dans Current Biology . Un choc ! car les deux espèces, génétiquement "déconnectées" depuis au moins 1,5 million d'années, auraient dû perdre la possibilité de se reproduire.

Cette découverte interroge la validité de la notion de spéciation -ou apparition de nouvelles espèces incapables de se reproduire entre elles. " L'évolution s'accélère tant qu'elle bouleverse nos expérimentations de terrain et nos certitudes , résume l'écologue Timothy Farkas qui travaille sur les phasmes verts et bruns et a vu ses expériences balayées par des phénomènes aussi rapides qu'inattendus. Le "graal" aujourd'hui, c'est l'évologie. La seule façon pour nous de tenter de comprendre l'ampleur du phénomène."
Le bec de "Rostrhamus sociabilis plumbeus"a grossi pour pouvoir s'attaquer à la coquille d'un escargot invasif, 2 à 5 fois plus gros que celui consommé jusque-là par le rapace (à droite). Crédit : PHOTOS : ROBERT FLETCHER
Des modifications morphologiques très marquées

Les comportements humains influencent l'évolution écologique depuis des siècles. La chasse de trophées conduit ainsi à une réduction de la taille des cornes ou crinières ; la prédation se traduit par un rapetissement des proies. L'extinction d'une espèce favorise la miniaturisation de ses ressources alimentaires, qui n'ont plus à résister en croissant. La domestication sélectionne des aliments - animaux ou végétaux - dépourvus de défenses et plus charnus. La disparition d'arbres au profit de constructions favorise la modification des membres des espèces qui explorent ces nouveaux terrains urbains. La sélection génétique, enfin, accélère notamment la croissance.

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Les humains précipitent l'évolution - Sciences et Avenir

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A priori condamnés à mourir de fail, des oiseaux de proie américains ont évité l'extinction en développant des becs plus longs... en dix ans seulement, selon des observations récentes publiées dans Nature Ecology and Evolution.

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Artificial intelligence finds surprising patt | EurekAlert!

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Artificial intelligence finds surprising patt | EurekAlert!

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Charles Darwin's landmark opus, On the Origin of the Species, ends with a beautiful summary of his theory of evolution, "There is a grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." In fact, scientists now know that most species that have ever existed are extinct. This extinction of species has on the whole been roughly balanced by the origination of new ones over Earth's history, with a few major temporary imbalances scientists call mass extinction events. Scientists have long believed that mass extinctions create productive periods of species evolution, or "radiations," a model called "creative destruction." A new study led by scientists affiliated with the Earth-Life Science Institute (ELSI) at Tokyo Institute of Technology used machine learning to examine the co-occurrence of fossil species and found that radiations and extinctions are rarely connected, and thus mass extinctions likely rarely cause radiations of a comparable scale.

Creative destruction is central to classic concepts of evolution. It seems clear that there are periods in which suddenly many species suddenly disappear, and many new species suddenly appear. However, radiations of a comparable scale to the mass extinctions, which this study, therefore, calls the mass radiations, have received far less analysis than extinction events. This study compared the impacts of both extinction and radiation across the period for which fossils are available, the so-called Phanerozoic Eon. The Phanerozoic (from the Greek meaning "apparent life"), represents the most recent ~ 550-million-year period of Earth's total ~4.5 billion-year history, and is significant to palaeontologists: before this period most of the organisms that existed were microbes that didn't easily form fossils, so the prior evolutionary record is hard to observe. The new study suggests creative destruction isn't a good description of how species originated or went extinct during the Phanerozoic, and suggests that many of the most remarkable times of evolutionary radiation occurred when life entered new evolutionary and ecological arenas, such as during the Cambrian explosion of animal diversity and the Carboniferous expansion of forest biomes. Whether this is true for the previous ~ 3 billion years dominated by microbes is not known, as the scarcity of recorded information on such ancient diversity did not allow a similar analysis.

Palaeontologists have identified a handful of the most severe, mass extinction events in the Phanerozoic fossil record. These principally include the big five mass extinctions, such as the end-Permian mass extinction in which more than 70% of species are estimated to have gone extinct. Biologists have now suggested that we may now be entering a "Sixth Mass Extinction," which they think is mainly caused by human activity including hunting and land-use changes caused by the expansion of agriculture. A commonly noted example of the previous "Big Five" mass extinctions is the Cretaceous-Tertiary one (usually abbreviated as "K-T," using the German spelling of Cretaceous) which appears to have been caused when a meteor hit Earth ~65 million years ago, wiping out the non-avian dinosaurs. Observing the fossil record, scientists came to believe that mass extinction events create especially productive radiations. For example, in the K-T dinosaur-exterminating event, it has conventionally been supposed that a wasteland was created, which allowed organisms like mammals to recolonise and "radiate," allowing for the evolution of all manner of new mammal species, ultimately laying the foundation for the emergence of humans. In other words, if the K-T event of "creative destruction" had not occurred, perhaps we would not be here to discuss this question.

The new study started with a casual discussion in ELSI's "Agora," a large common room where ELSI scientists and visitors often eat lunch and strike up new conversations. Two of the paper's authors, evolutionary biologist Jennifer Hoyal Cuthill (now a research fellow at Essex University in the UK) and physicist/machine learning expert Nicholas Guttenberg (now a research scientist at Cross Labs working in collaboration with GoodAI in the Czech Republic), who were both post-doctoral scholars at ELSI when the work began, were kicking around the question of whether machine learning could be used to visualise and understand the fossil record. During a visit to ELSI, just before the COVID-19 pandemic began to restrict international travel, they worked feverishly to extend their analysis to examine the correlation between extinction and radiation events. These discussions allowed them to relate their new data to the breadth of existing ideas on mass extinctions and radiations. They quickly found that the evolutionary patterns identified with the help of machine learning differed in key ways from traditional interpretations.

The team used a novel application of machine learning to examine the temporal co-occurrence of species in the Phanerozoic fossil record, examining over a million entries in a massive curated, public database including almost two hundred thousand species.

Lead author Dr Hoyal Cuthill said, "Some of the most challenging aspects of understanding the history of life are the enormous timescales and numbers of species involved. New applications of machine learning can help by allowing us to visualise this information in a human-readable form. This means we can, so to speak, hold half a billion years of evolution in the palms of our hands, and gain new insights from what we see."

Using their objective methods, they found that the "big five" mass extinction events previously identified by palaeontologists were picked up by the machine learning methods as being among the top 5% of significant disruptions in which extinction outpaced radiation or vice versa, as were seven additional mass extinctions, two combined mass extinction-radiation events and fifteen mass radiations. Surprisingly, in contrast to previous narratives emphasising the importance of post-extinction radiations, this work found that the most comparable mass radiations and extinctions were only rarely coupled in time, refuting the idea of a causal relationship between them.

Co-author Dr Nicholas Guttenberg said, "the ecosystem is dynamic, you don't necessarily have to chip an existing piece off to allow something new to appear."

The team further found that radiations may in fact cause major changes to existing ecosystems, an idea the authors call "destructive creation." They found that, during the Phanerozoic Eon, on average, the species that made up an ecosystem at any one time are almost all gone by 19 million years later. But when mass extinctions or radiations occur, this rate of turnover is much higher.

This gives a new perspective on how the modern "Sixth Extinction" is occurring. The Quaternary period, which began 2.5 million years ago, had witnessed repeated climate upheavals, including dramatic alternations of glaciation, times when high latitude locations on Earth, were ice-covered. This means that the present "Sixth Extinction" is eroding biodiversity that was already disrupted, and the authors suggest it will take at least 8 million years for it to revert to the long term average of 19 million years. Dr Hoyal Cuthill comments that "each extinction that happens on our watch erases a species, which may have existed for millions of years up to now, making it harder for the normal process of 'new species origination' to replace what is being lost."

###

Reference
J. F. Hoyal Cuthill 1,2,3*, N. Guttenberg 2,4,5 and G. E. Budd ⁶, Impacts of speciation and extinction measured by an evolutionary decay clock, Nature, DOI: 10.1038/s41586-020-3003-4

1. Institute of Analytics and Data Science and School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK

2. Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8550, Japan

3. Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EQ, UK

4. Cross Labs, Cross Compass Ltd., 2-9-11-9F Shinkawa, Chuo-ku, Tokyo 104-0033, Japan

5. GoodAI, Na Petynce, 213/23b, 169 00, Prague, Czech Republic

6. Department of Earth Sciences, Palaeobiology Programme, Uppsala University, Villavägen 16, SE752 36, Uppsala, Sweden

More information
Tokyo Institute of Technology (Tokyo Tech) stands at the forefront of research and higher education as the leading university for science and technology in Japan. Tokyo Tech researchers excel in fields ranging from materials science to biology, computer science, and physics. Founded in 1881, Tokyo Tech hosts over 10,000 undergraduate and graduate students per year, who develop into scientific leaders and some of the most sought-after engineers in industry. Embodying the Japanese philosophy of "monotsukuri," meaning "technical ingenuity and innovation," the Tokyo Tech community strives to contribute to society through high-impact research.

The Earth-Life Science Institute (ELSI) is one of Japan's ambitious World Premiere International research centers, whose aim is to achieve progress in broadly inter-disciplinary scientific areas by inspiring the world's greatest minds to come to Japan and collaborate on the most challenging scientific problems. ELSI's primary aim is to address the origin and co-evolution of the Earth and life.

The World Premier International Research Center Initiative (WPI) was launched in 2007 by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) to help build globally visible research centers in Japan. These institutes promote high research standards and outstanding research environments that attract frontline researchers from around the world. These centers are highly autonomous, allowing them to revolutionise conventional modes of research operation and administration in Japan.

Cross Labs is a research institute focused on machine intelligence, cognitive sciences, and artificial life, aimed at uncovering the mathematical principles of intelligence in natural and artificial systems. Cross Labs was founded in 2019 as a bridge between academia and the industry, by Cross Compass Ltd., a leading AI company providing state-of-the-art solutions to global industry leaders in manufacturing, robotics, gaming, healthcare, design, and marketing. Established in Tokyo in 2015, Cross Compass develops cutting-edge techniques in deep learning, machine learning, and artificial life, to increase safety, quality, and productivity for the benefit of society. For more information, please visit crosslabs.org and cross-compass.com.

GoodAI is a research and development organisation based in Prague with the goal to develop general artificial intelligence - as fast as possible - to help humanity and understand the universe. It was founded by CEO/CTO Marek Rosa in January 2014 and now has over 30 research scientists, engineers, and consultants working across its divisions.

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Artificial intelligence finds surprising patterns in Earth's biological mass extinctions

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Scientists have long believed that mass extinctions create productive periods of species evolution, or "radiations," a model called "creative destruction." However, new analysis provide evidence for different outcome.

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How Modern Genomics Is Rewriting Our Understanding of History | Technology Networks

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How Modern Genomics Is Rewriting Our Understanding of History | Technology Networks

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Genomics Research from Technology Networks

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A reduction in the cost and time required to conduct studies has seen genomics offer a helping hand in our efforts to understand history. By sequencing ancient DNA - whether it be human or animal in origin - scientists are contributing biological evidence to the words of history books, consolidating them, refuting them and sometimes completely rewriting them. Here is what the genetics research of 2020 taught us about the past. DNA sequencing

In a six-year research study by collaborators at the University of Cambridge and the University of Copenhagen, scientists conducted DNA sequencing of over 400 Viking skeletons. These remains had been obtained from a number of different archaeological sites in Europe and Greenland, and their analysis debunked several beliefs about Vikings, revealing:

Many Vikings were brunette, not blonde.

Early Viking raiding parties were an activity for local individuals and involved close family members.

The UK population carries up to six percent Viking DNA.

The skeletons obtained from Viking burial sites were actually local individuals who were buried as Vikings.

"The results change the perception of who a Viking actually was. The history books will need to be updated,"

An interdisciplinary team of researchers conducted a seven-year research study in which they analyzed the Dead Sea Scrolls - some 25,000 fragments of leather and papyrus that were discovered in 1947 - in an effort to piece together the puzzle. The parchments were discovered mainly in the Qumran caves and contain the oldest copies of biblical texts.

The scientists generated over 2.6 billion sequencing reads from the fragments they analyzed, and in doing so, learnt an awful lot about the history of the scrolls.

The DNA evidence enabled them to distinguish between different pieces of fragment that originated from different animals of the same species. If the fragments did belong to the same scroll, the likelihood is that they were from two different sheets.

Some pieces analyzed were also genetically different from other segments, which implies they are unrelated to the scrolls.

"You can extract enough authentic DNA from pieces that are over 2000 years old and use it to learn about the relationships of the different fragments. Aside from the fact that it's cool, it shows how interdisciplinary science can have real value," - Professor Oded Rechavi, in an exclusive interview

Scientists from Cornell University and Cold Spring Harbor Laboratory devised an algorithm for analyzing genomes that is able to pinpoint segments of DNA that came from other species. When applying the algorithm to DNA from two Neanderthals, two African humans and a Denisovan, they found that three percent of the Neanderthal genome came from ancient humans. One percent of the Denisovan genome came from an unknown, and slightly more distant relative. The scientists hypothesized that this may be Homo erectus, and 15% of these DNA regions may have been passed on to humans that are alive today.

"What I think is exciting about this work is that it demonstrates what you can learn about deep human history by jointly reconstructing the full evolutionary history of a collection of sequences from both modern humans and archaic hominins," - Adam Siepel.

The clinical variability of COVID-19 patients has proven a huge challenge to researchers and clinicians throughout 2020. Why are some patients completely asymptomatic, whilst others contract the virus and die?

Several large-scale research studies suggested a gene cluster, chr3p21.31, may be associated with disease severity. Scientists wanted to know more about this gene cluster and where it came from. In September 2020, researchers from the Karolinska Institute and the Max Planck Institute for Evolutionary Anthropology published a study reporting that the gene cluster on chromosome three is very similar to the DNA sequence of a 50,000-year-old Neanderthal.The study does not explain why this particular variant is associated with a higher risk of severe COVID-19, but the authors believe their findings are of historical interest and should be explored further, as it may offer novel insights into our ancestor's susceptibility to certain pathogens.

"It turns out that this gene variant was inherited by modern humans from the Neandertals when they interbred some 60,000 years ago. Today, the people who inherited this gene variant are three times more likely to need artificial ventilation if they are infected by the novel coronavirus SARS-CoV-2," Hugo Zeberg.

Regarded as man's best friend, dogs have been our close companions for thousands of years. Despite this, little is known about the origin of specific dog populations, how they diversified and spread across the globe, and how human movements might have influenced this.

In an international study, scientists sequenced 27 ancient dog genomes that were obtained from Europe, Siberia and the Near East. They found that the dogs had already diversified into distinct populations by the period from which the oldest sample was from, 10,900 years old. Interestingly, there was very little contribution of wild dogs and wolves in these genetic datasets, which the researchers attribute to human selection against wolf hybrids, which may have been vicious.

When exactly wolves were domesticated by humans remains elusive; but the results of this study - which show dogs had diversified by 10,900 years ago - imply it may have been earlier than once thought.

"We found that the genome of a dog found at a 5000-year-old site in Southern Sweden can explain practically all of the genetic heritage of modern European dogs. This means that a single population with ancestry similar to that of this individual replaced all other populations on the continent," - Laurent Frantz.

5. Bergström A, Frantz L, Schmidt R, et al. Origins and genetic legacy of prehistoric dogs. Science. 2020;370(6516)557-564. doi: 10.1126/science.aba9572 .

# data[].attributes.attachment_link.title
How Modern Genomics Is Rewriting Our Understanding of History

# data[].attributes.attachment_link.description
By sequencing ancient DNA - whether it be human or animal in origin - scientists are contributing biological evidence to the words of history books, consolidating them, refuting them and sometimes completely rewriting them. Here is what the genetics research of 2020 taught us about the past.

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Quand les serpents avaient des pattes... | Pour la Science

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Quand les serpents avaient des pattes... | Pour la Science

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Quand les serpents avaient des pattes...

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Il y a 90 millions d’années, les serpents étaient dotés de membres. L’analyse de leurs os fossiles montre que ces animaux, bien que marins, sont issus de lézards terrestres.

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RETRACTED ARTICLE: Complex societies precede moralizing gods throughout world history | Nature

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RETRACTED ARTICLE: Complex societies precede moralizing gods throughout world history | Nature

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Abstract

The origins of religion and of complex societies represent evolutionary puzzles. The 'moralizing gods' hypothesis offers a solution to both puzzles by proposing that belief in morally concerned supernatural agents culturally evolved to facilitate cooperation among strangers in large-scale societies. Although previous research has suggested an association between the presence of moralizing gods and social complexity, the relationship between the two is disputed, and attempts to establish causality have been hampered by limitations in the availability of detailed global longitudinal data. To overcome these limitations, here we systematically coded records from 414 societies that span the past 10,000 years from 30 regions around the world, using 51 measures of social complexity and 4 measures of supernatural enforcement of morality. Our analyses not only confirm the association between moralizing gods and social complexity, but also reveal that moralizing gods follow-rather than precede-large increases in social complexity. Contrary to previous predictions, powerful moralizing 'big gods' and prosocial supernatural punishment tend to appear only after the emergence of 'megasocieties' with populations of more than around one million people. Moralizing gods are not a prerequisite for the evolution of social complexity, but they may help to sustain and expand complex multi-ethnic empires after they have become established. By contrast, rituals that facilitate the standardization of religious traditions across large populations generally precede the appearance of moralizing gods. This suggests that ritual practices were more important than the particular content of religious belief to the initial rise of social complexity.

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Data availability

The full machine-readable dataset is available as Supplementary Data 1, and at http://seshatdatabank.info/datasets. Full coding data with detailed explanations and references are available at http://seshatdatabank.info/data, and are summarized in Supplementary Table 2. The data include the coded levels of uncertainty and disagreement, the textual explanations and the references for each of the variables for all polities used in our analysis. These webpages also make it possible to comment on each of our data points and suggest additions or corrections and thus provide an up-to-date and dynamic dataset that undergoes continual improvement by members of the Seshat team and external scholars. To maximize transparency, we have tied each cluster of variables to the names of the research assistants who gathered the data, and to the names of the experts who reviewed the data.

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Download references

Acknowledgements

We thank Q. Atkinson and A. Willard for feedback on an earlier version of the manuscript and E. Postma for discussions on parts of the statistical analyses. We acknowledge the contributions of our team of research assistants, post-doctoral researchers, consultants and experts. See http://www.seshatdatabank.info for a comprehensive list of private donors, partners, experts and consultants. This work was supported by an ESRC Large Grant entitled 'Ritual, Community, and Conflict' (REF RES-060-25-0085), a John Templeton Foundation grant to the Evolution Institute entitled 'Axial-Age Religions and the Z-Curve of Human Egalitarianism', a Tricoastal Foundation grant to the Evolution Institute entitled 'The Deep Roots of the Modern World: The Cultural Evolution of Economic Growth and Political Stability', an Advanced Grant ('Ritual Modes: Divergent modes of ritual, social cohesion, prosociality, and conflict', grant agreement no. 694986) and a Starter Grant ('The Cultural Evolution & Ecology of Institutions', grant agreement no. 716212) from the European Research Council (ERC) under the European Union's Horizon 2020 Research and Innovation Programme, an award from the Templeton World Charity Foundation entitled 'Cognitive and Cultural Foundations of Religion and Morality' (TWCF0164), a Keio Research Institute at SFC Startup Grant, a Keio Gijuku Academic Development Fund Individual Grant and a grant from the European Union Horizon 2020 Research and Innovation Programme (grant agreement no. 644055 (ALIGNED, www.aligned-project.eu)).

Reviewer information

Nature thanks Carol Ember, Peter J. Richerson and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Author information

Author notes

These authors contributed equally: Harvey Whitehouse, Pieter François, Patrick E. Savage

Affiliations

1. Centre for the Study of Social Cohesion, University of Oxford, Oxford, UK

Harvey Whitehouse, Pieter François, Patrick E. Savage & Robert M. Ross

2. St Benet's Hall, Oxford, UK

Pieter François

3. Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan

Patrick E. Savage

4. Human Behaviour & Cultural Evolution Group, Department of Biosciences, University of Exeter, Penryn, UK

Thomas E. Currie

5. School of Computer Science and Statistics, Trinity College Dublin, Dublin, Ireland

Kevin C. Feeney

6. Seshat: Global History Databank, Evolution Institute, San Antonio, FL, USA

Enrico Cioni & Rosalind Purcell

7. ARC Centre of Excellence in Cognition and its Disorders and Department of Psychology, Royal Holloway, University of London, Egham, UK

Robert M. Ross

8. Department of Anthropology and Archaeology, University of Bristol, Bristol, UK

Robert M. Ross

9. Department of Modern & Classical Language Studies, Kent State University, Kent, OH, USA

Jennifer Larson

10. Faculty of Oriental Studies, University of Oxford, Oxford, UK

John Baines

11. Department of Chinese Language and Culture, Asia-Africa-Institute, University of Hamburg, Hamburg, Germany

Barend ter Haar

12. Department of Anthropology, University of Texas at Austin, Austin, TX, USA

Alan Covey

13. Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA

Peter Turchin

14. Complexity Science Hub Vienna, Wien, Austria

Peter Turchin

Contributions

H.W., P.F. and P.E.S. designed the study, with input from P.T., T.E.C., K.C.F. and R.M.R.; E.C. and R.P. coded the religion and ritual data, with additional input from J.L., J.B., B.t.H and A.C.; P.E.S. analysed the data, with input from H.W., P.F., P.T., T.E.C. and R.M.R.; P.E.S., H.W. and P.F. drafted the manuscript.

Corresponding author

Correspondence to Patrick E. Savage.

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Competing interests

The authors declare no competing interests.

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Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data figures and tables

The 12 regions for which social complexity data are available both before and after the appearance of moralizing gods are shown. Vertical bands represent the period in which the first evidence of moralizing gods (red) and doctrinal rituals (blue) appeared. Grey shading represents 95% confidence intervals based on a PCA using multiple imputation8.

Source data

n = 12 regions with data before and after the appearance of moralizing gods. Social complexity has been scaled so that the society with the highest social complexity (Qing Dynasty, China, around ad 1900) has a value of 1 and the society with the lowest social complexity (Early Woodland, Illinois, USA, around 400 bc) has a value of 0. Vertical bands represent the period in which moralizing gods and doctrinal rituals first appeared. All errors represent 95% confidence intervals, with the exception of the vertical bar for moralizing gods, which represents the mean duration of the polity in which moralizing gods appeared (because times are normalized to the time of first evidence of moralizing gods, and there is thus no variance in this parameter). Lack of confidence intervals indicates data from only a single region. This figure is identical to Fig. 2a, except that it also includes all available data before and after moralizing gods, rather than being restricted to a window of 2,000 years before and after.

Source data

This is a version of Fig. 2 in which analyses are restricted to only MHG, rather than the broader definition of moralizing gods used in Fig. 2 and elsewhere (which includes BSP as well as MHG). a, Time series showing the mean social complexity over time for 2,000 years before and after the appearance of MHG. n = 10 regions with social complexity data for before and after moralizing high gods. Social complexity has been scaled so that the society with the highest social complexity (Qing Dynasty, China, around ad 1900) has a value of 1 and the society with the lowest social complexity (Early Woodland, Illinois, USA, around 400 bc) has a value of 0. Vertical bands represent the period in which MHG and doctrinal rituals first appeared. All errors represent 95% confidence intervals, with the exception of the vertical bar for MHG, which represents the mean duration of the polity in which MHG appeared (because times are normalized to the time of first evidence of MHG and there is therefore no variance in this parameter). b, Histogram of differences in rates of change in social complexity after minus before the appearance of MHG ( n = 158 time windows from the 10 regions). The y axis represents the number of time windows out of 158.

Source data

Supplementary information

This file contains Supplementary Material, including Supplementary Tables S1-S18.

This file contains the raw dataset containing all data analysed in the paper.

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Whitehouse, H., François, P., Savage, P.E. et al. RETRACTED ARTICLE: Complex societies precede moralizing gods throughout world history. Nature 568, 226-229 (2019). https://doi.org/10.1038/s41586-019-1043-4
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RETRACTED ARTICLE: Complex societies precede moralizing gods throughout world history - Nature

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The origins of religion and of complex societies represent evolutionary puzzles1-8. The 'moralizing gods' hypothesis offers a solution to both puzzles by proposing that belief in morally concerned supernatural agents culturally evolved to facilitate cooperation among strangers in large-scale societies9-13.

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Pourquoi les dieux sont devenus moraux - tous en même temps

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Pourquoi les dieux sont devenus moraux - tous en même temps

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Pour ne pas que ce blog se transforme en blog à parution bi-annuelle, un petit article différent de ce que je fais d'habitude: plus court, et basé sur un seul article scientifique.

Si de nos jours les religions sont facilement associées à la spiritualité et au contrôle de ses propres désirs, cela n'a pas toujours été le cas. Dans les sociétés de chasseurs-cueilleurs et les Etats primitifs, la religion se contente souvent de décrire des rituels et des tabous à respecter pour s'attirer prospérité et réussite. Cependant, vers 500-300 avant JC, une période que l'on nomme la période axiale, plusieurs doctrines insistant sur le contrôle de ses désirs matériels ont vu le jour. Il s'agit du bouddhisme et jaïnisme par exemple dans la vallée du Gange, du stoicisme et de l'épicurisme dans l'est de la Méditerranée, du Taoisme ou du Confucianisme en Chine.

La question du jour
La question du jour est donc : pourquoi d'un seul coup, en 400 avant JC environ, voyons-nous apparaître des religions similaires insistant sur l'autodiscipline et les comportements moraux dans trois régions du monde aussi éloignées que la vallée du Gange, la région méditerranéenne et la Chine ? Pourquoi sommes-nous passés de religions qui jusque-là postulent des dieux qu'il faut craindre mais qui ne disent pas ce qu'il est bien et mal de faire à des religions postulant des dieux moralisateurs ?
Un article récemment publié dans le journal Current Biology suggère une hypothèse basée sur la théorie des traits d'histoire de vie dont nous avons déjà parlé sur ce blog. Nous savons que la richesse d'un individu a des effets sur ses motivations et ses "systèmes de récompense". Quelqu'un qui vit de façon confortable a plus tendance à se fixer des objectifs à long terme, à s'éloigner de stratégies que l'on appelle "rapides" (obtenir des ressources rapidement, se reproduire rapidement...) et à se reporter vers une stratégie plus "lente" qui inclut des comportements plus coopératifs, inscrits dans la durée, privilégiant le self-control à l'impulsivité. L'étude montre précisément que lors de la période axiale, la capture d'énergie dans les trois régions sus-citées (vallée du Gange, Chine et Est de la Méditerranée) a augmenté de façon dramatique, dépassant les 20 000 kcal/jour/personne alors que les sociétés traditionnelles de chasseurs-cueilleurs ne dépassent pas les 4000 kcal et les grandes sociétés archaïques comme l'Egypte ou les Sumériens plafonnent à 15 000 kcal.

La capture d'énergie est un bon proxy pour la mesure de la richesse d'une civilisation. Elle est établie à partir de mesures variées qui peuvent inclure l'étude de squelettes, de restes de nourriture, d'outils, de pratiques agricoles, de maisons, monuments et épaves de bateaux. La taille des maisons par exemple est un proxy utilisé pour se faire une idée de la capture d'énergie. En Grèce, la taille des maisons a augmenté fortement pendant la période axiale :

L'hypothèse alternative majeure - et classiquement avancée - est que la complexité politique d'une société - et non pas sa richesse - permet d'expliquer l'apparition de ces religions. L'idée serait que plus une société devient grosse, plus elle a besoin de religions morales pour que ses individus continuent à coopérer à large échelle. Le reste de l'article est donc affaire de statistiques : différents "modèles bayésiens" cherchent à départager ces deux hypothèses, en estimant quels facteurs (de la richesse ou de la complexité politique) ont le plus de chance d'expliquer les données, c'est à dire l'apparition de religions morales à des moments précis de l'histoire. Par exemple, si dans une région du monde une religion morale apparaît alors que la complexité politique est faible et la richesse élevée, l'hypothèse "la richesse explique mieux l'apparition des religions morales" prendra du poids.

Le résultat, dont vous vous doutez sûrement maintenant, c'est que la capture d'énergie est un très bon prédicteur de l'apparition des religions morales à la période axiale. Le développement économique expliquerait donc l'apparition de ces religions plutôt que la complexité politique, un résultat aussi en concordance avec l'absence de doctrines ascétiques dans des sociétés politiquement complexes telles que l'Egypte antique ou la Perse.

Les auteurs interprètent ce résultat en termes de traits d'histoire de vie :

"Une augmentation massive de la richesse et de la sécurité matérielle pendant la période axiale pourrait avoir entraîné un changement drastique des stratégies, déplaçant les motivations pour des objectifs matérialistes (obtenir plus de richesses, un meilleur statut social) et des stratégies aggressives (oeil pour oeil, dent pour dent) à des motivations pour un investissement à long terme dans la coopération ("ne fais pas aux autres ce que tu ne voudrais pas qu'on te fasse") et des stratégies privilégiant le développement personnel. [...] Au cours du premier millénaire avant JC, les vieilles religions "rituelles" insistant sur les stratégies à court terme auraient été remplacées par les nouvelles religions "spirituelles" insistant plus sur les stratégies à long terme, l'ascétisme et le self-control."

Comme je le disais en intro, il s'agit d'une hypothèse nouvelle qui vient d'être suggérée par un papier et qui se base sur des données archéologiques forcément incomplètes. D'autres études devront donc venir confirmer ou infirmer cette hypothèse, mais elle a le mérite de proposer une alternative raisonnable et biologiquement fondée au mystère de l'apparition de ces religions morales au moment de la période axiale.

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Pourquoi les dieux sont devenus moraux - tous en même temps

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Pour ne pas que ce blog se transforme en blog à parution bi-annuelle, un petit article différent de ce que je fais d'habitude: plus court, et basé sur un seul article scientifique. Si de nos jours les religions sont facilement associées à la spiritualité et au contrôle de ses propres désirs, cela n'a pas toujours [...]

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For Darwin Day, 6 facts about the evolution debate | Pew Research Center

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For Darwin Day, 6 facts about the evolution debate | Pew Research Center

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Tuesday is the 210th anniversary of Charles Darwin's birth, a day now celebrated by some as Darwin Day. Darwin is best known for his theory of evolution through natural selection. When Darwin's work was first made public in 1859, it shocked Britain's religious establishment. And while today it is accepted by virtually all scientists, evolutionary theory still is rejected by many Americans, often because it conflicts with their religious beliefs about divine creation.

While not an official holiday, Darwin Day has been adopted by scientific and humanist groups to promote everything from scientific literacy to secularism. This year, dozens of events have been planned worldwide, many of them anchored by scientific talks or symposiums.

To mark the occasion, here are six facts about the public's views on evolution, as well as other aspects of the debate in the U.S. and elsewhere:

Roughly eight-in-ten U.S. adults (81%) say humans have evolved over time, according to data from a new Pew Research Center study. This includes one-third of all Americans (33%) who say that humans evolved due to processes like natural selection with no involvement by God or a higher power, along with 48% who believe human evolution occurred through processes guided or allowed by God or a higher power. The same survey found that 18% of Americans reject evolution entirely, saying humans have always existed in their present form. (See the full report for a deeper look at the ways question wording and format can affect survey results on evolution.)

2 Around four-in-ten white evangelical Protestants (38%) say humans have always existed in their present form, and about a quarter (27%) of black Protestants share this view, according to the new study. Among white mainline Protestants, just 16% say humans have always existed in their present form. Similar shares of Catholics (13%) and the religiously unaffiliated (11%) say the same. Only among the religiously unaffiliated - those who describe their religion as atheist, agnostic or "nothing in particular" - do a majority (64%) accept evolution via natural selection with no involvement from God or a higher power. Both Protestants and Catholics are considerably more likely to say evolution was guided or allowed by God than they are to say that humans evolved due to processes such as natural selection, or to say that humans have always existed in their present form.

3 Scientists overwhelmingly agree that humans evolved over time, and most Americans are aware that this is the case. Among scientists connected to the American Association for the Advancement of Science, 98% say they believe humans evolved over time. Roughly three-quarters (76%) of Americans perceive that most biological scientists hold this view, according to the new study. Those in the general public who reject evolution are divided on whether there is a scientific consensus on the topic: 46% say most biological scientists think humans have evolved due to processes such as natural selection, and 52% say most biological scientists think humans have always existed in their present form.

A series of court decisions have prohibited the teaching of creationism or intelligent design in public schools. In spite of efforts in many American states and localities to ban the teaching of evolution in public schools - or to teach alternatives to evolution - courts in recent decades have consistently rejected public school curricula that veer away from evolutionary theory. In Edwards v. Aguillard (1987), for instance, the U.S. Supreme Court ruled that a Louisiana law requiring public school students to learn both evolution and creation science violated the Constitution's prohibition on the establishment of religion.

While most Americans (59%) say science and religion are often in conflict, those who are more religiously observant are less likely than others to see this clash between faith and science,according to a 2015 Pew Research Center survey. Among those who attend church at least once a week, half (50%) view religion and science as in conflict, compared with nearly three-quarters (73%) of those who seldom or never attend worship services. At the same time, most people (68%) say that their own personal religious beliefs do not clash with accepted scientific doctrine.

Outside the U.S., there are many other countries where sizable shares of the population reject evolution. In Latin America, for example, roughly four-in-ten or more residents of several countries - including Ecuador, Nicaragua and the Dominican Republic - say humans and other living things have always existed in their present form. This is true even though the official teachings of Catholicism, which is the majority religion in the region, do not reject evolution. In Central and Eastern Europe, evolution is broadly accepted, but roughly half or more of adults in two countries - Armenia and Bosnia - reject it. Meanwhile, Muslims in many nations are divided on the topic, although majorities of Muslims in countries such as Afghanistan, Indonesia and Iraq reject evolution.

It's important to note that our international surveys have used a different approach to ask about evolution, so results are not directly comparable to our new U.S. survey (although some of our older U.S. surveys used similar questions).
Note: This is an update to a post originally published on Feb. 12, 2015.

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For Darwin Day, 6 facts about the evolution debate

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Tuesday is the 210th anniversary of Charles Darwin's birth, a day now celebrated by some as Darwin Day. Darwin is best known for his theory of evolution through natural selection. When Darwin's work was first made public in 1859, it shocked Britain's religious establishment.

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The prominent philosopher, Antony Flew, has famously converted to deism (Flew and Habermas, 2005).

Professor Flew was, also famously, a participant in a debate (reprinted, for example, in (Pojman, 1987)), wherein he argued that nothing can falsify a firmly held religious belief. Professor Flew, who claims never to have "attacked belief," (Ostling, 2005) has evidently changed his mind and is now a deist. (No, he did not convert to theism, and he rejects the Abrahamic God; his belief is far closer to deism, however much Gary Habermas stresses theism in the interview.)

Professor Flew's religious belief is his own concern and is unobjectionable inasmuch as it does not require denial of established facts. It is a pity, though, that Professor Flew, who admits he is "unable to keep up with the [scientific] literature," has based his change of heart in large measure on the writing of Gerald Schroeder and on the concept of intelligent design (Wavell, 2004).

Intelligent design theory is not testable and is based on very dubious propositions (Young and Edis, 2004). I will not discuss it here.

Gerald Schroeder's works are beyond dubious: they are wholly unscientific and distort both science and scripture to support a preconceived old-earth creationism. My colleague, Mark Perakh, and I have independently discussed various of Mr. Schroeder's opuses and found them wholly without merit. I will not repeat those discussions but rather will provide references below.

I wish that Professor Flew had read Mr. Schroeder's work more carefully or had consulted critical references to Mr. Schroeder's work before pronouncing Mr. Schroeder kosher.

References and bibliography.

Carrier, Richard, 2004, "Antony Flew Considers God - Sort of," The Secular Web, http://www.secweb.org/asset.asp?AssetID=369. The article, Flew, Antony, 2001, "Sorry to Disappoint, but I'm Still an Atheist," The Secular Web, http://www.secweb.org/asset.asp?AssetID=138, apparently no longer represents Flew's views.

Flew, Antony, and Gary R. Habermas, 2005, "My Pilgrimage from Atheism to Theism: An Exclusive Interview with Former British Atheist Professor Antony Flew," Philosophia Christi, Winter, in press. Available at http://www.biola.edu/antonyflew/flew-interview.pdf.

Ostling, Richard N., "One of the World's Leading Atheists Now Believes in God, More or Less," Boulder Daily Camera (AP release), 10 December 2004, http://www.dailycamera.com/bdc/religion/article/0,1713,BDC_2477_3389922,00.html.

Perakh, Mark, 1999, "Not a Very Big Bang about Genesis," http://www.talkreason.org/articles/schroeder.cfm.

Perakh, Mark, 2000, "O Bolshom Vzryve i Knige Bytiya (About the Big Bang and the Book of Genesis)," Vremya Iskat, no. 3, pp. 94-114 (in Russian).

Perakh, Mark, 2003, "Intelligent Design for Dummies," The Skeptic (Australia), vol. 23, no. 4, Summer 2003, pp. 22-27.

Perakh, Mark, 2004, Unintelligent Design, Prometheus, Amherst, N. Y., Chapter 10, "Not a Very Big Bang about Genesis."

Pojman, Louis P., 1987, Philosophy of Religion: An Anthology, Wadsworth, Belmont, California, pp. 359-364.

Wavell, Stuart, 2004, "In the Beginning There Was Something," Sunday Times (London), Dec 19, http://www.timesonline.co.uk/.

Young, Matt, 1998, "The Bible Code: Did God Write the Bible? Or Was It a Computer?" Rocky Mountain Skeptic, March-April, 1998, pp. 1, 4-6. Available at http://www.mines.edu/~mmyoung/BkRevs.htm.

Young, Matt, 1998, "The Bible as a Science Text," Rocky Mountain Skeptic, November, pp. 2-4. Review of The Science of God, by Gerald Schroeder, Free Press, New York, 1997. Available at http://www.mines.edu/~mmyoung/BkRevs.htm. See also "Correction and addendum," Rocky Mountain Skeptic, September, 1999, p. 2, at the same URL.

Young, Matt, and Taner Edis, eds., 2004, Why Intelligent Design Fails: A Scientific Critique of the New Creationism, Rutgers, New Brunswick, N. J., http://165.230.98.36/acatalog/____1147.html.

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The prominent philosopher, Antony Flew, has famously converted to deism (Flew and Habermas, 2005). Professor Flew was, also famously, a participant in a debate (reprinted, for example, in (Pojman, 1987)), wherein he argued that nothing can falsify a firmly held religious belief.

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Celebrating Darwin Day by Correcting Michael Behe on the Evolution of Polar Bears

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Celebrating Darwin Day by Correcting Michael Behe on the Evolution of Polar Bears

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Celebrating Darwin Day by Correcting Michael Behe on the Evolution of Polar Bears

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Les punaises d’eau, témoins de l’évolution | Pour la Science

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Les punaises d’eau, témoins de l’évolution | Pour la Science

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L'évolution incroyablement rapide des poux sur les pigeons - Sciences et Avenir

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L'évolution incroyablement rapide des poux sur les pigeons - Sciences et Avenir

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L’évolution incroyablement rapide des poux sur les pigeons - Sciences et Avenir

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L’étude des poux des plumes de pigeons a permis à une équipe de l’université d’Utah d’observer l’évolution d’une espèce en direct.

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Variation in genome-wide mutation rates within and between human families

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Variation in genome-wide mutation rates within and between human families

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Variation in genome-wide mutation rates within and between human families

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J.B.S. Haldane proposed in 1947 that the male germline may be more mutagenic than the female [] . Diverse studies have supported Haldane’s contention of a higher average mutation rate in the male germline in a variety of mammals, including humans ...

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Des chercheurs tentent de reproduire la recette de la vie sur Terre, pour la reconnaître sur d'autres planètes

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Des chercheurs tentent de reproduire la recette de la vie sur Terre, pour la reconnaître sur d'autres planètes

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Des chercheurs tentent de reproduire la recette de la vie sur Terre, pour la reconnaître sur d’autres planètes

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Des chercheurs tentent de recréer en laboratoire les ingrédients nécessaires à l’apparition de la vie autour des évents hydrothermaux. Les résultats de cette étude pourraient nous permettre de comprendre la manière dont la vie est

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Des chercheurs tentent de reproduire la recette de la vie sur Terre, pour la reconnaître sur d’autres planètes

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ADN : que change une différence de 1 ou 2 % d'avec les grands... - Science & Vie

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ADN : que change une différence de 1 ou 2 % d'avec les grands... - Science & Vie

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Selon les estimations les plus récentes, nous partageons 98,79 % de notre patrimoine génétique avec le chimpanzé, 98,47 % avec le gorille et 96,96 % avec l'orangoutan. En résumé, seul 1,2 % de notre génome a été modifié depuis que l'homme et le singe ont gagné chacun leur branche. 98 % d'ADN en commun, c'est énorme ! Oui, mais ce chiffre ne concerne que les gènes codants, qui commandent la synthèse de protéines.

Le rôle du reste, appelé à tort "ADN poubelle", reste mystérieux. Or, l'ADN codant ne représente que 1,5 % de notre génome. En clair, nous partageons en tout et pour tout 98,79 % de 1,5 % de nos gènes avec le chimpanzé. S'il semble logique que les modifications anatomiques liées à la bipédie se retrouvent dans ces 1,2 %, la connaissance parcellaire du génome humain et de celui des grands singes n'a pas encore permis de le démontrer.

Dans le cerveau, des différences substantielles

En revanche, des chercheurs ont identifié deux zones ayant subi d'importantes modifications après la divergence homme-chimpanzé : l'une impliquée dans le développement du cerveau, l'autre dans la position du pouce, deux caractéristiques qui nous distinguent des grands singes. Enfin, l'apparition du langage aurait favorisé les gènes impliqués dans l'audition.
D'après Science & Vie QR n°23 " Nos ancêtres & nous " - Feuilleter / Acheter A lire aussi : * Parler est-il vraiment impossible pour les chimpanzés ? * L'Homme a désormais un septième cousin

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ADN : que change une différence de 1 ou 2 % d'avec les grands singes ?

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Selon les estimations les plus récentes, nous partageons 98,79 % de notre patrimoine génétique avec le chimpanzé, 98,47 % avec le gorille et 96,96 % avec l'orangoutan. En résumé, seul 1,2 % de notre génome a été modifié depuis que l'homme et le singe ont gagné chacun leur branche.

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Evolution and Perceptions of Scientific Consensus | Pew Research Center

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Evolution and Perceptions of Scientific Consensus | Pew Research Center

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This chapter looks at public views about human evolution and perceptions of scientific consensus about evolution and the creation of the universe. Consistent with past Pew Research surveys and other public surveys, religious groups play a central role in beliefs about these topics. Numerous other factors also influence public views about evolution, however, including politics, education and science knowledge. We will examine respondents' views about the intersection of science and religion and religious groups' views about science-related topics in more detail in a follow-up report.

Beliefs About Human Evolution

Controversy over evolution has been a mainstay of American public life throughout much of the 20th century. The Pew Research survey asked about evolution using a set of two questions. Respondents were first asked whether "humans and other living things have evolved over time" or "have existed in their present form since the beginning of time." Those who say that humans and other living things have evolved are asked a follow-up question about the processes they believe account for evolution.

In the most recent survey, 65% of adults say that humans and other living things have evolved, while 31% say humans and other living things have existed in their present form since the beginning of time. Roughly half of those who say that humans have evolved over time believe that evolution has occurred from natural processes, such as natural selection (35% of all adults), while a somewhat smaller share (24% of all adults) believe a supreme being guided the evolution of humans and other living things. Another 5% of all adults are unsure how evolution occurred.

Among the public as a whole, beliefs about human evolution have been roughly stable since first asked in a 2009 Pew Research survey. As we show below, there are a number of differences among subgroups of the population in beliefs about evolution, as has also been the case in past surveys.

Gender, Age, Race and Ethnicity

View about evolution and the processes guiding evolution vary across a number of groups in the population, including gender, race and ethnic groups, as well as age groups. Women are more likely than men to say that humans have existed in their present form since the beginning of time (36% of women say this, compared with 26% of men). Among those who say that evolution has occurred, women are more likely than men to say that evolution was guided by a supreme being.

Younger adults are more likely than older adults to say that evolution has occurred. Those under age 30 are especially likely to say that evolution is due to natural processes (51% of all those ages 18-29 say this). By comparison, just 22% of adults ages 65 and older say that evolution has occurred due to natural processes; 25% of seniors say that evolution was guided by a supreme being and 37% say that humans and other living things have existed in their present form since the beginning.

African Americans are less likely than are whites to say that evolution has taken place.

Education and Knowledge

Three-quarters (75%) of all college graduates and fully 81% of those with a postgraduate degree believe that humans have evolved over time. By comparison, 56% of those with a high school diploma or less say evolution has occurred.

There are sizeable differences in views about evolution between those with more and less general knowledge about science. About three-quarters (76%) of those with more science knowledge say that humans have evolved, compared with 54% among those with less science knowledge.

Religion

Beliefs about evolution among the general public also vary by religious group, with white evangelical Protestants especially likely to say that humans have existed in their present form since the beginning (60%). Black Protestants are closely divided in their beliefs on this topic, with 49% saying that humans and other living things have evolved, and a nearly equal share (47%) saying humans and other living things have existed in their present form since the beginning. Those with no religious affiliation (including those who say they have no particular religion or are atheist or agnostic) stand apart from other groups in their beliefs about evolution. Fully 86% of the religiously unaffiliated say that humans have evolved over time, and two-thirds (67%) say that evolution occurred due to natural processes. By comparison, among all those with a religious affiliation, 59% say that humans have evolved and just 26% say that natural processes account for evolution. More analysis of the relationships between religious beliefs and views about science topics is forthcoming in a separate report.

Party and Ideology

Beliefs about evolution also differ strongly across political groups. Fully 72% of Democrats and independents who lean to the Democratic Party say that humans and other living things have evolved over time, and 46% of this group believes evolution has occurred due to natural processes. By contrast, 57% of Republicans and those who lean to the GOP say that humans have evolved, and just 26% of this group says evolution occurred through natural processes.

Similarly, liberals are more likely to say that humans have evolved and most believe evolution has occurred due to natural processes. Conservatives are closely divided over whether or not evolution has occurred (48% to 47%). Moderates fall in between these two groups, with 71% saying that humans have evolved over time; 38% of moderates say evolution is due to natural processes and 29% say a supreme being guided evolution "for the purpose of creating humans and other life in the form it exists today."

Both political and religious differences underlie beliefs about evolution. For example, partisans who are more religiously observant, measured by frequency of attending worship services, hold distinct views about evolution, as compared with fellow partisans who are less observant.

Among Republicans (including those who lean to the Republican Party) who attend church services at least weekly, fully 53% say that humans have existed in their present form since the beginning and just 9% say that evolution has occurred through natural processes. By contrast, a two-thirds majority (67%) of Republicans and leaning Republicans who attend worship services less often say that humans have evolved over time; 37% of this group says that evolution is due to natural processes.

A similar divide occurs among Democrats and leaning Democrats who regularly attend worship services and those who do not.

Multivariate Analyses

To look at the relative influence of these factors on beliefs about evolution, we conducted a series of multivariate regression analyses. The models shown here included religious affiliation and frequency of worship service attendance. The results underscore the importance of multiple influences on beliefs about evolution, especially religious tradition and church attendance, but, also, party and ideology, education and knowledge about science, age, gender and race. Belief that scientists generally agree that humans have evolved over time is also an independent predictor of beliefs about evolution.

We turn, first, to predicting the view that the humans and other living things have evolved over time (whether due to natural processes or guided by a supreme being) as compared with the view that humans and other living things have existed in their present form since the beginning.

We find religious tradition strongly associated with beliefs about whether or not humans have evolved. Evangelical Protestants are 30 percentage points less likely to say that humans have evolved over time and mainline Protestants are 18 percentage points less likely to say this than are the religiously unaffiliated. Other Christians (a small group in the sample composed primarily of Mormons) have a high predicted probability of saying that humans and other living things have existed in their present form since the beginning (+0.69). Catholics tend to be less likely than the religiously unaffiliated to say that humans have evolved, although this factor does not reach statistical significance once other factors are controlled. Black Protestants are closely divided over whether or not humans have evolved over time; a majority of black Protestants identify as evangelical and the remainder are included with mainline Protestants in the model. There is no statistically independent effect of being black on views about evolution once religious tradition, frequency of attendance and other factors are controlled, although the effect approaches customary levels of statistical significance.

Regular worship service attendance, regardless of tradition, also predicts a lower likelihood of saying that humans and other living things have evolved (-0.09 compared with seldom or never attending worship service).

In addition to religious factors, education and science knowledge play a role. Those who generally know more about science (+0.12) as well as those holding either a college degree or a postgraduate degree are more likely to say that humans have evolved (+0.10 and +0.08, respectively). Specifically, those with a high school degree or less science knowledge on this measure have a predicted probability of 0.64, those with a college degree and more science knowledge have a predicted probability of 0.85, and those with a postgraduate degree and more science knowledge have a predicted probability of 0.87 of saying humans evolved over time.

Those who believe there is scientific consensus about evolution are also 18 percentage points more likely to say that humans have evolved over time, compared with those who do not see broad scientific consensus on this issue.

Conservatives are less likely than liberals to say that humans have evolved over time (-0.18). And Republicans and independents who lean to the GOP are 10 percentage points less likely than are their Democratic counterparts to say that humans have evolved, after controlling for religious affiliation, service attendance and other factors.

Next, we show the results of a logistic regression predicting the view that humans have evolved due to natural processes, as opposed to other views (either that evolution was guided by a supreme being or that humans have existed in their present form since the beginning). A similar set of factors predicts this belief including religious, political, education level and other demographic differences. Those with a Christian religious affiliation (including evangelical Protestant, mainline Protestant, Catholic and other Christian) are less likely than the religiously unaffiliated to say that humans have evolved through natural processes. Those who attend services at least weekly are also less likely to believe that natural processes guided evolution (-0.14).

In addition, party and ideological factors significantly predict views about evolution with Republicans or leaning Republicans and those with no party affiliation or leaning less likely than Democrats and leaning Democrats to say that humans have evolved through natural processes (-0.14 for each). Conservatives are 12 percentage points less likely than are liberals to hold this view.

In addition, older adults (-0.21) and women (-0.12) are less likely to say that humans have evolved over time due to natural processes.

Those with a postgraduate degree are more likely to take the view that humans have evolved through natural processes (+0.13) as are those who say there is scientific consensus on this issue (+0.18).

Perceptions of Scientific Consensus About Human Evolution

As mentioned above, beliefs about whether scientists tend to agree about evolution are strongly related to respondent's views about evolution. These beliefs are independent predictors of views about evolution even after accounting for other factors.

Overall, two-thirds of adults (66%) say that scientists agree that humans have evolved over time, while 29% say that scientists do not agree about this.

About half (47%) of those who personally believe that humans have existed in their present form since the beginning of time also say scientists agree that humans have evolved. Three-quarters of those who believe humans have evolved also see scientists as largely in agreement about evolution.

Gender, Age, Race and Ethnicity

The perception that scientists generally agree about evolution is related to a number of respondent characteristics. Younger generations (ages 18 to 49) are more likely than older ones to see scientists as in agreement about evolution. There are no differences in perception of scientists between men and women or among whites, blacks and Hispanics, however.

Education and Knowledge

Perceptions of scientific consensus on evolution tend to vary by education and science knowledge. About three-quarters of college graduates (76%) say scientists generally agree about evolution, compared with 58% of those with a high school education or less. Fully 79% of those with more science knowledge say that scientists generally agree that humans have evolved; this compares with 54% among those who have less knowledge about science. There are no differences in perception of scientists' beliefs about evolution between college graduates with degrees in a scientific field and those with degrees in some other field, however.

Religion

Those who are religiously unaffiliated are also more inclined to say that scientists generally agree that humans have evolved over time: 78% do so compared with 62% among those with a religious affiliation. White evangelical Protestants are especially likely to say scientists disagree about evolution; 49% believe scientists do not agree that humans have evolved, while 46% say otherwise. However, a majority of black Protestants (63%) say scientists agree that humans have evolved over time. Those who attend services regularly are less likely than those who attend less often to see scientists as being in agreement about evolution.

Party and Ideology

Perceptions of scientific consensus about evolution are related to party affiliation and ideology. Six-in-ten Republicans and leaning Republicans say that scientists generally agree that humans have evolved compared with 72% among Democrats and those who lean to the Democratic Party. Conservatives are less likely than either moderates or liberals to say scientists generally agree that humans have evolved; 55% of conservatives say scientists agree, compared with 67% of moderates and 79% of liberals.

Multivariate Analyses

A multivariate logistic regression predicting the view that scientists generally agree that humans have evolved over time finds those with more science knowledge (+0.20) and postgraduate degree holders (+0.11) are more likely to believe there is scientific consensus about evolution. Those with a postgraduate degree and more science knowledge on this index are predicted to be 31 percentage points more likely to say that there is a scientific consensus on evolution than those with a high school degree or less and less science knowledge. Older adults are less likely than younger adults to say scientists are in agreement on this issue (-0.23). Conservatives (-0.12) and moderates (-0.09) are less likely than are liberals to say this. And, those who attend church services regularly (at least weekly) are less likely to believe that scientists are generally in agreement about human evolution (-0.13). There is no statistically independent effect of religious tradition in views of scientific consensus when it comes to evolution, however.

Perceptions of Scientific Consensus About the Creation of the Universe

The Pew Research survey included one question of perceived scientific consensus about the creation of the universe. Some 42% of the public as whole says that scientists generally agree the universe was created in a single event often called "the Big Bang," while 52% say that scientists are divided in their views about creation of the universe.

Gender, Age, Race and Ethnicity

As with perceptions of consensus about evolution, the belief that scientists generally agree about the creation of the universe is related to age. Younger generations (ages 18 to 49) are more likely than older ones to say scientists are in agreement about how the universe was created. Men are somewhat more likely than are women to say that scientists generally believe the universe was created in a single, violent event (48% of men say this, compared with 36% of women). There are no differences among whites, blacks and Hispanics in views about this.

Education and Knowledge

About half of those with at least a college degree (52%) and fully 61% of those with a postgraduate degree say that scientists generally believe the universe was created in a single, violent event compared with 33% of those with a high school degree or less who say the same. Similarly, those with more knowledge about science are more likely to view scientists as generally in agreement about the creation of the universe. There are no differences in perception of scientists' beliefs about the Big Bang between college graduates with degrees in a scientific field and those with degrees in some other field, however.

Religion

A 61% majority of the religiously unaffiliated say that scientists generally believe the creation of the universe occurred in a single, violent event. By contrast, a majority of those who identify with a religious tradition say that scientists generally are divided about how the universe was created (56%). A majority of white evangelical Protestants, black Protestants and Catholics hold the view that scientists are divided about the creation of the universe. White mainline Protestants are more evenly split, with 47% saying that scientists generally agree and 46% saying that scientists are divided about the Big Bang. Those who regularly attend worship services are less inclined than less frequent attenders to believe scientists are generally in agreement about the creation of the universe.

Party and Ideology

Partisan and ideological groups tend to hold differing beliefs about the Big Bang. A majority of Republicans and independents who lean to the GOP (61%) say scientists are divided in their views about the creation of the universe. By comparison 46% of those who identify with or lean to the Democratic Party say scientists are divided in their views about how the universe was created; a similar share (48%) says scientists generally agree that the universe was created in a single event. Close to half of moderates (47%) and liberals (50%) say scientists generally believe the universe was created in a single violent event. By contrast, a third (33%) of conservatives hold this view.

Multivariate Analyses

A multivariate logistic regression analysis finds science knowledge and education to predict views of scientific consensus. Those with more knowledge about science are 22 percentage points more likely than those with less knowledge to say that scientists generally believe the universe was created in a single, violent event. Those with a postgraduate degree are more likely than those with a high school degree or less schooling to say there is scientific consensus on this issue (+0.19). Controlling for other factors, adults with a high school education who also have less science knowledge have a predicted probability of 0.28 of saying that scientists believe the universe was created in a "Big Bang" event, compared to a predicted probability of 0.67 for those with a postgraduate degree who also have more science knowledge.

Other Christians (i.e., those who are Mormon or Orthodox Christian) are 35 percentage points less likely than the religiously unaffiliated to say that scientists generally agree about the universe was created in a single, violent event. Republicans and leaning Republicans are less likely than their Democratic counterparts to see scientists as in agreement about this issue (-0.16). Women are less likely than men to say that scientists believe the universe was created in a single, violent event (-0.10), controlling for other factors.

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Evolution and Perceptions of Scientific Consensus

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This chapter looks at public views about human evolution and perceptions of scientific consensus about evolution and the creation of the universe. Consistent with past Pew Research surveys and other public surveys, religious groups play a central role in beliefs about these topics.

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📰 Le lien entre diversité génétique et adaptation par sélection naturelle

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📰 Le lien entre diversité génétique et adaptation par sélection naturelle

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La diversité génétique des populations de plantes et d'animaux à l'échelle mondiale: mieux la comprendre pour mieux la conserver
La diversité génétique permet aux espèces de s'adapter face aux modifications de l' environnement (L'environnement est tout ce qui nous entoure. C'est l'ensemble des éléments naturels et...) . C'est un trésor façonné par l'évolution et la conserver efficacement à l'échelle du globe est devenu une priorité.

Dans un article paru dans Nature Communications le 22 janvier 2021, des scientifiques de la Station d'Ecologie Théorique et Expérimentale ( En art, il s'agit d'approches de création basées sur une remise en question des dogmes...) (SETE - CNRS), de l' Institut (Un institut est une organisation permanente créée dans un certain but. C'est...) de Systématique (En sciences de la vie et en histoire naturelle, la systématique est la science qui a pour...) , Evolution, Biodiversité (La biodiversité est la diversité naturelle des organismes vivants. Elle s'apprécie...) (ISYEB - MNHN / CNRS (Le Centre national de la recherche scientifique, plus connu sous son sigle CNRS, est le plus grand...) / Sorbonne (La Sorbonne est un complexe monumental du Quartier latin de Paris. Elle tire son nom du...) Université (Une université est un établissement d'enseignement supérieur dont l'objectif est la...) / EPHE / Université des Antilles) et de l'Université de Louvain analysent pour la première fois la distribution de la diversité génétique (La diversité génétique est une caractéristique décrivant le niveau de...) chez plus de 8000 populations de plantes et d'animaux à l'échelle du globe. Ils démontrent une distribution très hétérogène de cette diversité entre les espèces et les espaces, qui résulte de nombreux facteurs comme le climat (Le climat correspond à la distribution statistique des conditions atmosphériques dans une...) ou la longévité (La longévité d'un être vivant est la durée de vie pour laquelle il est...) des individus. Ces résultats ouvrent de nouvelles perspectives pour la conservation de la biodiversité à l'échelle du globe.

Face aux changements globaux comme le réchauffement climatique (Le réchauffement climatique, également appelé réchauffement planétaire, ou...) , la destruction des habitats ou la pollution (La pollution est définie comme ce qui rend un milieu malsain. La définition varie selon le...) , les espèces animales et végétales doivent s'adapter pour persister. La diversité génétique est l'essence qui permet aux espèces de s'adapter par sélection naturelle (En biologie, la sélection naturelle est l'un des mécanismes qui guident l'évolution...) ; plus elle est élevée, plus les capacités d'adaptation sont importantes. La conservation de cette facette de la biodiversité est donc essentielle. Toutefois, on sait encore mal comment elle est répartie sur Terre (La Terre est la troisième planète du Système solaire par ordre de distance...) ni quels sont les facteurs qui gouvernent sa distribution à une telle échelle. Ces connaissances sont requises pour développer des politiques de conservation qui soient pertinentes et durables.

Dans une récente étude parue dans Nature Communications, un groupe de chercheurs belges et français, issus de de la Station d'Ecologie Théorique et Expérimentale (SETE - CNRS), de l'Institut de Systématique, Evolution, Biodiversité (ISYEB - MNHN / CNRS / Sorbonne Université / EPHE / Université des Antilles) et de l'Université de Louvain, a synthétisé pour la première fois les données (Dans les technologies de l'information (TI), une donnée est une description élémentaire, souvent...) génétiques existantes dans la littérature pour plus de 8000 populations et plus de 700 espèces de plantes et d'animaux terrestres à l'échelle de la planète (Une planète est un corps céleste orbitant autour du Soleil ou d'une autre étoile de...) (Figure 1).

En collectant les données génétiques à l'échelle de la population, c'est à dire là où les contraintes environnementales agissent sur les organismes, les auteurs ont pu identifier les facteurs qui influencent la diversité génétique: des facteurs environnementaux (par exemple le climat actuel ou la variabilité climatique au cours des derniers millénaires), mais aussi des facteurs biologiques (les caractéristiques des individus comme leur taille, leur fécondité ou leur longévité) et biogéograhiques (la place de la population au sein de l'aire de répartition de l'espèce).

Leurs résultats indiquent que la diversité génétique est distribuée de façon très hétérogène à l'échelle de la planète, mais aussi entre les espèces (Figure 2). Par exemple, les plantes ont en moyenne (La moyenne est une mesure statistique caractérisant les éléments d'un ensemble de...) une diversité génétique beaucoup plus faible que les animaux. De la même façon, au sein des animaux, les amphibiens et les mollusques ont une diversité génétique particulièrement faible (Figure 2), ceci pouvant s'expliquer par la façon dont ces organismes se reproduisent. Certaines généralités ont par ailleurs émergé entre les espèces, comme par exemple l'impact consistant de facteurs climatiques contemporains comme le niveau de précipitation (En météorologie, le terme précipitation désigne des cristaux de glace ou des...) ou la température (La température est une grandeur physique mesurée à l'aide d'un thermomètre et...) , ou encore le rôle majeur de caractéristiques individuelles telles que la longévité (Figure 2).

Cette étude confirme par ailleurs l'hypothèse selon laquelle - de façon générale - la diversité génétique est plus forte au coeur de l'aire de répartition d'une espèce (Dans les sciences du vivant, l'espèce (du latin species, " type "...) plutôt qu'en périphérie (Le mot périphérie vient du grec peripheria qui signifie circonférence. Plus...) , même si des exceptions ont été identifiées, avec des implications importantes en matière (La matière est la substance qui compose tout corps ayant une réalité tangible. Ses...) de conservation. En revanche, et de façon très surprenante, les auteurs n'ont pas trouvé d'évidence que la diversité génétique était plus forte à l'équateur qu'aux pôles, ce qui remet en question l'idée reçue voulant que tous les niveaux de biodiversité soient plus riches à l'équateur. De manière générale, cette étude montre que la distribution de la diversité génétique est influencée par de nombreux facteurs qui parfois interagissent, ce qui implique que de nouvelles théories soient élaborées pour expliquer sa répartition à l'échelle du globe.

La plupart des plans internationaux de conservation de la biodiversité sont actuellement développés à l'échelle des espèces, avec comme principal enjeu le maintien de la diversité des espèces à l'échelle du globe. Néanmoins la diversité génétique propre aux espèces est essentielle car elle constitue le fondement de la biodiversité. Cette étude, en servant de de référence, est donc une première pierre à l'édification d'une politique globale de conservation de la biodiversité couvrant tous ses niveaux d' organisation (Une organisation est) , des gènes aux espèces et aux écosystèmes.

Ce travail contribue à comprendre la façon dont se répartit la biodiversité des plantes et des animaux à l'échelle du globe, et comment les activités humaines modifient cette répartition. En particulier, cette étude se concentre sur la diversité génétique des êtres vivants qui permet à ces derniers d'évoluer face aux nouvelles pressions comme le changement climatique.

Références:
De Kort H., Prunier J.G., Ducatez S., Honnay O., Baguette M., Stevens V.M., and Blanchet S. (2021). Life history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal (Un animal (du latin animus, esprit, ou principe vital) est, selon la classification classique, un...) populations. Nature Communications

Contact:
- Michel Baguette - Institut de Systématique, Evolution, Biodiversité (ISYEB - CNRS/Sorbonne Univ/MNHN/EPHE) - baguette at mnhn.fr
- Simon Blanchet - Station d'Ecologie Théorique et Expérimentale (SETE - CNRS) - Simon.blanchet at sete.cnrs.fr
- Hanne De Kort - Laboratory of Plant Conservation and Population Biology (KU Leuven) - hanne.dekort at kuleuven.be
- Olivier Guillaume (Guillaume est un prénom masculin d'origine germanique. Le nom vient de Wille, volonté et Helm,...) - Correspondant communication (La communication concerne aussi bien l'homme (communication intra-psychique, interpersonnelle,...) - Station d'Ecologie Théorique et Expérimentale (SETE - CNRS) - Olivier.GUILLAUME at sete.cnrs.fr
- Catherine Clerc - Correspondant communication - Station d'Ecologie Théorique et Expérimentale (SETE - CNRS) - catherine.clerc at sete.cnrs.fr

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📰 Le lien entre diversité génétique et adaptation par sélection naturelle

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La diversité génétique des populations de plantes et d'animaux à l'échelle mondiale: mieux la comprendre pour mieux la conserver La diversité génétique permet aux espèces de s'adapter face aux modifications de l' environnement (L'environnement est tout ce qui nous entoure. C'est l'ensemble des éléments naturels et...) .

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New Fish Data Reveal How Evolutionary Bursts Create Species | Quanta Magazine

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New Fish Data Reveal How Evolutionary Bursts Create Species | Quanta Magazine

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Africa's deepest freshwater lake holds a dizzying array of animals, including hundreds of species of cichlid fish found nowhere else in the world. They crowd the waters of Lake Tanganyika, with scales and stripes in most colors of the rainbow. One kind of cichlid there measures just over an inch; others are 2 to 3 feet long. "When you're snorkeling in the water with these fish, it's just incredibly striking how different they are," said Catherine Wagner, an assistant professor of botany at the University of Wyoming. Throughout history, local fishermen have pulled up the cichlids in nets for food, but for several decades researchers from around the globe have collected these fish as well in their quest to understand that lush diversity.

A recently published study in Nature offers a new wealth of data on Lake Tanganyika's cichlids and uses it to outline the wild ebb and flow of evolution for these fish, which diversified from one common ancestor to an astonishing 240 or so cichlid species in less than 10 million years.

That's a very small amount of time for so many species to evolve, said Walter Salzburger, an associate professor at the University of Basel's Zoological Institute and senior author on the study. And this process wasn't gradual or random - the data reveals that these cichlids evolved predominantly in bursts. "It's still surprising how clear and distinct these pulses of accelerated evolution are," Salzburger said.

Mapping out the emergence of all these species took Salzburger's team several years. The researchers compiled a list of the lake's cichlid species after they tracked down descriptions in scientific records as well as in books and magazines written about cichlids (which are so visually striking that they have become popular aquarium fish). In between encounters with crocodiles and hippos during their months in Africa, the researchers snorkeled and dived to gather examples of every cichlid they could. Fishermen on the lake provided specimens that live deeper than divers can reach. "Whenever we saw a boat, we would ask, 'What do you have?'" said Fabrizia Ronco, a postdoctoral researcher at the University of Basel and first author on the study. Eventually, they amassed a collection of almost every one of Lake Tanganyika's 240 cichlid species, including dozens that had not been described previously.

Back on land, the researchers scanned the fish to examine their skeletal structures, studied the differences in their genes, and analyzed their chemical composition for clues to the ecological niche each occupied. The team accumulated enough details to reveal how all the species are related and when they diverged from one another.

"It's just a fantastic amount of data," Wagner said. "This was just a dream, a sparkle in our eyes 10 years ago, that we would be able to sequence this many genomes."

One finding was that all but a handful of the species have a common ancestor that lived only about 9.7 million years ago. That corresponds to shortly after Lake Tanganyika is believed to have formed, which strongly implies that the species evolved within the lake from that one ancestral species, and not from multiple colonization events over the millennia.

This fact confirmed for the researchers that Tanganyika's cichlids were ideal subjects for testing ideas about adaptive radiation - an evolutionary event in which many diverse species emerge rapidly and adapt to new environmental niches. Evolutionary theorists have two models for how adaptive radiation might play out. In one, rapid diversification in some aspect of body morphology produces a burst of new species at first, and then speciation slows as the available niches fill up. In the other model, differences in species emerge in stages as a lineage cracks open opportunities available to it, which means that the rate of speciation can both rise and fall over time. Evolutionary biologists have turned up only limited evidence to bolster either of these theories.

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New Fish Data Reveal How Evolutionary Bursts Create Species

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Africa's deepest freshwater lake holds a dizzying array of animals, including hundreds of species of cichlid fish found nowhere else in the world. They crowd the waters of Lake Tanganyika, with scales and stripes in most colors of the rainbow. One kind of cichlid there measures just over an inch; others are 2 to 3 feet long.

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Fossil DNA Reveals New Twists in Modern Human Origins | Quanta Magazine

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Fossil DNA Reveals New Twists in Modern Human Origins | Quanta Magazine

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Humans today are mosaics, our genomes rich tapestries of interwoven ancestries. With every fossil discovered, with every DNA analysis performed, the story gets more complex: We, the sole survivors of the genus Homo, harbor genetic fragments from other closely related but long-extinct lineages. Modern humans are the products of a sprawling history of shifts and dispersals, separations and reunions - a history characterized by far more diversity, movement and mixture than seemed imaginable a mere decade ago.

But it's one thing to say that Neanderthals interbred with the ancestors of modern Europeans, or that the recently discovered Denisovans interbred with some older mystery group, or that they all interbred with each other. It's another to provide concrete details about when and where those couplings occurred. "We've got this picture where these events are happening all over the place," said Aylwyn Scally, an evolutionary geneticist at the University of Cambridge. "But it's very hard for us to pin down any particular single event and say, yeah, we're really confident that that one happened - unless we have ancient DNA."

The events that do get pinned down therefore tend to be relatively recent, starting with the migration of modern humans out of Africa 60,000 years ago, during which they interacted with hominin relatives (like the Neanderthals and Denisovans) they met along the way. Evidence of interbreeding during any migrations before then, or during events that transpired earlier within Africa, has been elusive.

Now that's starting to change. In part because of greater computational power, "we're starting to see the next wave of methods development," said Joshua Akey, a professor of genomics at the Lewis-Sigler Institute for Integrative Genomics at Princeton University. "And that's allowing us to start making new inferences from the data ... that the previous generation of methods couldn't make."

As scientists peer further back in time and uncover evolutionary relationships in unprecedented detail, their findings are complicating the narrative of human history and rescuing some formerly missing chapters from obscurity. Clues are emerging about the unexpected influence of gene flow from ancient hominins on modern human populations before the latter left Africa. Some researchers are even identifying the genetic contributions modern humans might have made to those other lineages, in a complete reversal of the usual scientific focus. Confusing and intertwined as these many effects can be, all of them shaped humanity as we now know it.

Old Humans, New Tricks

When researchers first recovered DNA from Neanderthal bones, the available techniques for making sense of it were powerful but relatively simple. Scientists compared ancient and modern sequences, tallied up shared sites and mutations, and conducted bulk statistical analyses. That's how they discovered in 2010 that Neanderthal DNA makes up approximately 2% of the genome of people today of non-African descent, a result of interbreeding that occurred throughout Eurasia beginning 50,000-60,000 years ago. That's also how they discovered that Denisovan DNA makes up approximately 3% of the genome of people in Papua New Guinea and Australia.

"But that kind of very simple approach isn't very good at sorting out the complexity" of how those lost populations interacted, said John Hawks, a paleoanthropologist at the University of Wisconsin, Madison. Nor does it allow researchers to test specific hypotheses about how that interbreeding unfolded.

Population geneticists could backtrack through the DNA data to identify common ancestors from hundreds of thousands of years ago, and they could detect recent incidents of gene flow from the past few tens of thousands of years. But discerning interbreeding that occurred between those periods, from events "old enough not to be recent but young enough not to be ancient," Hawks said, "that actually takes an extra trick." That's because the more recent events smear their footprints over the older ones; the DNA sequences left behind from those older events are so fragmented and mutated that they are difficult to recognize, and even more difficult to label with a date and location.

Adam Siepel, a quantitative biologist at Cold Spring Harbor Laboratory in New York, and his colleagues decided to focus on such gaps in the narrative. They were particularly interested in looking for signs of gene flow from modern humans into Neanderthals. That flow of genetic information is harder to study than the reverse, not only because of how long ago it happened, but also because there are fewer genomes to refer to: Think of all the present-day genomes at researchers' disposal, versus the handful of Neanderthal genomes left intact, or the single genome recovered from Denisovan remains. The challenge again prompted the need for new methods.

Using one such new technique, first in 2016 and then again in a preprint posted earlier this summer, Siepel and his team found that around 3% of Neanderthal DNA - and possibly as much as 6% - came from modern humans who mated with the Neanderthals more than 200,000 years ago. The same group who gave rise to modern humans throughout the world also furnished Neanderthals with (at least a little) more DNA than the Neanderthals would later give them. "You think you're just looking at a Neanderthal," Siepel said, "but you're actually looking at a mixture of Neanderthal and modern human."

"That's cool," Hawks said. Such a high level of genetic admixture, he added, "is like saying 6% of the cars on the road that you see are red, but somehow you never noticed any red cars. You ought to notice that." And yet the methods in general use had not. To Hawks, the omission suggests that there may be a lot more shared genetic material still to find even if it can't yet be quantified accurately. More advanced techniques may change that.

More Than a One-Off

The finding also adds to the already compelling body of evidence that there were multiple migrations of modern humans out of Africa, stretching back over hundreds of thousands of years. Modern humans were thought to have evolved in Africa after the departure of Neanderthals and Denisovans, and to have remained on the continent until their well-known out-of-Africa diaspora 60,000 years ago. But recently, fossil evidence has indicated otherwise: A human jawbone in Israel, reported last year to date back to 180,000 years ago, and a skull fragment in Greece that's even older, indicate earlier human migrations.

In fact, with that piece of skull, archaeologists may have stumbled across a possible member of the long-ago exodus that Siepel and his team inferred in their genomic study. The fossil, which was classified as Neanderthal when it was unearthed in Greece in the 1970s, was analyzed last month by the paleoanthropologist Katerina Harvati of the University of Tübingen and her colleagues. Structurally, it looked somewhat like a modern human skull, but it was estimated to be about 210,000 years old - supposedly too old to be modern at that location. (Because the structural similarities to modern skulls show up in reconstructive models of the Greek fossil, the conclusion is controversial and will probably continue to be until DNA can be recovered for a genetic study to confirm it.)

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Fossil DNA Reveals New Twists in Modern Human Origins | Quanta Magazine

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Humans today are mosaics, our genomes rich tapestries of interwoven ancestries. With every fossil discovered, with every DNA analysis performed, the story gets more complex: We, the sole survivors of the genus Homo, harbor genetic fragments from other closely related but long-extinct lineages.

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Sleep Evolved Before Brains. Hydras Are Living Proof. | Quanta Magazine

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Sleep Evolved Before Brains. Hydras Are Living Proof. | Quanta Magazine

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The hydra is a simple creature. Less than half an inch long, its tubular body has a foot at one end and a mouth at the other. The foot clings to a surface underwater - a plant or a rock, perhaps - and the mouth, ringed with tentacles, ensnares passing water fleas. It does not have a brain, or even much of a nervous system.

And yet, new research shows, it sleeps. Studies by a team in South Korea and Japan showed that the hydra periodically drops into a rest state that meets the essential criteria for sleep.

On the face of it, that might seem improbable. For more than a century, researchers who study sleep have looked for its purpose and structure in the brain. They have explored sleep's connections to memory and learning. They have numbered the neural circuits that push us down into oblivious slumber and pull us back out of it. They have recorded the telltale changes in brain waves that mark our passage through different stages of sleep and tried to understand what drives them. Mountains of research and people's daily experience attest to human sleep's connection to the brain.

But a counterpoint to this brain-centric view of sleep has emerged. Researchers have noticed that molecules produced by muscles and some other tissues outside the nervous system can regulate sleep. Sleep affects metabolism pervasively in the body, suggesting that its influence is not exclusively neurological. And a body of work that's been growing quietly but consistently for decades has shown that simple organisms with less and less brain spend significant time doing something that looks a lot like sleep. Sometimes their behavior has been pigeonholed as only "sleeplike," but as more details are uncovered, it has become less and less clear why that distinction is necessary.

It appears that simple creatures - including, now, the brainless hydra - can sleep. And the intriguing implication of that finding is that sleep's original role, buried billions of years back in life's history, may have been very different from the standard human conception of it. If sleep does not require a brain, then it may be a profoundly broader phenomenon than we supposed.

Recognizing Sleep

Sleep is not the same as hibernation, or coma, or inebriation, or any other quiescent state, wrote the French sleep scientist Henri Piéron in 1913. Though all involved a superficially similar absence of movement, each had distinctive qualities, and that daily interruption of our conscious experience was particularly mysterious. Going without it made one foggy, confused, incapable of clear thought. For researchers who wanted to learn more about sleep, it seemed essential to understand what it did to the brain.

And so, in the mid-20th century, if you wanted to study sleep, you became an expert reader of electroencephalograms, or EEGs. Putting electrodes on humans, cats or rats allowed researchers to say with apparent precision whether a subject was sleeping and what stage of sleep they were in. That approach produced many insights, but it left a bias in the science: Almost everything we learned about sleep came from animals that could be fitted with electrodes, and the characteristics of sleep were increasingly defined in terms of the brain activity associated with them.

This frustrated Irene Tobler, a sleep physiologist working at the University of Zurich in the late 1970s, who had begun to study the behavior of cockroaches, curious whether invertebrates like insects sleep as mammals do. Having read Piéron and others, Tobler knew that sleep could be defined behaviorally too.

She distilled a set of behavioral criteria to identify sleep without the EEG. A sleeping animal does not move around. It is harder to rouse than one that's simply resting. It may take on a different pose than when awake, or it may seek out a specific location for sleep. Once awakened it behaves normally rather than sluggishly. And Tobler added a criterion of her own, drawn from her work with rats: A sleeping animal that has been disturbed will later sleep longer or more deeply than usual, a phenomenon called sleep homeostasis.

Tobler soon laid out her case that cockroaches were either sleeping or doing something very like it. The response from her colleagues, most of whom studied higher-order mammals, was immediate. "It was heresy to even consider this," Tobler said. "They really made fun of me in my early years. It wasn't very pleasant. But I sort of felt time would tell." She studied scorpions, giraffes, hamsters, cats - 22 species in all. She was convinced that science would eventually confirm that sleep was widespread, and in later studies of sleep, her behavioral criteria would prove critical.

Those criteria were on the minds of Amita Sehgal at the University of Pennsylvania School of Medicine, Paul Shaw (now at Washington University School of Medicine in St. Louis) and their colleagues in the late 1990s. They were part of two independent groups that had begun to look closely at the quiescence of fruit flies. Sleep was still largely the domain of psychologists, Sehgal says, rather than scientists who studied genetics or cell biology. With respect to mechanisms, from a molecular biologist's perspective, "the sleep field was sleeping," she said.

However, the neighboring field of circadian clock biology was exploding with activity, following the discovery of genes that regulate the body's 24-hour clock. If molecular mechanisms behind sleep could be uncovered - if a well-understood model organism like the fruit fly could be used to study them - then there was the potential for a revolution in sleep science as well. Flies, like Tobler's cockroaches and scorpions, could not be easily hooked up to an EEG machine. But they could be observed minutely, and their responses to deprivation could be recorded.

With Less and Less Brain

In January 2000, Sehgal and her colleagues published their paper asserting that flies were sleeping. That March, Shaw and colleagues published their parallel work confirming the claim. The field was still reluctant to admit that true sleep existed in invertebrates, and that human sleep could be usefully studied using flies, Shaw says. But the flies proved their worth. Today more than 50 labs use flies to study sleep, generating findings that suggest that sleep has a set of core features present across the animal kingdom. And biologists did not stop with flies. "Once we showed that flies slept," Shaw said, "then it became possible to say that anything slept."

The sleep that researchers studied in other species was not always similar to the standard human variety. Dolphins and migrating birds can send half their brain to sleep while appearing awake, researchers realized. Elephants spend almost every hour awake, while little brown bats spend almost every hour asleep.

In 2008, David Raizen and his colleagues even reported sleep in Caenorhabditis elegans, the roundworm widely used as a model organism in biology laboratories. They have only 959 body cells (apart from their gonads), with 302 neurons that are mostly gathered in several clusters in the head. Unlike many other creatures, C. elegans does not sleep for a portion of every day of its life. Instead, it sleeps for short bouts during its development. It also sleeps after periods of stress as an adult.

The evidence for sleep in creatures with minimal nervous systems seemed to reach a new high about five years ago with studies of jellyfish. The Cassiopea jellies, about four inches long, spend most of their time upside down, tentacles reaching toward the ocean surface, and pulsating to push seawater through their bodies. When Michael Abrams, now a fellow at the University of California, Berkeley, and two other graduate students at the California Institute of Technology asked if Cassiopea might sleep, they were continuing the line of inquiry that Tobler had followed when she studied cockroaches, investigating whether sleep exists in ever simpler organisms. If jellyfish sleep, that suggests sleep may have evolved more than 1 billion years ago and could be a fundamental function of almost all organisms in the animal kingdom, many of which do not have brains.

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Sleep Evolved Before Brains. Hydras Are Living Proof. | Quanta Magazine

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The hydra is a simple creature. Less than half an inch long, its tubular body has a foot at one end and a mouth at the other. The foot clings to a surface underwater - a plant or a rock, perhaps - and the mouth, ringed with tentacles, ensnares passing water fleas.

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Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure | Nature Communications

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Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure | Nature Communications

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Introduction

Gene expression governs the development, adaptation, growth, and reproduction of all living matter. Understanding its regulatory code would provide us with the means to cure diseases, including heterogeneous tumours, and to control protein production for biotechnology purposes. Although transcriptional regulation has been a central area of research in the past decades, with advances that enable accurate measurement of mRNA levels ranging from just a few copies to several thousand per cell, we still cannot quantify to what extent the DNA code determines mRNA abundance, nor understand how this information is encoded in the DNA. Lack of such quantitative understanding hinders the potential of accurately controlling mRNA and protein levels by simply manipulating the sequence of the four DNA nucleotides.

A strong agreement between protein and mRNA levels in multiple organisms suggests that transcription is a major determinant of protein abundance. mRNA transcription is controlled via the gene regulatory structure, comprised of coding and cis-regulatory regions that include promoters, untranslated regions (UTRs) and terminators, each encoding a significant amount of information related to mRNA levels. For instance, in Saccharomyces cerevisiae, sequence properties of individual cis-regulatory regions can explain up to half of the variation in mRNA levels. Considering that each part of the gene regulatory structure is involved in specific processes related to mRNA synthesis, decay, and the overall transcription efficiency, all gene parts must cooperate in perfectly timed concerted action in order to regulate expression. However, despite the apparent importance of the non-coding regions in mRNA control, it remains unclear how they cooperatively regulate gene expression levels.

Much of the current knowledge on quantitative regulation of gene expression is based on high-throughput screens of thousands of synthetic sequences studied in isolation from their native gene regulatory structures. Although a de facto standard for expression tuning in synthetic biology, these techniques are (i) laborious and require expensive and highly-sophisticated equipment, (ii) are biased towards specificities of mutagenesis, and (iii) are generally restricted to particular experimental conditions. The major problem, however, is that the biological sequence space is so large that it cannot be explored experimentally or computationally. For instance, to analyze all the possible combinations of the four nucleotides in a 20 bp promoter would require iterating over a trillion (4 ²⁰) synthetic sequences. This limits the experimental studies to individual regulatory gene parts in the context of single reporter genes. Similarly, with natural systems, the majority of studies on mRNA transcription in the context of transcription factor (TF) binding, chromatin accessibility and ChIP-seq or DNase-Seq data, focus solely on promoter regions. Therefore, both the current natural and synthetic approaches are fundamentally limited in their ability to study the holistic relationship between the different parts of the gene regulatory structure and their joint regulation of expression.

Here, we consider that DNA sequences of all living systems, through evolution, have been fine-tuned to control gene expression levels. To learn from the natural systems, we analyse over 100,000 native gene sequences in over 20,000 RNA-Seq experiments from seven model organisms, including Homo sapiens and Saccharomyces cerevisiae. In the yeast S. cerevisiae, the variation of gene expression per gene across the entire repertoire of different experimental conditions is 340 times lower than the variation of expression levels across all genes. Consequently, the deep neural networks learn to predict gene expression levels directly from the native DNA sequences, without the need for screening experiments using synthetic DNA. Prediction of gene expression levels is highly accurate in all model organisms, and in S. cerevisiae ( R ² test = 0.82) shows strong agreement with fluorescence measurements from independent published experiments. This demonstrates that, in both eukaryotes and prokaryotes, mRNA levels are determined not by separate individual coding and cis-regulatory regions but rather collectively by the entire gene regulatory structure. In S. cerevisiae, as the coding and cis-regulatory regions contain both orthogonal as well as overlapping information on expression levels, the entire gene codon distribution can be predicted merely from the adjacent cis-regulatory regions ( R ² test = 0.58). Indeed, mutational analysis of orthologous genes in 14 yeast species provides evidence that each gene is a co-evolving unit. Next, we reconstruct the regulatory grammar of S. cerevisiae by measuring the co-occurrence of sequence motifs extracted from the deep models and present across the cis-regulatory regions. These motif co-occurrences are found to be highly predictive of expression levels and can differentiate the expression levels of single motifs in a range of over 3 orders of magnitude. Finally, by quantifying the variation present in all 36 million promoter-terminator combinations we observe that gene expression levels change, on average, over 10-fold in either direction of the native levels. Thus with each gene, merely exchanging one side of its regulatory regions with other natural variants unlocks enormous potential for future gene expression engineering. The potential of our models to guide gene expression engineering with any desired gene in S. cerevisiae is demonstrated experimentally using GFP fluorescence measurements.

Results

The dynamic range of gene expression levels is encoded in the DNA sequence

To explore the relationship between DNA sequence and gene expression levels, we compiled a dataset of 3025 high-quality Saccharomyces cerevisiae RNA-Seq experiments covering the majority of available experimental conditions from 2365 unique studies. By sorting 4975 protein-coding genes ("Methods", Supplementary Table 1) according to their median expression levels across the RNA-Seq experiments (expressed as TPM values, i.e. Transcripts Per Million), we observed a striking trend: expression levels varied within one-fold of values for 79% of the yeast protein-coding genes (Fig. 1a) and within 1 relative standard deviation ( RSD =  σ/ μ) for 85% of the genes (Fig. 1a, b and Supplementary Table 2). Conversely, the dynamic range of average TPM values across all the genes spanned over 4 orders of magnitude and the variance of expression levels within the whole genome was on average 340 times higher than the variance per gene across the experiments (Fig. 1c). The most variable genes across the entire range of biological conditions (Fig. 1b: RSD > 1) were significantly (Hypergeometric test BH adj. p-value < 0.05) enriched in metabolic processes, transport and stress response (Supplementary Fig. 2, "Methods"), while the most stable genes (RSD < 1) were significantly (Fisher's exact test p-value < 1e-16) enriched in TFIID-type constitutive promoters.

All results shown are for S. cerevisiae, except in (h). a Expression levels (transcripts per million, TPM) of protein-coding genes across 3025 RNA-seq experiments. Inset: distribution of genes with a relative standard deviation ( RSD =  σ/μ) below 1. b Experimental variation of the gene expression levels expressed as RSD. c Distribution of ratios between the variance of expression levels within a genome and the variance of expression levels per gene across the experiments. d Schematic diagram of the explanatory variables used for modeling, with distributions of the sequence lengths in the regions where the lengths varied. "TSS" denotes the transcription start site and "TTS" the transcription termination site. e The optimized deep neural network (NN) architecture, where "conv" denotes convolutional NNs, "FC" fully connected layers, and "max-pool" max-pooling layers. The values denoting sizes of parameters layers, stride, kernels, filters, max-pooling, and dilation are specified. f Experimentally determined (true) versus predicted expression levels with the S. cerevisiae model on the held out test dataset ( n = 425). Red line denotes least squares fit. g Comparison of published experimental fluorescence measurements with the predicted expression levels ( n = 625). Red line denotes least squares fit. h R 2 on held out test datasets across 7 model organisms. Red line denotes mean value. Source data are provided as a Source data file.

To test if the observed dynamic range of gene expression levels is encoded in the DNA, we extracted the DNA sequences of the regulatory and coding regions of all the genes with a relative standard deviation of expression variation less than 1 (Fig. 1a, b: 4238 genes with RSD < 1). A total of 2150 bp of regulatory sequences, 64 codon frequencies from coding regions and additional 8 mRNA stability variables, all known to be important for expression regulation, were used for prediction of mRNA levels (Fig. 1d and Supplementary Fig. 1, "Methods"). Using the DNA sequence information as input, we built a regression model based on deep convolutional neural networks (CNNs), capable of identifying functional DNA motifs across the sequence, and trained the model to predict the median gene expression levels (Fig. 1e, "Methods"). The median value was a good estimator of the expression differences between the genes, as it was strongly correlated with the first principal component of the entire expression matrix (Pearson's r = 0.990, p-value < 2e-16, Supplementary Fig. 3). To avoid potential technical biases related to read-based sequencing, mRNA levels were corrected for gene length bias (Supplementary Fig. 4, "Methods"). Overall, a total of 3433 gene sequences were used for training the model, 381 for tuning the model hyperparameters and 424 for testing. After optimizing the model ("Methods"), its predictive performance on the held out test set ( R ² test = 0.822, p-value < 1e-16, Fig. 1f and Supplementary Table 3) demonstrated that the DNA encodes the majority of the information about mRNA expression levels.

To validate the trained model on independent data, we used two published experimental datasets, where the effects of either promoter or terminator sequences were measured in yeast synthetic constructs combined with fluorescence reporters. For both studies, we only inferred expression levels based on the deep neural network trained on natural genomic sequences (Fig. 1e, f, "Methods"), meaning that the model was not exposed to the data from these studies in its training phase. The first dataset comprised measured activities of ~900 native yeast promoters recorded in synthetic constructs with a single strong terminator ( ADH1) and a YFP fluorescence reporter in 10 different conditions. In all 10 conditions, the predictions of mRNA levels inferred based on the DNA sequences of the synthetic constructs and YFP codon frequencies were in strong agreement (Pearson's r from 0.570 up to 0.718, p-value < 1e-16) with the experimental YFP readouts (Fig. 1g: median YFP readout shown, Pearson's r = 0.667, p-value < 1e-16, Supplementary Fig. 5a). Similarly, the second experimental dataset contained expression measurements of over 5,000 terminators with a fixed strong promoter ( TDH3) and a GFP fluorescence reporter. Despite the fact that predictions based on these synthetic constructs were only moderately correlated (Pearson's r = 0.310, p < 1e-16) with the measured protein fluorescence intensities (Supplementary Fig. 5b), this result was in fact stronger than the correlation between reporter fluorescence and measured mRNA abundances reported in the original study (Pearson's r  = 0.241).

To investigate if mRNA abundance can be predicted from the DNA sequence also in other model organisms, we processed an additional 18,098 RNA-Seq experiments from 1 prokaryotic and 5 eukaryotic model organisms equally as with yeast (Supplementary Tables 1 and 2, "Methods"). The organisms were selected to cover the whole known range of genome regulatory complexity, from 892 genes/Mbp ( Escherichia coli) to 6 genes/Mbp ( Homo sapiens), which is known to affect the gene structure and regulation. After training the models for each organism, the predictive power on test data ( R ² test) varied from 0.394 for Mus musculus to 0.725 for Drosophila melanogaster ( p-value < 1e-16, Fig. 1h, Supplementary Table 3). Overall, the predictions were less accurate for higher eukaryotes, which could be attributed to the increase in transcriptional complexity, e.g. due to alternative splicing, expression differences across tissues, and distant enhancer interactions, which were not accounted for in the present models. The prediction performance was thus correlated (Pearson's r = 0.616, p-value < 3e-3) with the genomic complexity of the model organisms (Supplementary Fig. 6). Nevertheless, the average performance across model organisms ( R ² test) of 0.6 (Fig. 1h) corroborated that the majority of mRNA expression differences in all organisms can be predicted directly from the DNA.

Coding and cis-regulatory regions jointly contribute to gene expression prediction

To evaluate the importance of each part of the gene regulatory structure (Fig. 1d) for the prediction of expression levels, we measured the amount of relevant information in each regulatory region. Similarly to the complete model (Fig. 1e, f), we trained multiple CNN models independently on promoter, 5′-UTR, 3′-UTR, and terminator regions as well as their combinations. To justify the use of deep convolutional networks, as a baseline we performed shallow modeling using a variety of regression algorithms, including multiple linear regression, elastic net, random forest, and support vector machines with nested cross-validation (Fig. 2a, "Methods"). We observed that, although a single regulatory region alone could explain less than 28% of the variation in mRNA abundance levels, when using combinations of regulatory regions, each region contributed to the prediction of mRNA levels and increased model performance (Fig. 2b, Supplementary Fig. 11). The model trained on all four regulatory regions thus accounted for approximately 50% of the mRNA abundance variation ( R ² test = 0.492, p-value < 1e-16, Fig. 2a, b and Supplementary Table 8), suggesting that the entire gene regulatory structure is important for controlling gene expression levels. In contrast, none of the shallow models could predict gene expression levels from the regulatory sequences ( R ² test < 0.031, Fig. 2a and Supplementary Table 9), likely since they cannot decode the information in a DNA sequence directly and thus rely on human-engineered features, such as k-mer frequencies, as a representation of the sequence properties. Despite the observation that the sole mRNA stability variables were also somewhat informative about gene expression levels ( R ² test = 0.378, p-value < 1e-16, Fig. 2a), they did not improve the overall model performance next to the codon frequencies and regulatory sequences, likely due to their information redundancy with these variables (Supplementary Fig. 12: R ² test was 0.779 when predicting mRNA stability variables using regulatory sequences).

a Test R 2 with different combinations of coding (codon prob.), mRNA stability (see Supplementary Fig. 1c) and cis-regulatory regions, using shallow (black) and deep modeling (red). b Test R 2 with deep models trained on different combinations of cis-regulatory regions. Red lines denote mean values. c Schematic depiction of deep neural network (NN) for prediction of codon probabilities (Y) based on regulatory DNA as input (X). d Actual versus predicted distribution of codon probabilities as predicted from non-coding DNA regions based on the model for prediction of codon probabilities based on regulatory DNA as input ( n = 11,947). Red line denotes least squares fit. e Evolutionary substitution rates in promoter vs. coding regions in orthologous genes of 14 yeast species ( n = 3248). Red line denotes least squares fit. f Evolutionary substitution rates in terminator vs. coding regions in orthologous genes of 14 yeast species ( n  = 3248). Red line denotes least squares fit. Source data are provided as a Source data file.

On the other hand, the codon frequencies alone explained well over 50% of mRNA level variation both with the shallow and deep models ( R 2 test was 0.681 and 0.690, respectively, p-value < 1e-16, Fig. 2a, Supplementary Table 9). Considering that the amount of information was comparable to, or greater than that of the regulatory sequences, we attempted to measure the amount of information overlap in these regions. We thus trained a CNN to predict the entire codon frequency vector for each gene using only its regulatory regions (Fig. 2c, Methods), which showed that over 58% of the gene's codon frequency variation was determined by its adjacent regulatory regions (Fig. 2d: R ² test = 0.582, p-value < 1e-16). This result suggested that the coding and noncoding regulatory regions might have co-evolved under common evolutionary pressure. To test this hypothesis, we composed a dataset of cis-regulatory regions of orthologous genes from a diverse set of 14 yeast species (Supplementary Table 10) and compared the mutation rates between the different regions of the yeast gene structure (Methods). The mutation rates of the promoter and terminator regions displayed a moderate positive correlation (Pearson's r = 0.423 and 0.471, p-value < 1e-16, respectively) with the mutation rates of the yeast coding regions (Fig. 2e, f) as well as among themselves (Supplementary Fig. 13), supporting the hypothesis that elements of the gene regulatory structure co-evolve.

Deep learning identifies specific DNA positions controlling gene expression levels

To explore the information learned by the deep neural network (Fig. 1e, f) and identify the specific parts of the DNA sequences that were most predictive of gene expression levels, we developed a pipeline for evaluating the relevance of each specific nucleotide position in relation to the predicted gene expression levels (Supplementary Fig. 14, "Methods"). Briefly, for each gene we removed sliding windows of 10 base pairs along its regulatory DNA sequence (Supplementary Fig. 15) and compared the predictions of the occluded sequences with those of the original unoccluded sequences. The occluded parts of the input DNA sequences that significantly deviated (exceeding ±2 standard deviations) from the original data were regarded as the most relevant for gene expression changes (Fig. 3a). The largest density of relevant regions was obtained in the direct vicinity of the boundary sites defining regulatory and coding sequences (see Fig. 1d). On average, 214 base pairs (bp) in promoters, 74 bp in 5′-UTRs, 94 bp in 3′-UTRs, and 127 bp in terminator regions of each gene significantly affected the prediction of its expression levels (Fig. 3a). Relevance profiles of promoter regions were also strongly correlated (Pearson's r = −0.7, p-value < 1e-16) with experimentally measured nucleosome occupancy scores (Supplementary Fig. 16), which suggested that the deep learning algorithms uncovered the intrinsic molecular information encoded in the nucleotide composition.

a Relevance profiles across cis-regulatory region sequences obtained by querying the deep models (Fig. 1f). Red lines denote cutoff of 2 standard deviations. The decrease in relevance of UTR sequences at left edges was due to the considerable number of sequences that were shorter than the analysed regions (see Fig. 1d). b Clustered relevance profiles across the cis-regulatory region sequences. The clusters 1 through 4 are colored dark red, light red, light blue and dark blue, respectively. Lines and shaded regions represent means and standard deviations, respectively. c GC content in the cis-regulatory regions ( n = 368, 383, 834 and 625, respectively). d Median expression levels of genes in the clustered relevance profiles ( n = 1385, 1187, 1206 and 460 with increasing cluster size, respectively). e Total amount of regulatory DNA motifs uncovered in the cis-regulatory regions, with the proportional amounts of motif overlap between adjacent regions (black) as well as with the Jaspar database (red) highlighted. f Examples of regulatory DNA motifs uncovered across all the cis-regulatory regions that correspond to published motifs and sequence elements (see Supplementary Fig. 1c). "TFBS" denotes transcription factor binding sites. For box plots in c, d, boxes denote interquartile (IQR) ranges, centres mark medians and whiskers extend to 1.5 IQR from the quartiles. Source data are provided as a Source data file.

Clustering the gene regulatory regions according to their expression relevance profiles (Methods) identified 4 stable clusters that significantly (Wilcoxon rank-sum test p-value < 1e-4) differed in the positional information (Fig. 3b) and were significantly (Wilcoxon rank-sum test p-value < 1e-16) informative about gene expression levels (Fig. 3d). Cluster 4, which contained highly expressed genes, was significantly (Hypergeometric test p-value < 1e-10) enriched in the occupied proximal-nucleosome (OPN) regulation strategy as opposed to the depleted proximal-nucleosome (DPN) strategy, which was likely related to the concurrent enrichment (Fisher's exact test p-value < 1e-12) of inducible SAGA promoters in the cluster. Cluster 4 also comprised genes with higher transcriptional plasticity spanning an over 4-fold higher variability of expression levels compared to the other clusters (Levene's test p-value < 1e-16). As is typical for highly abundant proteins, such as metabolic enzymes, that are linked to less defined nucleosome positions and higher dependence on nucleosome remodelling, the cluster was significantly enriched (Hypergeometric test BH adj. p-value < 0.01) mostly in metabolic processes (Supplementary Fig. 17). In contrast, Cluster 1, with lowly expressed genes, was related (Hypergeometric test BH adj. p-value < 0.01) to cell cycle regulation and DNA repair (Supplementary Fig. 17). The largest differences in positional expression relevance were identified in promoter and terminator sequences (Fig. 3b). For instance, in promoters of lowly and highly expressed genes (Clusters 1 and 4, respectively), occluding the original sequences yielded opposite effects. These positional differences were independent of the overall nucleotide composition (Supplementary Fig. 18), which indicated that specific regulatory DNA motifs were likely responsible for defining the expression levels.

We next identified the specific regulatory DNA motifs important for predicting expression levels from the set of all significantly relevant DNA sequences (Supplementary Fig. 19) using clustering and alignment ("Methods"). The highest quality motifs were obtained with the 80% sequence identity cutoff, according to the following criteria: (i) genome coverage, (ii) the amount of retained relevant sequences in motifs (seq. coverage) and (iii) % overlap with known motifs in databases (Supplementary Table 11). Over 2200 expression related regulatory DNA motifs were uncovered across all 4 regulatory regions (Fig. 3e). The majority of motifs were unique to each specific region, as analysis of motif similarity across the adjacent regulatory regions (Methods) showed that, on average, <16% of the motifs significantly (Tomtom BH adj. p-value < 0.05) overlapped between the regions (Fig. 3e and Supplementary Table 11). This further supported our observation that every regulatory region contains unique information related to the gene expression levels (see Fig. 2a). Further comparison to JASPAR and Yeastract databases ("Methods") showed that on average, 13% of the identified motifs (Fig. 3e) were significantly (Tomtom BH adj. p-value < 0.05) similar to the known transcription factor binding sites (TFBS) recorded in these databases (Supplementary Fig. 20), recovering 38% and 63%, respectively. The majority of these motifs were identified not only in the promoter, but also in the terminator region (Supplementary Fig. 20), due to the overlap between neighbouring genes. A significant (Wilcoxon rank-sum test p-value < 1e-8) decrease in GC content in the UTR regions (Fig. 3c) indicated that the identified motifs were likely to contain the regulatory DNA signals from UTR regions and terminators (Fig. 3f and Supplementary Fig. 1). This included the 5′-UTR Kozak sequences and 3′-UTR processing DNA elements that are enriched in the thermodynamically less stable A/T nucleotides. The deep models therefore successfully identified known regulatory signals (Fig. 3f), as well as uncovered new regulatory signals across all the gene regulatory regions.

Motif co-occurrence uncovers the regulatory rules of gene expression

To determine the functional meaning of the DNA motifs reconstructed from the deep learning relevance profiles (Fig. 3f), we analysed the informative power of the DNA motifs for predicting the specific gene expression levels. For this, we calculated the signal-to-noise ratio ( SNR =  μ/ σ) of expression levels across genes that carried the identified motifs (Fig. 4a and Supplementary Fig. 23). The spread of expression levels of motif-associated genes was over 2.5-fold larger than its expected (median) expression level (Supplementary Fig. 24), resulting in a low median SNR of under 0.4 (Fig. 4a). Of the full 4 order-of-magnitude range of gene expression levels observed in the data (Fig. 1a), only 57% could be recovered with the motifs, as indicated by the average expression level of genes per associated motif (Fig. 4b and Supplementary Fig. 23b). The range of gene expression levels for the identified motifs were thus too dispersed and overlapped, indicating that the predictions made by the model (Figs. 1f and 3b) were likely not based on single motif occurrences.

a Distribution of the signal-to-noise ratio ( SNR) of expression levels across genes carrying co-occurring motifs (co-occurrence rules, see Results text and Methods). Inset: comparison of SNR with single motifs ( n = 2098) and with motif co-occurrence rules ( n = 116,734). b The range of gene expression levels, relative to the full observed range in the initial RNAseq data (~4 orders of magnitude, Fig. 1a), that could be retrieved on average by genes carrying either single motifs or motif co-occurrence rules. c The amount of genes carrying a given motif co-occurrence rule versus the average expression level across the set of genes carrying the given rule, with increasing statistical significance levels from a chi-squared test. FDR denotes Benjamini-Hochberg (BH) adjusted p-value and data is colored gray except for significance cutoffs p < 0.05 (black), FDR < 0.05 (dark red) and FDR < 2.7e-6 (equals Bonferroni correction, red). Inset: distribution of the number of co-occurring motifs in significant (FDR < 0.05) rules. d Distribution of motif co-occurrence rules across single or multiple cis-regulatory regions, according to the locations of the co-occurring motifs. e Distribution of gene expression levels with groups of motif co-occurrence rules that have one motif in common (i.e. unchanged). f Illustration of four genes ( CDC6, RIO2, NSP1, EXG1) that carry a group of motif co-occurrence rules with a common motif (NHP6B transcription factor binding site, Tomtom BH adj. p-value < 0.005, SGD:S000002157, blue line) in their promoter region, whereas they all diverge in possessing 2 to 4 other DNA motifs (red lines) across the remaining regulatory regions. These genes span a 648-fold range of expression levels. Red lines in the histogram denote the specific expression levels of the genes. g Distribution of gene expression levels with groups of motif co-occurrence rules that differ by a single motif. Source data are provided as a Source data file.

On the other hand, the observed interactions across the regulatory regions (Fig. 2a, b) and positional differences in expression levels (Fig. 3b) suggested that certain combinations of motifs found in different regulatory regions might carry a greater indication of expression levels than single motifs (Fig. 3f). We, therefore, searched for patterns of co-occurring motifs, i.e. combinations of motifs that are statistically more likely to be present together in genes than alone, and termed these patterns 'regulatory rules'. For this we used Market basket analysis-a technique that is commonly used for identifying frequently bought items in market research ("Methods"). The number of identified rules corresponded to the quality of identified motifs and was largest at the 80% sequence identity cutoff, decreasing markedly when increasing the identity cutoff (Supplementary Table 11). A total of 9,962 rules were significantly overrepresented (Chi-squared test BH adj. p-value < 0.05) in at least 3 genes and across 93% of the analysed protein coding genome (Fig. 4c), and comprised 62% of all unique motifs that represented 86% of all motif occurrences (Supplementary Fig. 25). Importantly, the rules were frequently found in smaller groups of genes (at most 10 genes) and were crucial for discriminating genes with low and high expression levels, as the dynamic range of expression values decreased by 2-fold in rules present in more than 10 genes (Fig. 4c). Similarly, rules comprised of a larger number of motifs (Fig. 4c: rules of up to 6 motifs found) were also sparser and occurred in smaller groups of genes (Supplementary Fig. 26). In total, 88% of the significant rules (Chi-squared test BH adj. p-value < 0.05) occurred across the regulatory regions compared to the rest that were present within single regions (Fig. 4d). This resulted in over 8-fold more co-occurring motifs spread across multiple regulatory regions than within any single region.

We next compared the genes carrying the single motifs to those carrying the co-occurring motifs in rules. We observed that the range of average expression levels of genes spanned by the rules exceeded those of single motifs by over 11-fold (Levene's test p-value < 1e-16) (Supplementary Fig. 24) and recovered, in total, 84% of the whole range of gene expression levels (Figs. 4b and 1a). Furthermore, a significantly (Wilcoxon rank-sum test p-value < 1e-16) narrower window of expression levels was observed with rule-associated genes compared to single motifs, as the variance of expression levels was over 16-fold lower (Supplementary Fig. 24). This showed that the genes containing co-occurring motifs fall under the precise control of the specific co-occurrence rule. The signal-to-noise ratio, which exceeded 1 for over 60% of rules, in contrast to single motifs, of which 78% were below 1 (Fig. 4a and Supplementary Fig. 23b), demonstrated that the precision of expression control of the rule-associated genes was on average 3-fold higher (Wilcoxon rank-sum test p-value < 1e-16) than of single motifs (Supplementary Fig. 23). This again shows the presence of statistically measurable interactions across the entire gene regulatory structure, but this time at the level of motifs, thus supporting the existence of a coevolved interacting regulatory grammar.

To analyse how differences in the motif co-occurrence context across the regulatory regions affect the expression levels of genes, we grouped the motif co-occurrence rules, such that one motif was left unchanged and was common to all the rules, while the other motifs differed across the genes (Fig. 4e, rules with at least 3 motifs were used). We found that the motif co-occurrence context across the regulatory regions could repurpose a common motif in genes that exhibited a range of up to 1484-fold change of expression levels. Of the 1079 such rule sets that repurposed a given motif, 55% changed by at least one order of magnitude of expression levels (Fig. 4e). The repurposed motifs included significant (Tomtom BH adj. p-value < 0.05) hits to a range of Jaspar TFBS in promoter regions, and co-occurred with as well as were repurposed by motifs across all the cis-regulatory regions (Supplementary Table 12). For example, one of the largest ranges of expression levels was observed with a group of NHP6B-like motifs (SGD:S000002157, 648-fold change), a TF that binds to and remodels nucleosomes. The NHP6B-like motifs co-occurred with motifs from the adjacent regulatory regions that govern the expression levels of many essential yeast genes (Fig. 4f), including those involved in DNA replication ( CDC6), ribosomal RNA processing ( RIO2), and coding for nuclear ( NSP1) and cell membrane ( EXG1) proteins. Furthermore, a similar trend was observed by an alternative grouping of the motif co-occurrence rules, such that only one motif differed across the genes. Even a single motif substitution could achieve up to a 605-fold change of expression levels, where 24% of such rulesets were carried by genes that exhibited at least an order of magnitude change of expression levels (Fig. 4g). Finally, an analysis of gene sets containing the most widespread motif co-occurrence rules (that covered 20 or more genes) did not show any significant enrichment of specific cellular functions, which suggested that the uncovered gene expression grammar is shared across genes of all functions and is an integral part of the basic gene regulatory structure (Fig. 1d).

Since the regulatory regions were found to be coevolved with the coding region (Fig. 2e, f) and highly predictive of the codon frequencies (Fig. 2d), we analysed the properties of codon frequencies across the motifs and rules similarly as with the expression levels. The range of median Euclidean distances between codon frequencies, defined by the co-occurring motifs in rules, exceeded that of the single motifs by 6.5-fold (Levene's test p-value < 1e-16), whereas the average variance decreased almost 5-fold (Wilcoxon rank-sum test p-value < 1e-16, Supplementary Fig. 27). This shows that, compared to single motifs, co-occurrence rules define more conserved ranges of codon frequencies, and that the regulatory grammar learned by the deep models (and highly predictive of gene expression levels, Fig. 1f) is based on the combined properties of regulatory as well as coding regions.

Regulatory properties learned from native genome guide expression engineering

The common practice to manipulate gene expression levels is to use specific strong promoter (or terminator) sequences without much regard to which terminators (or promoters) they are combined with. Considering that our findings point to a strong dependence of gene expression on the interaction between all regions of the gene regulatory structure (Figs. 2a, b, d and 4e, f, g), we used the deep neural networks (Fig. 1e, f) to explore how much the expression level of each gene can be altered with all the possible promoter-terminator combinations, a task that is challenging to perform experimentally. To rationally simplify this analysis and retain just two global halves of the gene regulatory structure, here 5'-UTRs were combined with promoters and 3′-UTRs with terminators (Fig. 5a). For each half, 17,960,644 combinations of the native yeast promoters or terminators with their corresponding variable counterparts were tested using the same dataset as for training the models (Fig. 1a: RSD < 1). We observed that, on average, varying the terminator region introduced a significant (Wilcoxon rank-sum test p-value < 1e-16) 3-fold change in either direction of expression levels, compared to the native gene structure (Fig. 5b). The terminator constructs achieved up to a 130-fold increase (Fig. 5b: YOL097W-A promoter with TDH3 terminator) and 14-fold decrease (Fig. 5b: TIM10 promoter with TOP3 terminator) of expression levels compared to the native counterparts. This showed that with a given gene, a range of over two orders of magnitude of expression levels (Fig. 5b: 130-fold range with YOL097W-A) could be unlocked merely by exchanging the terminator region. This held true for both strong as well as weak promoters (Fig. 5c). For instance, with the commonly used strong yeast promoter YEF3 we identified a regulatory combination where the expression levels decreased 3.2-fold (Wilcoxon rank-sum test p-value < 1e-16) compared to the native counterpart. Conversely, with the natively weak promoter POP6, a terminator context with a significant (Wilcoxon rank-sum test p-value < 1e-16) increase of over 7-fold was identified (Fig. 5c). A further comparison of natively weak and strong promoters (100 top and bottom sorted constructs) confirmed that weak ones were expressed overall 2-fold more highly (Wilcoxon rank-sum test p-value < 1e-16), and strong ones overall 1.3-fold more lowly (Wilcoxon rank-sum test p-value < 1e-16) than the native sequences (Supplementary Fig. 28). The computed degree of regulatory freedom was supported also by published experimental results with the TDH3 promoter (Fig. 5d). Here, despite the specific experimental conditions leading to an offset in the measurements, we observed a moderate correlation (Pearson's r = 0.310, p-value < 1e-16) to the variability of the fluorescence intensities with 4005 different terminators as well as a comparable overall dynamic range (Fig. 5d).

a Two global halves of the gene regulatory structure where 5′-UTRs were combined with promoters and 3′-UTRs with terminators. b Maximum increases (red) and decreases (blue) of gene expression levels with combinations of 4238 native promoters with all terminator variants. c Distributions of gene expression levels for combinations of either strong (red) or weak (blue) promoters with all terminator variants ( n = 4238 for each construct). Black lines denote median exp. levels. d Comparison of changes in predicted TDH3 expression levels with measured fluorescence intensities when combining the promoter with n = 4005 terminator variants. Red line denotes least squares fit. e Maximum increases (red) and decreases (blue) of gene expression levels with combinations of 4238 native terminators with all promoter variants. f Distributions of gene expression levels for combinations of either strong (red) or weak (blue) terminators with all promoter variants ( n = 4238 for each construct). Black lines denote median expression levels. g Comparison of changes in predicted ADH1 expression levels with measured fluorescence intensities when combining the terminator with n = 625 promoter variants. Red line denotes least squares fit. For box plots in c, f, boxes denote interquartile (IQR) ranges, centres mark medians and whiskers extend to 1.5 IQR from the quartiles. Source data are provided as a Source data file.

When performing an analogous analysis using terminator regions and instead varying the promoters, expression levels changed on average over 20-fold (Wilcoxon rank-sum test p-value < 1e-16) in either direction and spanned a dynamic range of over 3 orders of magnitude (Fig. 5e: 2120-fold range with YNL146W). For all terminators, promoters could be identified that exerted a strong positive stabilizing effect, as the most pronounced variation was observed in the direction of increasing expression levels up to 1847-fold (Fig. 5e: YOL097W-A terminator with TDH3 promoter), compared with up to 32-fold decrease (Fig. 5e: MMF1 terminator with AMF1 promoter). Similarly as with promoters, strong and weak terminators (100 top and bottom sorted constructs) displayed stronger changes in the opposite directions of expression. Weak terminators were expressed overall 2.3-fold more highly (Wilcoxon rank-sum test p-value < 1e-16), and strong ones overall 2.4-fold more lowly (Wilcoxon rank-sum test p-value < 1e-16) than the native sequences (Supplementary Fig. 28), thus presenting many possibilities for gene expression engineering (Fig. 5f). Analysis of independent yeast experimental data confirmed the computationally predicted variability with the ADH1 terminator, as we measured a strong correlation (Pearson's r = 0.625, p-value < 1e-16) to the variability of fluorescence intensities with the 625 tested promoters (Fig. 5g).

We considered that changing the promoters and terminators could have affected gene expression predictions based either on (i) the specific regulatory signals present in the DNA (Figs. 3f and 4h) or (ii) the general sequence properties, such as GC content and di-nucleotide composition. We therefore evaluated the effect of removing high-order sequence information (ie. regulatory grammar) by randomly shuffling the regulatory DNA whilst preserving dinucleotide frequencies. On average, the native DNA regions demonstrated a significant (Levene's test p-value < 1e-16) 88% larger effect on expression variation and a 13.5-fold higher dynamic range compared to randomly shuffled sequences with the same nucleotide composition (Supplementary Fig. 29). Accordingly, random sequences could only increase the expression level up to 4.9-fold (Supplementary Fig. 29: YIL102C-A promoter with a shuffled variant of its terminator) and decrease it up to 3.2-fold (Supplementary Fig. 29: NCE102 promoter with a shuffled variant of its terminator) compared to the native expression level. The observed increase of expression signal by combining native regions with their adjacent counterparts indicated that the correct progression of gene expression requires the presence of a specific regulatory grammar, similar to the one detected above (see Fig. 4h), which can be lost when artificially manipulating or carelessly combining the sequences.

The computational results suggest that the model-based predictions could improve experimental design of gene expression systems and potentially decrease a part of the observed variability of gene expression levels (Fig. 5b, e). Therefore, using deep models to guide the development of experimental constructs, we set out to experimentally verify that a weak promoter can be driven to higher expression levels and vice versa, based on substituting its terminator with another natural variant (Fig. 6a, "Methods"). Since here the experimental design required models with limited 500 bp regions on either side of the CDS, we constructed a new model based on constricted input data that contained only the most relevant parts of the regulatory regions, as determined from the relevance profiles (Fig. 3a: 400 bp, 100 bp, 250 bp and 250 bp, respectively, Supplementary Fig. 30a). This model achieved similar performance ( R ² test = 0.797, Supplementary Fig. 30b and 31) as the previous one, despite requiring regulatory sequences that were approximately half the length. Compared to the above computational analysis, where only one side of the regulatory regions was perturbed (Fig. 5a), development of experimental constructs for the fluorescence measurements additionally required the substitution of all coding sequences (codon frequencies) with a GFP variant (Methods), which represented approximately half of the model input response (Supplementary Fig. 31). In order to retain the predictive power of the model despite these large perturbations, we selected 6 promoter variants from the set of constitutive genes. The data was subset to the 10th percentile, based on the similarity between native and GFP coding sequences, as well as the model predictive accuracy (Supplementary Fig. 32). These GFP-substituted genes covered a 16-fold range of predicted expression levels from 26 to 420 TPM (Supplementary Table 13). Similarly, a weak and a strong terminator were selected according to the strength of their effects on increasing or decreasing the GFP-substituted gene expression levels compared to the native terminators (Supplementary Table 13). Experimental measurements with the resulting 18 constructs (Fig. 6a: 6 each with native terminator, weak terminator, strong terminator, respectively, Methods) achieved good correlation to the predicted levels (Pearson's r = 0.647, p-value < 1.8e-3, Fig. 6b). We observed, on average, a corresponding 20% change in GFP fluorescence levels with all constructs, in accordance with the predicted expression level changes (Supplementary Table 13), with the exception of the YBL036C promoter with the strong terminator and the HIS1 promoter with the weak terminator (Fig. 6c). We identified a strong promoter with HIS1 that consistently (duplicate tests) achieved a 3440% increase in GFP intensity (Supplementary Fig. 33) and, conversely, a weak promoter with RPC40 leading to a 61% decrease in GFP intensity (Fig. 6c). In addition, we tested the well known weak POP6 and strong RPL3 promoters, which showed considerable divergence of properties and model predictions between the native and GFP coding sequence (Supplementary Table 13 and Supplementary Fig. 34). Despite this, we were able to obtain a weak terminator variant with the RPL3 promoter leading to strong decrease in gene expression (Fig. 6d: 75% decrease in GFP intensity), whereas the POP6 promoter achieved a smaller 30% increase and 13% decrease, respectively. To conclude, even in the highly perturbed state with multiple substitutions to the gene regulatory structure, our models enabled computational pre-screening of optimized candidates from millions of combinations and thus demonstrated the feasibility of model guided fine-tuning of gene expression levels.

a Conceptual diagram of experiment and constructs. b Correlation analysis between model predictions and measured GFP fluorescence levels for constructs with 6 promoters in combination with native (grey) as well as strong (red) and weak (blue) terminators ( n = 18). Black line denotes least squares fit. c Relative change in measured GFP fluorescence levels of the constructs, where native terminators were replaced with either strong (red bars) or weak (blue bars) variants with n = 2 technical replicates indicated as grey points (see text and Supplementary Table 13). On average, the GFP fluorescence levels shifted by 20% in the directions of the predicted levels. Red and blue lines denote median values with strong and weak promoters, respectively. d Additional tests with the weak POP6 and strong RPL3 promoters, whose CDS were more dissimilar to GFP. Native terminators were replaced with either strong (red bars) or weak (blue bars) variants with n  = 2 technical replicates indicated as grey points. Source data are provided as a Source data file.

Discussion

In the present study we asked the question: to what extent are gene expression levels encoded in the coding and cis-regulatory DNA regions of the gene regulatory structure? This question followed our observation that with all known biological variation of gene expression, based on a collection of RNA-Seq experiments across the majority of presently tested conditions, 79% of protein coding genes were merely within a ±1-fold change of their median expression levels in 2/3 of the conducted experiments (Fig. 1a). By training deep neural networks on the sequences from the entire gene regulatory structure (Fig. 1d), we demonstrated that most gene expression levels in S. cerevisiae are predictable using only DNA encoded information (Fig. 1f: R ² test = 0.822). Therefore, 4 orders of magnitude of the transcriptional repertoire can be directly determined from the DNA sequence, irrespective of the experimental condition. Of course, this statement does not object to the reality that regulation of gene expression can be highly dynamic between different conditions. However, for the majority of genes, this biological variation across conditions is much smaller than the magnitude of expression levels between the genes (Fig. 1a), meaning that genes which are highly expressed in the majority of conditions will likely always (79% of protein coding genes) be highly expressed and vice-versa. These differences in gene expression levels are encoded in the DNA and can be read using machine learning. Accordingly, similar results were obtained in 6 other model organisms spanning multiple kingdoms of life (including bacteria and eukaryotes such as fruit fly, zebrafish, mouse and human), that covered the complete range of genetic regulatory complexity, as measured by coding gene density (Supplementary Table 1).

The models in the present study mapped the relations of input DNA sequence variables to the continuous target mRNA levels, where model performance was assessed with the coefficient of determination R2 on the test data. This is an intuitive measure signifying the proportion of the variance in the dependent variable (mRNA levels) that can be predicted from the independent DNA sequence variables (Fig. 1d and Supplementary Fig. 1c)-i.e. how much could be learned from the sequence data using our machine learning approach. We emphasize that for the actual model selection during training, the mean squared error (MSE) was used, as this is a robust goodness-of-fit measure that makes no assumptions about the data distributions. For each model: (i) the model was trained on the training set using minimization of MSE criteria, (ii) Hyperparameter tuning was performed on the validation set, (iii) a model with minimal MSE on the validation set was chosen and (iv) for final testing evaluation the model with the minimal MSE criteria was accessed again to ensure that it did not overfit the data (Supplementary Tables 3 and 8). As an alternative statistical approach and a measure of goodness of fit, we also performed the F-test with all models (Supplementary Tables 3 and 8). Although not informative about a model's predictive performance, this tested whether the model in question fits the data significantly better than the null model based only on the intercept (i.e. average over data) to make predictions. Moreover, to clearly differentiate between reporting model performance with R 2 and the strength of a linear relation between independent variables (such as predicted expression levels and measured GFP fluorescence in Fig. 1g), for the latter the Pearson's correlation coefficient r was used.

Since individual coding and non-coding parts of the gene regulatory structure (Fig. 1d) all play a crucial role in the regulation of gene expression, we inquired which particular regions contained the highest amounts of information on gene expression levels. While codon frequencies were highly informative about mRNA levels (Fig. 2b), we observed that a similar amount of information was encoded in the flanking regions (Fig. 2a). Indeed, this was further supported by the result that deep neural networks could predict the codon usage of a gene merely based on that gene's regulatory sequence (Fig. 2c, d). Although the effect of codon usage on overall transcription has been widely studied and debated, their surprisingly strong effects on transcription, also supported by our results (Fig. 2b), have only recently started coming to light. The hypothesized mechanisms through which codons affect transcription are: (i) effects on nucleosome positioning, (ii) premature termination of transcription, usually by mimicking poly-A signals, or (iii) mRNA toxicity. Generally, the differences in codon usage between bacterial species can be explained from the dinucleotide content in their non-coding regions and it is widely assumed that most inter-species variation in codon usage is attributed to mutational mechanisms. Within a genome, however, given that codon usage can be predicted from non-coding regions (Fig. 2d), and both coding and regulatory regions are similarly predictive of gene expression levels (Fig. 2b), it is likely that the entire gene regulatory structure undergoes a common selection pressure. Multiple lines of evidence support this both in higher eukaryotes and yeast, as (i) approximately half of all functional variation is found in non-coding regions, with cis-regulatory regions undergoing not only purifying negative but also positive selection, (ii) findings indicate a similar selective pressure on gene expression and protein evolution, and (iii) instances of coupled protein and regulatory evolution were observed. Accordingly, mutation rates in orthologs from 14 yeast species supported the notion of coevolution between the coding and regulatory regions (Fig. 2e, f), indicating that the gene regulatory structure is a co-evolving unit. However, despite the ensuing information overlap among the different regions (Fig. 2b, d: up to 58%), each region contributed to mRNA level prediction (Fig. 2a, b) and the entire gene regulatory structure was required to define over 82% of the gene expression variability (Fig. 1f).

The multiple regulatory elements of the gene regulatory structure individually or jointly control the different DNA processing phases required for mRNA transcription, including nucleosome positioning, mRNA synthesis, and mRNA maturation and decay (Supplementary Fig. 1a). To control enzyme interactions, DNA, therefore, contains a plethora of statistically identifiable DNA motifs. The question remains though, which of those motifs are relevant signals for regulating mRNA levels? For instance, based on currently identified JASPAR motifs, a significant enrichment of known promoter TF binding sites was found particularly in highly expressed genes (Supplementary Fig. 21). However, such an analysis does not uncover which motifs or combinations of motifs is found to be important by a predictive model of mRNA abundance (Fig. 1e). To resolve this, we opened the neural network "black box" (Fig. 1e and Supplementary Fig. 14) and determined which DNA sequences were causing significant neural network responses (Fig. 3a). Although thousands of DNA motifs were uncovered across all regulatory regions (Fig. 3d, f), individual motifs could not explain the entire dynamic range of gene expression, i.e. the same motifs were found in both lowly and highly expressed genes (Fig. 4a, Supplementary Fig. 23). However, by statistically analysing the interactions between motifs, we could retrieve a much more accurate (Fig. 4a) and comprehensive (Fig. 4b) indication of expression levels than with single motifs, where an almost 3-fold higher amount of co-occurrence rules surpassed a SNR of 1 (Fig. 4a) and recovered almost the whole (84%) dynamic range of expression levels as opposed to 57% with motifs (Fig. 4b). 9,962 combinations of 2 to 6 motifs were found to co-occur more frequently together than alone across the gene regions (Fig. 4c) and were informative of almost the entire dynamic range of expression (Fig. 4a, b, f). Moreover, the motif co-occurrence rules also defined more specific ranges of codon usage than single motifs (Supplementary Fig. 27), further supporting our results that the entire gene regulatory structure (Fig. 1d), including both coding and non-coding regions, is a single co-evolved interacting unit (Fig. 2d, e, f).

Finally, we demonstrated that deep neural networks can learn the complex regulatory grammar of gene expression directly from an organism's genome (Fig. 1f, h), without any prior knowledge of genetic regulation or the need to perform laborious high-throughput screening experiments with synthetic constructs. Despite the fact that the machine learning model had never seen the synthetic DNA data, it was able to successfully recapitulate fluorescence readouts from published experimental studies and demonstrate a strong agreement between model predictions and experimental measurements (Fig. 1g and Supplementary Fig. 5), even on constructs containing de novo generated sequences (Supplementary Fig. 5c). Furthermore, since the trained models encapsulate the whole interacting regulatory grammar that must be present to correctly drive expression, they can be used to enhance experimental techniques and improve control over gene expression in synthetic biology. We show that the standard approach of introducing a variety of terminators (or promoters) in combination with strong promoters (or terminators) can in fact lead to large variability in each direction of the actual measured levels of expression (Fig. 5c, f). Our model was however ~1.6-fold more capable of predicting downregulation compared to upregulation (Fig. 6b), which was likely due to the average native expression level being over 2-fold higher from a predicted average basal expression level (Supplementary Fig. 35a: 64.5 TPM). From an evolutionary perspective, this suggests that the regulatory grammar might be specifically adapted not only for higher expression levels but also for lower ones below the basal expression level, whereas around the basal level the grammar is less specific and possibly more diverse (Supplementary Fig. 35c). This is also in agreement with the observations that highly expressed genes are under stronger selection pressure than average ones and thus altering these highly optimized sequences likely results in downregulation. The implications for future experiments are that (i) separate models for different classes of expression as well as accounting for different conditions or tissues to decrease the experimental variation might provide more accurate predictions, and (ii) more computational and experimental work is required to decipher the evolutionary strategies of regulatory grammars and define the properties of underlying basal and targeted-evolved regulation. Nevertheless, using the deep learning models, researchers can now computationally test the effects of the different combinations of regions (Fig. 5b, e), even with specific perturbations to gene coding sequences (Fig. 6b). This way, they can obtain candidate variants that enable rapid development of constructs with desired levels of gene expression (Fig. 6c, d). This has potential to greatly decrease experimental noise, accelerate experimental throughput and thus decrease the overall costs of microorganism and cell-line development in biotechnology.

Methods

Data

Genomic data, including gene sequences, as well as transcript and open reading frame (ORF) boundaries, were obtained from Ensembl ( https://www.ensembl.org/index.html). The exceptions were organisms (i) S. cerevisiae S288C, for which data were obtained from the Saccharomyces Genome Database ( https://www.yeastgenome.org/) and additional published transcript and ORF boundaries were used with this organism, and (ii) E. coli K-12 MG1655, where all data were obtained from the RegulonDB database ( http://regulondb.ccg.unam.mx/) (Supplementary Table 1). For each organism, coding and regulatory regions were extracted based on the transcript and ORF boundaries. DNA sequences were one-hot encoded, UTR sequences were zero-padded up to the specified lengths (Fig. 1d and Supplementary Figs. 9 and 10), codon frequencies were normalized to probabilities, and 8 mRNA stability variables were computed that included: lengths of 5′-UTR, ORF and 3′-UTR regions, GC content of 5′- and 3′-UTR regions, and GC content at each codon position in the ORF.

For gene expression levels, processed raw RNA sequencing Star counts were obtained from the Digital Expression Explorer V2 database ( http://dee2.io/index.html) and filtered for experiments that passed quality control. Raw mRNA data were transformed to transcripts per million (TPM) counts and genes with zero mRNA output (TPM < 5) were removed (Supplementary Table 2). Prior to modeling (Supplementary Fig. 7), the mRNA counts were Box-Cox transformed (see lambda parameters in Supplementary Table 4).

Modeling datasets were obtained with the above data processing and comprised paired gene regulatory structure explanatory variables (Fig. 1d and Supplementary Fig. 1c) and mRNA abundance response variables (Fig. 1a). No significant pairwise correlations were found between the variables (Supplementary Fig. 4 and Supplementary Table 5), except between mRNA counts and ORF lengths, due to the technical normalization bias from fragment-based transcript abundance estimation. To obtain mRNA counts that were uncorrelated to gene length, the residual of a linear model, based on ORF lengths as the response variable and mRNA counts as the explanatory variable, was used as the corrected response variable (Supplementary Fig. 4). When testing whether the introduced correction could potentially remove biological signal associated with gene length, using data from whole molecule RNA sequencing that does not rely on short-read assembly, no correlation between gene length and its expression was found (Pearson's r = −0.08, p-value < 1e-6; Supplementary Fig. 8).

Statistical hypothesis testing

For enrichment analysis, gene ontology slim terms were obtained from the Saccharomyces Genome Database and published promoter classifications were used. For statistical hypothesis testing, Scipy v1.1.0 was used with default settings. All tests were two-tailed except where stated otherwise.

Supervised deep methods

Different neural network architectures were tested that combined: (i) 1 to 4 convolutional neural network (CNN) layers (see tested parameters in Supplementary Table 6), which included inception layers (ii) 1 to 2 bidirectional recurrent neural network (RNN) layers, and (iii) 1 to 2 fully connected (FC) layers, in a global architecture layout CNN-RNN-FC. Training the networks both (i) concurrently or (ii) consecutively, by weight transfer on different variables (regulatory sequences to CNN and RNN, numeric variables to FC), showed that the architecture yielding best results was a concurrently trained CNN (3 layers)-FC (2 layers), which was used for all models. Batch normalization and weight dropout were applied after all layers and max-pooling after CNN layers (Supplementary Table 6). The Adam optimizer (Supplementary Table 6) with mean squared error (MSE) loss function and ReLU activation function with uniform weight initialization were used. In total, 26 hyper-parameters were optimized using a tree-structured Parzen estimators approach via Hyperopt v0.1.1 at default settings for 1500 iterations.

The explanatory input data and corresponding response variables were divided into training (80%), validation (10%) and test (10%) sets. Tests with different sizes of input regulatory sequences showed that whole regions resulted in the most accurate models (Supplementary Fig. 10). The best models were chosen according to the minimal MSE on the validation set with the least spread between training and validation sets. The coefficient of determination ( R ²) computed on the test set is reported in the main text and was defined as \(R^2 = 1 - {\mathrm{SS}}_{{\mathrm{Residual}}}/{\mathrm{SS}}_{{\mathrm{Total}}}\) [Eq. 1], where SS Residual is the sum of residual squares of predictions and SS Total is the total sum of squares, and statistical significance was evaluated using the two-tailed F-test.

To assess model predictions by varying either promoter or terminator regions, input explanatory variables were constructed based on the specified coding (fluorescence reporters codon frequencies) and regulatory regions (variable region combined with specified adjacent regions). For building and training models Keras v2.2 and Tensorflow v1.10 software packages were used and accessed using the python interface.

Supervised shallow methods

For shallow modeling the following regression algorithms were used: linear regression, ridge regression, lasso, elastic net, random forest, support vector machines with nested cross-validation, and k-nearest neighbour regression. To include information from the regulatory DNA sequences in the shallow models, k-mers of lengths 4-6 bp were extracted from the regulatory DNA sequences and used as additional explanatory variables. Nested cross validations by selecting the best models with the lowest MSE on held-out sets were performed with these algorithms and GridSearchCV using the Scikit-learn package v0.20.3 with default settings. The coefficient of determination ( R 2) (Eq. 1) computed on the test is reported in the main text analogously as with deep models in M3.

Analysis of evolutionary rates

Multi-sequence alignments of 3800 orthologous protein-coding genes (each gene divided into separate promotor, 5′- and 3′-UTR, terminator and coding regions) from fourteen fungal species were generated using Mafft v7.407 with the Linsi algorithm and default settings. Orthologs were defined according to Ensembl Compara. The resulting 19,000 alignments were analysed with Zorro v1.0 to identify regions of high sequence variability and possible misalignment that could have a negative effect on the phylogenetic signal in the overall sequence. After excluding sites with a confidence score ≤ 0.2, each individual alignment was analysed for 1,000,000 generations in MrBayes v3.2.6, with the number of substitution types set to one, and a gamma distribution of substitution rates, to obtain the estimated mean substitution rate (alpha) for each dataset.

DNA relevance analysis

To calculate the relevance of different DNA sequences for model predictions, defined as \({\mathrm{Relevance}} = (Y - Y_{{\mathrm{Occluded}}})/Y\) [Eq. 2], where Y is the model prediction, an input dataset with sliding window occlusions was used with the deep models to obtain predictions (Supplementary Fig. 14). The window size of the occlusions was set to either: (i) whole regions, to analyze the relevance of region combinations and sensitivity analysis or (ii) 10 bp for motif analysis, determined based on the analysis of relevance profiles at difference occlusion sizes using the FastDTW v0.3.2 alignment method and analysis of the distribution of DNA sequence motif sizes in the JASPAR database (Supplementary Fig. 15). For clustering of relevance profiles, the consensus clustering approach was used, as implemented in the package ConsensusClusteringPlus v1.48.0 with the method Partition around medoids (pam) set to 50-fold subsampling of 80% of data points and using the Pearson correlation distance. The number of clusters ( k) was determined at k = 4, for which the relative consensus did not increase more than 10% (Supplementary Fig. 22).

DNA motif analysis

Extraction of relevant sequences, i.e. those that significantly (standard deviation ≥ 2) affected gene expression prediction, yielded 169,763 sequences that spanned all the analysed genes ( RSD < 1) (Supplementary Fig. 18). To identify regulatory motifs, clustering of the relevant sequences was performed using CD-HIT v4.8.1, with recommended settings (a k-mer size of 4, 5 and 6 was used in correspondence with sequence identity cutoff 0.8, 0.85, and 0.9, respectively) and a cluster size of 5 sequences, based on the amount of recovered sequences and unique motifs. Multiple sequence alignment on the clustered sequences was performed using Mafft v7.407, with the Linsi algorithm and default settings. Position weight motifs (PWMs) were processed using the Biopython package v1.73 and motif edges were trimmed below a cutoff of 0.2 bits. Pairwise comparisons of the PWMs across the regulatory regions and comparisons to JASPAR (core fungi, non-redundant) and Yeastract databases was performed using Tomtom and Meme suite v4.12, with recommended settings. Motif co-occurrence was analysed using the FP-growth algorithm as implemented in Apache Spark v2.4, with default settings accessed through the Python interface, where support, confidence and lift were calculated as defined in. The statistical significance level of co-occurring motifs was determined using the chi-squared test.

Experimental strain construction

The S. cerevisiae strain CEN.PK113-7D was used as the base strain for all genetic engineering. Integration of the promoter-GFP-terminator constructs was done using the CRISPr/Cas9 plasmid as well as the gRNA Helper vectors from the EasyClone marker-free system at the XI-2 locus (using pCFB2312 + pCFB3044). All transformation steps were performed according to the published manual, with the exception that the repair fragment was provided as three fragments: the promoter with 30 bp overlap to the genome and 30 bp overlap to the GFP gene, the GFP gene, and the terminator with 30 bp overlap to the GFP gene and 30 bp overlap to the genome. For each fragment, 250 µg of DNA were used for the transformation. The DNA fragments for the promoters and terminators were obtained using PCR (see Supplementary Table 14 for the list of primers). All PCR products were purified using the Thermo Scientific GeneJET PCR Purification Kit. For the GFP gene, the UBIMΔ kGFP* version from Houser et al. was used (see Supplementary Table 15 for sequence), where the DNA sequence was ordered as a gene fragment from Eurofins.

Fluorescence measurements and analysis

The yeast cells were pre-cultured overnight in 96 deep well plates in 0.5 ml of minimal media with 2% glucose (see Supplementary Table 16 for media composition) at 30 °C and 300 rpm. The following day, the cultures were set up in 96 deep well plates with a starting OD600 of 0.1. After 5 h of cultivation, when the cells were in mid-exponential growth phase, the cells were diluted with water to a final OD600 of 0.02 in a total volume of 200 µl in 96-well round plates in technical duplicates. Using the Guava easyCyte 8HT flow cytometry system the GFP (green fluorescence) intensity as well as cell size (forward scatter) and granularity (side scatter) were measured (Supplementary Fig. 36). The cells were gated based on the forward and side scatter intensity in order to exclude a few very large and very small cells (Supplementary Fig. 37). For each technical duplicate the median GFP intensity value is reported.

Software

Python v3.6 ( www.python.org) and R v3.6 ( www.r-project.org) were used for computations. Code for the data analysis is available at https://github.com/JanZrimec/DeepExpression and data at https://doi.org/10.5281/zenodo.3905251 (see also section on Data Availability).

Reporting summary

Further information on research design is available in the Nature Research Reporting Summary linked to this article.

Data availability

Genomic data, transcript and gene boundaries were obtained from Ensembl Genomes release 41 and Ensembl release 94 ( https://www.ensembl.org/), Saccharomyces Genome Database ( https://www.yeastgenome.org/) and RegulonDB v10.5 database ( http://regulondb.ccg.unam.mx/) (links to raw data in Supplementary Tables 4 and 10). RNA sequencing data was obtained from the Digital Expression Explorer V2 database ( http://dee2.io/mx/), DNA sequence motifs from the Meme suite motifs databases file ( http://meme-suite.org/) and additional data from the cited references (links to raw data in Supplementary Table 7). The Source Data file was deposited to the Zenodo repository and is available at https://doi.org/10.5281/zenodo.3905251.

Code availability

Code for the data analysis was deposited to the Github repository and is available at https://github.com/JanZrimec/DeepExpression.

Acknowledgements

We thank Hal Alper for kindly sharing data from his lab, Victor Garcia for insightful discussions on codon usage, and Clara Correia-Melo and Simran Aulakh for commenting on the manuscript. We gratefully acknowledge the NVIDIA Corporation for supporting this research as well as the Chalmers Centre for Computational Science and Engineering (C3SE) and the Swedish National Infrastructure for Computing (SNIC) for providing computational resources. Mikael Öhman and Thomas Svedberg at C3SE are acknowledged for technical assistance. J.Z., F.B. and A.Z. were supported by SciLifeLab funding. CSB was supported by the European Union's Horizon 2020 research and innovation programme [Marie Skłodowska-Curie grant agreement No 722 287]. The study was supported by the BIGDATA@Chalmers funding initiative (Area of Advance ICT).

Funding

Open Access funding provided by Chalmers University of Technology.

Author information

Affiliations

1. Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden

Jan Zrimec, Christoph S. Börlin, Filip Buric, Verena Siewers, Jens Nielsen & Aleksej Zelezniak

2. Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden

Christoph S. Börlin, Verena Siewers & Jens Nielsen

3. Computer Science and Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden

Azam Sheikh Muhammad, Rhongzen Chen & Vilhelm Verendel

4. Department of Marine Sciences, University of Gothenburg, Box 461, SE-405 30, Gothenburg, Sweden

Mats Töpel

5. Gothenburg Global Biodiversity Center (GGBC), Box 461, 40530, Gothenburg, Sweden

Mats Töpel

6. Science for Life Laboratory, Tomtebodavägen 23a, SE-171 65, Stockholm, Sweden

Aleksej Zelezniak

Contributions

J.Z. and A.Z. conceptualized the project; J.Z., F.B., A.S.M., R.C., V.V., M.T. and A.Z. designed and performed the computational analysis; J.Z., C.B., V.S. and A.Z. designed the experimental analysis; C.B. performed the experimental analysis; J.Z. and A.Z. interpreted the results; J.Z. and A.Z. wrote the initial draft paper; J.Z., C.B., F.B., V.S., J.N., M.T. and A.Z. revised the initial draft and wrote the final paper.

Corresponding author

Correspondence to Aleksej Zelezniak.

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The authors declare no competing interests.

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Zrimec, J., Börlin, C.S., Buric, F. et al. Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure. Nat Commun 11, 6141 (2020). https://doi.org/10.1038/s41467-020-19921-4
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# data[].attributes.attachment_link.title
Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure

# data[].attributes.attachment_link.description
Regulatory and coding regions of genes are shaped by evolution to control expression levels. Here, the authors use deep learning to identify rules controlling gene expression levels and suggest that all parts of the gene regulatory structure interact in this.

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Genes and speciation | Nature Reviews Genetics

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Genes and speciation | Nature Reviews Genetics

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Nature Reviews Genetics 5, 114-122 (2004) Cite this article

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Key Points

Studies of reproductive isolation have shown that the number of genes that are involved is often large. Between closely related species of Drosophila, the number of such genes might often be in the hundreds.

Speciation genes - that is, the genes that underlie reproductive isolation - can contribute to hybrid inviability, sterility or behavioural aberration, as well as ecological maladaptation.

In the genic view of speciation, loci that are not closely linked to speciation genes might continue to be shared between nascent species, as in parapatric speciation.

At least five cases of speciation genes have been confirmed so far. Most bear a strong signature of positive selection. Three of the five known speciation genes are related to transcriptional regulation, supporting the postulate that species divergence is often regulatory in nature.

For a gene to diverge in function, it needs to be released from the old functional niche (genetic 'niche-release'). So, speciation genes are often non-essential, with functions that are only loosely coupled to reproductive isolation. In a few cases, gene knock-out studies - the ultimate way to test the dispensability of a gene - have been able to show the non-essential nature of specific speciation genes.

Genomic data might help to resolve the long-running debate on the relative importance of allopatric and parapatric modes of speciation. Models of allopatric speciation make specific testable predictions about the level of divergence across the whole genome.

Abstract

It is only in the past five years that studies of speciation have truly entered the molecular era. Recent molecular analyses of a handful of genes that are involved in maintaining reproductive isolation between species (speciation genes) have provided some striking insights. In particular, it seems that despite being strongly influenced by positive selection, speciation genes are often non-essential, having functions that are only loosely coupled to reproductive isolation. Molecular studies might also resolve the long-running debate on the relative importance of allopatric and parapatric modes of speciation.

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Acknowledgements

We thank S. Shi and N. Osada for technical help and two anonymous referees for critical comments. Grants from the National Institutes of Health (USA) to C.-I Wu and from the National Science Council (ROC) to C.-T. Ting are gratefully acknowledged.

Author information

Affiliations

1. Department of Ecology and Evolution, University of Chicago, Chicago, 60637, Illinois, USA

Chung-I Wu

2. Department of Life Science, National Tsing Hua University, Hsinchu, 300, Taiwan, Republic of China

Chau-Ti Ting

Corresponding author

Correspondence to Chung-I Wu.

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Competing interests

The authors declare no competing financial interests.

Related links

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DATABASES

FlyBase

desat2

Hmr

Nup96

OdsH

unc-4

Glossary

NEO-DARWINIAN (SYNTHESIS)

The modern theory of evolution that combines both natural selection and population genetics, in which the Darwinian concept of spontaneous variation is explained in terms of mutation and genetic recombination.

CO-ADAPTATION

Selection by which harmoniously interacting genes accumulate in the gene pool of a population.

INTROGRESSION

The integration of a genomic region from one species into the genome of another species. Even a few percent of the introgressed genome can lead to hybrid incompatibility.

POSITIONAL CLONING

The procedure by which we identify and isolate genes on the basis of their location in the genome, involving detailed genetic and physical maps of chromosomes.

DEFICIENCY MAPPING

Uses chromosomes that have different sections deleted to locate the position of a gene of interest. Without the deficiency, the normal functional gene usually masks the effect of (that is, complements) the defective or foreign copy that we wish to identify.

ALLELE COMPLEMENTATION

A test of whether a wild-type phenotype can be restored with two given alleles in a diploid genome.

RECEPTOR TYROSINE KINASE SUPERFAMILY

One of the important cell-surface receptors that interacts with water-soluble ligands.

ONCOGENE

A gene that induces uncontrolled cell proliferation.

MATERNAL EFFECT

The effect of the maternal genotype on the phenotype of the offspring, or the zygotes, usually at the embryonic stage (see also zygotic effects).

ZYGOTIC EFFECT

The effect of the zygotes' own genotype on their own phenotype.

MCDONALD AND KREITMAN TEST

A test that contrasts interspecific divergence against intraspecific polymorphism. It is a powerful test to detect excess of non-synonymous substitutions between species.

CONTACT PHEROMONES

Chemical signals that are transmitted through the direct physical contact of two individuals. Contact pheromones in Drosophila are often sexual signals.

KA/KS RATIOS

Ratios of non-synonymous substitutions to synonymous substitutions per site.

INCIPIENT SPECIATION

The initial stage of species formation during which reproductive isolation is only partial.

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Wu, CI., Ting, CT. Genes and speciation. Nat Rev Genet 5, 114-122 (2004). https://doi.org/10.1038/nrg1269
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It is only in the past five years that studies of speciation have truly entered the molecular era. Recent molecular analyses of a handful of genes that are involved in maintaining reproductive isolation between species (speciation genes) have provided some striking insights.

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The genes that drive speciation : Nature News

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The genes that drive speciation : Nature News

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Published online 11 December 2008 | Nature | doi:10.1038/news.2008.1297

News

Mouse and fruitfly studies provide clues to the origins of species.

A gene that drives speciation in mice has been discovered.Getty

Geneticists have identified two genes, one in mice and one in fruitflies, that stop the offspring of different species from reproducing - driving the evolution of new species.

A species can be defined as a group of organisms that can interbreed to produce fertile offspring. Hybrid animals, bred from inter-species pairings - such as mules, from the pairing of a male donkey and a female horse - are usually infertile and many such hybrids do not survive. Sometimes, however, pairings of closely related species, or subspecies, produce hybrids with limited fertility.

Identifying the genes that block reproduction in hybrids can reveal the genetic forces that drive speciation. However, fewer than 10 such genes have been identified to date.

Now Jiri Forejt, a geneticist at the Academy of Sciences of the Prague-based Czech Republic, and his colleagues have identified a speciation gene in mice - the first to be found in mammals.

Tracking down the gene "was terrible work", says Forejt, who has spent the last 30 years trying to identity a suspected speciation gene in two subspecies of mice.

Relying on extensive crossing and genetic modification of animals, and thanks to whole-genome data that has only recently become available, Forejt found that male hybrids of these subspecies are infertile because of the Prdm9 gene.

The finding that Prdm9 encodes a protein that silences genes also confirms suspicions that epigenetic changes - traits that can be inherited without changes to the underlying DNA sequence - are important in speciation.

The fruit of the fruitfly hybrid

"The genetics of speciation are almost by definition inherently problematic - speciation means no crosses, and no crosses means it's very difficult to do genetics," says Nitin Phadnis, a geneticist at the Fred Hutchinson Cancer Research Center in Seattle.

Phadnis and his colleague, H. Allen Orr at Rochester University in New York, were searching for a speciation genes that caused peculiar hybrids when two related subspecies of Drosophila mated. These male hybrids are infertile for most of their lives, but recover some fertility in their old age - but then can produce only daughters.

The existence of these hybrids suggested to Phadnis and Orr that a segregation distorter - a gene that causes chromosomes bearing it to pass more frequently to offspring, in this case by controlling the sex of progeny - might be linked to speciation.

Because segregation distorters can be involved in an arms race with genes that try to prevent such distortion, they may evolve rapidly, says Phadnis. Although it has been proposed that the rapid evolution of 'cheating' genes and their repressors could cause functional divergence between populations resulting in speciation, evidence for this theory has been scarce.

Using similar techniques to the ones Forejt used, however, Phadnis showed that a single gene caused both hybrid sterility and segregation distortion.

"What this works shows you is that speciation can happen not only because of adaptation to the external environment, but also because of adaptation to the internal genomic environment," Phadnis says.

"Since there are so few speciation genes identified to the sequence level, adding one more to the list is exciting," says Roger Butlin, a geneticist at Sheffield University, UK. "I think there will be a lot more interest in segregation distortion and its relationship to speciation."

Gene bonanza

Both papers are published in Science and could pave the way to the discovery of more speciation genes in the near future. Forejt is already working to identify additional speciation genes that work with Prdm9 to cause infertility in hybrid mice, but says that other researchers are hot on his heels.

"There is no question that in this era of whole-genome sequences and genomic data it is much easier to identify speciation genes than it used to be" says Michael Nachman, who studies mouse genetics at the University of Arizona in Tucson.

With more genes should come greater insight into speciation. Some geneticists wonder whether only particular classes of genes are important in speciation - such as epigenetic genes or segregation distorters - or whether many sorts of genes help to drive species apart.

"What is surprising about the speciation genes that have been identified [so far] is that there is a whole hodgepodge of different kinds of genes with different functions," says Nachman. "I don't think we're going to see [trends] until dozens of genes are identified, and there's just a handful now."

References

1. Mihola, O., Trachtulec, Z., Vlcek, C., Schimenti, J. C. & Forejt, J. Science advance online publication, doi:10.1126/science.1163601 (11 December 2008).

2. Phadnis, N. & Orr, H. A. Science advance online publication, doi:10.1126/science.1163934 (11 December 2008).

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Published online 11 December 2008 | Nature | doi:10.1038/news.2008.1297 News Mouse and fruitfly studies provide clues to the origins of species. A gene that drives speciation in mice has been discovered.Getty Geneticists have identified two genes, one in mice and one in fruitflies, that stop the offspring of different species from reproducing - driving the evolution of new species.

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Life on Earth may be carbon-based, but another element matters, too

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Viewed from space, a bloom of the nitrogen-fixing phytoplankton Trichodesmium spans hundreds of square miles in the Coral Sea off the northeast Australian coast. Credit: Joshua Stevens/NASA Earth Observatory

Middle school students learn in science class about the carbon cycle-the flow of carbon among the atmosphere, living organisms, soil and the oceans. But another, less familiar cycle also plays a crucial role in the balance of nature: the nitrogen cycle.

Nitrogen constitutes about 78% of the Earth's atmosphere, where it exists mainly in its most stable form, a gas called dinitrogen, or N ₂. A significant amount also resides in the oceans as dissolved gas.

Most animals and plants can't use N ₂; they first need it turned into a more reactive form, such as ammonia, through a process called nitrogen fixation. But only certain microorganisms can fix nitrogen, and many of those live in marine environments. They draw the N ₂ from the water and, using a specialized enzyme, break the bond between the two nitrogen atoms and attach other atoms to each, making new molecules that other living organisms can use.

The process is crucial to life on Earth and directly affects humans.

"The oceans are becoming an ever-increasing source of food for humanity, and nitrogen fixation is critical in maintaining many marine food webs," said Doug Capone, professor of biological sciences at the USC Dornsife College of Letters, Arts and Sciences. His research focuses on understanding how ocean microbes affect the movement of important elements, including carbon and nitrogen, through plants and animals and from land to sea to air and back.
Getting a fix on global fixation
Capone has studied diverse ecological systems throughout the world, including the tropical open ocean, coral reefs, mangroves, temperate estuaries, groundwater aquifers and Antarctic snows.

A thorough understanding of the factors involved in nitrogen fixation in the oceans could help future generations safely and sustainably farm the oceans, he said.

Capone, collaborating with Jonathan Zehr of the University of California, Santa Cruz, recently published Marine Nitrogen Fixation (Springer, 2021), which summarizes the extensive research and current understanding of marine nitrogen fixation. The book builds on an article the pair wrote and published last year at the request of the journal Science.

Capone, who holds the William and Julie Wrigley Chair in Environmental Studies, and Zehr, a Distinguished Professor at UC Santa Cruz, are widely respected authorities on marine nitrogen fixation.

"I've been working on aspects of marine N ₂ fixation since my days as a Ph.D. student," Capone said. His dissertation focused on the importance of N ₂ fixation in the tropical seagrass Thalassia, also known as turtle grass.

In shallow tropical waters, turtle grass forms dense "meadows" that many sea-going species-from microbes to mollusks to manatees-call home. Nitrogen-fixing microbes, known scientifically as diazotrophs, live on the plant's leaves and its roots, providing a critical source of nitrogen in the nutrient-depleted tropical waters, Capone said.
Combined expertise in a vital field of study
After landing his first faculty position at New York's Stony Brook University in the late '70s, Capone turned his attention to the open ocean, and in the decades since, he has led many research cruises to locations throughout the globe and conducted extensive research on the physiology, ecology and biogeochemical impact of open ocean diazotrophs.

He's also spent a large share of his career mentoring young scientists and brought many others into this field.

"I've trained a gaggle of researches in this area-undergrads, grad students and postdocs-as well as having entrained researchers from diverse fields into the area of marine nitrogen fixation," he said.

Zehr is among those researchers, having joined Capone's Stony Brook University Lab as a postdoctoral fellow in 1980.

"His postdoc with me was not on N ₂ fixation, but he subsequently joined me on many of the cruises I led to study this process in the tropical ocean," said Capone.

Zehr has gone on to establish one of the best model systems for studying functional genes in the environment, according to Capone. Major advances in uncovering the vast biodiversity of microbes in the environment have generally relied upon analyzing the ribosomal genes-genes involved in creating ribosomes-that are common to all life to establish relationships and diversity. Zehr has instead used the genes directly involved with nitrogen fixation to find and characterize previously unknown microbes capable of fixing N ₂ in the ocean and to track the expression of these genes.

Well-known for his work among the tiniest marine plankton, Zehr discovered a biological partnership, or symbiosis, of two microorganisms found throughout much of the world's upper ocean.

One partner, the host alga, is eukaryotic-meaning it has a nucleus and is autotrophic, able to use light energy and fix carbon; that is, take up carbon dioxide to feed itself and produce new organic molecules.

The other partner is a small, unicellular cyanobacterium, or blue-green alga, that can also derive energy from light but is unable to fix carbon. However, it does fix N ₂.

The two exchange metabolites in their symbiosis, and the cyanobacterium is a major player in fixing N ₂ in the oceans, says Capone, who also hints that his and Zehr's combined expertise is a kind of symbiosis in its own right, making them particularly well-suited to put together Marine Nitrogen Fixation.

"In many ways, we complement each other-Jon on the molecular biology, physiology and biogeography of nitrogen fixation, myself focusing on ecology and biogeochemistry," Capone says.

In the book, which is primarily intended for scientists, graduate students and upper division undergraduates, he and Zehr give a detailed overview of the current understanding of global marine nitrogen fixation. Topics include which marine microorganisms are fixing nitrogen, where they live and what environmental factors-including human-caused changes such as ocean warming and acidification-impact microbial activity. And they point out that much about the physiology and regulation of N ₂ fixation remains to be uncovered.

More information: Marine Nitrogen Fixation: www.springer.com/gp/book/9783030677459

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Life on Earth may be carbon-based, but another element matters, too

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Middle school students learn in science class about the carbon cycle-the flow of carbon among the atmosphere, living organisms, soil and the oceans. But another, less familiar cycle also plays a crucial role in the balance of nature: the nitrogen cycle.

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Molecular and evolutionary processes generating variation in gene expression | Nature Reviews Genetics

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Molecular and evolutionary processes generating variation in gene expression | Nature Reviews Genetics

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Acknowledgements

The author thanks members of the Wittkopp laboratory for helpful discussions during drafting of the manuscript. Support for this work was provided by the John Simon Guggenheim Memorial Foundation, Alexander von Humboldt Foundation, National Science Foundation (DEB-1911322) and National Institutes of Health (NIH) (R35GM118073) to P.J.W. and the NIH Training Grant T32GM007544 to P.V.Z.

Author information

Author notes

These authors contributed equally: Mark S. Hill, Pétra Vande Zande.

Affiliations

1. Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA

Mark S. Hill & Patricia J. Wittkopp

2. Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA

Pétra Vande Zande & Patricia J. Wittkopp

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The authors contributed equally to all aspects of the article.

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Correspondence to Patricia J. Wittkopp.

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Glossary

Genetic drift

Variation in allele frequencies caused by random sampling of individuals.

Pleiotropy

The phenomenon whereby a single genetic variant affects multiple independent traits.

Bulk segregant analysis

A technique used to associate genetic markers with trait variation by contrasting allele frequencies between two groups of individuals defined by differences in trait values.

TATA box

An element of some promoter sequences that serves as a binding site for certain general transcription factors and is rich in T/A nucleotides.

Core promoter element

Functional sequences proximal to the transcription start site that are sufficient to initiate transcription.

CpG islands

Regions of the genome containing a large number of CpG dinucleotide repeats, found in the promoters of many mammalian genes.

Initiator region

An element of the core promoter sequence located downstream of the TATA box that overlaps with the transcription start site.

Skew

A measure of the asymmetry of a distribution about its mean.

Kurtosis

A measure of how much weight is concentrated in the tails of a distribution, relative to its centre.

Dispersion

The extent to which a set of values is clustered or dispersed, often measured by the variance or standard deviation of a distribution.

Gene expression noise

The variability of expression level among genetically identical cells in the same environment.

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Hill, M.S., Vande Zande, P. & Wittkopp, P.J. Molecular and evolutionary processes generating variation in gene expression. Nat Rev Genet 22, 203-215 (2021). https://doi.org/10.1038/s41576-020-00304-w
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Further reading

Joachim M. Surm

& Yehu Moran

Trends in Genetics (2021)

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Molecular and evolutionary processes generating variation in gene expression

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Heritable variation in gene expression is common within and between species. This variation arises from mutations that alter the form or function of molecular gene regulatory networks that are then filtered by natural selection.

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Scientists discover new organic compounds that could have helped form the first cells -- ScienceDaily

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Scientists discover new organic compounds that could have helped form the first cells -- ScienceDaily

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Chemists studying how life started often focus on how modern biopolymers like peptides and nucleic acids contributed, but modern biopolymers don't form easily without help from living organisms. A possible solution to this paradox is that life started using different components, and many non-biological chemicals were likely abundant in the environment. A new survey conducted by an international team of chemists from the Earth-Life Science Institute (ELSI) at Tokyo Institute of Technology and other institutes from Malaysia, the Czech Republic, the US and India, has found that a diverse set of such compounds easily form polymers under primitive environmental conditions, and some even spontaneously form cell-like structures.

Understanding how life started on Earth is one of the most challenging questions modern science attempts to explain. Scientists presently study modern organisms and try to see what aspects of their biochemistry are universal, and thus were probably present in the organisms from which they descended. The best guess is that life has thrived on Earth for at least 3.5 billion of Earth's 4.5 billion year history since the planet formed, and most scientists would say life likely began before there is good evidence for its existence. Problematically, since Earth's surface is dynamic, the earliest traces of life on Earth have not been preserved in the geological record. However, the earliest evidence for life on Earth tells us little about what the earliest organisms were made of, or what was going on inside their cells. "There is clearly a lot left to learn from prebiotic chemistry about how life may have arisen," says the study's co-author Jim Cleaves.

A hallmark of life is evolution, and the mechanisms of evolution suggest that common traits can suddenly be displaced by rare and novel mutations which allow mutant organisms to survive better and proliferate, often replacing previously common organisms very rapidly. Paleontological, ecological and laboratory evidence suggests this occurs commonly and quickly. One example is an invasive organism like the dandelion, which was introduced to the Americas from Europe and is now a commo weed causing lawn-concerned homeowners to spend countless hours of effort and dollars to eradicate. Another less whimsical example is COVID-19, a virus (technically not living, but technically an organism) which was probably confined to a small population of bats for years, but suddenly spread among humans around the world. Organisms which reproduce faster than their competitors, even only slightly faster, quickly send their competitors to what Leon Trotsky termed the "ash heap of history." As most organisms which have ever existed are extinct, co-author Tony Z. Jia suggests that "to understand how modern biology emerged, it is important to study plausible non-biological chemistries or structures not currently present in modern biology which potentially went extinct as life complexified."

This idea of evolutionary replacement is pushed to an extreme when scientists try to understand the origins of life. All modern organisms have a few core commonalities: all life is cellular, life uses DNA as an information storage molecule, and uses DNA to make ribonucleic RNA as an intermediary way to make proteins. Proteins perform most of the catalysis in modern biochemistry, and they are created using a very nearly universal "code" to make them from RNA. How this code came to be is in itself enigmatic, but these deep questions point to their possibly having been a very murky period in early biological evolution ~ 4 billion years ago during which almost none of the molecular features observed in modern biochemistry were present, and few if any of the ones that were present have been carried forward.

Proteins are linear polymers of amino acids. These floppy strings of polymerised amino acids fold into unique three-dimensional shapes, forming extremely efficient catalysts which foster precise chemical reactions. In principle, many types of polymerised molecules could form similar strings and fold to form similar catalytic shapes, and synthetic chemists have already discovered many examples. "The point of this kind of study is finding functional polymers in plausibly prebiotic systems without the assistance of biology, including grad students," says co-author Irena Mamajanov.

Scientists have found many ways to make biological organic compounds without the intervention of biology, and these mechanisms help explain these compounds' presence in samples like carbonaceous meteorites, which are relics of the early solar system, and which scientists don't think ever hosted life. These primordial meteorite samples also contain many other types of molecules which could have formed complex folded polymers like proteins, which could have helped steer primitive chemistry. Proteins, by virtue of their folding and catalysis mediate much of the complex biochemical evolution observed in living systems. The ELSI team reasoned that alternative polymers could have helped this occur before the coding between DNA and protein evolved. "Perhaps we cannot reverse-engineer the origin of life; it may be more productive to try and build it from scratch, and not necessarily using modern biomolecules. There were large reservoirs of non-biological chemicals that existed on the primeval Earth. How they helped in the formation of life-as-we-know-it is what we are interested in," says co-author Kuhan Chandru.

The ELSI team did something simple yet profound: they took a large set of structurally diverse small organic molecules which could plausibly be made by prebiotic processes and tried to see if they could form polymers when evaporated from dilute solution. To their surprise, they found many of the primitive compounds could, though they also found some of them decomposed rapidly. This simple criterion, whether a compound is able to be dried without decomposing, may have been one of the earliest evolutionary selection pressures for primordial molecules.

The team conducted one further simple test. They took these dried reactions, added water and looked at them under a microscope. To their surprise, some of the products of these reaction formed cell-sized compartments. That simple starting materials containing 10 to 20 atoms can be converted to self-organised cell-like aggregates containing millions of atoms provides startling insight into how simple chemistry may have led to complex chemistry bordering on the kind of complexity associated with living systems, while not using modern biochemicals.

"We didn't test every possible compound, but we tested a lot of possible compounds. The diversity of chemical behaviors we found was surprising, and suggests this kind of small-molecule to functional-aggregate behavior is a common feature of organic chemistry, which may make the origin of life a more common phenomenon than previously thought," concludes co-author Niraja Bapat.

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organic; biology; biochemistry research; organic chemistry; chemistry; biochemistry; geochemistry; earth science; biodiversity; origin of life; charles darwin; evolution

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Scientists discover new organic compounds that could have helped form the first cells

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Chemists studying how life started often focus on biopolymers like peptides and nucleic acids, but modern biopolymers don't form easily without help from living organisms. A possible solution to this paradox is that life started using different components, and many non-biological chemicals were likely abundant in the environment.

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How organ functions were shaped over the course of evolution

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How organ functions were shaped over the course of evolution

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Credit: CC0 Public Domain

A large-scale study conducted by molecular biologists from Heidelberg University has yielded groundbreaking new insights into the evolution and regulation of gene expression in mammalian organs. The scientists investigated RNA synthesis and subsequent protein synthesis in the organs of humans and other representative mammals, and with the aid of sequencing technologies, they analyzed more than 100 billion gene expression fragments from various organs. They were able to demonstrate that the finely tuned interplay of the two synthesis processes during evolution was crucial for shaping organ functions.

A complex interplay of activity between a large number of genes -known as gene expression-underlies organ functions. "Until now, our understanding of these essential genetic programs in mammals was limited to the first layer of gene expression-the production of messenger RNAs," explains Prof. Dr. Henrik Kaessmann, group leader of the "Functional evolution of mammalian genomes" research team at the Center for Molecular Biology of Heidelberg University (ZMBH). "The next layer-the actual synthesis of proteins at the ribosome through the translation of the messenger RNAs-remained largely unknown."

It is this second synthesis process that the Heidelberg researchers have now studied more closely. Using so-called next-generation sequencing technologies, they analyzed the gene expression of various organs on both layers. They studied the brain, liver and testes from humans and other selected mammals, including rhesus monkeys, mice, opossum and platypus. "On the basis of these data, we could jointly investigate both gene expression layers and compare them across mammalian organs using state-of-the-art bioinformatics approaches," explains Dr. Evgeny Leushkin of the ZMBH.

In their large-scale study, the ZMBH researchers showed that the finely tuned interplay of the two synthesis processes during evolution was critical for shaping organ functions. For the first time, they were able to show that-in addition to regulation of messenger RNA production-other regulatory mechanisms at the layer of translation are crucial for optimizing the amount of protein produced in all organs. This is especially true in the testes, where translational regulation is key for sperm development. Another important finding concerns mutational changes in gene expression regulation that arose during evolution. These changes were often balanced between the two layers. Changes that offset one another were primarily maintained to ensure the production of consistent amounts of protein.

Researchers from France and Switzerland contributed to the study. Funding was provided by the German Research Foundation and European Research Council. The data are available in a public access database. Their research results were published in Nature.

More information: Zhong-Yi Wang et al, Transcriptome and translatome co-evolution in mammals, Nature (2020). DOI: 10.1038/s41586-020-2899-z

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How organ functions were shaped over the course of evolution

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A large-scale study conducted by molecular biologists from Heidelberg University has yielded groundbreaking new insights into the evolution and regulation of gene expression in mammalian organs. The scientists investigated RNA synthesis and subsequent protein synthesis in the organs of humans and other representative mammals, and with the aid of sequencing technologies, they analyzed more than 100 billion gene expression fragments from various organs.

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For Darwin Day, 6 facts about the evolution debate | Pew Research Center

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For Darwin Day, 6 facts about the evolution debate | Pew Research Center

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Tuesday is the 210th anniversary of Charles Darwin's birth, a day now celebrated by some as Darwin Day. Darwin is best known for his theory of evolution through natural selection. When Darwin's work was first made public in 1859, it shocked Britain's religious establishment. And while today it is accepted by virtually all scientists, evolutionary theory still is rejected by many Americans, often because it conflicts with their religious beliefs about divine creation.

While not an official holiday, Darwin Day has been adopted by scientific and humanist groups to promote everything from scientific literacy to secularism. This year, dozens of events have been planned worldwide, many of them anchored by scientific talks or symposiums.

To mark the occasion, here are six facts about the public's views on evolution, as well as other aspects of the debate in the U.S. and elsewhere:

Roughly eight-in-ten U.S. adults (81%) say humans have evolved over time, according to data from a new Pew Research Center study. This includes one-third of all Americans (33%) who say that humans evolved due to processes like natural selection with no involvement by God or a higher power, along with 48% who believe human evolution occurred through processes guided or allowed by God or a higher power. The same survey found that 18% of Americans reject evolution entirely, saying humans have always existed in their present form. (See the full report for a deeper look at the ways question wording and format can affect survey results on evolution.)

2 Around four-in-ten white evangelical Protestants (38%) say humans have always existed in their present form, and about a quarter (27%) of black Protestants share this view, according to the new study. Among white mainline Protestants, just 16% say humans have always existed in their present form. Similar shares of Catholics (13%) and the religiously unaffiliated (11%) say the same. Only among the religiously unaffiliated - those who describe their religion as atheist, agnostic or "nothing in particular" - do a majority (64%) accept evolution via natural selection with no involvement from God or a higher power. Both Protestants and Catholics are considerably more likely to say evolution was guided or allowed by God than they are to say that humans evolved due to processes such as natural selection, or to say that humans have always existed in their present form.

3 Scientists overwhelmingly agree that humans evolved over time, and most Americans are aware that this is the case. Among scientists connected to the American Association for the Advancement of Science, 98% say they believe humans evolved over time. Roughly three-quarters (76%) of Americans perceive that most biological scientists hold this view, according to the new study. Those in the general public who reject evolution are divided on whether there is a scientific consensus on the topic: 46% say most biological scientists think humans have evolved due to processes such as natural selection, and 52% say most biological scientists think humans have always existed in their present form.

A series of court decisions have prohibited the teaching of creationism or intelligent design in public schools. In spite of efforts in many American states and localities to ban the teaching of evolution in public schools - or to teach alternatives to evolution - courts in recent decades have consistently rejected public school curricula that veer away from evolutionary theory. In Edwards v. Aguillard (1987), for instance, the U.S. Supreme Court ruled that a Louisiana law requiring public school students to learn both evolution and creation science violated the Constitution's prohibition on the establishment of religion.

While most Americans (59%) say science and religion are often in conflict, those who are more religiously observant are less likely than others to see this clash between faith and science,according to a 2015 Pew Research Center survey. Among those who attend church at least once a week, half (50%) view religion and science as in conflict, compared with nearly three-quarters (73%) of those who seldom or never attend worship services. At the same time, most people (68%) say that their own personal religious beliefs do not clash with accepted scientific doctrine.

Outside the U.S., there are many other countries where sizable shares of the population reject evolution. In Latin America, for example, roughly four-in-ten or more residents of several countries - including Ecuador, Nicaragua and the Dominican Republic - say humans and other living things have always existed in their present form. This is true even though the official teachings of Catholicism, which is the majority religion in the region, do not reject evolution. In Central and Eastern Europe, evolution is broadly accepted, but roughly half or more of adults in two countries - Armenia and Bosnia - reject it. Meanwhile, Muslims in many nations are divided on the topic, although majorities of Muslims in countries such as Afghanistan, Indonesia and Iraq reject evolution.

It's important to note that our international surveys have used a different approach to ask about evolution, so results are not directly comparable to our new U.S. survey (although some of our older U.S. surveys used similar questions).
Note: This is an update to a post originally published on Feb. 12, 2015.

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For Darwin Day, 6 facts about the evolution debate

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Tuesday is the 210th anniversary of Charles Darwin's birth, a day now celebrated by some as Darwin Day. Darwin is best known for his theory of evolution through natural selection. When Darwin's work was first made public in 1859, it shocked Britain's religious establishment.

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Evolution of bacterial movement revealed

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Evolution of bacterial movement revealed

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An international team with researchers from Leiden revealed how a bacterium repurposed an internal system to control its movements. Movement control is very important in host invasion, which can lead to disease. Publication on 27 April in Nature Communications.
Bacteria from 'nose' to 'tail'
Cells are full of complex systems of which the origins are a mystery. In bacteria nineteen different systems based on 'smell' are known, so-called chemosensory systems (see frame). In the study published, the researchers found an ancestral chemosensory system of the model species of the bacterium Escherichia coli in several other bacteria like the pathogenic bacterium Pseudomonas aeruginosa and in Vibrio cholerae, the bacterium that causes cholera. Furthermore, the study revealed the origin of the chemosensory system of E. coli, including the evolutionary steps that led to the modern E. coli. These findings may help in the development of anti-microbial remedies using the chemosensory system as a target. From Leiden co-corresponding author Ariane Briegel, Professor of Ultrastructural biology at the Institute of Biology Leiden, and Ph.D. student and second author Wen Yang were involved in the study.

Bacteria move based on chemosensory 'smell' signals in their surroundings. The 'smell' signals reach the bacterium through its 'nose," activating a system within the bacterium to control the spinning direction of the flagella. Flagella are rotating 'tails' that many bacteria use to navigate their environment. They guide the bacterium towards something attractive and away from something repelling. These 'smell' signals are very important for pathogenic bacteria to be able to invade their host.
System under stress

Image of the 'nose' of an E. coli bacterium. The pattern looks a bit like a honeycomb. Credit: Wen Yang.

When the researchers looked at the bacteria under stress conditions by starvation, they discovered that under these conditions, a different form of the chemosensory system appeared in the Vibrio cholerae and Pseudomonas aeruginosa bacteria. Tracing the evolutionary history of the system, it turned out to be the ancestral form of the system that is present in E. coli. The researchers discovered that this ancient form took over another chemosensory system in a series of evolutionary steps and gained control of the flagellar motor. The combination of the two systems now makes up the chemosensory system in modern E. coli bacteria. This finding shows an example of how complex systems were being repurposed during evolution.
Ice-cold microscopy
The researchers were able to study the bacteria with the use of cryo-electron microscopy and bioinformatics. Inside a cryo-electron microscope, the temperature is almost 200°C below zero. By freezing microbes very quickly they are pristinely preserved in a glass-like ice. With cryotomography, the researchers take hundreds of photos of bacteria in different stages and are able to reconstruct the microbes in three dimensions at macromolecular resolution. Briegel and others collected the data at Caltech, Pasadena, California. Leiden holds similar cryo- electron microscopy facilities at the Netherlands Center for Electron Nanoscopy (NeCEN), where Briegel holds a position as co-director.

More information: Davi R. Ortega et al. Repurposing a chemosensory macromolecular machine, Nature Communications (2020). doi.org/10.1038/s41467-020-15736-5

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Evolution of bacterial movement revealed

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An international team with researchers from Leiden revealed how a bacterium repurposed an internal system to control its movements. Movement control is very important in host invasion, which can lead to disease. Publication on 27 April in Nature Communications. Bacteria from 'nose' to 'tail' Cells are full of complex systems of which the origins are a mystery.

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Review of Michael Behe's Darwin's Black Box | National Center for Science Education

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Review of Michael Behe's Darwin's Black Box | National Center for Science Education

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Perhaps the single most stunning thing about Darwin's Black Box, Michael Behe's "Biochemical Challenge to Evolution," is the amount of territory that its author concedes to Darwinism. As tempted as they might be to pick up this book in their own defense, "scientific creationists" should think twice about enlisting an ally who has concluded that the Earth is several billion years old, that evolutionary biology has had "much success in accounting for the patterns of life we see around us ," that evolution accounts for the appearance of new organisms including antibiotic-resistant bacteria, and who is convinced that all organisms share a "common ancestor." In plain language, this means that Michael Behe and I share an evolutionary view of the natural history of the Earth and the meaning of the fossil record; namely, that present-day organisms have been produced by a process of descent with modification from their ancient ancestors. Behe is clear, firm, and consistent on this point. For example, when Michael and I engaged in debate at the 1995 meeting of the American Scientific Affiliation, I argued that the 100% match of DNA sequences in the pseudogene region of beta-globin was proof that humans and gorillas shared a recent common ancestor. To my surprise, Behe said that he shared that view, and had no problem with the notion of common ancestry. Creationists who believe that Behe is on their side should proceed with caution - he states very clearly that evolution can produce new species, and that human beings are one of those species.

Michael Behe is Associate Professor of Biochemistry at Lehigh University, and not surprisingly, biochemistry, his own discipline, is at the heart of his argument. Simply stated, he claims that Darwinism, whatever it may explain at the organismic level, fails to account for the evolution of the complex biochemical machinery that is found in every living cell. He writes: "for the Darwinian theory of evolution to be true, it has to account for the molecular structure of life. It is the purpose of this book to show that it does not."

Behe engages in some rhetorical heavy-lifting to support this contention. In the first half of his book the reader is treated to a lively description of some of the most intricate of life's microscopic machinery - the cilia and flagella that produce cell movement, the cascade of blood-clotting proteins, the systems that target proteins to specific sites within the cell, the production of antibodies by the immune system, and the intricacies of biosynthetic pathways. Behe's descriptions of these systems are a delight to read. He is an excellent writer, and describes the complexities of the cell with the flair of a gifted teacher.

Why does the existence of these (and many other) systems rule out evolution? Because they are "irreducibly complex," meaning that if they are missing just one of their many parts, they cannot function. Behe writes that "Irreducibly complex systems ... cannot evolve in a Darwinian fashion." Why not? Because natural selection works on small mutations in just one component at a time. If dozens or even hundreds of distinct proteins, precisely fashioned, are required to make a functional cilium, how could natural selection slowly and patiently craft them, one at a time, while waiting for the complex function of ciliary movement to emerge? It couldn't, so, according to Behe, the hypothesis that the cilium was produced by evolution is therefore disproved. If evolution did not make the cilium, then "intelligent design" must have. He writes: "life on earth at its most fundamental level, in its most critical components, is the product of intelligent activity."

If all of this has a familiar ring, it should. It is the classic "Argument from Design," articulated so well by William Paley nearly 200 years ago in his book Natural Theology. Behe is candid in his admiration for Paley, and although he takes care to point out some of Paley's mistakes, he leaves no doubt that he views the Argument from Design as his principal logical weapon against Darwinism. To Behe, the intricacy and complexity of natural systems at the biochemical level shows evidence of intelligent design.

At its core, Behe's argument is about the mechanism of evolution, which distinguishes him from "young-earth creationists" who deny the validity of the geological ages, the appearance of new species, and attempt to prove that the fossil record is either an illusion or a vast conspiracy. Behe will have none of this, and explicitly denies any connection with "creationism." Nonetheless, he recognizes that his ideas do have theological implications as well as scientific ones. He is not at all modest about these implications, comparing the discovery of design to achievements of "Newton and Einstein, Lavoisier and Schrödinger, Pasteur and Darwin." And he believes that he knows why the scientific community has not embraced intelligent design to explain cellular complexity: "Why is the observation of design handled with intellectual gloves? The dilemma is that while one side of the elephant is labeled intelligent design, the other side might be labeled God." So, according to Behe, design is rejected by the scientific community for the most non-scientific of reasons - its theological significance.

Behe has gone two centuries into the past to find the argument from design, dusted it off, and invigorated it with the modern language of biochemistry. But there are problems in this excursion. Not the least of these is the fact that the argument from design has been answered, not once, but many times by writers such as Dawkins, Gould, and even Darwin himself. The multiple parts of complex, interlocking biological systems do not evolve as individual parts, despite Behe's claim that they must. They evolve together, as systems that are gradually expanded, enlarged, and adapted to new purposes. As Richard Dawkins successfully argued in The Blind Watchmaker, natural selection can act on these evolving systems at every step of their transformation.
As factual examples we could choose any of the systems whose evolution is documented by the fossil record, a source apparently acceptable to Behe. The three smallest bones in the human body, the malleus, incus, and stapes, carry sound vibrations across the middle ear, from the membrane-like tympanum (the eardrum) to the oval window. This five component system fits Behe's test of irreducible complexity perfectly - if any one of its parts are taken away or modified, hearing would be lost. This is the kind of system that evolution supposedly cannot produce. Unfortunately for "intelligent design," the fossil record elegantly and precisely documents exactly how this system formed. During the evolution of mammals, bones that originally formed the rear portion of the reptilian lower jaw were gradually pushed backwards and reduced in size until they migrated into the middle ear, forming the bony connections that carry vibrations into the inner ears of present-day mammals. A system of perfectly-formed, interlocking components, specified by multiple genes, was gradually refashioned and adapted for another purpose altogether - something that this book claims to be impossible. As the well-informed reader may know, creationist critics of this interpretation of fossils in the reptile to mammal transition once charged that this could not have taken place. What would happen, they joked, to the unfortunate reptile while he was waiting for two of his jaw bones to migrate into the middle ear? The poor creature could neither hear nor eat! As students of evolution may know, A. W. Crompton of Harvard University brought this laughter to a deafening halt when he unearthed a fossil with a double articulation of the jaw joint - an adaptation that would allow the animal to both eat and hear during the transition, enabling natural selection to favor each of the intermediate stages.

Is there something special about biochemistry that prevents evolution from doing exactly the same thing to a microscopic system composed of proteins? Absolutely not. But evolution does make a testable prediction with respect to such systems. That prediction is that the degree of similarity in DNA sequences of organisms should correspond to their evolutionary histories. And, as the author is all too well aware, that prediction has been borne out a thousand times over.

Despite the close correspondence of gene sequence to fossil sequence, Behe demands that evolutionary biologists should tell us exactly "how" evolution can produce a complex biochemical system. This is a good strategic choice on his part, because the systems he cites, being common to most eukaryotic cells, are literally hundreds of millions of years old. And, being biochemical, they leave no fossils. Once burned, twice shy, Behe may be hoping to avoid the fate of his 1994 claim that there were no transitional fossils linking the first fossil whales with their land-dwelling Mesonychid ancestors . Less than a year after that prediction, the existence of not one, not two, but three transitional species between whales and land-dwelling eocine Mesonychids was confirmed. Nonetheless, it is quite possible to rise to the occasion and answer his challenge in biochemical terms. In fact, Russell Doolittle, whose investigations on the evolution of blood clotting are discussed in this text, has done exactly this. Behe is at great pains to disqualify this work, even though Doolittle has not only shown how such a complex system might evolve, but has also produced comparative studies showing how it probably did evolve.

In dismissing Doolittle's work, and in preempting any attempt to show how evolution might produce a complex biochemical system, Behe scoffs at the notion that a biochemical system adapted for one purpose might be adapted by evolution for a totally different function, despite physiological examples to the contrary in the fossil record. He dismisses, for example, the notion that the parts of a cilium, including proteins like dynein and tubulin, could have evolved by gene duplication even though similar forms of dynein and tubulin are used for other purposes in the cell. Most cell biologists will be unconvinced by his explanations of why the cilium could not have been assembled from proteins originally used for other purposes - especially since the cilium itself has been adapted for another purpose in one of the very tissues that Behe uses as an example of design - the vertebrate photoreceptor cell.

As the book draws to a conclusion, Behe attempts to develop the idea of intelligent design into a testable, scientific hypothesis. This is a lofty goal, but this is also where his argument collapses. Scientific ideas must be formulated in terms that make them testable. Indeed, Darwin himself proposed several ways in which his theory might be tested and disproved. And one of these ways - the contention that organisms contain biochemical parts that could not have been produced by Darwinian means - is the basis of Behe's criticisms of evolution. Being a trained experimental scientist, one would have expected that Behe would have seen the need to do likewise. Unfortunately, he did not.

Let's suppose, for example, that a fellow scientist were to take Behe's challenge to evolution seriously, and attempted to show how a specific biochemical system composed of multiple parts could have evolved. A hypothesis for design, formulated in genuinely scientific terms, must be disprovable, and this is exactly the kind of evidence that might disprove it. Incredibly, Behe has intentionally insulated "intelligent design" from this and any other scientific test. How has he done this? In the penultimate chapter of his text, he lists some of the driving forces associated with evolutionary change, including natural selection, genetic drift, founder effects, gene flow, meiotic drive, and transposition . Behe states that all of these agents can effect change in biological systems, and admits that they may account completely for at least some of the biochemical features of a living cell. So, if our colleague were to show how these forces could have produced, say, the bacterial flagellum, would he be entitled to say: "I have disproved design?" Not at all, according to Behe. "The production of some biological improvements by mutation and natural selection - by evolution - is quite compatible with intelligent design theory." In other words, any evidence for the evolution of complexity is dismissed in advance as being irrelevant to the problem of design. "Design" exists only when and where evolution cannot explain it!

This sterile definition of design means that Behe is free to ignore any conceivable evidence for the evolution of any biochemical system. Such an idea, intentionally placed outside the realm of testability, is not science, whatever the pretentions of its advocates.

If Behe's formulation of intelligent design as science is illogical, his mechanism for how the work of the designer was inserted into living systems is almost laughable. Remember that Behe accepts the validity of the geological ages and the fossil record - an open-minded scientist can hardly do otherwise - and yet he claims that the complex biochemical systems he extols were fashioned by an intelligent agent. When did this agent go to work, and when were the genes encoding them engineered? He has an answer ready:

"Suppose that nearly four billion years ago the designer made the first cell, already containing all of the irreducibly complex biochemical systems discussed here and many others. (One can postulate that the designs for systems that were to be used later, such as blood clotting, were present but not "turned on." In present-day organisms plenty of genes are turned off for a while, sometimes for generations, to be turned on at a later time.)"

This means that billions of years ago a humble prokaryote was packed with genes that would be turned off for hundreds of millions of years before they produced the eukaryotic cilium, and genes for blood clotting proteins that would pass more than a billion inactive years in genetic "cold storage." And what happens during those billions of years? As any student of genetics will tell you, because those genes are not expressed, natural selection cannot weed out genetic mistakes. This means that mutations will accumulate in these genes at breathtaking rates, rendering them hopelessly changed and inoperative hundreds of millions of years before Behe says that they will be needed.

Contrary to Behe's claims, the evidence of evolution in the fossil record is not irrelevant to his argument. It has forced him, for the sake of consistency, to cobble his acceptance of the earth's well-documented natural history together with the doctrine of intelligent design. The result is an absolutely hopeless genetic fantasy of "pre-formed" genes waiting for the organisms that might need them to gradually appear. This absurdity is the unavoidable result of trying to make "design" conform to that troublesome fossil record. The very same fossil record that provides the primary evidence for evolution.

However serious its scientific flaws, this interesting and colorful book is sure to attract attention. Michael Behe would like us to believe that he has discovered a new biological principle. But the real news in Darwin's Black Box is that a contemporary scientist has dipped back into the past and wrapped the remains of the Argument from Design in a shiny cloth of biochemistry. In this new clothing, the old idea may surprise a few unsuspecting readers who have not thought long or seriously about the mechanisms of evolution. They may be entertained by Behe's energy, and sustained by his enthusiasm. But ultimately, the careful reader will recognize this book for what it truly is - an argument against evolution that concedes nearly all the contested ground to Darwin's edifice, and then ends up teetering on little more than rhetoric and personal skepticism

Notes:

¹ Darwin's Black Box, Page 4.
² Page 25
³ Page 111
⁴ Page 193.
⁵ Page 5.
⁶ Page 233
⁷ Page 233.
⁸ Behe wrote: "...if random evolution is true, there must have
been a large number of transitional forms between the Mesonychid
and the ancient whale. Where are they? It seems like quite a
coincidence that of all the intermediate species that must have
existed between Mesonychid and whale, only species that are very
similar to the end species have been found." page 61.
(MJ Behe in Darwinism, Science or Philisophy? © 1994.
Jon Buell & Virginia Hearn, eds. Published by the Foundation for
Thought and Ethics, Houston, Texas).
⁹ This listing is at the bottom of page 229.
¹⁰ Page 228.
¹¹ Page 228.

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Review of Michael Behe's Darwin's Black Box

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Perhaps the single most stunning thing about Darwin's Black Box, Michael Behe's "Biochemical Challenge to Evolution," is the amount of territory that its author concedes to Darwinism.

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C'est la fête à Darwin. Fêté par un article et un éditorial de la revue Science pour les 150 ans de la parution de The Descent of Man, le 24 février 1871, où le célèbre biologiste ose enfin appliquer à l'homme sa théorie de l'évolution. Et par la publication d'une nouvelle traduction, bien supérieure à l'ancienne, de son ouvrage de 1872 : L'expression des émotions chez l'homme et l'animal.

Dans Science, Agustin Fuentes, professeur d'anthropologie à l'Université de Princeton (NJ USA) se voit confier l'éditorial de cette revue très lue dans les laboratoires du monde entier pour célébrer le 150ème anniversaire de la parution de The Descent of Man fort intelligemment traduit par La Filiation de l'Homme dans la traduction par une équipe dirigée par Patrick Tort et Michel Prum (1).
Descendance avec modifications
L'anthropologue souligne l'extraordinaire fécondité scientifique et intellectuelle de la rupture introduite par Charles Darwin dans la réflexion de l'être humain sur lui même. Une rupture qui consiste à placer l'humanité et son origine dans l'histoire naturelle, elle-même conçue et analysée à travers le concept de la sélection naturelle des variations lors de la reproduction des individus. La fameuse " descendance avec modifications ". Une rupture qui, dans absolument tous les domaines, exclut toute... rupture entre l'homme et l'animal. Y compris sur son esprit et ses émotions. Ainsi dans La Filiation, Darwin écrit déjà : " la différence entre l'esprit de l'homme et celui des animaux supérieurs, aussi grande soit-elle, est certainement une différence de degré et non de nature ".

Un article de la revue, signé de Peter Richerson, Sergey Gavrilets et Frans de Waal, se veut une démonstration de ce que les théories modernes de l'évolution humaine ont été annoncées par le livre cent cinquantenaire de Darwin. Notre parenté génétique - un génome identique à 96% avec celui des chimpanzés, bonobos et gorilles - s'accompagne d'un partage avec eux de nombre de traits de " développement, physiologiques, morphologiques, cognitifs et psychologiques", précisent les auteurs. Logique puisque la paléoanthropologie a révélé que nous partagions " un ancêtre commun vivant entre 6 et 8 millions d'années ". En Afrique, comme prédit par un Darwin qui ne disposait pourtant d'aucun fossile à l'appui de son idée.
formule darwinienne
Toutes les tentatives de découvrir un fossé infranchissable entre l'homme actuel et ces grands singes - fabrication d'outils, enseignements culturels et imitation, empathie, pro-socialité et coopération, capacité de planification et de prévision, mémoire épisodique et métacognition, théorie de l'esprit (je sais que l'autre sait ce que je sais) - ont échoué, confirmant la formule darwinienne, c'est une question de degré, non de nature. Eh oui, il y a du deep ecologist chez Darwin. Mais, à condition de ne pas oublier, notent les trois auteurs, que pour Darwin la différence de degré entre les capacités intellectuelles de l'homme et ceux des " plus avancés " des animaux est... " enormous " (in The Descent of Man).

Les trois auteurs soulignent ainsi la fécondité scientifique de l'idée darwinienne d'aller fouiller les racines biologiques profondes de nombre de traits humains dans l'histoire évolutionniste de nos ancêtres et de nos " cousins " actuels, chimpanzés et bonobos en particulier. Les découvertes passionnantes de l'éthologie des grands singes, excellement relatées dans les ouvrages de Frans de Waal pour le grand public, en témoignent abondamment. On y découvre notamment que la " politique " de ces grands singes offre tout aussi bien des sociétés où violences et conflits abondent (chimpanzés) que d'autres où s'observent coopérations pacifiques et domination des femelles (bonobos).

Quant au trait le plus distinctif de l'homme, le langage, il est fortement lié à l'accroissement des coopérations et de l'apprentissage culturel cumulatif entre individus dans des groupes de plus en plus vastes, unis par le fait que l'union fait la force dans la sélection naturelle. Patrick Tort y voit " l'effet réversif de l'évolution " : la sélection naturelle de comportements coopératifs de plus en plus étendus qui s'opposent à l'élimination des plus faibles et donnent finalement à l'évolution culturelle le pilotage de l'espèce humaine à la place... de la sélection naturelle (2) ! Avec un effet contraire, soulignent les trois auteurs, lorsque cette force est utilisé non contre la nature, mais contre d'autres groupes humains. Une compétition et des affrontements qualifiés de " sous-produit indésirables " de l'évolution humaine.
suprématie blanche
Mais c'est la fête à Darwin aussi dans le sens négatif du terme, avec cet éditorial qui souligne également tout ce que l'anthropologue Agustin Fuentes estime être, dans T he Descent of Man, des signes de " racisme ", de " suprématie blanche " et de " sexisme " (anti-féminin bien sûr). Or, affirme Fuentes, la " race " n'est pas une description valide des variations biologiques chez les humains, et il n'y a " pas de cohérence biologique divisant les cerveaux entre male et femelle". Il appelle donc à " une science de l'évolution des humains à la place de celle de l'homme ".

Cette lecture de Darwin fera bondir le philosophe Patrick Tort, à l'origine de la nouvelle traduction de l'ensemble de l'œuvre du biologiste (1) afin de la guérir de contresens issus des premières. Pour Tort, en effet, au delà des expressions de Darwin reflétant l'esprit et le vocabulaire de son temps et des préjugés, sur les femmes ou des peuples, dont il n'a pu se défaire, le biologiste est fondamentalement anti-raciste.

Et d'ailleurs violemment anti-esclavagiste au point d'accepter la mort " horrible" de millions d'hommes dans la guerre de Sécession qui vient tout juste de commencer entre Nord et Sud aux Etats-Unis si c'est le prix à payer pour mettre fin à " cette malédiction grande entre toutes : l'esclavage ! " (lettre à Asa Gray, 5 juin 1861).

En témoigne cet extrait de La Filiation: " A mesure que l'homme avance en civilisation, et que les petites tribus se réunissent en communautés plus larges, la plus simple raison devrait aviser chaque individu qu'il doit étendre ses instincts sociaux et ses sympathies à tous les membres de la même nation, même s'ils lui sont personnellement inconnus. Une fois ce point atteint, seule une barrière artificielle peut empêcher ses sympathies de s'étendre à tous les hommes de toutes les nations et de toutes les races " (chap IV, III dans la première édition). Dans La Filiation, Darwin s'oppose à la plupart de ses contemporains pour affirmer l'unité biologique profonde de l'espèce humaine, soulignent les trois auteurs de Science. Et sa vision de la civilisation comme l'extension à l'ensemble des êtres humains de la " sympathie" qui doit les relier par des normes sociales et la morale est à l'opposé de toute hiérarchisation des populations.
Coup de massue intellectuelle
Quant au racisme supposé de Darwin, ce qui frappe surtout à la lecture de La Filiation, c'est qu'il y applique un adage darwinien majeur et ironique : " l'ignorance engendre plus fréquemment l'assurance que ne le fait la connaissance ; et ce sont ceux qui connaissent peu, et non ceux qui connaissent beaucoup, qui affirment aussi positivement que tel ou tel problème ne sera jamais résolu par la science. " Sa conclusion principale de son long essai, s'appuyant sur la littérature scientifique de son époque, pour expliquer " les différences externes caractéristiques entres les races de l'homme " est un très prudent : je sais que je ne sais pas. Il conclut en effet sur ces différences : " (elles) ne peuvent s'expliquer d'une manière satisfaisante ni par l'action directe des conditions de vie, ni par les effets de l'usage continu de certains membres, ni par le principe de corrélation ".

Il assène donc un coup de massue intellectuelle : " Nous avons donc jusqu'ici été mis en échec dans toutes nos tentatives pour expliquer les différences entre les races de l'homme ". Savoir qu'on ne sait pas est précieux en science, et savoir l'admettre est le signe d'un scientifique de bon aloi. Mais il se promet d'analyser si " la sélection sexuelle " (des mâles par les femelles), si efficace chez nombre d'animaux, pourrait avoir joué un rôle. En fait, Darwin vit avant la découverte de la base matérielle de l'hérédité (l'ADN), avant la découverte de l'histoire du peuplement de la Terre par l'homme moderne, avant la découverte du réseau historico-géographique de ce peuplement révélé par la génétique, il lui manque donc des faits essentiels à déconstruction de la notion de races chez l'homme suggérée par des variations d'aspects dont les bases biologiques et l'horizon temporel lui sont inconnus. Ce serait un anachronisme que de le lui reprocher.
Préjugés de l'époque
En revanche, on peut lui reprocher de n'avoir pas appliqué son adage à sa propre approche des différences, physiques et mentales, entre les deux sexes, tant ses conclusions sont marquées par les préjugés de l'époque... paradoxalement renforcés par sa tentative permanente d'y voir les traces d'une évolution ancienne, chez les ancêtres simiens de l'homme et chez l'homme " primitif ", afin de replacer l'humanité dans une histoire naturelle faite de variations et de sélections.

Son livre sur L'expression des émotions chez l'homme et les animaux n'est, dans l'esprit de Charles Darwin, qu'un chapitre (très) long de son ouvrage The Descent of Man . Il s'agit pour lui, explique Patrick Tort dans sa très érudite introduction, d'explorer l'expression des émotions chez l'homme et l'animal afin de contredire l'idée que l'un des signes de la création divine de l'homme est qu'il est doté de muscles exclusivement destinés à exprimer des émotions qu'aucun animal ne peut ressentir. Le biologiste part alors dans une longue exploration de tout ce qui pouvait être disponible à son époque sur l'expression des émotions chez l'homme - avec une vaste collecte d'informations auprès de correspondants à l'étranger -, guidé par son principe directeur : il n'y aura de différence que de degrés entre les grands singes et l'homme actuel et l'on peut chercher l'expression des émotions chez de très nombreux animaux, signe de nos ascendances communes.

La lecture de ce livre offre des moments précieux, où l'on voit l'émergence d'une approche scientifique, mélangée à des préjugés non critiqués, et entravée par des trous béants dans les connaissances. Trous béants souvent comblés par la recherche des 150 ans qui ont suivi. Ainsi, Darwin suppose que les gros chiens descendent des loups et les petits des chacals. Cela ferait bien rire un étudiant en première année de biologie qui sait que la génétique a démontré que l'ancêtre commun de tous les chiens se situe chez les loups, les deux espèces partageant 99,9% de leurs génomes. Finalement, ce qui en ressort est l'immense effort intellectuel produit par le biologiste pour raisonner juste à partir de données encore très éparses et lacunaires, guidé par des principes théoriques dont la fécondité extraordinaire a fait dire à Théodosius Dobzhansky " rien en biologie n'a de sens, si ce n'est à la lumière de l'évolution ".
Sylvestre Huet
(1) Patrick Tort et Michel Prum dirigent un programme de traduction et de publication de l'intégralité de l'œuvre de Charles Darwin, que l'on peut trouver aux éditions Honoré Champion .

(2) La formule la plus ramassée de Patrick Tort est : " Par la voie des instincts sociaux, la sélection naturelle sélectionne la civilisation, qui s'oppose à la sélection naturelle " (voir ici).

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C'est la fête à Darwin. Fêté par un article et un éditorial de la revue Science pour les 150 ans de la parution de The Descent of Man, le 24 février 1871, où le célèbre biologiste ose enfin appliquer à l'homme sa théorie de l'évolution.

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Comment expliquer qu'une macaque se masturbe sur le dos d'un cerf | Slate.fr

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Comment expliquer qu'une macaque se masturbe sur le dos d'un cerf | Slate.fr

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Temps de lecture: 6 min

C'est ce qu'on nous apprend à l'école: en général, les animaux d'espèces différentes ne copulent pas. Exceptionnellement, cela peut arriver, mais c'est toujours entre espèces très proches et fortement anthropisées (le cheval et l'âne, par exemple, ou encore les lions et les tigres de Thoiry). Et s'il y a reproduction, la descendance est stérile. En termes scientifiques, on parle là d' interférence reproductive et d'interactions hétéro-spécifiques mal-adaptatives, vu qu'elles peuvent mener ( entre autres) à l'extinction d'une population si les individus qui la constituent prennent un peu trop goût à la gaudriole entre partenaires un peu trop phylogénétiquement éloignés.

L'erreur de partenaire

Mais l'hybridation n'est pas forcément ni toujours délétère -elle peut engendrer une progéniture reproductivement viable- et, surtout, elle est loin d'être aussi rare que nos vieux cours de SVT pouvaient nous le laisser penser. En réalité, les interactions sexuelles hétéro-spécifiques courent les rues dans "la nature" (guillemets avec les doigts), principalement entre espèces du même genre. Des études existent ainsi sur les acariens rouges ( Panonychus), les papillons ( Papilio), les saumons et les truites ( Salmo), les geckos ( Hemidactylus), les canards ( Anas), les cervidés ( Cervus) ou encore les babouins (Papio).

Parce que les individus qui se grimpent dessus sont issus d'espèces physiquement assez similaires, l'explication la plus courante du phénomène évoque l'erreur de casting -la bestiole voulait tellement baiser qu'elle a loupé l'étape "mon partenaire est-il bien de la même espèce que moi?" avant de satisfaire ses impérieux désirs. D'autres hypothèses -qui ne sont pas obligatoirement contradictoires- envisagent ces interactions hétéro-spécifiques comme des sous-produits de stratégies reproductives, qui pour leur part sont directement adaptatives. Par exemple, si une espèce se caractérise par un dimorphisme sexuel conséquent et que les femelles sont bien plus grosses que les mâles, les mâles d'une espèce X vont chercher à copuler avec des grosses femelles, qu'importe qu'elles appartiennent aux espèces Y ou Z. Dans d'autres espèces, ce sont les femelles qui se "trompent" et en viennent à privilégier des partenaires qui ne sont pas de leur bande.

Dans la plupart des cas, les copulations sont forcées

Reste que ce sont bien les mammifères qui, en l'état actuel de nos connaissances, sont les plus créatifs en matière de copulation chez (et avec) des voisins. On a vu des éléphants de mer du nord ( Mirounga angustirostris) se taper des bébés phoques ( Phoca vitulina); des otaries à crinière ( Otaria flavescens) saillir des otaries à fourrure australe ( Arctocephalus australis); des éléphants de mer du sud se hisser (le mâle peut peser jusqu'à quatre tonnes) sur des otaries à fourrure d'Afrique du sud; des loutres marines embabouiner des pinnipèdes et même des phoques violer des manchots.

De fait, dans la plupart des cas, ces copulations sont forcées et il n'est pas rare que les victimes (des femelles et/ou des juvéniles) finissent gravement blessées, voire mortes, éventrées ou étouffées. Ici, trois hypothèses ont été avancées pour expliquer ces phénomènes:

1/ La confusion entre une pratique prédatrice et une pratique sexuelle -Maurice était parti pour bouffer, il a fini par coïter.

2/ Des jeunes mâles qui s'exercent sur à peu près n'importe quoi (ou qui) avant d'arriver à maturité reproductive.

3/ Un déséquilibre démographique (un trop plein de mâles), facteur connu de violences en général et de violences sexuelles en particulier, y compris dans notre bonne vielle espèce.

La sexualité récréative n'est pas propre à l'homme

Dans la réserve naturelle de Minoh, au Japon, l'insolite est monté d'un cran, puisque ce sont des jeunes macaques femelles ( Macaca fuscata) que l'on voit régulièrement se masturber sur le dos de cerfs Sika mâles ( Cervus nippon).

Via YouTube.

Comme le consigne une étude publiée en décembre dernier, ce ne sont pas moins de 257 interactions hétéro-spécifiques qui ont été analysées par Noëlle Gunst, Paul L. Vasey et Jean-Baptiste Leca, chercheurs en psychologie biologique et évolutionnaire à l'université de Lethbridge, au Canada. Les scientifiques y affirment que ces "montes et sollicitations démonstratives effectuées par des femelles macaques japonaises adolescentes" sont bien "de nature sexuelle", vu que ces copulations sont très semblables -au niveau du planning, de la structure comportementale ou du choix de partenaire- à celles que ces macaques accomplissent entre femelles, entre mâles ou entre mâles et femelles. Des recherches qui clouent une énième fois le cercueil d'un soi-disant "propre de l'homme" que serait la dissociation de la reproduction et de la sexualité et la pratique d'une sexualité purement récréative.

Quelques mois plus tôt, a u printemps 2017, une équipe de chercheurs affiliés (notamment) au CNRS avait publié une étude de cas sur les échanges hétéro-spécifiques entre un mâle macaque et une femelle sika sur l'île de Yakushima, à plus d'un millier de kilomètres au sud de Minoh. Selon les scientifiques, à l'exception d'une pénétration tout bonnement impossible du fait de contraintes anatomiques, "toute la séquence comportementale d'une saillie" avait été observée. Et le macaque avait éjaculé.

Échange de bons procédés

Ces dernières années, d'autres observations ont été faites aux quatre coins du Japon et tendent à prouver que les relations entre macaques et sikas dépassent un simple cadre sexuel. En effet, les singes et les cervidés semblent entretenir des rapports dits commensaux -où chaque espèce profite de l'autre. Notamment, les cerfs s'aventurent sur le territoire des macaques pour grignoter ce que les singes laissent tomber des arbres lorsqu'ils se nourrissent -des fruits, des feuilles, des graines. Une source d'énergie à laquelle les cerfs ne pourraient avoir accès sans "l'aide" de leurs copains et copines primates.

Selon Gunst et al., les rapprochements sexuels entre macaques et cerfs seraient donc un cas particulier de leurs échanges écologiques.

"À Minoh", écrivent-ils, les cerfs "se rassemblent occasionnellement autour des zones où les macaques vont pour se nourrir", ce qui relève là encore d'une curiosité, vu que les cerfs ne "sont pas en général une espèce grégaire", avec des mâles demeurant "solitaires la plupart de l'année".

En temps normal, les mâles et les femelles sika occupent des territoires différents et ne se croisent qu'au moment du rut, entre septembre et décembre.

Une saison des amours qui chevauche celle que les jeunes macaques femelles -âgées entre 3 à 4 ans, soit le début de la puberté chez ces singes- choisissent pour grimper sur les cerfs: les observations de Gunst et ses collègues ont toutes été effectuées entre novembre et janvier (2012, 2013, 2014 et 2015). Et si le Kamasutra des macaques comprend plusieurs positions comme le "chien de chasse" (la macaque se fige en présentant son arrière-train) ou la "grosse colère" (elle s'accroupit et hurle), 75% des frottages se concentrent sur la tête, la croupe et la nuque du cerf, qui reste docile la plupart du temps -dans un cas, parce que la guenon s'excitait un peu trop sur ses bois, le cervidé a préféré ruer et la catapulter histoire de la calmer. En tout, les scientifiques n'ont noté que trois interactions avortées -et deux fois sur trois, parce que la macaque allait se faire déloger par une autre qui ne voulait pas attendre son tour.

Un mystère, des hypothèses

Qu'est-ce qui pourrait expliquer ces comportements? Déjà, les scientifiques sont à peu près certains qu'ils ne sont pas "induits par l'homme", car même si les macaques du Parc de Minoh peuvent être mieux nourris que ceux d'autres régions japonaises, leur commensalisme avec les sikas demeure structurellement identique dans tout le pays. Alors quoi? Gunst et ses collègues proposent principalement quatre hypothèses, loin d'être mutuellement exclusives.

La première, c'est que les jeunes macaques s'exercent à la séduction et au sexe avec les cerfs, dans une interaction de "nature" et de "culture" que l'on a trop souvent tendance à considérer comme spécifique à notre espèce. Ici, si les jeunes macaques peuvent être physiologiquement prédisposées à tel ou tel comportement sexuel, c'est bien leur environnement social (en compagnie de cerfs) qui modèlera l'expression de ces comportements et leur donnera, au cours du développement des guenons, leur forme définitive. Une forme, dès lors, profondément variable.

La seconde, dite hypothèse du "safe sex", c'est que par leur carrure relativement chétive, les jeunes macaques ont tout intérêt à jouer la prudence en choisissant des partenaires doux et accommodants -d'autres femelles de leur espèce ou des cerfs sika, bien moins dangereux que les mâles macaques dans la force de l'âge.

La troisième, c'est que les jeunes macaques se rabattent sur des cerfs faute d'avoir trouvé des partenaires consentants dans leur espèce -femelles comme mâles, vu que les macaques adolescentes sont fréquemment rejetées par leurs camarades plus âgé(e)s lorsqu'elles veulent batifoler. Une hypothèse que privilégient par ailleurs les spécialistes des phoques violeurs de manchots pour expliquer ce comportement (attention, ces images peuvent choquer).

Via YouTube.

La quatrième et dernière hypothèse, c'est que les macaques adolescentes découvrent le plaisir sexuel avec les cerfs en jouant "innocemment" avec eux.

"Les macaques femelles juvéniles pourraient faire leurs premières expériences de stimulation génitale lors d'interactions hétéro-spécifiques ludiques", écrivent les chercheurs et, sous l'effet du rush hormonal pubertaire, chercher ensuite à "retrouver de telles gratifications sexuelles avec leurs partenaires cervidés".

Des interactions par ailleurs hygiéniquement bénéfiques pour les cerfs, que les femelles macaques n'oublient pas d'épouiller dans la manœuvre.

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Comment expliquer qu'une macaque se masturbe sur le dos d'un cerf

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C'est (encore) un "propre de l'homme" qui en prend un coup. C'est ce qu'on nous apprend à l'école: en général, les animaux d'espèces différentes ne copulent pas. Exceptionnellement, cela peut arriver, mais c'est toujours entre espèces très proches et fortement anthropisées (le...

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Qui a peur du grand méchant Darwin? | Slate.fr

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Qui a peur du grand méchant Darwin? | Slate.fr

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Temps de lecture: 15 min

Il n'y a pas que les militants qui s'en prennent aux scientifiques. Il arrive que des scientifiques eux-mêmes prennent les armes de l'activisme pour nuire à des collègues dont ils redoutent les travaux, tant ils risquent d'éclipser les leurs. Et pour ce faire, rien de mieux que la stratégie de l'homme de paille: dépeindre votre "adversaire" non pas tel qu'il est, mais sous les traits d'une caricature conçue pour rallier le maximum de soutiens à votre croisade, présentée comme l'éternel combat du bien contre le mal -et, au passage, braquer les projecteurs sur des théories qui auraient pu passer inaperçues. Une stratégie dont aura fait les frais Edward Osborne Wilson, entomologiste et créateur de la sociobiologie, soit l'étude systématique des fondements biologiques du comportement social animal, sous tous ses aspects et sans la moindre dérogation pour les sociétés humaines et les individus qui les composent.

C'est en étudiant les fourmis que Wilson ressent la nécessité d'une synthèse sur la biologie évolutionnaire des comportements sociaux. En effet, chez ces minuscules invertébrés, Wilson retrouve des traits comportementaux de certaines espèces vertébrées. "Marx avait raison pour la lutte des classes, sauf qu'il s'était trompé d'espèce", aime-t-il à plaisanter. Simple homologie ou loi de l'évolution? Sa rencontre avec William Hamilton, auteur de la mathématisation de l'altruisme, lui fait pressentir "un changement de paradigme". Il se met alors au travail pour produire son grand œuvre, Sociobiology, une synthèse encyclopédique de la génétique des populations, de l'écologie comportementale et évolutionnaire, de l'éthologie et de la biologie moléculaire. Le livre sort en 1975 et Wilson y présente les grands concepts de la discipline -la sélection sexuelle, la dominance et la hiérarchie, l'altruisme réciproque, la sélection de parentèle, les modalités de la communication intraspécifique, les lois mathématiques de la biologie des populations, les formes élémentaires de la vie sociale. Ensuite, il se focalise sur quatre sommets de la vie sociale dans l'histoire évolutive: les coraux et siphonophores, les insectes sociaux, les primates et l'homme.

La tentative sociobiologique est celle d'une réconciliation a priori impossible entre les deux sœurs ennemies de la recherche, d'un côté les sciences naturelles et de l'autre les sciences humaines et sociales. Mais loin d'opposer la nature à la culture, Wilson tente de déchiffrer leur co-évolution: comment se mêlent chez l'homme les règles épigénétiques primaires -la perception du monde et sa traduction immédiate par le cerveau- et secondaires -la régularisation culturelle dans le traitement de l'information? Wilson décrit en ces termes les rétroactions à l'œuvre dans la démarche sociobiologique (ou "consiliente"):

"Les gènes prescrivent des règles épigénétiques; ce sont des régularités de la perception sensorielle et du développement mental ambiant, animant et canalisant l'acquisition de la culture. La culture aide à déterminer quels gènes prescripteurs survivent et se multiplient d'une génération à l'autre. Des gènes nouveaux qui réussissent altèrent les règles épigénétiques des populations. Les règles épigénétiques, une fois modifiées, changent la direction et l'efficacité des canaux d'acquisition culturelle."

Réductionnisme

Si Wilson est réductionniste, c'est au sens scientifique du terme: la réduction du plus complexe au plus simple est le principe commun de la science moderne depuis des siècles. Et les extraordinaires découvertes de la physique, de la chimie ou de la biologie indiquent que cette démarche n'est pas tout à fait vaine lorsqu'on la pratique avec rigueur. Parallèlement, du fait même de ces découvertes, l'humanité se trouve désormais obligée de penser les événements en sens inverse, du plus simple au plus complexe. Et Wilson de conclure:
"Il est urgent de faire appel à tous les pans de la connaissance humaine et de viser une unité entre toutes les branches du savoir: la mise en commun de ce que l'humanité a de meilleur est nécessaire".
L'appel de Wilson ne sera pas entendu: il a péché en intégrant l'espèce humaine dans son champ d'analyse et son livre provoquera une polémique comme rarement les sciences contemporaines en ont connue. En l'espèce, c'est son dernier chapitre (28 pages sur plus de 700) qui soulève un tollé quasiment aux quatre coins de la planète. Intitulé "L'homme: de la sociobiologie à la sociologie", il affirme qu'un certain nombre de comportements sont inscrits dans la phylogenèse de l'espèce (c'est-à-dire, à un degré ou à un autre, dans nos gènes), une théorie que l'on peut très rapidement résumer à ces deux principes:

1. La hiérarchie rencontrée dans la plupart des sociétés animales est d'origine génétique et tient à des comportements d'agressivité et de dominance. Biologiquement, certains sujets seraient "faits pour" commander, alors que d'autres "sont faits pour" obéir -la position que chacun occupe dans la hiérarchie sociale serait le fruit de la compétition.

2. Les comportements d'un individu obéiraient à une loi fondamentale: diffuser ses propres gènes d'une façon aussi large que possible. Une réalité qui s'appliquerait à l'agressivité (qui conduit à éliminer tout rival sexuel) et à l'altruisme (qui s'applique aux membres d'une même famille portant certains gènes identiques). Quant à l'altruisme que nous manifestons pour nos amis et autres non-apparentés, il tiendrait au fait que ceux-ci peuvent nous aider à élever notre progéniture et donc à diffuser plus efficacement nos propres gènes (comme le veut l' "altruisme réciproque", théorisé par Trivers). Ainsi, les inégalités sociales, les conflits entre individus, familles ou peuples auraient des fondements biologiques.

Ou pour le dire encore plus succinctement: malgré l'originalité exceptionnelle que représentent dans l'évolution le langage et la culture d'Homo sapiens, notre espèce n'a pas rayé en quelques dizaines de millénaires les milliards d'années d'évolution qui ont précédé son apparition...

"Provocation scientiste"

Qu'importe. Si Wilson dit chercher à aider les humains à mieux se comprendre, il est accusé de promouvoir une science penchant dangereusement vers la droite, de faire dans "la provocation scientiste" ou le "réductionnisme génétique dangereux". Dans un article collectif publié en novembre 1975 dans la New York Review of Books, une quinzaine de chercheurs et d'étudiants menés par le paléontologue Stephen Jay Gould et le biologiste marxiste Richard C. Lewontin le situent dans le "long défilé de déterministes biologiques ayant œuvré à conforter les institutions sociales en les exonérant de la responsabilité des problèmes sociaux"; un cortège fédérant racisme, eugénisme, sexisme, lois anti-immigration, stérilisation des "déviants", jusqu'aux "chambres à gaz dans l'Allemagne nazie". Sous la bannière de l'organisation Science for the People, puis du Sociobiology Study Group, Gould et Lewontin soutiendront les actions d'une association étudiante anti-raciste, le CAR, émanation du Progressive Labor Party, selon laquelle "La sociobiologie, en encourageant des explications biologiques et génétiques du racisme, de la guerre et du génocide, exonère et protège les groupes et les individus ayant commis et exploité ces crimes monstrueux".

En février 1978, des militants du CAR débarquent au beau milieu d'une conférence de l'Association américaine pour l'avancement des sciences ( AAAS) dédiée aux travaux de Wilson. Il s'en prennent à l'entomologiste -immobilisé ce jour-là, suite à une fracture de la jambe, par un plâtre montant de la cheville à la hanche- en hurlant "Wilson le raciste, tu ne peux pas nous échapper, on t'inculpe de génocide!", avant de lui renverser un pichet d'eau glacé sur la tête. Dans Naturalist, son autobiographie parue en 1994, Wilson se rappelle que "Personne ne leur a demandé de quitter les lieux ni n'a appelé la police et aucune action ni sanction n'a été prise contre eux plus tard". Le chercheur, trempé, continuera son exposé, qui sera salué par une standing-ovation.

Si les attaques contre la sociobiologie ont été si violentes, précise la sociologue des sciences Ullica Segerstrale dans Defenders of the Truth, un ouvrage datant de 2001 qui leur est entièrement consacré, c'est qu'elles ne visaient rien de moins que la définition de la nature humaine, "l'âme de la science" et la manière dont nos sociétés doivent être structurées. Et c'est bien là où le bât blesse. Au beau milieu d'une décennie caractérisée par une valorisation de l'égalitarisme et du déterminisme culturel, Wilson ne pouvait ignorer que son livre allait faire pas mal de remous. Dans son autobiographie, il se demande "naïvement" pourquoi, pour exprimer leurs griefs, Gould et Lewontin ne sont pas simplement venus le voir à Harvard -leurs bureaux respectifs n'étaient qu'à un étage du sien. Pourquoi choisir, avec leur article-pétition de la New York Review of Books, de les porter immédiatement sur un terrain public et de shunter les canaux consacrés des débats et des revues scientifiques? Parce que, comme le détaille Segerstrale, Gould et Lewontin n'avaient pas qu'un projet politique à faire valoir, ils avaient aussi et surtout un programme scientifique à faire connaître: que toute l'histoire du vivant ne peut être "réduite" à des arguments adaptationnistes, centrés sur des "gènes égoïstes", et que l'évolution se joue sur différents niveaux de sélection via des processus souvent non adaptatifs. Sauf que parler d'exaptations, d'équilibres ponctués, de pendentifs ou de cooptations n'aurait pas passionné les foules, ni braqué les projecteurs sur leurs travaux, contrairement à l'annonce du retour des théories raciales, de l'eugénisme et des camps de la mort.

"Quels actes misérables naissent de la ferveur de la renommée", écrivait Darwin dans une lettre à Joseph Dalton Hooker datée du 10 mai 1848, "l'amour de la vérité seul ne poussera jamais un homme à s'en prendre cruellement à un autre". L'observation sied à merveille à Stephen J. Gould et le paléontologue ne s'en cachera même pas. En 1984, lors d'une conférence relatée par Segerstrale, il déclare: "Nous avons ouvert le débat par une position de force. Cette position définitive, nous l'avons prise afin d'ouvrir le débat à la critique scientifique. Tant que des opinions contraires n'auront pas de légitimité pour s'exprimer, les scientifiques tiendront leur langue". Ce que Gould semble vouloir dire, commente Segerstrale, "c'est que la controverse scientifique sur l'adaptation n'aurait pas vu le jour sans la controverse politique sur la sociobiologie". En matière de " rénovateur respectueux " de l'édifice darwinien, on a fait mieux.

La France, bastion de résistance

Aujourd'hui, si la polémique sociobiologique n'est pas totalement terminée -la France s'illustre comme un bastion de résistance particulièrement tenace, Sociobiology n'ayant été que partiellement traduit, et dans une édition aujourd'hui épuisée-, la controverse scientifique, elle, s'est considérablement calmée, tant les avancées de ces quarante dernières années penchent en faveur de Wilson. En 2001, John Alcock, diplômé de Harvard et professeur de biologie à l'Université d'État de l'Arizona, parlera même d'un "triomphe de la sociobiologie" et montrera combien les années suivant la publication de Sociobiology n'auront fait que confirmer ses hypothèses.

Mais E.O.Wilson n'a pas été le seul faire-valoir (et bouc émissaire) des ambitions "rénovatrices" de Gould. En 1981, dans La mal-mesure de l'homme, Gould construit toute son argumentation hostile à une "prétendue" objectivité scientifique - "les scientifiques sont des êtres humains enracinés dans des contextes culturels, pas des automates programmés pour la recherche d'une vérité extérieure"- en démontant les travaux de Samuel George Morton, dans lesquels il décèle à, juste titre, des préjugés racistes . "La prédominance du trucage inconscient amène (...) une conclusion générale sur le contexte social dans lequel s'élabore la science", écrit-il. "Car si les savants peuvent en toute honnêteté s'illusionner comme Morton le fit, c'est que l'on peut trouver des préjugés partout, même dans les méthodes de mensuration des ossements et dans les additions de chiffres". Alors que fermentent les " science wars", cet ouvrage ne pouvait pas mieux tomber. Il sera largement cité par les tenants du postmodernisme et Morton deviendra, pendant près de trente ans, le parangon de la fraude et de la falsification scientifiques à visée réactionnaire -et même, pour beaucoup, de la science intrinsèquement méphitique.

Sauf qu'en 2011, six anthropologues menés par Jason E. Lewis de Stanford décident de refaire les mesures de Gould sur les mesures de Morton et trouvent... que c'est Gould qui s'est bel et bien planté. Leur conclusion: oui, Morton était raciste, mais reste que ses " données sur la capacité crânienne (...) sont généralement fiables et méticuleusement consignées", écrivent-ils. "Dans l'ensemble, nous trouvons que la réputation initiale de Morton, comme objectiviste de son temps, est bien méritée".

Ils ajoutent: "Que les données de Morton soient fiables malgré ses évidents préjugés tempère l'argument de Gould et d'autres voulant que des résultats biaisés soient endémiques en science. Gould avait certainement raison de noter que les scientifiques sont des êtres humains et qu'ils sont, en tant que tels, inévitablement biaisés (...). Mais le pouvoir de l'approche scientifique est tel qu'une méthodologie convenablement conçue et suivie peut très largement protéger les résultats de l'influence des préjugés du chercheur".

Avant de conclure, comme un coup de grâce: "La science ne dépend pas de chercheurs "automates" parfaitement impartiaux, elle dépend de méthodes qui limitent la capacité des préjugés des chercheurs, certes inévitables, à influer sur les résultats. Les méthodes choisies par Morton étaient solides et notre analyse montre qu'elles auront empêché les préjugés de Morton d'affecter significativement ses résultats. Le cas Morton n'illustre pas tant l'omniprésence des biais en science que la capacité de la science à échapper aux contraintes et aux angles morts des contextes culturels".

Le problème, c'est que les manœuvres "malhonnêtes" ( Ernst Mayr) de Gould et de ses acolytes pourrissent encore (et probablement pour longtemps) les recherches darwiniennes. Face à l'évolution, leurs divers représentants n'ont eu de cesse de se chercher querelle comme les aveugles du conte indien face à l'éléphant, où chacun est persuadé que l'autre a tort sans voir que tous disent une partie de la vérité. Et le "grand public" demeure convaincu que la sociobiologie -et ses héritières contemporaines que sont la psychologie évolutionnaire ou la génétique comportementale- méritent autant les soupçons que les craintes et les censures.

Les peurs

"Dans Comprendre la nature humaine ", m'écrit Steven Pinker, "j'ai détaillé quatre raisons (toutes fausses) expliquant pourquoi tant de gens ont peur des explications biologiques de la nature humaine". La première, c'est la "peur de l'inégalité: si tout un chacun est une page blanche, alors tout le monde doit être identique, car 0=0, à l'inverse, si la nature humaine existe, alors certaines personnes sont peut-être différentes des autres de manière innée, ce qui pourrait justifier les préjugés".

Une appréciation "illogique", tranche Pinker, "l'égalité, c'est traiter tous les individus de la même façon, pas que nous sommes tous des clones".

La seconde peur, tout aussi fallacieuse, est celle de "l'imperfectibilité: si l'évolution a doté les individus de vilains traits, comme l'égoïsme, l'agressivité, le goût de la vengeance et de la lubricité, cela les rend "naturels" et donc bons, mais si les gens sont des pages blanches, nous pouvons espérer les perfectionner par le biais de l'éducation". Ici, outre le sophisme naturaliste, "les gens sont capables d'apprendre à se contrôler et à assimiler des normes sociales".

Vient ensuite la peur du déterminisme: "si nous ne sommes que l'activité de notre cerveau, personne ne peut être jugé responsable de ses actions". Sauf que, précise Pinker, "juger quelqu'un responsable de ses actions signifie simplement que nous l'estimons ou que nous le punissons pour ses actions, et que cette estime et ces sanctions peuvent, en elles-mêmes, être la cause de certains comportements".

Enfin, la biologie rebute à cause du "nihilisme" qu'elle semble générer: "Si nous n'avons pas d'âme immortelle, alors la vie n'a pas de sens ou de signification. C'est tout aussi faux: les individus peuvent souffrir ou prospérer, et nous avons comme objectif moral d'améliorer notre existence, notre santé, notre bonheur et notre connaissance".

A l'instar de Tchekhov, Pinker estime que "l'homme ne deviendra meilleur que lorsque nous lui aurons donné la possibilité de se voir tel qu'il est". C'est aussi le cas de bon nombre de chercheurs évolutionnaires avec lesquels je me suis entretenue -une vision à laquelle j'adhère mais beaucoup moins visible et audible dans notre environnement culturel et médiatique. Un "empoisonnement de l'atmosphère intellectuelle", déplore Pinker, "qui nous prive des outils nous permettant d'analyser convenablement les questions les plus urgentes sur notre humaine nature, à l'heure où des découvertes scientifiques les rendent d'autant plus cruciales".

"Les gens n'aiment pas ce que j'ai à leur dire", confirme Jesse Bering, chercheur en psychologie évolutionnaire aujourd'hui affilié à l'université d'Otago (Nouvelle Zélande) et par ailleurs contributeur de Slate. "Pas parce que ce n'est pas vrai, mais parce que cela les met mal à l'aise. De plus, en tant que société, nous faisons désormais tellement gaffe au moindre signe d'inégalité que discuter de différences innées (soit une construction insignifiante) vous fait automatiquement passer pour le méchant de l'histoire".

La difficulté de vulgarisation

Résultat, un décalage s'est créé entre l'état réel de la science et l'idée que s'en fait le grand public. "Je pense que les journalistes devraient être plus critiques, explique Michel Raymond, directeur de recherches au CNRS et spécialiste de biologie évolutive humaine. Certaines personnes sont régulièrement sollicitées par les médias, souvent pour la seule raison qu'elles sont médiatiquement connues et politiquement correctes. Parfois même, au vu de leur liste de publications, leur légitimité scientifique n'est pas évidente." Ce qui permet d'expliquer, comme l'écrit Pinker, pourquoi "la position extrême (que tout est culturel) est si souvent considérée comme modérée, alors que la modérée (que nous sommes la somme de facteurs biologiques et culturels) est considérée comme extrémiste".

Geoffrey Miller, l'un des papes de la psychologie évolutionnaire et l'un de mes tous premiers mentors me précise: "L'application de la biologie évolutionnaire à l'étude de la nature humaine est loin d'être balbutiante. Elle a été menée avec beaucoup de sérieux et de succès depuis 1871 et la publication par Darwin de son livre La descendance de l'homme. En particulier, depuis les années 1990, nous avons assisté à l'éclosion et au développement de centaines de théories et d'observations en psychologie, en médecine, en anthropologie, en esthétique évolutionnaires. Ces champs de recherche prospèrent depuis des décennies".

Le problème, ajoute-t-il, "c'est que les approches évolutionnaires sont conspuées par des chercheurs en sciences sociales (...) prétendant que l'esprit humain est une page blanche, que l'évolution n'a pas joué sur nos instincts, nos motivations ou nos préférences. Des chercheurs qui affirment que tous les aspects de la nature humaine sont "socialement construits", qu'il n'y a pas d'influences génétiques sur les différences entre individus, entre sexes ou entre groupes. Ils sont presque toujours persuadés qu'une idéologie de gauche exige de croire à la page blanche, et que si jamais ils admettent la moindre influence de l'évolution ou des gènes sur l'esprit humain, cela aura forcément des conséquences politiques conservatrices. Ils ont raison de penser qu'une perspective évolutionnaire est incompatible avec le dogme gauchiste de la page blanche, le même que soutenaient Staline, Mao ou Pol Pot. Mais ils ont tort de croire que cette perspective mène automatiquement au conservatisme, au réactionnarisme ou à l'extrême-droite. Selon mon expérience, plus vous comprenez l'évolution, plus vous aurez de difficultés à vous situer sur l'échiquier politique et plus vous aurez de mal à vous reconnaître dans le simplisme des étiquettes. Prendre Darwin au sérieux, c'est avoir la liberté de ne prendre aucune idéologie trop au sérieux".

Dans The unnatural nature of science, paru en 1994, Lewis Wolpert, professeur de biologie appliquée à la médecine à l'University College de Londres, explique combien la communication et la vulgarisation scientifiques n'ont jamais autant relevé d'une gageure, du fait du caractère fondamentalement "contre-intuitif" de la science contemporaine. Une science des plus complexes, confrontée à une intuition et à un "bon sens" issus, comme le dirait Richard Dawkins, d'un temps où le cerveau humain n'avait que trois tâches fondamentales à maîtriser: bouffer, baiser et grimper dans un arbre au moindre signe de danger.

Cette description ne correspond que trop bien à la biologie évolutionnaire et à ses "applications" à nos comportements. "Le problème de l'évolution", tranche Miller, "c'est que tout le monde a l'impression de la comprendre. Ce n'est pas le cas des sciences dures, comme la physique quantique ou la biochimie, et ce n'est pas non plus le cas des sciences humaines, comme l'histoire ancienne ou la théorie littéraire. Mais parce qu'ils ont de vagues souvenirs de leurs cours de biologie au lycée et qu'ils ont vu deux ou trois documentaires de David Attenborough, les gens se croient capables de juger la psychologie évolutionnaire, alors qu'il s'agit d'un des domaines les plus complexes et les plus sophistiqués des sciences comportementales."

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Temps de lecture: 15 min Il n'y a pas que les militants qui s'en prennent aux scientifiques. Il arrive que des scientifiques eux-mêmes prennent les armes de l'activisme pour nuire à des collègues dont ils redoutent les travaux, tant ils risquent d'éclipser les leurs.

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Some Viruses Have a Completely Different Genome to The Rest of Life on Earth

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In the world of microbial warfare, sometimes you have to change the very fabric of who you are.

Viruses that infect bacteria - fittingly called bacteriophages - and their prey have been at war for eons, each side evolving more devilish tactics to infect or destroy each other. Eventually, some bacteriophages took this arms race to a new level by changing the way they code their DNA.

At least, that's what we think happened. Once thought to be an outlier, new research published in three separate papers shows that there's a whole army of bacteriophages with non-standard DNA, which researchers call a Z-genome.

"Genomic DNA is composed of four standard nucleotides ... These nucleobases form the genetic alphabet, ATCG, which is conserved across all domains of life," biologists Michael Grome and Farren Isaacs write in a recent Science editorial accompanying the new research on bacteriophage genetics.

"However, in 1977, the DNA virus cyanophage S-2L was discovered with all instances of 'A' substituted with 2-aminoadenine (Z) throughout its genome forming the genetic alphabet ZTCG."

The reason appeared to be self-protection. Within the connecting 'rungs' of a DNA double helix, the 'Z' base forms a triple bond to the opposite 'T' base, one more than the two bonds of the regular A:T connection. This makes the viral genome hardier and more difficult for bacteria to prise apart with chemicals called nucleases.

Although scientists were fascinated, no other bacteriophages were found with the Z-genome, and with the difficulty of culturing S-2L in a lab, the Z-genome was set aside as a curiosity.

Now, research documented in three separate studies from researchers in France and China shows that this was not a one-off, whilst also characterizing how the Z-genome works and how it's assembled.

"Scientists have long dreamed of increasing the diversity of bases. Our work shows that nature has already come up with a way to do that," one of the teams, led by first author Yan Zhou from Tianjin University, wrote in their paper.

Zhou's team, along with another group led by Institut Pasteur microbiologist Dona Sleiman, found two major proteins which they called PurZ and PurB; these make up the 'Z' base.

A third group, led by Université Paris-Saclay synthetic biologist Valerie Pezo, corroborated those findings and analysed an enzyme - called DpoZ - which is responsible for assembling the whole Z-genome together.

All three searched genetic sequence databases for the sequences relating to their proteins and enzymes, and found a wide variety of bacteriophages with similar genes.

"[The authors] have done an amazingly comprehensive job of showing that this is not one crazy outlier, but there's a whole group of bacteriophages that have this kind of genetic material," Jef Boeke, a molecular biologist at New York University who was not involved in the work, told The Scientist.

There are still plenty of questions to answer about the Z-genome.

For example, is a Z-genome compatible with regular cell machinery such as ours? And could it be used in the same way that artificial DNA is starting to be?

"The Z base has been unambiguously identified in a carbonaceous meteorite and proposed as a nucleobase that could have been available for the origin of life," the team lead by Zhou wrote in their paper.

"Considering that the Z base was discovered in a meteorite, our work may spark interest in interdisciplinary research on the origins of life and astrobiology."

The three papers have been published in Science here, here, and here.

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Some Viruses Have a Completely Different Genome to The Rest of Life on Earth

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In the world of microbial warfare, sometimes you have to change the very fabric of who you are. Viruses that infect bacteria - fittingly called bacteriophages - and their prey have been at war for eons, each side evolving more devilish tactics to infect or destroy each other.

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Crocodile evolution rebooted by Ice Age glaciations

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Crocodile evolution rebooted by Ice Age glaciations

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Crocodile from a population living on the coast of Panama. Credit: José Avila-Cervantes

Crocodiles are resilient animals from a lineage that has survived for over 200 million years. Skilled swimmers, crocodiles can travel long distances and live in freshwater to marine environments. But they can't roam far overland. American crocodiles (Crocodylus acutus) are found in the Caribbean and Pacific coasts of the Neotropics but they arrived in the Pacific before Panama existed, according to researchers from McGill University.

Over 3 million years ago, the formation of the Isthmus of Panama altered global ocean circulation, connecting North and South America and establishing the Caribbean Sea. This resulted in widespread mixing of species on the continent and separation in the seas. On land, mammals from North America such as mammoths, saber-toothed cats, horses, and camels invaded South America, and strange mammals like giant ground sloths, armadillos, and opossums from South America invaded North America. This event is known as the Great American Interchange, and the opposite happened in the seas, where new species of corals, clams, and fishes evolved in the separated Pacific and Caribbean waters.

The question a group of McGill and Panamanian researchers asked was: how distant are the Pacific and Caribbean populations from each other and does it match the geological record? Researchers have long suspected that American crocodiles living on the Pacific coast should have diverged genetically enough from Caribbean populations to become unique species.

"We assumed we would detect significant genetic differences between Pacific and Caribbean crocodile populations that were isolated for the past 3 million years," thought José Avila-Cervantes, a recent Ph.D. graduate of McGill University under the supervision of Professor Hans Larsson.

Researchers captured and took blood samples of crocodiles from several populations living on both coasts of Panama. Credit: Luis Felipe Estrada

Capturing crocodiles
To test this, Avila-Cervantes captured and took blood samples of crocodiles from several populations living on both coasts of Panama. Back at McGill University, he sequenced their genomes to look for small variations in their DNA. He used the genetic differences to estimate how much evolutionary divergence and gene flow existed between populations. With this information, the team found that Pacific and Caribbean crocodile populations have been separated for only about 100,000 years.

"This time of separation is a far cry from the 3 million years we were expecting," said Professor Larsson, Director of the Redpath Museum at McGill. "But it did match the last interglacial period of the Ice Age."

Glacial and interglacial cycles in the Ice Age mark periods of peak polar glaciations separated by relatively warm times. These warm times caused sea levels to rise over 100 meters globally compared to present-day levels. Using the record of Ice Age sea levels, Avila-Cervantes was able to reconstruct what Panama would have looked like during these peak cold and warm periods of the Ice Age.

At McGill University, researchers sequenced the genomes of crocodiles to look for small variations in their DNA. Credit: José Avila-Cervantes

Coastal movements explained
"It surprised us to see that during the warm inter-glacial periods, most of Panama was underwater with the coasts separated by brackish lagoons, small rivers, and thin stretches of land," said Avila-Cervantes. "These are the reasons why we think crocodiles were able to pass from coast to coast freely and explain why their oldest genetic signature of separation coincides with this time." A second younger signature of genetic separation is timed to about 20,000 years ago and coincides with the last glaciation cycle that they found made Panama about twice as wide as it is today, and probably a good barrier for these crocodiles. "This is one of the first studies to implicate Ice Age glaciation-interglaciation cycles with the evolution of a tropical organism."

Yet the researchers discovered there is some genetic divergence between the populations on each coast despite the frequent inter-glaciations, and this diversity is at risk due to habitat destruction from human development. "It was difficult to find any population living on the Pacific coast near the Panama Canal," said Avila-Cervantes.

One of the best-preserved populations is in the middle of the Panama Canal on the Barro Colorado Island Nature Monument. "Preserving the population around this island may be our best chance to preserve the unique genetic signatures of Panamanian American crocodiles," said Professor Larsson. "Our study not only highlights the resilience of crocodiles to ancient climate changes and their great capacity to survive large geological events, but also their vulnerability to our voracious need to modify their environments."

"Effect of the Central American Isthmus on gene flow and divergence of the American crocodile ( Crocodylus acutus)" by Jose Avila-Cervantes, Carlos Arias, Miryam Venegas-Anaya, Marta Vargas, Hans C.E. Larsson, and W. Owen McMillan was published in the journal Evolution.

More information: Jose Avila‐Cervantes et al, Effect of the Central American Isthmus on gene flow and divergence of the American crocodile ( Crocodylus acutus ), Evolution (2020). DOI: 10.1111/EVO.14139

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Crocodile evolution rebooted by Ice Age glaciations

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Crocodiles are resilient animals from a lineage that has survived for over 200 million years. Skilled swimmers, crocodiles can travel long distances and live in freshwater to marine environments. But they can't roam far overland. American crocodiles (Crocodylus acutus) are found in the Caribbean and Pacific coasts of the Neotropics but they arrived in the Pacific before Panama existed, according to researchers from McGill University.

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The most popular textbook example of punctuated evolution debunked

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The most popular textbook example of punctuated evolution debunked

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The picture shows the seven species of bryozoans that were used in the debunking.The white line is only 500 micrometers in length. Credit: JoAnn Sanner, The University of Chicago

Evolutionary biologists have for a long time disagreed on the rate of evolution when new species emerge. Are new species the result of gradual changes-as Charles Darwin suggested-or is evolution speeding up for short periods of time when new species evolve?

World renowned paleontologist Stephen Jay Gould (1941-2002) formulated the theory of punctuated equilibrium together with Niles Eldredge (1943-) in 1972. The theory states that species remain more or less unaltered during their existence, with major evolutionary change happening during rapid events of speciation. As evidence for this view, Gould pointed to the fossil record.

According to Gould, the fossil record typically show that species do not change significantly after they emerge, and that major changes occurred when new species appeared.

Stephen Jay Gould was one of the twentieth century's most famous evolutionary biologists and a bestselling popular science writer. Some even claimed that Gould was the foremost biologist of his time-perhaps the greatest since Charles Darwin himself-so his words have carried a lot of weight to this day.

In a new paper from researchers at the University of Oslo, the authors claim to have found several methodological problems in the most famous and well-trusted example supporting the theory of punctuated equilibrium.

"We find no evidence for punctuated evolution in our reanalysis of the most recognized dataset that Gould used to support his theory", says Kjetil Lysne Voje at UiO's Center for Ecological and Evolutionary Synthesis (CEES) at the Department of Biosciences.
Textbook example is rejected
Fossils of the bryozoan genus Metrarabdotos-a group of aquatic invertebrates thoroughly investigated by the excellent paleobiologist Alan Cheetham-have been the prime example of punctuated evolution.

Gould called Metrarabdotos "the most brilliantly persuasive, and most meticulously documented, example ever presented for predominant (in this case, exclusive) punctuated equilibrium in a full lineage" (Gould 2002, page 827).

"We detected some critical methodological issues in the original work on Metrarabdotos. When we take the methodological issues into account, we do not find any evidence of punctuated evolution in our reanalysis of the Metrarabdotos data", says Kjetil Lysne Voje.

Bryozoans are so small that scientists have to use an electron microscope to study them in detail, but they form colonies that can be quite large (up to 1 meter). Most bryozoans live in the sea, but there are also many species in fresh water. The bryozoan genus Metrarabdotos has been used as a textbook example in evolutionary biology and paleontology, showing how evolution speeds up when new species form compared to a much slower evolution of already established species.

"But our new results show nothing else than a gradual evolution of the bryozoan species both before, during and after the formation of new species", emphasizes Voje.

The idea of fast-track evolution during speciation has been controversial. Critics of the theory of punctuated equilibrium found it difficult to believe that the evolutionary processes leading to new species should be markedly different from the processes that cause already existing species to change.

"Species are continuously evolving and our results support the hypothesis that evolution does not "behave" differently when new species emerge", says Voje.

The paper with the new results was published in the May issue of The American Naturalist.

More information: Kjetil Lysne Voje et al. Revisiting a Landmark Study System: No Evidence for a Punctuated Mode of Evolution in Metrarabdotos, The American Naturalist (2019). DOI: 10.1086/707664

# data[].attributes.attachment_link.title
The most popular textbook example of punctuated evolution debunked

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Evolutionary biologists have for a long time disagreed on the rate of evolution when new species emerge. Are new species the result of gradual changes-as Charles Darwin suggested-or is evolution speeding up for short periods of time when new species evolve?

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Facultative oviparity in a viviparous skink (Saiphos equalis) | Biology Letters

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Facultative oviparity in a viviparous skink (Saiphos equalis) | Biology Letters

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1. Introduction

Viviparity has evolved from ancestral oviparity at least 115 times in squamate reptiles [ 1, 2]. Reversals from viviparity to oviparity are rare [ 3- 6], yet recent phylogenetic work suggesting frequent reversals [ 7] has rekindled debate about their adaptive significance for squamate evolution. Dollo's Law of irreversibility predicts that complex traits, once lost, either cannot re-evolve or will do so in a different way [ 3, 5, 8, 9]. The evolution of viviparity involves loss of complex structures, including the eggshell and oviductal glands that produce shell material, and requires changes in maternal vasculature and timing of reproductive events [ 8]. Physiological challenges associated with re-evolution of these structures and processes likely constrain reversals to oviparity [ 2, 5]. Additionally, intermediate phenotypes 'in transition' to oviparity from viviparity may be inviable, as re-evolution of an eggshell could restrict embryonic gas exchange in utero [ 5, 10- 13]. Obligate viviparity may thus be a 'fitness valley' [ 10] that is difficult to emerge from once viviparity is acquired [ 3, 5].

By contrast, facultative switches in parity mode (oviparity to viviparity and vice versa), while rare, involve fewer modifications than complete reversals, and suggest that an intermediate, reproductively labile stage can exist before obligate viviparity [ 14]. Facultative viviparity (capacity to deposit either eggs or developed offspring, depending on circumstance; [ 14]) is relatively common in invertebrates [ 14], including thrips [ 15], dipteran flies [ 14] and onycophorans [ 14, 16]. In vertebrates, facultative viviparity is rare, yet likely occurs in the olm ( Proteus anguinus) [ 17, 18], and several species of poeciliid fish [ 19, 20]. While facultative viviparity has never been reported for squamate reptiles, several oviparous squamate species show plasticity in timing of oviposition [ 21- 24], demonstrating facultative changes in length of internal egg-retention. Species that can reproduce via either parity mode are evolutionarily significant as they demonstrate retention, rather than re-evolution, of oviparous traits. Since neither parity mode is selectively advantageous in all environments [ 3], persistence of an 'intermediate' transitional form (facultative viviparity) could convey a reproductive advantage, irrespective of the direction of selection [ 3, 10]. Parition (giving birth or laying eggs) is rarely observed for many species; facultative changes in parity mode, and mixed modes within a clutch, could go unreported and may be more biologically significant than previously acknowledged.

Species in which viviparity has evolved relatively recently are ideal models for investigating reproductive lability in squamate evolution [ 9, 22]. The three-toed skink, Saiphos equalis, endemic to southeastern Australia, is one of very few reptile species with intraspecific variation in parity mode [ 2, 25]. Reproduction varies geographically: S. equalis is viviparous in its northern high-elevation range and oviparous in northern and southern coastal regions [ 26]. Oviparous squamates typically lay eggs at embryonic stage 30, which hatch at stage 40 [ 27]. Unusually, oviparous females of S. equalis oviposit shelled eggs at stages 38-39 and undergo a shorter incubation period (mean 5.5 days) than sympatric skink species [ 26, 28]. By contrast, viviparous S. equalis neonates are enclosed by transparent membranes that are broken on average 1.5 days after birth [ 26, 29].

Here we report an observation of facultative oviparity in S. equalis. A viviparous female in our laboratory colony oviposited three eggs at embryonic stage 33, followed by a single fully developed offspring. As far as we are aware, this is the first report of a facultative change in parity mode within a vertebrate clutch, offering a rare opportunity to investigate reproductive lability in an unusual and evolutionarily important skink species. We used scanning electron microscopy (SEM) to compare shell morphology of facultatively oviposited eggs with those of normal oviparous and viviparous S. equalis to determine: (1) if shells of eggs deposited facultatively were more similar to those of viviparous or oviparous S. equalis and (2) whether viviparous S. equalis retain the machinery required for oviparous egg production.

2. Methods

(a) Animals

Female S. equalis ( n = 40) were collected in November 2013 from a northern high-elevation population previously shown to be viviparous [ 26, 28] (Mummel Gulf National Park, NSW, 31°21′ S 151°43′ E), and from a known oviparous population at southern low-elevation (Sydney, NSW, 33°50′ S 151°12' E; [ 25]). Animals were housed under standard protocols [ 30] in cages lined with damp peat moss (50 mm) with a heat strip at one end to provide a temperature gradient (17-26°C) for 6 h d −1. Photoperiod : scotoperiod reflected natural periods and incrementally increased from 14 to 15 h d −1. Crickets and water were provided ad libitum.

(b) Egg treatment and shell collection

One shelled embryo was dissected from each of nine of S. equalis females at four different reproductive stages, according to the staging system of Dufaure and Hubert [ 31] (from 0 (fertilization) to 40 (fully developed)): oviparous stage 36/37 (O36/37; n = 2 embryos), oviparous stage 39 (O39; n = 2 embryos), viviparous stage 36 (V36; n = 3 embryos) and viviparous stage 39/40 (V39/40; n = 2 embryos). We also dissected two embryos from 'unusual' eggs oviposited facultatively by a single viviparous female (V unusual, deposited at stage 33; post-oviposition ( n = 1 embryo), post-hatching ( n = 1 egg-covering)). Eggs and egg coverings were fixed in 10% neutral buffered formalin overnight followed by 70% ethanol. After staging, shells were dissected, air dried, then processed for SEM. Two 'unusual' eggs deposited facultatively were incubated in moist vermiculite (100% water by dry mass of vermiculite) at 22°C until hatching.

(c) Scanning electron microscopy

Shell fragments (greater than 3 × 5 mm ²) stored in 70% ethanol (34-46 months) were dried using a Leica EM CPD300 (Leica, Wetzlar, Germany), using CO ₂. To embed, upright shell fragments were secured flat between rings of copper coils, then cold-mounted in epoxy resin overnight at room temperature. The upper surface was ground flat using a RotoPol-22 (Struers, Copenhagen, Denmark) to expose the sample. Blocks were polished on a TegraPol-25 (Struers) to remove imperfections, then mounted onto aluminium stubs and coated with gold (15 nm). Images were captured using a Zeiss Sigma HD VP-STEM (Zeiss, Oberkochen, Germany).

SEM images were used to measure shell thicknesses. At least 10 measurements were taken of the crust and shell membrane layers of at least three shell regions per sample (1000-9000× magnification), although fewer measurable regions were intact for 'unusual' samples (two regions). Shell layer measurements were taken using ImageJ (v.1.51) and used to calculate: (1) total shell thickness, (2) relative thicknesses of crust (crust/total) and shell membrane (shell membrane/total) and (3) ratio of crust to shell membrane thickness (crust/shell membrane).

3. Results

During routine checks, and prior to parturition of any of the other 39 viviparous females from the same collecting trip, a viviparous female oviposited two eggs (24 January 2014), followed by a third (25 January 2014). Eggs were covered with a thin transparent membrane consistent with published descriptions of viviparous S. equalis at parturition [ 25] (electronic supplementary material). One egg was fixed (10% NBF) and found to be at stage 33 (electronic supplementary material), much earlier than typical for oviparous S. equalis (stage 38-39). The remaining two eggs were incubated. One died during incubation; the other resulted in a viable neonate that was observed 'hatching' from its thin membranes 37 days after oviposition. These membranes were fixed as per the first egg (electronic supplementary material figure B). The same female then gave birth to a single live neonate 41-48 days after oviposition of the first egg.

(a) Oviparous

Shells of oviparous S. equalis consist of an outer crust layer overlying a shell membrane layer consisting of interwoven fibres embedded in a dense crystalline matrix ( figure 1 a,b). Outermost fibres are thickest; many contain a globular material ( figure 1 c). The crust and shell membrane are separated by an additional thin membrane ( figure 1 a,b). The shell membrane overlays a thin inner boundary layer comprised of a dense matrix of thin fibres. Shell morphology is similar between stages 36/37 and 39, including shell layer proportions ( figure 2), although total shell thickness decreases by 45.5% from 32.9 ± 1.3 µm (stage 36/37) to 17.9 ± 2.5 µm (stage 39)].

(b) Viviparous

Shells of viviparous S. equalis are structurally similar to those of oviparous S. equalis ( figure 1 d-e), although the inner boundary layer is often difficult to discern, particularly at stage 39/40 ( figure 1 e). At stage 36, the shell membrane consists of thicker fibres towards the outer surface, with thinner fibres embedded in a dense matrix ( figure 1 d). Shell membrane fibres become more uniform in diameter by stage 39/40 ( figure 1 e). Shells are 28.5% thicker at stage 36 (11.67 ± 1.9 µm) than at stage 39/40 (8.35 ± 2.1 µm), with the reduction primarily in the shell membrane ( figure 2).

(c) 'Unusual' viviparous

Morphology was similar for both 'unusual' shells (post-oviposition (stage 33, figure 1 f) and post-hatching (stage 40)). An inner boundary layer could not be discerned, possibly as an artefact of sample preparation. Shell membrane fibres are relatively uniform and dense ( figure 1 f). Total thickness (9.27 ± 0.25 µm ( figure 2 a)) and shell layer proportions ( figure 2 c) are most similar to those of viviparous egg coverings at stage 36, yet layer proportions are also similar to oviparous S. equalis. Qualitatively, the thickness and proportions appear intermediate between the products of oviparous and viviparous individuals at the time of parition (O39 and V39/40, respectively; figure 2).

4. Discussion

This is the first description of both oviparity and viviparity within a single clutch in a reptile. Our observations suggest that oviparity may be facultative in viviparous S. equalis under some conditions. A mixed mode of parity within a clutch may reflect lability in timing of parition and suggests fine-scale control over neonate deposition within the uterus. The oviposition we observed (stage 33 versus 40) overlaps with oviposition of some oviparous species [ 22, 24] and is close to the typical range for most oviparous squamates (embryonic stages 25-31; [ 22]). Hence, the oviposition observed here is likely to be biologically significant. While our observation could be aberrant, the neonate that hatched from an egg oviposited at stage 33 was apparently healthy. We have also observed earlier than normal egg deposition (approx. stage 30) in captive S. equalis several times previously (M. B. Thompson 2018, personal communication). We thus suggest that reproductive lability is part of a viable reproductive strategy for S. equalis, at least in captivity.

Similarities of facultatively oviposited 'unusual' shells to those of oviparous and viviparous S. equalis suggest that the machinery for producing oviparous egg coverings is retained in viviparous S. equalis. Since 'unusual' shells were thinner than those of normally oviparous S. equalis, the capacity of oviductal glands to deposit shell material may be reduced [ 32], possibly as a result of reduced gland density [ 29]. However, as eggshells of both viviparous and oviparous S. equalis are relatively similar [ 29, 33, 34], the 'unusual' shell characteristics may be within the normal range of variation for viviparous S. equalis. Indeed, the eggshell thickness difference between oviparous and viviparous S. equalis is less than other bimodal squamates [ 35, 36, 37]. Hence shells of S. equalis eggs oviposited facultatively, intermediate in thickness at parition, may incur minimal fitness consequences during external incubation under some environmental conditions.

Lability in parity mode and timing of parition may confer an adaptive advantage in species in which viviparity has evolved relatively recently. 'Unusual' eggs were oviposited even earlier than those from normally oviparous S. equalis populations, which may be advantageous where inter- or intraspecific competition is high. Intra-clutch variation in timing of oviposition may be an adaptive strategy to ensure asynchronous hatching for offspring dispersal, similar to asynchronous birth in the viviparous skink, Liopholis whitii [ 38]. By contrast, since oviposited eggs with thinner shells are less likely to survive due to embryonic water balance constraints [ 13, 22], the capacity to carry offspring to term could increase survival during dry periods. The ability to reproduce via either parity mode could, therefore, act as a bet-hedging strategy in variable environments. Field monitoring, as well as experimental tests of the relationship between parity mode and environmental and physiological variables, could determine if wild S. equalis demonstrate such intra-clutch variation, and identify its adaptive significance.

Potential facultative oviparity in S. equalis suggests that a shift to obligate oviparity may still be possible for species early in the transition to viviparity. Investigating oviparous traits retained in facultatively oviparous species could identify which remain selectively advantageous in a mixed parity mode. While viviparous individuals of bimodally reproductive species such as S. equalis may retain oviparous traits, shifts to obligate oviparity are less likely for species representing more ancient origins of viviparity [ 3], particularly after the evolution of complex placentation and/or complete loss of an eggshell [ 5]. We suggest that reproductive lability may be an unacknowledged source of adaptation during squamate evolution.

Ethics

Ethics approval for this project was obtained from the University of Sydney Animal Ethics committee (688; L04/10-2011/3/5607). Fieldwork was conducted under NSW collection permit SL100401.

Data accessibility

Measurement data and image files. Data are available from the Dryad Digital Repository: https://doi.org/10.5061/dryad.6q3d110 [ 39].

Authors' contributions

M.K.L., C.M.W. and M.B.T. performed the study and wrote the manuscript. All authors agree to be held accountable for the content therein and approve the final version of the manuscript.

Competing interests

We declare we have no competing interests.

Funding

This study was funded by the Australian Research Council (DP120100649).

Acknowledgements

We acknowledge the Australian Centre for Microscopy and Microanalysis (University of Sydney), particularly N. Gokoolparsadh and J. Byrnes. We also thank J. Herbert for assistance with animal collection/husbandry, and J. Van Dyke, O. Griffith and M. Brandley for field assistance and useful discussions.

Footnotes

Electronic supplementary material is available online at https://dx.doi.org/10.6084/m9.figshare.c.4441844.

References

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Facultative oviparity in a viviparous skink (Saiphos equalis)

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Viviparity has evolved from ancestral oviparity at least 115 times in squamate reptiles [ 1, 2]. Reversals from viviparity to oviparity are rare [ 3- 6], yet recent phylogenetic work suggesting frequent reversals [ 7] has rekindled debate about their adaptive significance for squamate evolution.

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The three-toed skink is a bizarre lizard that is still evolving

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The three-toed skink is a bizarre lizard that is still evolving

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Evolution is usually something that science textbooks refer to as having happened however many million years ago. Then you have a freak of nature that defies whatever you learned in Bio 101.

The three-toed skink gives birth to live young. Wait, it lays eggs. No, it lays eggs and also gives birth to live young.

As biologists Dr. Charles Foster and Dr. Camilla Whittington of the University of Sydney, who recently published a paper in Biology Letters, found out, this bizarre lizard was literally evolving as they studied its DNA. Their research team was in for a shock when one of the normally live-bearing females laid eggs. As if that wasn't unexpected enough, she gave birth again a few weeks later.

"What is clear in biology is that evolution is a near-constant process. Organisms are always changing, whether they are sharks, humans, or the three-toed skink," Foster, the paper's lead author, told SYFY WIRE. "It's likely that both egg-laying and live-bearing three-toed skinks will continue to evolve over time."

This indecisive reptile is one of only a few species known to be bimodally reproductive. This rare phenomenon means it may either lay eggs or give birth to live young, but never before have scientists observed a vertebrate doing both during one pregnancy.

Environment can be a determining factor for whether or not it's going to be a birthday or a hatchday. Three-toed skinks are native to Australia's east coast, and it has been observed that those crawling around on the lower ground around Sydney lay eggs, while those that live in higher and cooler areas of New South Wales tend to bear live young. So why the transition from oviparity (egg laying) to viviparity (live birth)?

"Viviparity allows mothers to have greater control over the development of embryos," Foster explained. "In general, this means that viviparity might be favored in situations where it's expected that the embryo has more chance to develop to maturity with the mother's help as opposed to developing externally inside an egg. For example, laid eggs might be more susceptible to poaching by predators, or to fluctuations in environmental conditions such as water or temperature."

The earliest vertebrates that emerged - like the textbooks say, millions of years ago - laid eggs. Squamate reptiles (lizards and snakes) are of so much interest to study the evolution of viviparity since it has evolved at least 115 times in these creatures. Live births started to appear in these reptiles when some species started holding the eggs, in which embryos were developing, inside their bodies for longer and longer, until these species started giving birth to live offspring. Going back to how environmental conditions have separated the skinks that lay eggs from those that give birth, their bodies must react to where they prefer to hang out.

"Our work has shown that the egg-laying populations closer to Sydney are more of a transitional form between true egg-laying and live birth. It's possible that the Sydney populations are either in the process of transitioning from egg-laying to live birth, or from live birth back to 'true' egg-laying," said Foster.

What is even weirder is that egg coverings for both oviparous and viviparous embroys are produced the same way in a female skink's body. Viviparity changes things such as the glands that produce eggs and eggshells in the female, as well as blood flow, metabolism, and how long it takes for embryos to develop; but it may go back and forth if it has evolved recently in a previously egg-laying species. These are the rare species that Foster and Whittington feel are the most ideal for studying the likelihood of change in how snakes and lizards reproduce. They aren't going to be done evolving anytime soon, either.

So how is the three-toed skink most likely to create more skinks in the future?

"I would say that the forecast of more variable environmental conditions induced by climate change will favor live birth in the three-toed skink, since mothers will have more control over embryonic development compared to eggs developing in the fluctuating external environment," Foster said.

Millions of years from now, maybe someone will know.

(via University of Sydney/ Biology Letters)

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Thought evolution was ancient? This lizard is evolving, like, right now

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Evolution is usually something that science textbooks refer to as having happened however many million years ago. Then you have a freak of nature that defies whatever you learned in Bio 101. The three-toed skink gives birth to live young. Wait, it lays eggs. No, it lays eggs and also gives birth to live young.

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The most popular textbook example of punctuated evolution debunked

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The most popular textbook example of punctuated evolution debunked

# data[].attributes.attachment_link.readable_text
The picture shows the seven species of bryozoans that were used in the debunking.The white line is only 500 micrometers in length. Credit: JoAnn Sanner, The University of Chicago

Evolutionary biologists have for a long time disagreed on the rate of evolution when new species emerge. Are new species the result of gradual changes-as Charles Darwin suggested-or is evolution speeding up for short periods of time when new species evolve?

World renowned paleontologist Stephen Jay Gould (1941-2002) formulated the theory of punctuated equilibrium together with Niles Eldredge (1943-) in 1972. The theory states that species remain more or less unaltered during their existence, with major evolutionary change happening during rapid events of speciation. As evidence for this view, Gould pointed to the fossil record.

According to Gould, the fossil record typically show that species do not change significantly after they emerge, and that major changes occurred when new species appeared.

Stephen Jay Gould was one of the twentieth century's most famous evolutionary biologists and a bestselling popular science writer. Some even claimed that Gould was the foremost biologist of his time-perhaps the greatest since Charles Darwin himself-so his words have carried a lot of weight to this day.

In a new paper from researchers at the University of Oslo, the authors claim to have found several methodological problems in the most famous and well-trusted example supporting the theory of punctuated equilibrium.

"We find no evidence for punctuated evolution in our reanalysis of the most recognized dataset that Gould used to support his theory", says Kjetil Lysne Voje at UiO's Center for Ecological and Evolutionary Synthesis (CEES) at the Department of Biosciences.
Textbook example is rejected
Fossils of the bryozoan genus Metrarabdotos-a group of aquatic invertebrates thoroughly investigated by the excellent paleobiologist Alan Cheetham-have been the prime example of punctuated evolution.

Gould called Metrarabdotos "the most brilliantly persuasive, and most meticulously documented, example ever presented for predominant (in this case, exclusive) punctuated equilibrium in a full lineage" (Gould 2002, page 827).

"We detected some critical methodological issues in the original work on Metrarabdotos. When we take the methodological issues into account, we do not find any evidence of punctuated evolution in our reanalysis of the Metrarabdotos data", says Kjetil Lysne Voje.

Bryozoans are so small that scientists have to use an electron microscope to study them in detail, but they form colonies that can be quite large (up to 1 meter). Most bryozoans live in the sea, but there are also many species in fresh water. The bryozoan genus Metrarabdotos has been used as a textbook example in evolutionary biology and paleontology, showing how evolution speeds up when new species form compared to a much slower evolution of already established species.

"But our new results show nothing else than a gradual evolution of the bryozoan species both before, during and after the formation of new species", emphasizes Voje.

The idea of fast-track evolution during speciation has been controversial. Critics of the theory of punctuated equilibrium found it difficult to believe that the evolutionary processes leading to new species should be markedly different from the processes that cause already existing species to change.

"Species are continuously evolving and our results support the hypothesis that evolution does not "behave" differently when new species emerge", says Voje.

The paper with the new results was published in the May issue of The American Naturalist.

More information: Kjetil Lysne Voje et al. Revisiting a Landmark Study System: No Evidence for a Punctuated Mode of Evolution in Metrarabdotos, The American Naturalist (2019). DOI: 10.1086/707664

# data[].attributes.attachment_link.title
The most popular textbook example of punctuated evolution debunked

# data[].attributes.attachment_link.description
Evolutionary biologists have for a long time disagreed on the rate of evolution when new species emerge. Are new species the result of gradual changes-as Charles Darwin suggested-or is evolution speeding up for short periods of time when new species evolve?

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Origine de la vie : un scénario alternatif défendu par de... - Science & Vie

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Origine de la vie : un scénario alternatif défendu par de... - Science & Vie

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"Nos résultats ont été accueillis comme une hérésie !" , s'exclame Gustavo Caetano-Anollés. Ce biologiste du laboratoire de bio-informatique évolutionnaire à l'université de l'Illinois (Etats-Unis) ne s'en étonne guère : on ne s'attaque pas impunément à un mythe. A fortiori celui de l' origine de la vie.

Car le récit largement admis aujourd'hui remonte à la fin des années 1970. Il y a 3,8 à 3,5 milliards d'années, quelques centaines de millions d'années après la formation de la Terre, plusieurs entités cellulaires vivantes se disputaient les ressources de la " soupe primordiale", cet océan chaud planétaire contenant des molécules en perpétuelle inter action. La lignée qui s'est le plus reproduite a fini par monopoliser les ressources de ce maelström, engendrant par la suite tout le vivant.

Repères

Le modèle ou arbre "phylogénétique" établit que tous les organismes vivants descendent d'une seule lignée de cellules, nommée "Luca" ("Last universal common ancestor"), qui se serait divisée en trois "royaumes" : les archées, les bactéries et les eucaryotes. Tous les organismes multicellulaires, dont l'homme, appartiennent à la lignée des eucaryotes.

Ce gagnant se nomme "Luca" (pour "Last universal common ancestor", ou "Dernier ancêtre commun universel"), et sa descendance couvre, à travers un gigantesque arbre évolutif, les trois royaumes du vivant (lire "Repères" ci-contre), des bactéries aux éléphants. Face à sa force multiplicatrice, toutes les autres lignées de protocellules ont périclité et disparu.

Toutes... sauf celle des virus, affirment aujourd'hui Gustavo Caetano-Anollés et son collègue Arshan Nasir. Selon eux, les virus modernes sont les descendants directs, non de Luca, mais de cellules concurrentes. Autrement dit, ils procèdent d'une autre façon d'être vivant !

Dans un premier temps, ces ancêtres des virus seraient devenus des parasites de Luca, détournant la machinerie cellulaire tout en abandonnant certaines de leurs fonctions internes, ainsi que les gènes qui les pilotent - un phénomène classique de "réduction évolutive". Ils auraient ensuite continué à se simplifier jusqu'à se reposer totalement sur la machine moléculaire de leur hôte, perdant les attributs des êtres vivants aujourd'hui considérés comme essentiels (telle la capacité à dupliquer soi-même son information ou à puiser de l'énergie de l'extérieur) et ne conservant que le strict nécessaire pour mettre les cellules à leur service et se disséminer.

Voilà qui ne cadre pas vraiment avec le scénario officiel de l'histoire de la vie. Lequel voit dans les virus de simples rejets accidentels des protocellules de Luca. Selon lui, les protocellules ont inondé durant des millions d'années la soupe primordiale de morceaux de leur anatomie - fragments d'ADN, d'ARN ou de membrane cellulaire. Du matériel inerte biologiquement, mais actif chimiquement. "Le hasard a voulu qu'un nombre infime de ces fragments se trouve doté de propriétés physico-chimiques leur permettant de se répliquer au sein des cellules, et donc de perdurer" , précise Purificación Lopez-Garcia, directrice de l'équipe Diversité, écologie et évolution microbiennes de l'université Paris-Sud, qui ne croit pas au nouveau récit.

11 MILLIONS DE PROTÉINES

Les deux "hérétiques" ont publié en septembre leurs arguments. Contrairement à la plupart des études visant à construire les arbres généalogiques de la vie, leurs travaux ne reposent pas sur la comparaison entre des gènes, mais entre les formes des protéines, plus précisément entre les divers "domaines structuraux" (les "plis" en 3D des protéines) qui les constituent. Ce sont eux qui agissent chimiquement sur l'environnement, conférant ainsi leurs fonctions aux protéines.

"On compare non pas les séquences génétiques, mais les structures 3D des protéines qu'elles produisent , résume Gustavo Caetano-Anollés. Et, comme on le fait avec les séquences génétiques, nous pouvons retracer l'histoire évolutive de ces structures." Avec la même logique : deux entités produisant des protéines aux structures proches partagent un ancêtre commun. Le bio-informaticien exploite cette méthode depuis son émergence, à la fin des années 1990. Et les arbres de la vie qu'il a ainsi tracés ont toujours été compatibles avec ceux de la méthode phylogénétique traditionnelle - du moins jusqu'ici.

Pour lui, cette méthode est même plus fiable : "Les gènes mutent beaucoup plus vite que les structures des protéines qu'ils produisent." Pour dresser ce nouvel arbre des virus, Arshan Nasir et lui ont brassé large : ils ont passé au crible de puissants algorithmes statistiques 11 millions de protéines produites par 3 460 espèces de virus et 1 620 espèces de cellules appartenant aux trois royaumes du vivant.

En comparant leur composition chimique à l'aide d'une "bibliothèque" de quelques milliers de protéines dont on connaît exactement la composition et la structure 3D, ils ont d'abord déduit la forme des domaines structuraux de ces millions de protéines. Un calcul probabiliste complexe, mais dont les prévisions, assure Gustavo Caetano-Anollés, "ont jusqu'ici été confirmées par l'étude par rayons X des protéines avec un taux de réussite de 95 % à 98 %" .

Les chercheurs ont ensuite identifié les domaines structuraux les plus répandus parmi les espèces. Ils en ont dénombré 1 995, dont 66 n'appartiennent qu'aux virus. Difficile de croire que les gènes qui produisent ces protéines soient issus de ceux de Luca - on en retrouverait la trace dans les trois royaumes du vivant.

D'où leur conclusion : les virus sont issus de plusieurs cellules distinctes de la lignée de notre ancêtre universel, et ont coexisté avec lui. Ils ont leur propre arbre évolutif, qui s'entremêle avec le nôtre (voir le schéma ci-contre). Et ils devraient dès lors être considérés comme des êtres vivants, puisqu'étant issus d'ancêtres vivants - la théorie de l'évolution ne permet pas d'imaginer qu'une espèce vivante devienne inerte en évoluant.

Une branche du vivant à part entière

Ce nouvel arbre du vivant intègre une quatrième branche, celle des virus, en plus des trois "royaumes" du vivant déjà connus (archées, bactéries et eucaryotes). Les virus descendraient de cellules préexistantes au dernier ancêtre commun de ces trois royaumes : Luca (point rouge). L'importance de la lignée des virus sur cet arbre tient uniquement au fait qu'elle est ici détaillée.

UNE CLÉ DE L'ÉVOLUTION

Cette idée avait déjà été avancée par les virologistes français Didier Raoult et Jean-Michel Claverie après leur découverte, en 2003, de "virus géants" (photo ci-contre).

"Nous avions aussi mis au jour des gènes n'appartenant qu'aux virus , s'enthousiasme Jean-Michel Claverie. Je ne vois pas comment interpréter la présence de structures ou de gènes communs aux virus, mais absents du règne des cellules, si ce n'est en supposant qu'ils proviennent d'ancêtres cellulaires préexistant à Luca."

Les défenseurs de cette hypothèse d'une origine cellulaire des virus restent minoritaires. Mais Gustavo Caetano-Anollés n'en démord pas : "Nos résultats sont robustes. Les évolutionnistes sont trop attachés aux séquences génétiques. La plupart n'ont pas vu la montée en puissance de l'analyse structurelle des protéines."

Tout en avouant qu' "il reste beaucoup à faire avant de disposer d'arbres évolutifs corrects retraçant l'histoire des virus" , Patrick Forterre, spécialiste de l'évolution à l'Institut Pasteur, se réjouit de la controverse : "Cela favorise le retour des virus dans la mire des évolutionnistes, alors qu'ils en étaient les grands absents." Le débat est en cours : et si les virus étaient les autres survivants de la soupe primordiale ?
Une version précédente de cet article est parue le 25 novembre 2015

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Origine de la vie : un scénario alternatif défendu par des chercheurs

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"Nos résultats ont été accueillis comme une hérésie !" , s'exclame Gustavo Caetano-Anollés. Ce biologiste du laboratoire de bio-informatique évolutionnaire à l'université de l'Illinois (Etats-Unis) ne s'en étonne guère : on ne s'attaque pas impunément à un mythe. A fortiori celui de l' origine de la vie.

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Global human genomes reveal rich genetic diversity shaped by complex evolutionary history

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Global human genomes reveal rich genetic diversity shaped by complex evolutionary history

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Credit: CC0 Public Domain

A new study has provided the most comprehensive analysis of human genetic diversity to date, after the sequencing of 929 human genomes by scientists at the Wellcome Sanger Institute, the University of Cambridge and their collaborators. The study uncovers a large amount of previously undescribed genetic variation and provides new insights into our evolutionary past, highlighting the complexity of the process through which our ancestors diversified, migrated and mixed throughout the world.

The resource, published in Science (20 March), is the most detailed representation of the genetic diversity of worldwide populations to date. It is freely available to all researchers to study human genetic diversity, including studies of genetic susceptibility to disease in different parts of the world.

The consensus view of human history tells us that the ancestors of present-day humans diverged from the ancestors of extinct Neanderthal and Denisovan groups around 500,000-700,000 years ago, before the emergence of 'modern' humans in Africa in the last few hundred thousand years.

Around 50,000-70,000 years ago, some humans expanded out of Africa and soon after mixed with archaic Eurasian groups. After that, populations grew rapidly, with extensive migration and mixture as many groups transitioned from hunter-gatherers to food producers over the last 10,000 years.

This study is the first to apply the latest high-quality sequencing technology to such a large and diverse set of humans, covering 929 genomes from 54 geographically, linguistically and culturally diverse populations from across the globe. The sequencing and analysis of these genomes, which are part of the Human Genome Diversity Project (HGDP)-CEPH panel, now provides unprecedented detail of our genetic history.

The team found millions of previously unknown DNA variations that are exclusive to one continental or major geographical region. Though most of these were rare, they included common variations in certain African and Oceanian populations that had not been identified by previous studies.

Variations such as these may influence the susceptibility of different populations to disease. However, medical genetics studies have so far predominantly been conducted in populations of European ancestry, meaning that any medical implications that these variants might have are not known. Identifying these novel variants represents a first step towards fully expanding the study of genomics to underrepresented populations.

However, no single DNA variation was found to be present in 100 per cent of genomes from any major geographical region while being absent from all other regions. This finding underlines that the majority of common genetic variation is found across the globe.

Dr. Anders Bergström, of the Francis Crick Institute and an alumnus of the Wellcome Sanger Institute, said: "The detail provided by this study allows us to look deeper into human history, particularly inside Africa where less is currently known about the timescale of human evolution. We find that the ancestors of present-day populations diversified through a gradual and complex process mostly during the last 250,000 years, with large amounts of gene flow between these early lineages. But we also see evidence that small parts of human ancestries trace back to groups that diversified much earlier than this."

Hélène Blanché, Head of the Biological Resource Centre at the Centre d'Etude du Polymorphisme Humain (CEPH) in Paris, France, said: "The Human Genome Diversity Project resource has facilitated many new discoveries about human history in the past two decades. It is exciting to see that with the latest genomic sequencing technology, these genomes will continue to help us understand our species and how we have evolved."

The study also provides evidence that the Neanderthal ancestry of modern humans can be explained by just one major 'mixing event', most likely involving several Neanderthal individuals coming into contact with modern humans shortly after the latter had expanded out of Africa. In contrast, several different sets of DNA segments inherited from Denisovans were identified in people from Oceania and East Asia, suggesting at least two distinct mixing events.

The discovery of small amounts of Neanderthal DNA in west African people, most likely reflecting later genetic backflow into Africa from Eurasia, further highlights how human genetic history is characterised by multiple layers of complexity. Until recently, it was thought that only people outside sub-Saharan Africa had Neanderthal DNA.

Dr. Chris Tyler-Smith, recently retired from the Wellcome Sanger Institute, said: "Though this resource is just the beginning of many avenues of research, already we can glimpse several tantalising insights into human history. It will be particularly important for better understanding human evolution in Africa, as well as facilitating medical research for the full diversity of human ancestries."

More information: A. Bergström el al., "Insights into human genetic variation and population history from 929 diverse genomes," Science (2020). science.sciencemag.org/cgi/doi ... 1126/science.aay5012

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Global human genomes reveal rich genetic diversity shaped by complex evolutionary history

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A new study has provided the most comprehensive analysis of human genetic diversity to date, after the sequencing of 929 human genomes by scientists at the Wellcome Sanger Institute, the University of Cambridge and their collaborators.

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The COVID-19 Pandemic Exposes The Harm Of Denying Scientific Facts

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The COVID-19 Pandemic Exposes The Harm Of Denying Scientific Facts

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In 2016, an Italian virologist named Roberto Burioni was invited to appear on television alongside two celebrities: Red Ronnie (a DJ) and actress Eleonora Brigliadori. Near the end of the program, the host turned to Burioni for the first time. His response is now legendary:

"The Earth is round, gasoline is flammable, and vaccines are safe and effective. All the rest are dangerous lies."

Over the past few months, the COVID-19 pandemic has spread around the world, aided and abetted by millions upon millions of people - including many of the most powerful politicians in the world - who failed to heed the warnings of public health and scientific experts. But this is not a new problem. People deny scientific facts all the time when facing up to them is the more fearsome option. But science is real whether we accept it or not, and denying it harms the whole of human society.

Science is the most valuable tool we have for exploring the natural world and Universe around us. If we want to figure out how any physical system works, all we have to do is investigate it scientifically: by asking it the right questions about itself. That means performing experiments, measurements, and observations - under the right, relevant, controlled conditions - to reveal the answers.

It's true that science is always a work-in-progress. Sometimes, new data comes along to overturn the previously prevailing consensus. Sometimes, flaws are found in the data, methods, or analysis of what we thought we had understood, changing the conclusions. And sometimes, effects that had previously been neglected turn out to be important, altering what we thought we knew.

Science isn't just a body of facts, it's a process, and part of that process necessarily involves reaching preliminary, provisional conclusions that may later turn out to be wrong. But the only thing that has ever overturned a previously held scientific consensus is additional scientific inquiry: i.e., more and better science. Moreover, the more we learn about the natural world, the smaller and more esoteric those changes and effects tend to generally be.

Right now, we are seeing the consequences unfold, worldwide, of ignoring the science of epidemiology, virology, disease ecology, and public health. The current COVID-19 coronavirus pandemic, as of today, has infected a minimum of 850,000 people already, with over 40,000 confirmed deaths. Even today, many are failing to practice social (i.e., physical) distancing, convinced that the scientific conclusions reached by the field are mistaken.

Of course, the physical and biological sciences will continue to do what they do irrespective of human opinion. Politics may be a team-based sport while science most certainly is not. But a society that embraces scientific thinking - and incorporates the best scientific evidence and knowledge into their public policies - is a society where we're all better off. COVID-19 is only the most immediate example of science denialism, but it's one where the consequences are the most clear-cut, particularly in the short term.

Science, on the whole, is the best guide we have for predicting what will happen in the future. If we understand any system successfully, we can understand at least the basics of what consequences our actions (or inactions) will have. They say that the first stage of grief is often denial, often accompanied by anger, and yet when it comes to a scientific or health issue, denial, particularly in the early stages, is the worst thing we can collectively engage in if we don't want to exacerbate the problem.

Scientific consensus isn't something that's arrived at lightly. Consensus is not a compromise; it's not a matter of opinion; it's not immune to challenge. Instead, consensus is a fact-based starting point for any reasonable discussion among professionals: it's the point where the overwhelming majority of professionals are all in agreement with one another.

There are often legitimate challenges to any scientific consensus, but the legitimate ones always come from a purely scientific point-of-view. Typically, there's a new piece of evidence that's come to light that conflicts with the prevailing consensus, and more and better science is required to put that into context with the rest of the field. Most frequently, the consensus holds up. It's only on rare occasions that a true scientific revolution occurs.

And yet, most people hold at least one belief, often based on anecdotal or (perceived) personal experience, that wholly conflicts with the available scientific evidence. The flu vaccine, available every year or two, would prevent tens of thousands of deaths annually if vaccination rates were high, and yet the percentage of Americans who get the flu vaccine annually has dropped to a decades-long low for the most recent year available: below 40%.

Anti-vaccination sentiment continues to remain a problem in the country, even as preventable, dangerous, and highly contagious diseases like the measles have returned. Measles, in particular, is so contagious that it requires that approximately 95% of the population have immunity against it to prevent its spread to vulnerable, necessarily unvaccinated populations. And yet, denial of the safety and effectiveness of vaccines, along with a long-debunked conspiracy that they cause autism, remains widespread.

This is one dangerous type of science denialism: denying the safety or effectiveness of something that has been robustly established to be safe and effective. This includes examples such as:

5G wireless technology, which poses no health risks to humans in the doses that even those with the greatest exposure endure,

fluoridated drinking water, which reduces cavities and bone fractures in the recommended dosages while not increasing any ill effects until much higher doses are reached,

glyphosate (RoundUp), which not only doesn't cause cancer, but the only environmental problem it causes is the development of glyphosate-resistant weeds.

It's very easy to make people afraid of something that they themselves don't understand well, but the science is very clear on these issues. The societal benefits of a vaccinated population, of widespread and available high-speed internet, of reduced cavities, and of improved crop yields are not disputed by any mainstream scientific source.

However, the other major form of science denialism is even more potentially hazardous: denying the real risks and dangers that science has established. COVID-19 is a dangerous, deadly, and contagious disease, and can be combatted through a variety of medical and social interventions. Yet, even today (March 31, 2020, at the time of this writing) many people are publicly denying the well-established dangers that the novel coronavirus presents.

Examples of this type of denialism include:

Science denialism is not just someone glorifying an obviously ignorant position, like a flat Earth or declaring that the Moon landings were a hoax. It's a common form of self-deception, where many of us think (either consciously or subconsciously) that we won't need to reckon with an inconvenient aspect of reality if we reject it. But that's never what actually happens. Instead, we harm ourselves, others, and society as a whole through our selfish self-delusions.

And it is a delusion to think that we, as non-expert individuals, know more than the experts do. As I've written previously,

All of the solutions that require learning, incorporating new information, changing our minds, or re-evaluating our prior positions in the face of new evidence have something in common: they take effort. They require us to admit our own limitations; they require humility. And they require a willingness to abandon our preconceptions when the evidence demands that we do. The alternative is to live a contrarian life where you're actively harming society.

The COVID-19 pandemic is likely to have widespread consequences for the entire world on a wide variety of fronts: social, economic, and political all included. But the biggest lesson of all should be the scientific one: when we ignore the best recommendations of science, our entire society suffers unnecessarily. There's the old saying that an ounce of prevention is worth a pound of cure, and the dangerous lie that harms all of society is the idea that the ounce of prevention is expendable. In many cases, such as COVID-19, the prevention is so necessary exactly because there is no cure.

There are many challenges we all face in our day-to-day lives that consume us, and it's a challenge to plan ahead weeks or months in advance, much less years, decades, or centuries, which is where the effects of global warming and climate change are most severe. But the science is real regardless of our beliefs and irrespective of our actions, and listening to it is one thing we can all do to improve not only our own lives, but to serve the public good.

... Read More

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The COVID-19 Pandemic Exposes The Harm Of Denying Scientific Facts

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In 2016, an Italian virologist named Roberto Burioni was invited to appear on television alongside two celebrities: Red Ronnie (a DJ) and actress Eleonora Brigliadori. Near the end of the program, the host turned to Burioni for the first time. His response is now legendary: "The Earth is round, gasoline is flammable, and vaccines are safe and effective.

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L'aveuglement des sciences sociales aux sciences naturelles creuse leur propre tombeau | Slate.fr

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L'aveuglement des sciences sociales aux sciences naturelles creuse leur propre tombeau | Slate.fr

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Temps de lecture: 8 min

C'est rigolo comme file l'actualité. Il n'y a pas si longtemps (surtout si l'on compare à l'âge de l'univers), les nouvelles n'étaient pas monopolisées par les "gilets jaunes", mais par les rixes entre jeunes de quartiers plus ou moins sensibles. "Depuis près de trois ans", pouvait-on ainsi lire dans Le Monde en octobre dernier, "la capitale voit augmenter à un rythme préoccupant le phénomène des rixes entre bandes de jeunes. Pour tenter de l'enrayer, la maire de Paris, Anne Hidalgo, le procureur de la République, le préfet de police et le recteur d'académie de Paris ont lancé [...] des états généraux sur ce phénomène à l'hôtel de ville".

Invitée pour en discuter dans l'émission de France Culture "Du grain à moudre", Colombe Brossel, adjointe à la Mairie de Paris chargée des questions relatives à la sécurité, la prévention, aux quartiers populaires et à l'intégration, s'étonnait de plusieurs caractéristiques d'un phénomène dont le bilan s'élevait alors à trois morts et plusieurs centaines de blessés en un peu moins d'un an.

D'abord sa démographie: "Ce sont des jeunes gens très jeunes, quasi exclusivement des garçons", s'était stupéfaite l'élue, avant que sa surprise ne soit confirmée par Hervé Gardette, l'animateur de l'émission ( "entre 12 et 14 ans, c'est vraiment très jeune, c'est contre-intuitif", avait-il commenté). Puis certaines de ses répercussions sociales: "Il nous a fallu quelques mois pour comprendre, déceler et [...] mettre en place des actions qui permettent de marquer le coup, notamment sur la violence et la réalité que peut engendrer la violence." La raison de ce retard à l'allumage? Le fait que, malgré l'intensité des échauffourées (parfois agrémentées de "feuilles de boucher") et le "vrai risque de mort" qu'il y avait à y prendre part, "les gamins qui sortaient de l'hôpital" devenaient des "héros" une fois revenus au collège.

J'avoue, j'ai moi aussi été sidérée par ces propos et j'en ai d'abord ri, à la manière d'un Figaro dans Le Barbier de Séville de Beaumarchais, qui se "presse de rire de tout, de peur d'être obligé d'en pleurer"). Ce qu'ils révèlent? L'ignorance d'un ensemble de connaissances scientifiques pourtant parmi les plus solides et les plus en consilience que l'esprit humain a pu pondre au cours de sa longue maturation: la théorie de l'évolution.

Car, pour expliquer ces rixes, tout allait y passer: précarité, échec scolaire, ultra-libéralisme, désaffection des pères et travail des mères jusqu'à l'influence (forcément délétère) des jeux vidéo... Sans que jamais personne ne fasse remarquer qu'en des circonstances équivalentes, un tel schéma de violence -à la fois coalitionnelle, majoritairement masculine, essentiellement adolescente, extrêmement agonistique et lourdement pourvoyeuse de statut et d'opportunités sexuelles chez celles et ceux qui en sortent vainqueurs (qu'importe, et peut-être même surtout, s'ils en sont marqués dans leur chair)- se retrouve dans toutes les cultures.Sans compter une palanquée d'espèces autres que la nôtre, à commencer par les primates. Ou, pour le dire autrement, qu'il n'y a pas lieu de s'en étonner ni de passer des mois à se demander ce qui peut bien "clocher" dans la cervelle de jeunes mâles qui se mettent sur la gueule à intervalles réguliers avant d'en tirer divers avantages sociaux vu que la chose n'a absolument rien d'une aberration.

Limites du paradigme constructiviste

Mais pour le savoir, il aurait fallu que l'analyse soit fondée sur autre chose que le paradigme constructiviste encore dominant en sciences humaines et statuant que si oui, les humains ont des organes et une physiologie lentement façonnés selon la double loi du hasard et de la nécessité, non, les logiques s'appliquant à l'intégralité du vivant ignorent sa psychologie et ses comportements, pour leur part dépendants de facteurs à la fois socioculturels et spécifiques à notre espèce. Une idéologie qui n'en finit plus d'être scientifiquement intenable.

C'est sur cette déconnexion entre sciences naturelles et sciences sociales, du fait et aux frais des secondes, que porte La nature du social de Laurent Cordonier. Dans cet ouvrage, le sociologue affilé à l'université Paris-Diderot se donne comme objectif "d'étudier l'hypothèse selon laquelle les sciences de la nature humaine contemporaines sont susceptibles de nous apporter un éclairage nouveau et complémentaire sur certains objets classiques de la sociologie et de l'anthropologie, sans pour autant nous contraindre à réduire l'explication des phénomènes sociaux ou culturels à un ensemble d'activités neuronales, ni nous conduire à légitimer quelque inégalité sociale que ce soit".

Une logique proprement intégrative que l'on retrouvait, entre autres, chez E.O. Wilson et son Unicité du savoir, projet sociobiologique que Cordonier assimile à tort à du réductionnisme et dans lequel il voit un "exercice périlleux" à forte charge "politiquement problématique" -cette dernière appréciation ciblant en particulier un de ses héritiers, à savoir ma petite personne.

Qu'on se rassure, c'est bien là le seul et maigre défaut du livre de Cordonier -et je me demande même s'il ne nous pas jette sous le bus avec Wilson comme offrandes expiatoires,histoire d'atténuer l'ire de ses nombreues et nombreux collègues qui nous assimilent (toujours à tort) à Belzébuth, mais c'est un autre débat. Car s'il se montre sans doute par trop précautionneux sur le sujet épineux de notre cognition sexuelle, dans le reste de son ouvrage, Cordonier détaille bien comment "vivre en société n'est absolument pas une option facultative pour l'être humain, pas plus qu'elle ne l'est pour nos cousins non humains".

Un cerveau "modelé par et pour la société"

De fait, les sciences cognitives, ces multiples disciplines qui étudient la manière dont notre cerveau traite les informations et réagit en fonction par des comportements, " ont démontré qu'au cours de l'histoire évolutive de notre espèce, notre cerveau a été modelé par et pour la vie en société. Il est ainsi de plus en plus évident qu'il n'existe pas de frontière stricte entre ce qui relèverait du social et de la nature", m'explique l'auteur. Et il n'est donc évidemment plus possible de défendre les antiques oppositions entre matière et esprit, nature et culture ou inné et acquis sans se retrouver en porte-à-faux avec l'état actuel des connaissances scientifiques.

Nos interactions socio-comportementales sont encodées dans notre patrimoine génétique et dans son histoire évolutive comme des notes sur une portée de musique.

" L'environnement social dans lequel s'est déroulée la phylogenèse de notre espèce, écrit Cordonier, a littéralement modelé notre cerveau, nous dotant progressivement de compétences cognitives naturellement adaptées au traitement de l'information sociale pertinente au sein de groupes fortement hiérarchisés et parcourus de réseaux de relations interindividuelles allant de l'antagonisme à la bienveillance, en passant par l'association et l'engagement réciproque". Nos interactions socio-comportementales sont encodées dans notre patrimoine génétique et dans son histoire évolutive comme des notes sur une portée de musique -la mélodie et le rythme peuvent varier, mais dans un cadre modal et tonal qui n'a rien d'infini.

La nature du social de Cordonier est une adaptation de sa thèse de doctorat en sociologie, dirigée par Laurence Kaufmann. "Notre intérêt commun portait sur l'étude de la cognition sociale, à savoir les mécanismes mentaux qui nous permettent de nous orienter en société, me précise-t-il. Cette thématique de recherche nous a naturellement conduits à nous pencher sur les travaux des sciences cognitives -psychologie cognitive et psychologie du développement, principalement. Durant ma thèse, j'ai donc entrepris de me former à ces disciplines. J'ai ainsi effectué plusieurs séjours de recherche dans des laboratoires de sciences cognitives en Europe et aux États-Unis, où j'ai eu l'opportunité de conduire des recherches expérimentales."

C'est là qu'il se rend compte de l'énorme fossé qui sépare beaucoup de sociologues et de spécialistes des sciences cognitives. "J'ai rapidement été marqué par l'indifférence, voire le mépris de mes collègues sociologues pour les travaux en sciences cognitives portant sur des sujets qui auraient pourtant dû les intéresser, regrette Cordonier. Comme celui du traitement des informations hiérarchiques ou des mécanismes de catégorisation sociale, par exemple." Un rejet qu'il explique principalement par "le fait que les sciences cognitives sont profondément ancrées sur la biologie".

Rejet de l'approche biologisante du social

Cordonier observe en effet que bon nombre de sociologues "voient d'un très mauvais œil toute approche potentiellement "biologisante" du social. Selon eux, soutenir que notre fonctionnement social résulte en partie de mécanismes cognitifs sélectionnés au cours de l'évolution de notre espèce aboutirait à "naturaliser" et, ce faisant, à légitimer diverses inégalités (les inégalités de genre, par exemple)". Soit, encore et toujours, une variation sur un même thème fait d' erreur naturaliste, de créationnisme mental -l'évolution se serait arrêtée comme par magie chez l'humain au niveau du cou- et d' "anthropodéni", pour reprendre la formule du primatologue Frans de Waal.

Au printemps 2015, une revue de psychologie du développement sortait un numéro spécial sur le harcèlement scolaire dans laquelle on apprenait que la grande majorité des interventions visant à endiguer le phénomène se soldaient par un échec. Pourquoi? Principalement parce que si elles supprimaient les avantages du harcèlement -un statut social augmenté parmi ses pairs-, elles n'offraient aucune gratification alternative équivalente. Les harceleurs étaient donc toujours incités à harceler vu qu'ils ne trouvaient pas dans d'autres comportements l'estime sociale qu'ils tiraient du harcèlement. À l'instar de la violence coalitionnelle des rixes entre adolescents débordant d'ennui et de testostérone, le harcèlement est loin d'être une interaction inter-individuelle purement négative -au contraire, elle sert aussi et surtout à gagner en statut et en prestige. Une fonction sociale qu'il est nécessaire de comprendre si l'on veut la combattre et, à cette fin, le cadre conceptuel évolutionnaire n'est pas accessoire.

"La question n'est plus de savoir s'il faut chercher à intégrer le travail des sciences naturelles et sociales, mais comment il s'agit de le faire! "

Laurent Cordonier, sociologue.

De fait, si "rien n'a de sens en biologie, si ce n'est à la lumière de l'évolution", comme l'écrivait en 1973 Theodosius Dobzhansky, alors, rappelle Cristine Legare, spécialiste d'évolution cognitive et culturelle au sein de l'université du Texas, rien n'a non plus de sens dans "la culture, la psychologie et le comportement humains" sans cet éclairage. Un fait que les recherches en sciences sociales se doivent aujourd'hui de prendre en compte, ce que Cordonier confirme: "La question n'est plus aujourd'hui de savoir s'il faut chercher à intégrer le travail des sciences naturelles et sociales, mais comment il s'agit de le faire! Je tiens à souligner qu'une telle intégration ne bénéficierait pas uniquement à la sociologie. Les sciences cognitives ont également besoin d'enrichir leurs recherches sur la cognition sociale en recourant au savoir sociologique."

Il est courant d'opposer le chercheur militant, qui veut changer le monde, et la chercheuse observante, qui veut le comprendre. Mais s'il est un "exercice périlleux" entre tous, c'est de croire que la première entreprise peut se passer de la seconde. Une volonté de réforme se condamne à demeurer dans la sphère de l'utopie -avec tout son cortège de tragédies- si elle s'obstine à ignorer les réseaux nomologiques de preuves cumulées constituant l'état de nos connaissances sur la nature humaine.

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L'aveuglement des sciences sociales aux sciences naturelles creuse leur propre tombeau

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Comme l'expose le sociologue Laurent Cordonier, il n'est plus possible d'ignorer la nature du social. C'est rigolo comme file l'actualité. Il n'y a pas si longtemps (surtout si l'on compare à l'âge de l'univers), les nouvelles n'étaient pas monopolisées par les "gilets jaunes",...

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Un oiseau fossile au bec de toucan avec des dents - Sciences et Avenir

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Un oiseau fossile au bec de toucan avec des dents - Sciences et Avenir

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Cet oiseau vieux de 70 millions d'années possède un bec de toucan avec des dents

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Les pinsons ! Ce sont eux, ou plutôt la grande variété de formes que peuvent adopter leurs becs, qui ont largement inspiré Charles Darwin pour sa théorie de l'Evolution. Et depuis, l'observation des oiseaux et l'étude de leurs fossiles a largement contribué à étayer et à compléter cette théorie.

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PhyML, le logiciel français au coeur des recherches sur le Covid-19 | Les Echos

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PhyML, le logiciel français au coeur des recherches sur le Covid-19 | Les Echos

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PhyML, le logiciel français au coeur des recherches sur le Covid-19

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Le logiciel de bioinformatique français PhyML, qui permet de reconstruire la généalogie des virus et leurs chaînes de transmission, est au coeur de la recherche mondiale sur le coronavirus. Il s'avère être un outil précieux pour aider à contrôler l'épidémie, trouver des cibles thérapeutiques et mettre au point un futur vaccin.

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These bizarre ancient species are rewriting animal evolution

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These bizarre ancient species are rewriting animal evolution

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The revolutionary animal lived and died in the muck. In its final hours, it inched across the sea floor, leaving a track like a tyre print, and finally went still. Then geology set to work. Over the next half a billion years, sediment turned to stone, preserving the deathbed scene. The fossilized creature looks like a piece of frayed rope measuring just a few centimetres wide. But it was a trailblazer among living things.

This was the earliest-known animal to show unequivocal evidence of two momentous innovations packaged together: the ability to roam the ocean floor, and a body built from segments. It was also among the oldest known to have clear front and back ends, and a left side that mirrored its right. Those same features are found today in animals from flies to flying foxes, from lobsters to lions.

Palaeontologist Shuhai Xiao marvels at the tracks left by this creature, Yilingia spiciformis, and how they captured evidence of its movement. In his cluttered office at Virginia Tech in Blacksburg, he shows off a slab of beige resin - a reproduction of the fossil, which was found in China's Yangtze Gorges region and is now kept in a Chinese research institute. The replica captures a snapshot of a moment from 550 million years ago. Xiao, whose team formally described Yilingia last year, traces the bumpy tracks it made immediately before its death. "It was just moving around, and it died suddenly," he says.

But that's not the end of this creature's story. Although nobody knows which category of life it belonged to - the group that includes earthworms is one possibility - Yilingia is helping to fill in key details about the evolution of animals. Most importantly, Yilingia shows that some quintessential animal traits had appeared half a billion years ago, earlier than previous definitive evidence, Xiao says.

Yilingia is not the only creature from that region to provide some of the earliest fossil evidence for an important animal feature. In 2018, Xiao and his team reported on tracks found in the Yangtze Gorges consisting of two parallel rows of dimples. The researchers propose that the trails were made by an animal from 550 million years ago that might have been able to burrow and had multiple pairs of appendages - which would make it one of the earliest-known animals with legs.

These Chinese fossils hail from a time right before the Cambrian explosion, the evolutionary transformation when most of the animal groups that populate the planet today first made their appearance in the fossil record. Scientists long regarded the boundary between the Cambrian period and the Precambrian as a dividing point in evolution - a transition from a world in which simple, strange organisms flourished, to a time when the seas teemed with complex creatures that are the forebears of nearly everything that followed.

But a growing number of findings reveal that the time slice just before the Cambrian, known as the Ediacaran (635 million to 541 million years ago), was a pivot point of animal evolution - a period that includes the earliest fossil records of anatomical innovations, such as guts and legs, and the first appearance of complex behaviours such as burrowing. The insights into the Ediacarans' powers lend support to a provocative idea: that the Cambrian explosion, that iconic evolutionary burst, was actually less revolutionary than many had thought.

The Cambrian explosion "is just another phase of evolution", says palaeobiologist Rachel Wood at the University of Edinburgh, UK. "It's not a single flash event. It could not have happened without previous waves of innovation."

Tumultuous times

The Ediacarans' innovations came against a backdrop of planetary cataclysms. During this time, Earth was still recovering from a long, shivery chapter when ice covered much of the seas. A gigantic meteor slammed into what is now Australia and probably kicked up enough dust to trigger catastrophic changes around the globe. The planet's very surface was splitting: during the Ediacaran, one supercontinent broke apart and another took shape as land masses smashed together. On the continents, no plants grew. In the ocean, oxygen levels swung wildly.

Scientists once thought that complex life did not start until after all this tumult. In Charles Darwin's day, no fossils had been found below the rock layers documenting the Cambrian explosion. That blank rock record troubled Darwin, who reasoned that if his theory of evolution were correct, there must have been life before the Cambrian's riches. "The case at present must remain inexplicable," he wrote in On the Origin of Species in 1859.

'Darwin's dilemma' would remain unsolved for a century. In the 1930s and 1940s, researchers found intriguing imprints in rocks in Australia and elsewhere, but those rocks were not definitively Precambrian. Then, several English schoolchildren finally gave the Ediacarans their big break in 1957. Scrambling through a local quarry, the students noticed a leaf-shaped imprint in the ancient stone. Geologist Trevor Ford at the University of Leicester, UK, went to see it - and recognized that it had been made by a living thing. Ford's paper about the imprint provided definitive evidence that large, complex species lived in the Precambrian. He ventured that the type of organism was probably "an algal frond".

It almost certainly wasn't. Ford's proposal was among the first in a long list of mistaken ideas about the identity of Ediacaran organisms. As more were discovered, scientists tried valiantly to place them on the tree of life. Some of the fossils were towering structures that stood one metre tall; others resembled deflated air mattresses. They have been called lichens and algae, fungi and bacterial colonies. "Basically any interpretation you can name has been suggested," says geobiologist Lidya Tarhan at Yale University in New Haven, Connecticut.

Finally, an audacious theory broke through the welter of competing claims. In the 1980s and 1990s, palaeontologist Adolf Seilacher at the University of Tübingen in Germany proposed, that many Ediacaran life forms were not animals, but instead belonged to a single, bizarre group that he called the Vendobionta. These organisms were "an evolutionary experiment that failed" when formidable predators arrived on the scene, Seilacher wrote. His ideas have fallen out of favour, but they challenged researchers to question their assumptions. "At the time it was brilliant thinking," says geobiologist Simon Darroch at Vanderbilt University in Nashville, Tennessee. "Before that, everyone assumed they were all jellyfish, which was even more wrong."

Now, most scientists are reaching agreement that the Ediacarans were a grab bag of disparate life forms, rather than the self-contained group proposed by Seilacher. "It's inappropriate to consider them a failed experiment," says palaeontologist Frances Dunn at the University of Oxford, UK. "They represent the ancestors, probably, of lots of different things." Many scientists - although not all - are also signing up to the idea that some fraction of the Ediacaran organisms were probably animals, including some that don't look like any animal alive today.

That idea dovetails with genetic evidence that animals, or metazoans, first appeared more than 600 million years ago, well before the Ediacaran. There are no definitive fossils to illustrate the dawn of the animals, but the early metazoans were probably small, soft, simple things, including ancestors of modern creatures such as sponges and corals. Eventually, animals developed left-right symmetry, which is packaged with a gut, mouth and anus.

But it's not easy to define which fossils are animals and which are not. "Would we know the first metazoan if we tripped over it?" Wood wonders. "Is our search image correct?" Those questions still dog scientists.

Insight from imprints

Although the Ediacaran fossils have bedevilled researchers for decades, new techniques are coaxing fresh insights out of previously intractable imprints. Take the baffling organisms in the genus Dickinsonia. Rounded and flat, they resembled segmented bath mats only a few millimetres thick, although they could reach nearly 1.5 metres in length. Their strange construction spawned theories that they were protists - a diverse group of mostly single-celled organisms that includes protozoa and some algae - or lichens, although many researchers suspected that they were animals.

To try to settle the long-standing dispute, geobiologist Ilya Bobrovskiy, now at the California Institute of Technology in Pasadena, and his colleagues took a biochemical approach. Bobrovskiy used tweezers to harvest thin films of organic matter - the remnants of Dickinsonia specimens that lived more than 550 million years ago. Analysis of the fat molecules in these biofilms showed that they were breakdown products of cholesterol, which is found in animals' cell membranes. " Dickinsonia was indeed an animal," Bobrovskiy says.

Dickinsonia was a rather simple animal: it showed no evidence of a mouth or a gut. But earlier this year, scientists detailed what might be the oldest-known animal that had both. Called Ikaria wariootia, it lived at roughly the same time as the Dickinsonia specimens that Bobrovskiy's team studied, or perhaps earlier.

This discovery resolves a long-standing Ediacaran whodunnit: what made the narrow, twisting burrows that cut through Ediacaran sediments? They are among the most common Ediacaran calling cards, but are so small - only 1.5-2 millimetres wide - that they must have been created by an elusively tiny organism. "We never thought we'd see it," says palaeontologist Mary Droser at the University of California, Riverside. Then she got her hands on a 3D laser scanner.

Droser and her colleagues used the scanner to image hundreds of tiny blobs found near the twisting burrows. The team's high-resolution 3D reconstructions show that the blobs were, in fact, organisms. They were smaller than grains of rice, but they had left-right symmetry and both a front and back end, and features of the burrows suggest that the creatures could control where they moved. Previous analysis showed that some burrows wend into and out of the buried bodies of larger organisms, implying that Ikaria was a scavenger - the earliest known. Droser's team suggests that, to support Ikaria 's burrowing and scavenging habits, the tiny animal probably had a mouth, anus and gut.

More evidence that Ediacarans had guts comes from tubular organisms called cloudinids that arose around 550 million years ago. Using high-resolution X-ray imaging to peer inside cloudinids' outer tubes, researchers saw a long, cylindrical feature, which the authors say is the oldest gut in the fossil record. The team found this feature in a cloudinid that most probably belonged to the genus Saarina, and it bolsters the case that some cloudinids were animals with left-right symmetry, says palaeobiologist and study co-author Jim Schiffbauer at the University of Missouri, Columbia. The gut's shape and other clues hint that Saarina could be an early annelid, an animal grouping that includes modern earthworms.

Alien animals

New approaches are producing evidence that even the most alien-looking Ediacarans might have been animals. Take the 'frondose' Ediacarans, which were built from collections of miniature branches reminiscent of a fern's lacy foliage. Some frondose organisms resembled heads of lettuce, whereas the organism Charnia masoni looked like a palm branch stuck into the sea floor. Charnia and its close relatives had a 'pseudo-fractal' organization like that of no living creature: the fronds were made up of branches, which were made up of sub-branches, which were made up of still-smaller branches.

Dunn and her colleagues borrowed tools from developmental biology to understand these oddities. The researchers noted that Charnia's fronds invariably have the same outline: widest at the bottom, smallest at the tip, with no short branches in the middle. This uniformity, a product of how the organism grows, is not seen in plants or algae. Despite the other-worldly appearance of Charnia and its kin, "they're more closely related to animals than they are to anything else", Dunn says.

Researchers studying the Ediacaran have revealed other frondose quirks by turning to the tools of modern ecology. One such technique is spatial analysis, which involves ultra-precise mapping of a large set of organisms that are preserved precisely where they lived - information that is rarely available in palaeontology. But scientists have exactly such an array at their disposal in Newfoundland, Canada, which has thousands of frondose imprints. Among them are examples that date back 571 million years, making them the oldest-known organisms that are big enough to be seen without magnification.

Some of Newfoundland's most abundant residents from around this time belong to the genus Fractofusus, whose members looked like mounds of fronds in the shape of an overturned saucer. Like its cousin Charnia, Fractofusus might have been an animal with no modern analogue. Spatial analysis showed that many large Fractofusus specimens are surrounded by clusters of small ones. "Children," says palaeobiologist Charlotte Kenchington at the University of Cambridge, UK, who was a member of the team that published the findings in 2015. This pattern suggests that Fractofusus multiplied in part by shooting out long runners on which its young developed.

In a paper published earlier this year, scientists describe long, thin, fossilized threads, some stretching 4 metres, between frondose organisms in Newfoundland. These threads might have been reproductive runners, and could also have been used for nutrient transport or communication. Perhaps these organisms were "acting in each other's best interests rather than just for themselves", says palaeobiologist Alex Liu at the University of Cambridge, who co-wrote the paper.

Before the Big Bang

As evidence mounts for Ediacaran innovation, a group of researchers is using these finds to question an icon of evolutionary history: the Cambrian explosion. In the past, researchers often spoke of this event as the Big Bang of evolution - a single, supreme episode that had no prelude and suddenly changed everything. But some researchers take the view that Ediacaran organisms were the founders of this revolution. The burst of new species in the Cambrian "didn't just come out of thin air", says Wood. "It must have been derived from something in the Ediacaran."

A common view holds that many Ediacaran organisms vanished at the Ediacaran-Cambrian boundary some 540 million years ago. But while excavating in a remote spot in Siberia, Wood and her team found Cambrian-type fossils, such as animals that lived in mineral-laden, tube-shaped shells, in Ediacaran-age rock.

Wood and her co-authors cited these fossils in a provocative 2019 paper, which also noted that Ediacaran animals capable of burrowing into sediments survived into the Cambrian period. The ability to burrow is a hallmark of that time, when animals dug so enthusiastically that they tore up the sea floor, creating new ecological niches. But the Ediacarans took the first step, the authors say. The vaunted Cambrian explosion, "was simply one phase" in the rise of animal diversity, they contend.

All of these findings tell a new story of animal evolution - but it is not yet clear whether the revision will stick. Some palaeontologists say that Wood's argument, in trying to give the Ediacaran its due, gives short shrift to the Cambrian explosion - which marked the appearance of a vast number of creatures that fit clearly into modern animal groups. Xiao agrees that some Ediacaran animals survived into the Cambrian, but he argues that the big picture shows a mass die-off at the boundary between the two periods. And invertebrate palaeontologist Jean-Bernard Caron at the Royal Ontario Museum in Toronto, Canada, questions Wood's tally of Ediacaran species that survived into the Cambrian. "We don't really have the fossil record to support that," he says. Wood responds that although the critique is fair, it's clear that multiple Cambrian-style creatures first appeared in the Ediacaran.

For all the contention, however, some researchers think that answers are just around the corner. Continued work on biomarkers could pin down whether various Ediacaran organisms were, in fact, animals. And palaeontologists are excavating new Ediacaran finds in places such as Iran and Russia, Darroch says. The latest approaches, such as spatial analysis, hold promise too, says Xiao. These could flesh out - at long last - what was going on in the oceans during the pivotal Ediacaran period.

"I would just love to be swimming over these communities and see, finally, how are they really growing? What on Earth are they?" Wood says. "So much would become obvious."

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These bizarre species are rewriting animal evolution

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Early fossils with guts, segmented bodies and other sophisticated features reveal a revolution in animal life - before the Cambrian explosion. Early fossils with guts, segmented bodies and other sophisticated features reveal a revolution in animal life - before the Cambrian explosion.

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Study investigates evolution during Cambrian Explosion

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Study investigates evolution during Cambrian Explosion

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The hypothetical ancestral echinoderm is at the center of the graph with evolutionary pathways radiating outward during and following the Cambrian Explosion to establish the major echinoderm body plans from sea urchins to sea lilies. Credit: Deline, et. al.

A new study by an international team of scientists has revealed the developmental and evolutionary mechanisms underlying the origin of a major phylum.

The Cambrian Explosion was a pivotal event in the history of life half a billion years ago with the sudden appearance of dozens of distinctive animal body plans. After this initial burst of innovation, the appearance of new body plans slowed to a halt. This pattern has puzzled and intrigued scientists and led to hypotheses regarding the ecological and developmental influences on animal evolution.

The study investigates the questions of whether this pattern resulted from abundant ecological opportunity early in the history of life, which became dampened with competition through time, or from evolutionary shifts in growth and development that limit evolutionary innovation through time.

Bradley Deline-lead author in the study, from the University of West Georgia (USA)-assembled a team of experts to address this question by compiling the vast anatomical features found within echinoderms.

This phylum that includes sea stars and sea urchins, was ideal for this study because it contains an incredible richness of forms and features, especially early in its evolutionary history.

"With this information, we can trace the evolution of complex forms and address fundamental questions regarding the mechanisms that govern the overall appearance of animals through time," Deline said.

Scientists have argued that features defining animal body plans have become increasingly elaborate through time such that they become burdened by their own complexity. This burden could prevent change and would explain the lack of new phyla since the Cambrian Explosion.

Recent studies in modern animals show genetic interactions that mirror this hypothesis in which the genes and gene interactions that govern complex features are conserved through time. However, modern animals are 500 million years removed from the origin of their phylum, such that these questions can only be answered with the fossil record.

Colin Sumrall from the University of Tennessee (USA), worked to integrate this wealth of information with a new and expansive evolutionary tree of early echinoderms. This showed the steady exploration of body plans through time that ultimately became distinctive with the extinction of transitional forms.

However, body plans' distinctiveness was subsequently diminished with animals independently converging on similar forms.

"This highlights the amazing complexity within echinoderms with so many groups arriving on similar solutions to become successful," Sumrall explained. "There are many examples of echinoderms continuing to change dramatically long after the Cambrian Explosion."

Co-author Jeffrey Thompson, from University College London (UK), suggested testing developmental mechanisms by comparing the evolutionary stability of both complex and simple features within echinoderms.

"We see no difference in the stability or evolutionary patterns in simple and complex features," Thompson exclaimed. "Large-scale characters are flexible allowing echinoderms to routinely break through constraints allowing for continued evolutionary innovation."

Therefore, based on the results of this study, the major factor limiting this vast potential for evolutionary change seems to be ecological opportunity rather than rigidly constrained developmental processes.

This study, along with work on modern animals, clarifies evolution and development during the Cambrian Explosion and beyond in which complex and burdened features retain flexibility enabling continued change and anatomical innovation in an ever-changing world.

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Study investigates evolution during Cambrian Explosion

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A new study by an international team of scientists has revealed the developmental and evolutionary mechanisms underlying the origin of a major phylum. The Cambrian Explosion was a pivotal event in the history of life half a billion years ago with the sudden appearance of dozens of distinctive animal body plans.

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Scientists have discovered the origins of the building blocks of life

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Scientists have discovered the origins of the building blocks of life

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A fold (shape) that may have been one of the earliest proteins in the evolution of metabolism. Credit: Vikas Nanda/Rutgers University

Rutgers researchers have discovered the origins of the protein structures responsible for metabolism: simple molecules that powered early life on Earth and serve as chemical signals that NASA could use to search for life on other planets.

Their study, which predicts what the earliest proteins looked like 3.5 billion to 2.5 billion years ago, is published in the journal Proceedings of the National Academy of Sciences.

The scientists retraced, like a many thousand piece puzzle, the evolution of enzymes (proteins) from the present to the deep past. The solution to the puzzle required two missing pieces, and life on Earth could not exist without them. By constructing a network connected by their roles in metabolism, this team discovered the missing pieces.

"We know very little about how life started on our planet. This work allowed us to glimpse deep in time and propose the earliest metabolic proteins," said co-author Vikas Nanda, a professor of Biochemistry and Molecular Biology at Rutgers Robert Wood Johnson Medical School and a resident faculty member at the Center for Advanced Biotechnology and Medicine. "Our predictions will be tested in the laboratory to better understand the origins of life on Earth and to inform how life may originate elsewhere. We are building models of proteins in the lab and testing whether they can trigger reactions critical for early metabolism."

A Rutgers-led team of scientists called ENIGMA (Evolution of Nanomachines in Geospheres and Microbial Ancestors) is conducting the research with a NASA grant and via membership in the NASA Astrobiology Program. The ENIGMA project seeks to reveal the role of the simplest proteins that catalyzed the earliest stages of life.

"We think life was built from very small building blocks and emerged like a Lego set to make cells and more complex organisms like us," said senior author Paul G. Falkowski, ENIGMA principal investigator and a distinguished professor at Rutgers University-New Brunswick who leads the Environmental Biophysics and Molecular Ecology Laboratory. "We think we have found the building blocks of life-the Lego set that led, ultimately, to the evolution of cells, animals and plants."

The Rutgers team focused on two protein "folds" that are likely the first structures in early metabolism. They are a ferredoxin fold that binds iron-sulfur compounds, and a "Rossmann" fold, which binds nucleotides (the building blocks of DNA and RNA). These are two pieces of the puzzle that must fit in the evolution of life.

Proteins are chains of amino acids and a chain's 3-D path in space is called a fold. Ferredoxins are metals found in modern proteins and shuttle electrons around cells to promote metabolism. Electrons flow through solids, liquids and gases and power living systems, and the same electrical force must be present in any other planetary system with a chance to support life.

There is evidence the two folds may have shared a common ancestor and, if true, the ancestor may have been the first metabolic enzyme of life.

More information: Hagai Raanan el al., "Small protein folds at the root of an ancient metabolic network," PNAS (2020). www.pnas.org/cgi/doi/10.1073/pnas.1914982117

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Scientists have discovered the origins of the building blocks of life

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Rutgers researchers have discovered the origins of the protein structures responsible for metabolism: simple molecules that powered early life on Earth and serve as chemical signals that NASA could use to search for life on other planets.

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Cryptic transmission of novel coronavirus revealed by genomic epidemiology

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Cryptic transmission of novel coronavirus revealed by genomic epidemiology

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The field of genomic epidemiology focuses on using the genetic sequences of pathogens to understand patterns of transmission and spread. Viruses mutate very quickly and accumulate changes during the process of transmission from one infected individual to another. The novel coronavirus which is responsible for the emerging COVID-19 pandemic mutates at an average of about two mutations per month. After someone is exposed they will generally incubate the virus for ~5 days before symptoms develop and transmission occurs. Other research has shown that the "serial interval" of SARS-CoV-2 is ~7 days. You can think of a transmission chain as looking something like:

where, on average, we have 7 days from one infection to the next. As the virus transmits, it will mutate at this rate of two mutations per month. This means, that on average every other step in the transmission chain will have a mutation and so would look something like:

These mutations are generally really simple things. An 'A' might change to a 'T', or a 'G' to a 'C'. This changes the genetic code of the virus, but it's hard for a single letter change to do much to make the virus behave differently. However, with advances in technology, it's become readily feasible to sequence the genome of the novel coronavirus. This works by taking a swab from someone's nose and extracting the RNA in the sample and then determining the 'letters' of this RNA genome using chemistry and very powerful cameras. Each person's coronavirus infection will yield a sequence of 30,000 'A', 'T', 'G' or 'C' letters. We can use these sequences to reconstruct which infection is connected to which infection. As an example, if we sequenced three of these infections and found:

We could take the "genomes" ATTT, ATCT and GTCT and infer that the infection with sequence ATTT lead to the infection with sequence ATCT and this infection lead to the infection with sequence GTCT. This approach allows us learn about epidemiology and transmission in a completely novel way and can supplement more traditional contact tracing and case-based reporting.

For a few years now, we've been working on the Nextstrain software platform, which aims to make genomic epidemiology as rapid and as useful as possible. We had previously applied this to outbreaks like Ebola, Zika and seasonal flu. Owing to advances in technology and open data sharing, the genomes of 140 SARS-CoV-2 coronaviruses have been shared from all over the world via gisaid.org. As these genomes are shared, we download them from GISAID and incorporate them into a global map as quickly as possible and have an always up-to-date view of the genomic epidemiology of novel coronavirus at nextstrain.org/ncov.

The big picture looks like this at the moment:

where we can see the earliest infections in Wuhan, China in purple on the left side of the tree. All these genomes from Wuhan have a common ancestor in late Nov or early Dec, suggesting that this virus has emerged recently in the human population.

The first case in the USA was called "USA/WA1/2020". This was from a traveller directly returning from Wuhan to Snohomish County on Jan 15, with a swab collected on Jan 19. This virus was rapidly sequenced by the US CDC Division of Viral Diseases and shared publicly on Jan 24 (huge props to the CDC for this). We can zoom into the tree to place WA1 among related viruses:

The virus has an identical genome to the virus Fujian/8/2020 sampled in Fujian on Jan 21, also labeled as a travel export from Wuhan, suggesting a close relationship between these two cases.

Last week the Seattle Flu Study started screening samples for COVID-19 as described here. Soon after starting screening we found a first positive in a sample from Snohomish County. The case was remarkable in that it was a "community case", only the second recognized in the US, someone who had sought treatment for flu-like symptoms, been tested for flu and then sent home owing to mild disease. After this was diagnostically confirmed by Shoreline Public Health labs on Fri Feb 28 we were able to immediately get the sample USA/WA2/2020 on a sequencer and have a genome available on Sat Feb 29. The results were remarkable. The WA2 case was identical to WA1 except that it had three additional mutations.

This tree structure is consistent with WA2 being a direct descendent of WA1. If this virus arrived in Snohomish County in mid-January with the WA1 traveler from Wuhan and circulated locally for 5 weeks, we'd expect exactly this pattern, where the WA2 genome is a copy of the WA1 genome except it has some mutations that have arisen over the 5 weeks that separate them.

Again, this tree structure is consistent with a transmission chain leading from WA1 to WA2, but we wanted to assess the probability of this pattern arising by chance instead of direct transmission. Scientists often try to approach this situation by thinking of a "null model", ie if it was coincidence, how likely of a coincidence was it? Here, WA1 and WA2 share the same genetic variant at site 18060 in the virus genome, but only 2/59 sequenced viruses from China possess this variant. Given this low frequency, we'd expect probability of WA2 randomly having the same genetic variant at 2/59 = 3%. To me, this not quite conclusive evidence, but still strong evidence that WA2 is a direct descendent of WA1.

Additional evidence for the relationship between these cases comes from location. The Seattle Flu Study had screened viruses from all over the greater Seattle area, however, we got the positive hit in Snohomish County with cases less than 15 miles apart. This by itself would only be suggestive, but combined with the genetic data, is firmer evidence for continued transmission.

I've been referring to this scenario as "cryptic transmission". This is a technical term meaning "undetected transmission". Our best guess of a scenario looks something like:

We believe this may have occurred by the WA1 case having exposed someone else to the virus in the period between Jan 15 and Jan 19 before they were isolated. If this second case was mild or asymptomatic, contact tracing efforts by public health would have had difficulty detecting it. After this point, community spread occurred and was undetected due to the CDC narrow case definition that required direct travel to China or direct contact with a known case to even be considered for testing. This lack of testing was a critical error and allowed an outbreak in Snohomish County and surroundings to grow to a sizable problem before it was even detected.

Knowing that transmission was initiated on Jan 15 allows us to estimate the total number of infections that exist in this cluster today. Our preliminary analysis puts this at 570 with an 90% uncertainty interval of between 80 and 1500 infections.

Back on Feb 8, I tweeted this thought experiment:

We know that Wuhan went from an index case in ~Nov-Dec 2019 to several thousand cases by mid-Jan 2020, thus going from initial seeding event to widespread local transmission in the span of ~9-10 weeks. We now believe that the Seattle area seeding event was ~Jan 15 and we're now ~7 weeks later. I expect Seattle now to look like Wuhan around ~1 Jan, when they were reporting the first clusters of patients with unexplained viral pneumonia. We are currently estimating ~600 infections in Seattle, this matches my phylodynamic estimate of the number of infections in Wuhan on Jan 1. Three weeks later, Wuhan had thousands of infections and was put on large-scale lock-down. However, these large-scale non-pharmaceutical interventions to create social distancing had a huge impact on the resulting epidemic. China averted many millions of infections through these intervention measures and cases there have declined substantially.

This suggests that this is controllable. We're at a critical junction right now, but we can still mitigate this substantially.

Some ways to implement non-pharmaceutical interventions include:

Practicing social distancing, such as limiting attendance at events with large groups of people

Working from home, if your job and employer allows it

Staying home if you are feeling ill

Take your temperature daily, if you develop a fever, self-isolate and call your doctor

Implementing good hand washing practices - it is extremely important to wash hands regularly

Covering coughs and sneezes in your elbow or tissue

Avoiding touching your eyes, nose, and mouth with unwashed hands

Disinfecting frequently touched surfaces, such as doorknobs

Beginning some preparations in anticipation of social distancing or supply chain shortages, such as ensuring you have sufficient supplies of prescription medicines and ensuring you have about a 2 week supply of food and other necessary household goods.

With these preparation in mind, it is important to not panic buy. Panic buying unnecessarily increases strain on supply chains and can make it difficult to ensure that everyone is able to get supplies that they need.

For more information please see:

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Cryptic transmission of novel coronavirus revealed by genomic epidemiology

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The field of genomic epidemiology focuses on using the genetic sequences of pathogens to understand patterns of transmission and spread. Viruses mutate very quickly and accumulate changes during the process of transmission from one infected individual to another. The novel coronavirus which is responsible for the emerging COVID-19 pandemic mutates at an average of about two mutations per month.

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Researchers discover new mechanism for the coexistence of species

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Researchers discover new mechanism for the coexistence of species

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Cartoon of experiment showing coexistence between bacteria (red and blue) that cyclically colonize nutrient patches (green). Credit: AMOLF

Researchers from the AMOLF institute in Amsterdam and Harvard have shown that the ability of organisms to move around plays a role in stabilizing ecosystems. In their paper published 19 February 2020 in Nature, they describe how the competition between 'movers' and 'growers' leads to a balance in which both types of bacteria can continue to exist alongside each other.

We are all too familiar with the threats to our planet's ecosystems: global warming, forest fires, nitrogen deposition, biodiversity decline, and even mass extinctions. But what actually makes ecosystems stable or fragile? What prevents one species from outcompeting all others, and hence driving them to extinction?

These questions have captivated biologists since Darwin. We have learned that food webs and cooperation between species are key pieces to this puzzle, because they help explain how species depend on one another to survive. Now, a group of biophysicists from the Netherlands and the U.S. have advanced a startling finding: The active movement of organisms can also drive ecosystem diversity and stability through a remarkably simple mechanism that does not require food webs or cooperation.

"Movement is fundamental to essentially all organisms-even plants move by seed dispersal," says Sander Tans at the AMOLF institute in Amsterdam. "Bacteria are well known to move actively. Our experiments show how this movement can keep different bacterial species, typically called strains, together in a larger population. There is a rich literature on the possible roles of movement in such coexistence of species, but direct experiments that can exclude other explanations were lacking.

Bacterial strains A and B were show to both outcompete the other when rare, and hence coexist. Credit: AMOLF

The coexistence paradox-what prevents extinctions in a competitive world?
To find bacterial species that might form a minimal stable ecosystem in the lab, the Ph.D. student Sebastian Gude took two species (also called strains) from the gut of the same animal. If both survived there, perhaps they would also do so in his experiments. To follow their competition, he colored one blue and the other red. However, all his first attempts failed in the beginning. One of the two strains always lost the competition when grown together, with these bacteria always producing fewer offspring than the other. This blue 'loser' strain would thus become outnumbered by the red 'winner' strain, and was ultimately driven to extinction.

Gude's luck took a dramatic upturn, however, when he changed the design of the experiment. He took the sugary liquid in which the bacteria normally grew, and turned it into a gel reminiscent of a jelly desert. When the blue 'loser' bacteria growing on the gel became outnumbered by the reds, they started to produce more offspring than the reds, and were thus winning. But in turn, the reds also became more competitive when rare. In this way, both strains escaped extinction, and hence coexisted together. These results underscore the fundamental paradox of the coexistence debate: What causes losers that are close to extinction to suddenly start winning?

Fluorescence microscopy of bacterial populations across the gel after the competition. Credit: AMOLF

Getting territorial
To resolve this conundrum, Gude followed the competition by making movies. "The results were quite striking," says Tom Shimizu. "We saw the populations migrating into the gel like a wave, where they multiplied using the sugars they encountered. Initially, red dominated the expansion and blue was barely seen. But then the red advance suddenly stopped just when the blues emerged, and were seen to overtake the reds' front, where they formed a thin layer. After that, the wave was blue only. The blue bacteria could thus proliferate alone in the deeper regions of the gel, freed from competition from the reds that could not reach that far. This also explained the coexistence: Whenever blue were rare, they could build up their population in the deeper regions of the gel."

Accelerated movie of competing bacterial strains. Credit: AMOLF

Should I spread or should I grow?
But how did the blue bacteria organize themselves and efficiently confine the red? Did they signal to each other or secrete toxins, as is known for some bacteria? In trying to address these questions the team discovered a rather different mechanism. The blue bacteria were indeed worse at proliferating, as they lost in a direct competition. But they compensated by migrating faster. By reaching the farther regions first, they could finish the local sugars. Hence, they gave the red no chance there, and could thus block their advance, a bit like in a scorched earth strategy.

Tans: "Some bacteria apparently are good at proliferating, and others at migrating. But they cannot excel at both. This makes sense because both activities cost a lot of energy. Such specialization is often observed, though effects on coexistence are often difficult to prove. Here we could manipulate the capacity to migrate and proliferate by genetic engineering, and show it alone is enough for coexistence. Other mechanisms like exchanging toxins or dependencies like in food webs are thus not required per se."

Slowed-down movie of motile E. coli cells. Credit: AMOLF

Disturbance ecology
Of course, in the real world, bacteria cannot count on encountering bowls of Jello left out of the fridge. Luckily for them, they don't need to, as pristine pastures of fresh nutrients do arise more often than expected. Much like the vegetation that colonize cleared soil after forest fires, many bacteria grow on patches of resources, from fallen fruits to decomposing animals, or-for those microbes that inhabit your gut-the lunch you just had.

Shimizu says, "We demonstrated this migration-proliferation mechanism in motile bacteria. But what we found is for instance evocative of models of plant ecology where fast-growing plants compete with plants that invest more in spreading their seeds." He added that there is a lot to be learned about more complex scenarios. "There is a lot of interest in explaining the diversity of bacteria in the human gut, which we now know, thanks to modern DNA analysis, is intimately related to our health. Our findings suggest that looking at motility genes and their spatial distribution within the gut might help explain some of that diversity."

More information: Bacterial coexistence driven by motility and spatial competition, Sebastian Gude, Erçağ Pinçe, Katja M. Taute, Anne-Bart Seinen, Thomas S. Shimizu, and Sander J. Tans, Nature 2020, DOI: 10.1038/s41586-020-2033-2

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Researchers discover new mechanism for the coexistence of species

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Researchers from the AMOLF institute in Amsterdam and Harvard have shown that the ability of organisms to move around plays a role in stabilizing ecosystems. In their paper published 19 February 2020 in Nature, they describe how the competition between 'movers' and 'growers' leads to a balance in which both types of bacteria can continue to exist alongside each other.

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Des fossiles d'algues vertes vieux d'un milliard d'années - Sciences et Avenir

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Des fossiles d'algues vertes vieux d'un milliard d'années - Sciences et Avenir

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C'est dans la province de Liaoning, en Chine, plus exactement dans la formation Nanfen connue pour ses fossiles datés d'un milliard d'années, qu'ont été découvert ces traces d'algues vertes, imprimées sur plusieurs roches. "Vertes" parce que ce sont des organismes photosynthétiques capables de transformer l'énergie lumineuse en matière organique grâce à un pigment principal, la chlorophylle. La découverte de ces fossiles permet de préciser l'évolution de ces algues qui ont transformé la Terre puisqu'une de leur branche a colonisé la surface terrestre et donné naissance à toutes les plantes actuelles.

Datation imprécise

Les analyses génétiques, notamment l'étude des horloges moléculaires, indiquent que les algues vertes sont apparues il y a entre 1,6 milliard d'années et 720 millions d'années. Mais la datation précise de cet essor reste difficile à déterminer : il existe très peu de fossiles portant la trace de ces organismes. Et on ne sait pas non plus quand ils ont opté pour la multicellularité. La découverte des roches de Nanfen permet de préciser ces deux interrogations. " Elles représentent les plus vieilles traces d'algues vertes et elles indiquent que les plantes vertes sont apparues il y a au moins un milliard d'années. De plus, cette découverte confirme qu'elles ont commencé leur histoire dans l'océan avant d'étendre leur territoire aux terres" explique Qing Tang, géoscientifique à l'Institut de technologie de Virginie, aux Etats-Unis.
Un des fossiles découverts. Crédit : Nature ecology & evolution/Qing Tang
Il y a un milliard d'années, les océans étaient dominés par les cyanobactéries, des bactéries photosynthétiques autrefois appelées, à tort, algues bleues. " Même si elles étaient présentes, les algues vertes étaient encore peu nombreuses à l'époque. Et même si elles étaient plus grosses que les cyanobactéries, elles ne dépassaient pas l'échelle millimétrique ou centimétrique. Ce qui assez petit si l'on considère les plantes terrestres actuelles" précise le chercheur.

La transformation du monde

Les fossiles découverts on été analysés et sont présentés dans une étude publiée dans la revue Nature ecology & evolution. Ils représentent une nouvelle espèce nommée Proterocladus antiquus qui possède une gamme de caractéristiques compatibles avec les algues vertes actuelles, y compris la multicellularité, des cellules différenciées et ramifiées et des structures en forme de racine. Preuve que la multicellularité et les cellules spécialisées étaient déjà apparues à cette époque chez les algues vertes. " Ces fossiles déjà évolués indiquent qu'elles étaient déjà un des acteurs importants dans l'océan bien avant que leurs descendants, les plantes terrestres, ne prennent le contrôle de la Terre, il y a 450 millions d'années" souligne Qing Tang.

Fossile d'algues vertes centimétriques. Crédit : Nature ecology & evolution/Qing Tang

Avant d'envahir la Terre, les algues vertes ont pris le contrôle de l'océan en dominant les cyanobactéries environ 300 millions d'années après leur apparition. Elles sont alors devenues la principale ressource alimentaire de l'écosystème marin. Et depuis, elles n'ont cessé d'évoluer ; la plus grande transition qu'elles aient connue est le passage à la vie terrestre qui a été le point de départ de tous les développements génétiques futurs. Une fois la Terre conquise, elles ont radicalement modifié son aspect et son climat et continué à se diversifier pour constituer aujourd'hui un groupe rassemblant plus de 500 000 espèces.

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Découverte de fossiles d'algues vertes vieux d'un milliard d'années

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C'est dans la province de Liaoning, en Chine, plus exactement dans la formation Nanfen connue pour ses fossiles datés d'un milliard d'années, qu'ont été découvert ces traces d'algues vertes, imprimées sur plusieurs roches. "Vertes" parce que ce sont des organismes photosynthétiques capables de transformer l'énergie lumineuse en matière organique grâce à un pigment principal, la chlorophylle.

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SARS-CoV-2 : les scientifiques savaient que ce n'était qu'une question de temps

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SARS-CoV-2 : les scientifiques savaient que ce n'était qu'une question de temps

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Dans un article scientifique publié en 2007, les scientifiques annonçaient déjà qu'une telle pandémie était très probable, surtout à cause de la consommation d'animaux exotiques en Chine.

Avant l' du Sars-CoV-1 en 2003, seulement 12 coronavirus étaient connus chez l'Homme ou chez d'autres animaux. La découverte de ce a amplifié l'étude des coronavirus chez les animaux et cette surveillance a agrandi notre connaissance : on sait désormais qu'il existe au moins, chez des animaux particulièrement, 36 coronavirus différents. Pourtant, cela n'a pas empêché la de Sars-CoV-2 que nous connaissons actuellement. Pourquoi ?

La consommation d'animaux exotiques : une bombe à retardement

C'est après avoir fait un inventaire conséquent des caractéristiques du Sars-CoV-1 en 2007 concernant les aspects épidémiologiques, cliniques, pathologiques , immunologiques, virologiques et autres aspects scientifiques de base du virus et de la maladie que les scientifiques osent ce propos dans un article publié dans la revue Clinical Microbiology Reviews .

Dans un paragraphe intitulé " Devons-nous êtres prêt pour la ré-émergence du SARS ? ", ils énoncent " la présence d'un grand réservoir de virus de type chez les chauves-souris "en à cheval", ainsi que la culture de manger des mammifères exotiques dans le sud de la Chine, [qui] est une bombe à retardement. Il ne faut pas ignorer la possibilité de réapparition du et d'autres nouveaux virus provenant d'animaux ou de laboratoires et, par conséquent, le besoin de préparation. " Pour ce qui est du , coupons court aux théories du complot : un article paru dans la revue Nature démontre que le virus est d'origine naturelle .

Bien sûr, il n'est pas question ici de juger ni de porter atteinte à la culture ou à la population chinoise. Simplement, on peut regretter que des mesures plus conséquentes n'aient pas été prises pour limiter considérablement le passage d'un telle famille de virus de l'animal à l'Homme. En effet, quand on se souvient du contexte potentiel de la première contamination (un marché aux avec des règles d'hygiènes laissant à désirer), on en conclut rapidement que cette pandémie aurait pu être évitée. Prudence cependant, cette hypothèse semble maintenant remise en question par des scientifiques chinois : le patient zéro n'aurait eu aucun lien avec le marché de Whuan. Affaire à suivre.

La mondialisation : l'aubaine des pandémies

La faute ne peut pas être jetée uniquement sur la Chine. L'une des grandes différences entre l' de Sars-CoV qui n'avait pas quitté la Chine en 2003 et la pandémie que nous connaissons aujourd'hui est que le traffic aérien ne cesse de s'accroître. entre 2003 et aujourd'hui. Forcément, cela crée les conditions propices à la propagation d'un virus aussi contagieux . Surtout que dans nos démocraties libérales, les mesures drastiques mettent souvent du temps à être effectives comme nous avons pu le constater.

Si, en temps normal, c'est une bonne chose pour nos libertés individuelles, en temps de pandémie, on constate la faiblesse de nos systèmes politiques et l'irresponsabilité de la population. De même, on espère qu'à l'avenir, on écoutera enfin, sur tous les sujets importants, comme , par exemple, la voix des scientifiques.

Des scientifiques avaient déjà pointé comme très probable la ré-émergence d'un coronavirus, surtout à cause de la consommation d'animaux exotiques qu'ils qualifiaient de " bombe à retardement ".

À la suite de l'inventaire effectué sur le Sars-CoV-1, il apparaît que cette pandémie aurait pu être évitée si les avis des scientifiques avaient été entendus.

À l'avenir, il faut espérer encore et toujours que les scientifiques seront écoutés...

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SARS-CoV-2 : les scientifiques savaient que ce n'était qu'une question de temps

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Dans un article scientifique publié en 2007, les scientifiques annonçaient déjà qu'une telle pandémie était très probable, surtout à cause de la consommation d'animaux exotiques en Chine. Avant l' du Sars-CoV-1 en 2003, seulement 12 coronavirus étaient connus chez l'Homme ou chez d'autres animaux.

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Plus de religion égale moins de sciences – {Sciences²}

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Plus de religion égale moins de sciences – {Sciences²}

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Peut-on concilier la croyance religieuse et une attitude scientifique ? Les partisans de cette thèse mettent en avant quelques noms de grands scientifiques ayant affirmé que leurs recherches ne les empêchaient pas de croire en Dieu. Mais les sociologues - des scientifiques eux aussi - n'acceptent pas de se contenter de quelques exemples. Ils veulent vérifier si cette thèse tient toujours debout lorsqu'on la confronte à des données issues d'une pratique sociologique classique : l'enquête sur les opinions et attitudes des populations.

Spoil direct : non, la thèse ne tient pas debout, elle s'écroule. Du moins pour les populations des Etats-Unis d'Amérique et d'Europe, montre une étude publiée récemment (1). Le résumé de l'étude l'affirme sans vraiment prendre de précautions oratoires : " quel que soit le pays considéré, plus les individus s'identifient à une religion et la pratiquent fortement, moins ils ont de compétence scientifique. D'autre part, c'est l'ensemble des représentations des sciences qui est affecté par l'univers religieux des individus. Plus les individus adhèrent à une religion, moins ils ont des attitudes positives envers les sciences. Les Européens et les Américains les moins religieux sont ceux dont les représentations des sciences et de leurs répercussions sociales sont les plus positives. "
Effet cognitif de la croyance en Dieu
Yves Gingras et Kristoff Tallin, deux sociologues patentés du Centre interuniversitaire de recherche sur la science et la technologie (CIRST, Québec, Canada), le second étant chercheur au CNRS, ont utilisé des résultats d'enquêtes sur les croyances et pratiques religieuses (2) permettant de dépasser les " inévitables variations individuelles qui n'ont qu'une valeur anecdotique" afin d'accéder aux " tendances sociales lourdes". Chez les scientifiques eux-mêmes, la dite tendance est anciennement mesurée : la " croyance en un Dieu personnel" n'était en 1914 que de " 27% de l'élite scientifique américaine" (Leuba, 1916). Une part qui avait chuté à 15% en 1933 (Leuba, 1934). Un demi-siècle plus tard, une enquête similaire mesurait une accélération du déclin de cette croyance en milieu scientifique, limitant à " 7% la proportion de croyants en un Dieu personnel " (Larson et Witham, 1998)

L'effet cognitif de la pratique scientifique sur la croyance en Dieu semble donc massif, mais qu'en est-il de la population générale ? Comment, s'interrogent les deux sociologues, " les attitudes envers les sciences varient en fonction du type et du niveau de croyances religieuses " ?
+ de religion = - de sciences
Premier résultat, massif, des trois enquêtes, une corrélation d'airain : plus on connait de sciences et moins le niveau de croyances religieuses est élevé... et inversement. Un constat dont la régularité est impressionnante surtout lorsque l'on se penche sur l'intensité des pratiques religieuses. A l'exception des musulmans (mais c'est là un résultat jugé douteux par les deux sociologues en raison d'un trop faible effectif), on observe un gradient. Plus la fermeté de l'opinion des non religieux est élevée (l'athéisme revendiqué étant son degré le plus haut) et plus les compétences scientifiques sont affirmées.

A l'inverse, plus les pratiques religieuses sont intenses (fréquences des prières, etc) et moins les connaissances scientifiques sont partagées. La conclusion des deux auteurs s'exprime ainsi : " Les résultats présentent donc une logique très structurée par rapport à la compétence scientifique : plus les personnes sont intégrées à une religion, moins elles sont performantes sur le plan des connaissances scientifiques. Par ailleurs, les indicateurs du niveau de pratique religieuse, de la prière et de l'importance de la religion dans la vie quotidienne varient tous dans le même sens : plus l'individu est pratiquant, priant ou religieux, moins son score de compétence scientifique est élevé. "

L'étude américaine permet de cibler des groupes particuliers, comme celui des évangélistes (à 86% se déclarant protestants, et 12% catholiques). Ce groupe particulièrement pratiquant affiche les plus mauvais résultats en connaissances scientifiques.
l'athée plus compétent
Mais dans quel sens fonctionne la causalité ? Nos deux sociologues n'ont évidemment pas négligé les autres causes possibles des corrélations observées. Et ont donc creusé les variables d'âges, de genre et de niveau d'études.

Les résultats sont assez peu surprenants. Dans l'enquête américaine, les hommes affichent de meilleures connaissances que les femmes (3). En dessous de 55 ans, pas de différences notables... et au dessus de 55 ans il s'agit d'un effet de l'âge de fin de scolarité. Une relation linéaire apparaît entre niveau d'études et score moyen de compétences scientifiques. Mais... Mais si l'on croise avec les données sur les religions, l'effet de ces dernières réapparaît sans l'ombre d'un doute : quel que soit l'âge de fin d'études, les sans religions sont toujours plus compétents en science que les religieux à âge égal. Plus encore : un individu " agnostique ou athée" de niveau d'étude " secondaire ou moins" sera en moyenne plus compétent en science qu'un " protestant ou catholique" de niveau " baccalauréat ou plus " ! Un résultat qui ne peut s'expliquer que par un rapport plus positif aux sciences et à leurs utilisations par les sociétés, général chez les sans religions, agnostiques et athées, favorable à la mémorisation de savoirs. Un rapport plus positif qui se lit dans les questions portant non sur les connaissances mais sur l'appréciation de l'apport des sciences aux sociétés humaines.

Dans les enquêtes européennes, " seule l'appartenance au protestantisme n'affecte pas la compétence scientifique de manière notable ", notent les deux sociologues.

Exit, donc, le soit disant bénéfice d'un " dialogue sciences/religions " au service de la rationalité. Les convictions religieuses pèsent manifestement sur la capacité des populations à s'approprier les résultats d'une approche scientifique du monde. Elles pèsent donc négativement sur leurs capacités à discuter en démocratie des usages des technologies qui en sont issues. La vogue du " naturel " - au sens ancien d'un ordre divin puisque la Nature est création divine - opposé à l'artificiel, et cela sans aucune analyse des avantages et des risques des objets naturels et artificiels en débat, en témoigne abondamment. Ainsi, la péridurale proposée à la femme qui accouche devient une pratique artificielle, donc mauvaise par principe, opposée à la douleur " naturelle " de l'accouchement " naturel " qu'il faudrait donc accepter sans se rebeller. Exemple facile. En voici un moins aisé : tout organisme génétiquement modifié est nécessairement mauvais, sans analyse de ses avantages et inconvénient, parce qu'il n'est pas " naturel " (alors que les ravageurs des cultures ou les adventices, eux, sont naturels...).
Sylvestre Huet
(1) Note de recherche 2020-02, CIRST.

(2) Les deux enquêtes Eurobaromètres menées en 2005 et en 2010 auprès des pays membres de l'Union européenne dont les données incluent les variables concernant la religion d'appartenance, le niveau de pratique religieuse et la croyance en l'existence d'un Dieu. Cela permet de prendre en compte différentes dimensions du rapport aux religions. La représentation des sciences est abordée sous plusieurs angles différents (à partir des connaissances scientifiques, des explications scientifiques et des attitudes par rapport aux sciences). Et l'enquête menée par le Pew Research Center en 2018 aux États-Unis. Les données nous informent sur l'appartenance à une religion, l'intensité de la pratique religieuse, la fréquence de la prière et l'importance de la religion dans la vie quotidienne. Les connaissances scientifiques sont mesurées à partir d'une série de neuf variables permettant d'élaborer un score de connaissance scientifique.

(3) Les questionnaires ne permettaient pas de creuser avec précision l'effet " prudence féminine " qui conduit ces dernières à répondre plus souvent " je ne sais pas " lorsque c'est possible tandis que les hommes ont plus souvent tendance à répondre au pif plutôt que d'admettre leur ignorance ce qui gonfle équitablement les bonnes... et les mauvaises réponses aux questions de connaissances scientifiques. Un résultat connu par ailleurs. Cette " prudence féminine " peut d'ailleurs s'interpréter de manière positive : savoir qu'on ne sait pas est une attitude profondément scientifique puisqu'elle conduit à la recherche (lire Sciences, les Français sont-ils nuls ?).

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Plus de religion égale moins de sciences

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Peut-on concilier la croyance religieuse et une attitude scientifique ? Les partisans de cette thèse mettent en avant quelques noms de grands scientifiques ayant affirmé que leurs recherches ne les empêchaient pas de croire en Dieu. Mais les sociologues - des scientifiques eux aussi - n'acceptent pas de se contenter de quelques exemples.

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Americans are still scientifically illiterate — and scientists still need a PR team - The Washington Post

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Americans are still scientifically illiterate — and scientists still need a PR team - The Washington Post

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Back in 2009, the Pew Research Center and the American Association for the Advancement of Science released a survey that I'll never forget.

" Public Praises Scientists; Scientists Fault Public, Media," it was entitled. And it was revolutionary, because it went so dramatically against the grain for these kinds of reports.

Usually when Americans gets surveyed about science, we learn that they don't know a lot about it - and then we proceed to lament how dumb they are. In fact, we did that just last week, when we learned that Americans want to label food containing DNA. (Har har.)

But in 2009, Pew and AAAS dared to treat the problem as two-sided. They surveyed scientists, not just citizens - members of the American Association for the Advancement of Science, no less. And they found that, hey, it takes two to tango in the science-society relationship, and scientists might, if anything, be more down on the public than the public actually was on them!

I recall all this now because a long-awaited successor to this classic report has now come out. Same game plan, same structure. Except for one thing - the overall framing seems to have subtly shifted back toward the old "public doesn't know stuff" presentation. Perhaps not intentionally, but that's how I suspect the report is going to be interpreted (whether its authors intend it or not).

The reason is the prominence of figures like this, showing just how wrong people are about factual stuff:

So let's discuss this. You will not be shocked to learn that scientists accept climate change and evolution much more than do average Americans. Or that scientists are more supportive of nuclear power.

You might be a bit more surprised to find that the biggest gap of all exists over GMO safety - I was, it's stunningly big. But in general, we know this stuff already. We know that people deny a lot of science when they really shouldn't.

So I feel that with this report now out, it's actually important to reemphasize a key implication of the old report: namely, that scientists have also traditionally disengaged from the public and sometimes blamed the public over findings like these, while failing to understand the root causes of science resistance - and that what they really need is to engage the public if they ever want the situation to change.

Granted, since 2009, there's been a great deal of that happening. A public communication wave has swept the world of science. You can't go to a big scientific meeting without wading through session after session on communication.

That's to the good. But the observation still really matters - and to show as much, let's just go through two of the issues above and briefly try to explain why there's really such a gap between science and the public.

Evolution. Basically, a lot of people are afraid that if they accept the science of evolution, life becomes meaningless, morality collapses, and death becomes just the end. (Yeah, it's really that big of a deal for them.) To address this fear, scientists need to show how religious believers (like Pope Francis) actually have no problem with the theory of evolution. Some have adopted this wise strategy, but many have instead opted to slam religion, which, obviously, is likely to backfire.

Climate Change. Here, resistance to the science is driven by an ideology and an identity called individualism, which centers on the belief that a fair society is one in which a person succeeds on his or her own merits. What does that have to do with the climate, you ask? Well, nothing obvious - except that libertarian individualists think that the climate issue is a way of clamping down on something they hold in very high regard indeed: the free market. Scientists can try to explain the facts here till they're blue in the face, but if they don't disarm the concerns rooted in ideology, they'll never disarm the resistance.

In both of these cases, if you just call the public dumb, and try to set them straight about the facts, and don't understand where the resistance actually comes from....well, then, the truth is that you're not being so perceptive yourself.

The point is, we have a lot of problems at the interface between science and society. But none of them are simple, and when people disagree with scientists, there's often a lot more going on than mere scientific illiteracy.

In fact, in many cases, scientists' opponents are deeply ideological and deeply dedicated - and, yes, smart. That's the real science-society problem, and it's one that we're still only beginning to grapple with.

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Americans are still scientifically illiterate - and scientists still need a PR team

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Back in 2009, the Pew Research Center and the American Association for the Advancement of Science released a survey that I'll never forget. " Public Praises Scientists; Scientists Fault Public, Media," it was entitled. And it was revolutionary, because it went so dramatically against the grain for these kinds of reports.

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La recette pour l’apparition de la vie sur Terre enfin découverte ?

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La recette pour l’apparition de la vie sur Terre enfin découverte ?

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Des chimistes ont développé une nouvelle théorie concernant les origines de la vie sur Terre et démontré que ses éléments constitutifs auraient bien pu être présents sur notre planète il y a 4 milliards d'années.

Une étude parue ce 8 janvier dans la revue Natureapporte une nouvelle compréhension sur la façon dont la vie aurait pu apparaître sur notre planète, il y a environ 4 milliards d'années. D'après l'équipe de recherche du Scripps Research Institute (SRI), les éléments nécessaires à l'apparition de la vie auraient bien été disponibles sur Terre à cette époque.

"C'était une "boîte noire" pour nous", explique le docteur Ramanarayanan Krishnamurthy, professeur de chimie agrégé à l'IRS et co-auteur, " mais si l'on se concentre sur la chimie, la question des origines de la vie devient moins décourageante".
Le cycle de Krebs
Pour cette nouvelle étude, Krishnamurthy et son équipe se sont focalisés sur une série de réactions biochimiques qui constituent ce que les chercheurs appellent le cycle de l'acide citrique, plus connu par les amateurs de biologie sous le nom de cycle de Krebs. Il est utilisé par tous les organismes dits aérobies, c'est-à-dire ceux ayant besoin d'oxygène (nom plus communément donné au dioxygène) pour vivre : oiseaux, mammifères, champignons, végétaux, etc.

Ces organismes utilisant le cycle de Krebs peuvent récupérer de l'énergie chimique à partir de différents substrats, présents stockés et exploitables, dans leurs cellules. Par le passé, les chercheurs ont tenté d'imaginer une vie primitive dont le cycle de Krebs utiliserait les mêmes molécules que celles que nous employons actuellement. Néanmoins, cette approche menait à une impasse, ces molécules étant fragiles et les ingrédients nécessaires au bon déroulement du cycle tel que nous le connaissons n'étant tout simplement par disponibles au cours des premiers milliards d'années de la Terre.

L'équipe du SRI a donc décidé de prendre le problème dans l'autre sens. Elle a commencé par poser sur le papier les recettes de chacune des réactions chimiques composant le cycle de Krebs. Puis, elle a identifié parmi les ingrédients nécessaires à ces réactions ceux étant disponibles sur Terre à l'époque du développement de la vie. Leurs résultats ont révélé que malgré l'indisponibilité de certains éléments fondamentaux, l'apparition d'un cycle biologique aurait bien pu avoir lieu.
De l'inorganique à l'organique
L'étude montre comment l'interaction entre deux cycles non-organiques auraient pu déclencher l'apparition d'une version primitive du cycle de Krebs, lui-même un cycle organique : la synthèse malonique et le cycle HKG. Lorsque la vie émerge de matière non-vivante, on parle d' abiogenèse. Ces deux cycles utilisent des réactions exploitant la même chimie fondamentale que le cycle de Krebs pour certains éléments (les alpha-cétoacides et les bêta-cétoacides).

Ces réactions impliquent notamment le rejet de molécules sous la forme de dioxyde de carbone, mais ce n'est pas tout. Durant leurs expérimentations, les chercheurs ont découvert qu'elles pouvaient également produire des acides aminés, produits issus du cycle de Krebs et jouant un rôle capital dans le bon fonctionnement des cellules. Les chercheurs pensent que dès que des molécules biologiques comme des enzymes deviennent disponibles, elles sont en mesure de remplacer les réactions initiales, en les complexifiant et en les rendant plus efficaces.

"Cette forme de chimie aurait pu se maintenir au fil du temps, seule la nature des molécules aurait changé", explique Krishnamurthy. " Les molécules ont évolué au cours du temps temps, devant plus complexes selon les besoins de la biologie". "Le métabolisme moderne a un précurseur : un modèle primitif non-biologique ", s'exclame le docteur Greg Springsteen, premier auteur de l'étude et professeur agrégé de chimie à l'université Furman.

Ces réactions sont rendues d'autant plus plausibles par le fait qu'en leur centre, on trouve une molécule appelée glyoxylate, dont les études ont pu démontrer qu'elle aurait été disponible sur notre jeune Terre et joue aujourd'hui un rôle dans le cycle de Krebs (on parle de cycle du glyoxylate). Mais Krishnamurthy souligne que de plus amples recherches sont nécessaires pour mieux comprendre comment ces réactions se seraient par la suite stabilisées, jusqu'à donner naissance au cycle de Krebs que nous utilisons tous aujourd'hui.
Merci à Dimitri Garcia, enseignant à l'université de Nice, pour sa relecture attentive.

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La recette pour l'apparition de la vie sur Terre enfin découverte ?

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Des chimistes ont développé une nouvelle théorie concernant les origines de la vie sur Terre et démontré que ses éléments constitutifs auraient bien pu être présents sur notre planète il y a 4 milliards d'années.

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Théorie de l'évolution : ce que Darwin ne savait pas - Science & Vie

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Théorie de l'évolution : ce que Darwin ne savait pas - Science & Vie

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ADN, cellules souches... Depuis la publication, il y a 150 ans, de la théorie de l'évolution, la science n'a cessé d'accumuler les découvertes. Or, non seulement celles-ci s'éclairent à l'aune de Darwin, mais elles font évoluer sa théorie. Explications.

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Théorie de l'évolution : ce que Darwin ne savait pas

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ADN, cellules souches... Depuis la publication, il y a 150 ans, de la théorie de l'évolution, la science n'a cessé d'accumuler les découvertes. Or, non seulement celles-ci s'éclairent à l'aune de Darwin, mais elles font évoluer sa théorie. Explications.

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DE l'EVOLUTION : la théorie des équilibres ponctués - Le blog de cepheides

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DE l'EVOLUTION : la théorie des équilibres ponctués - Le blog de cepheides

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Comme l'a très bien expliqué Darwin, la transformation des espèces se déroule sur un temps très long, proche des temps géologiques, c'est-à-dire portant sur des centaines de milliers, voire des millions d'années. L'apparition de différences entre individus, différences se maintenant chez leurs descendants, explique cette évolution ; les individus les mieux adaptés dans leur milieu (surtout si celui-ci se transforme rapidement) sont les plus aptes à survivre et donc à se reproduire : c'est la sélection naturelle (voir sujet : les mécanismes de l'Evolution). Rappelons que ces transformations se font surtout par mutations mais pas seulement puisque d'autres mécanismes génétiques, quoique moins fréquents, sont également à l'œuvre (échange de matériel génétique, épimutations, etc.). Il paraît également justifié de mentionner qu'il ne faut jamais considérer ces transformations d'un point de vue généalogique mais phylogénétique : les espèces ne descendent pas les unes des autres mais se transforment en parallèle. Par exemple, deux populations d'une même espèce longtemps séparées l'une de l'autre finissent par " diverger ", c'est-à-dire que leurs représentants sont devenus incapables de se reproduire entre eux, formant alors des espèces distinctes mais coexistant encore dans un environnement voisin (c'est le phénomène de dérive génétique). En pareil cas, on pourra affirmer que ces deux espèces ont un " ancêtre commun " (l'espèce de départ) et, par exemple, c'est bien le cas de l'Homme qui ne descend pas du singe (comme l'ont un peu stupidement déclaré certains antidarwiniens) mais possède un lointain ancêtre commun avec lui.

Quoi qu'il en soit c'est par l'intermédiaire des gènes que ces transformations opèrent mais Darwin ne pouvait que le supposer puisque la génétique était à son époque encore inconnue. C'est la raison pour laquelle, dès les années 1930-40, de nombreux scientifiques cherchèrent à compléter la théorie de Darwin avec des acquisitions plus récentes : la génétique évidemment mais aussi la biologie, l'embryologie, la paléontologie, la génétique des populations, la systématique, etc. Du fait, on s'intéressa non plus seulement aux individus mais à des groupes entiers et c'est la fréquence des mutations dans une population qui devint le critère principal. La grande majorité de ces mutations - rappelons-le - sont déclarées neutres (elles n'ont aucune incidence sur les individus), quelques unes sont létales ou très défavorables (et leurs porteurs n'ont pas de descendants), quelques unes enfin apportent un avantage sélectif et se transmettent aux générations suivantes. Lorsque la fréquence de ces mutations devient élevée, on peut assister à la modification de l'espèce.

Quelques décennies plus tard (1960), grâce à la compréhension de la nature des chromosomes et des gènes, la biologie moléculaire vint compléter le néodarwinisme (autre appellation de la théorie synthétique) en donnant les bases expérimentales qui manquaient.

En relisant avec attention l'ouvrage principal de Darwin (l'origine des espèces au moyen de la sélection naturelle, 1859), on se rend compte que le grand scientifique s'était interrogé sur un fait qui lui paraissait curieux : si l'on pense à une transformation graduelle, comment se fait-il que les fossiles jusqu'alors retrouvés (et la même remarque prévaut encore" aujourd'hui) ne concernent presque toujours que des espèces déjà formalisées et très peu d'espèces dites " intermédiaires " chez lesquelles on pourrait reconnaître une partie seulement des caractères définitifs de l'espèce considérée. La réponse, pour lui évidente, est simplement que ces fossiles n'ont pas encore été trouvés... Il le dit de la façon suivante : .../... que l'accumulation de dépôts riches en espèces fossiles diverses, et assez épais pour résister aux dégradations ultérieures, n'étant guère possible que pendant des périodes d'affaissement du sol, d'énormes espaces de temps ont dû s'écouler dans l'intervalle de plusieurs périodes successives ; qu'il y a probablement eu plus d'extinctions pendant les périodes d'affaissement et plus de variations pendant celles de soulèvement, en faisant remarquer que ces dernières périodes étant moins favorables à la conservation des fossiles, le nombre des formes conservées a dû être moins considérable.../... ". Il ne resterait donc plus qu'à trouver ces fameux " chaînons manquants "...

En 1972, deux paléontologues, Stephen J. Gould et Niles Eldredge, publièrent un article qui prit tout le petit monde néodarwinien à contrepied : selon les deux chercheurs, ces fameux fossiles intermédiaires ne pouvaient pas être retrouvés pour la bonne raison qu'ils n'existent pas ! La raison en est que, pour eux, le gradualisme n'est qu'une supposition et que les transformations apparaissent en fait d'un coup, très rapidement, sur quelques milliers d'années (un temps infime à l'échelle géologique) ; survient ensuite pour les espèces une longue période d'équilibre, dite de stase, au cours de laquelle il ne se passe rien. Gould explique ainsi pourquoi on peut trouver des espèces n'ayant pas changé durant des millions d'années. Il avance que, loin d'une transformation progressive, une espèce peut disparaître rapidement car remplacée par l'espèce mutante qui recolonise la niche écologique jusque là occupée par celle dont elle est issue ; parfois, il peut même arriver, ajoute-t-il, que les deux espèces continuent d'exister l'une à côté de l'autre.

C'était le retour à une certaine forme de catastrophisme, la théorie qui prévalait avant le gradualisme (voir le sujet : la querelle sur l'âge de la Terre) et, bien entendu, les néodarwiniens classiques furent consternés au point qu'ils crièrent au retour d'un certain créationnisme. Il s'agissait là certainement d'un mauvais procès fait à Gould et Eldredge qui estimaient, bien au contraire, qu'ils ne faisaient que compléter - ou affiner - le darwinisme qui restait à leurs yeux la seule explication possible. Certains créationnistes, notamment religieux, s'emparèrent sans la comprendre de la nouvelle idée pour asseoir leurs propres arguments antidarwiniens ce qui ne contribua pas, on le comprend, à la sérénité du débat ! Il n'y avait pourtant pas là une idée véritablement révolutionnaire puisque, à bien le relire, on s'aperçoit que Darwin lui-même avait évoqué cette hypothèse sans s'y arrêter définitivement...

En somme, le ponctuationnisme (équilibres ponctués) n'est qu'une autre façon d'interpréter le transformisme et la sélection naturelle ; là où le gradualisme ne voit qu'une transformation progressive apparue par petites touches sur un temps très long, Gould penche plutôt pour l'apparition brutale de mutations importantes permettant d'un seul coup la transformation d'une espèce qui se met alors à concurrencer celle dont elle est issue et, le plus souvent, la supplante en quelques milliers d'années grâce à son avantage sélectif. On est toujours dans le cadre d'un darwinisme bien compris.

En ce début de millénaire, les scientifiques s'accordent pour reconnaître la validité à la fois du gradualisme et du ponctuationnisme : certaines espèces se transforment lentement au gré du temps (géologique) mais d'autres semblent apparaître en un laps de temps très court suivi d'une longue période d'absence de changement. La grande majorité des espèces ayant un jour vécu sur Terre ont aujourd'hui disparu (99% d'entre elles avancent les spécialistes). Certaines ont été emportées, comme les dinosaures du Crétacé, par un événement cataclysmique. D'autres se sont transformées en de nouvelles espèces mieux adaptées à un milieu donné. Dans tous les cas, le hasard est à l'œuvre puisqu'il entraîne aussi bien mutations soudaines qu'extinctions massives accidentelles. Et, on le sait bien, le hasard est imprévisible.

The Structure Of Evolutionary Theory (Stephen J. Gould, Belknap-Harvard, 2002). On trouvera une intéressante analyse de cet ouvrage ICI

1. combat entre un allosaure et un stégosaure (sources: http://www.linternaute.com/science/)

3. dérive génétique artificielle (sources : http://e-sante.futura-sciences.com/)

4. chromosome (sources : http://www.beltina.org/health-dictionary )

5. Stephen Jay Gould (sources : http://www.vetopsy.fr/)

6. Niles Eldredge (sources : http://www.amnh.org/exhibitions/darwin)

7. strates du temps (sources : http://fr.wikipedia.org/wiki/Tronc )

8. slection naturelle (sources : http://us2.harunyahya.com)

Charles Darwin - théorie synthétique de l'Evolution - Stephen J Gould - Niles Eldredge - sélection naturelle - mutations - phylogénétique - dérive génétique - extinctions de masse - génétique des populations - systématique - avantage sélectif - gradualisme - période de stase - catastrophisme

Sujets apparentés sur le blog

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DE l'EVOLUTION : la théorie des équilibres ponctués - Le blog de cepheides

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La théorie de l'Evolution explique la transformation des espèces au fil des âges mais, en réalité, c'est bien plus qu'une simple théorie tant les preuves abondent en son sens. De ce fait, on devrait plutôt dire les lois de l'Evolution (c'est également...

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Evolution Doesn’t Give a Damn About Us, or the USA | The Nation

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Evolution Doesn’t Give a Damn About Us, or the USA | The Nation

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In 1859, Charles Darwin published On the Origin of Species. At the end of the book, there is this wonderful passage about the power of natural selection. Darwin writes: "There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." The fact that you are reading this now is a product of billions of years of evolution, no small miracle in and of itself.

Darwin wrote these words several years before Louis Pasteur would conduct his experiments across the English Channel in Paris on the germ theory of disease, but all creatures, great and small, operate according to the basic laws of evolution, from the bacteria that caused the puerperal fever that Pasteur first investigated, to the creature (or, rather, more correctly described as a collection of genetic material encased in a protective coat of protein), the virus, that plagues us today: SARS-CoV2.

Organisms evolve by random changes in their genetic makeup as they replicate, whether they can do it on their own, like all living things, or viruses, which straddle the world of the animate and inanimate, and require hosts to parasitize for their own reproduction. What Darwin noted is that the world around us drives evolution in nonrandom ways. The sheer variety of the natural world is driven by adaptations over time to our environments, where those individual organisms with mutations that confer protection against harm or offer a competitive advantage against other individuals of our own kind prosper over the generations.

What we are now seeing with SARSCoV2's variants emerging around the world is evolution in action. Although SARC0V2 has a proof-reading enzyme-which slows the accumulation of mutations compared to other viruses (e.g., HIV)-over the past year, we've seen the virus adapt to its surroundings. All SARSC0V2 wants to do is to find a home, a host, and share the same place with us to reproduce. The B.1.1.7 variant first documented in the United Kingdom is hypothesized to have come from a chronically ill patient, perhaps immunocompromised, where the virus found a home, lingered and replicated happily for longer than it would have in a typical patient, probably in the presence of treatments like convalescent plasma or remdesivir, which would have driven mutations to escape these interventions. Unfortunately, the evolution of the virus within this host ended up conferring another benefit on this viral lineage making it 50-70 percent more infectious than the strains we've been dealing with thus far. Other variants are showing reduced susceptibility to neutralization by antibodies raised by some vaccines, which may confer greater lethality in those infected.

None of this is a surprise. Evolution is happening all around us among animals, plants, bacteria, and viruses. But what is clear is that if you want to stop SARSC0V2 and stop the generation of variants-the endless forms most beautiful and most wonderful that Darwin described-you have to eradicate it before it becomes an endemic disease, lingering like the many infections that we've tried to outwit and outlast over the centuries.

What is discouraging is that our attempts to address the pandemic have been hyper-local, nationalistic, and mired in short-term thinking and myopia. Depending on where you live in the United States, control efforts are taken more or less seriously. Meanwhile, in Washington, D.C, politicians quibble over what is already a modest pandemic relief package from the virus's point of view, offering not nearly enough to allow every American to stay at home to protect themselves and their families, ramp up testing and disease surveillance, and get vaccination efforts on track. In fact, I'm already hearing that public health departments are having to choose between vaccination and testing efforts because of staff shortages. Meanwhile, Democratic dinosaurs like Larry Summers think this is 2008 and we are merely having an academic argument about the size of an economic stimulus bill, while Republicans in Congress think we're spending too much on it all right now. We're furiously debating who should get $1,400 one-time checks across the country; meanwhile, the virus is being fruitful and multiplying, along with its mutations.

If the US response domestically is still akin to bringing a knife to a gunfight-better than Trump's mismanagement and chaos, but still not setting us up for containment of the pandemic anytime soon-the global response remains a catastrophe unfolding in plain sight. Right now, the absence of plans to vaccinate people outside of the rich countries of the world is a recipe for disaster. COVAX, the main multilateral initiative on worldwide vaccination for SARSCoV2, said it will be able to vaccinate 27 percent of individuals in poor countries in 2021. The initial estimate was 20 percent. But back to Darwin. What happens with an intervention that cannot eradicate an organism but while in operation lets it generate mutations? Low-level vaccination in poorer countries, along with scarce support for other control measures, risks creating environments for, and selective pressure on, SARSCoV2 to evade the immunogens we develop to prevent serious disease and blunt transmission.

Why is no one screaming bloody murder at this point about this? It's barbaric in human terms-letting the rest of the world suffer mostly uncontrolled epidemics for the next several years-while Europe, the United States, Canada and other wealthy countries jab up, perhaps requiring vaccine passports for entry by foreigners. But it's also folly and hubris of the worst kind. Unless we stop SARSCoV2 everywhere, we won't stop it anywhere. We will be chasing variants across the globe for many years at this rate, all because we cannot raise our heads above the parapets of our own countries to see that all of us are inextricably linked together in viral destiny.

One last thing about evolution. It doesn't care about us. Modern humans have only been on this planet for about 200,000 years out of the 4 billion of so years of life on earth. It's all a blink of an eye. We're just not that important in cosmic terms. To survive against SARSC0V2, against the near-future threats of climate change and whatever else this way comes, humanity is going to have to adapt-and do it quickly. Sadly, we haven't yet shown ourselves to be up to the task.

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Evolution Doesn't Give a Damn About Us, or the USA

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In 1859, Charles Darwin published On the Origin of Species. At the end of the book, there is this wonderful passage about the power of natural selection.

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Ce que le Covid-19 nous rappelle sur l’évolution – Libération

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Ce que le Covid-19 nous rappelle sur l’évolution – Libération

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Si elle est une mauvaise nouvelle pour les services de soins et les pays éprouvés par la pandémie depuis plus d'un an, l'émergence des variants du Covid-19 nous rappelle que le vivant est dynamique, qu'il change, qu'il s'adapte et qu'il... évolue. Quelques jours après l'anniversaire de la naissance de Darwin (12 février), le #DarwinDay sur les réseaux sociaux, nous constatons que le virus permet cette chose fascinante : nous montrer l'évolution à l'œuvre.

Ce virus est un être vivant à génération rapide. Il ne lui faut que 10 heures pour se reproduire. Un individu infecté peut rapidement présenter des millions voire des milliards de virus. Chaque virus possède un génome de 29 000 lettres, soit autant de possibilités de mutations. Dès lors, on comprend bien qu'un événement rare, comme une mutation viable, a statistiquement des chances de se produire. "On estime qu'une lignée du virus accumule une à deux mutations par m...

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Ce que le Covid-19 nous rappelle sur l'évolution

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Si elle est une mauvaise nouvelle pour les services de soins et les pays éprouvés par la pandémie depuis plus d'un an, l'émergence des variants du Covid-19 nous rappelle que le vivant est dynamique, qu'il change, qu'il s'adapte et qu'il... évolue.

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Case for Evolutionary Genomics and the Comprehensive Examination of Sequence Biodiversity | Molecular Biology and Evolution | Oxford Academic

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Case for Evolutionary Genomics and the Comprehensive Examination of Sequence Biodiversity | Molecular Biology and Evolution | Oxford Academic

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Abstract

Comparative analysis is one of the most powerful methods available for understanding the diverse and complex systems found in biology, but it is often limited by a lack of comprehensive taxonomic sampling. Despite the recent development of powerful genome technologies capable of producing sequence data in large quantities (witness the recently completed first draft of the human genome), there has been relatively little change in how evolutionary studies are conducted. The application of genomic methods to evolutionary biology is a challenge, in part because gene segments from different organisms are manipulated separately, requiring individual purification, cloning, and sequencing. We suggest that a feasible approach to collecting genome-scale data sets for evolutionary biology (i.e., evolutionary genomics) may consist of combination of DNA samples prior to cloning and sequencing, followed by computational reconstruction of the original sequences. This approach will allow the full benefit of automated protocols developed by genome projects to be realized; taxon sampling levels can easily increase to thousands for targeted genomes and genomic regions. Sequence diversity at this level will dramatically improve the quality and accuracy of phylogenetic inference, as well as the accuracy and resolution of comparative evolutionary studies. In particular, it will be possible to make accurate estimates of normal evolution in the context of constant structural and functional constraints (i.e., site-specific substitution probabilities), along with accurate estimates of changes in evolutionary patterns, including pairwise coevolution between sites, adaptive bursts, and changes in selective constraints. These estimates can then be used to understand and predict the effects of protein structure and function on sequence evolution and to predict unknown details of protein structure, function, and functional divergence. In order to demonstrate the practicality of these ideas and the potential benefit for functional genomic analysis, we describe a pilot project we are conducting to simultaneously sequence large numbers of vertebrate mitochondrial genomes.

Introduction

Following the first complete genome sequence from a free-living organism ( Fleischmann et al. 1995 ), the complete genomes of a number of crown eukaryotes have been sequenced (i.e., Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and a draft of Homo sapiens [ C. elegans Consortium 1998 ; Adams et al. 2000 ; Ball et al. 2000] ). The sequencing of D. melanogaster was particularly notable in that it was completed via whole-genome shotgun sequencing, a method previously thought applicable only to bacterial-sized genomes ( Fleischmann et al. 1995 ; Adams et al. 2000 ). The human genome is also being sequenced utilizing a total-genome shotgun approach in combination with the standard directed approach ( Venter, Smith, and Hood 1996 ; Weber and Myers 1997 ; Venter et al. 1998 ). While the data from these genomes can provide many insights into evolution, the inherent comparative nature of evolutionary biology limits the evolutionary questions that can be addressed with only these few genomes.

The paucity of genomes available from crown eukaryotes leads to common challenges for phylogenetics, molecular evolution, and functional genomics analysis, since parameters of evolutionary models, including topology and rates, will tend to have high variances as a result. This situation is particularly unacceptable for functional genomics analysis: with the completion of sequencing of the human genome, one of the most important problems of the coming century will be to develop a complete understanding of how that sequence functions to carry out essential life processes, and a major route to that understanding will be comparative analysis of sequence biodiversity. Despite the accomplishments of genomics research and the associated development of strategies, techniques, and tools for large-scale sequencing, these advances have had very limited influence on the way molecular-based evolutionary studies are conducted. In order to reduce the variance of evolutionary model parameters and increase the accuracy of comparative analysis, we need data sets from large genomic regions with much more extensive sampling of divergent taxa than in data sets that are currently available.

To address this problem, we describe here the potential challenges of evolutionary genomics, which we define as the application of genome research strategies to comparative studies in evolution. We consider possible solutions to these challenges, outline a research design for applying evolutionary genomics to vertebrate mitochondria, and describe simulated sequence assembly experiments to verify the feasibility of our design.

A key element of our plan is to reduce costs associated with cloning and handling of materials by pooling DNA samples from different gene regions and diverse species prior to cloning. Thus, the costs specific to individual samples are limited to those that occur prior to cloning, and the costs of all subsequent steps are shared by all samples. Although breaking the direct association between sequences and samples is a counterintuitive approach, these associations can be re-created using automated assembly programs in combination with preexisting sequence information which can be used as an evolutionary reference. In cases where there is ambiguous assignment of sequences to samples, limited PCR and sequencing can be performed on the original samples to resolve these uncertainties. The simulated resampling and assembly experiments indicate that this strategy will be practical and cost-effective. Individuals from the same species can also be pooled but are unlikely to be separable into unique contiguous sequences, or haplotypes; rather, they would contribute to estimates of intraspecific variation.

Our focus is thus on large-scale sequence analysis of samples from divergent taxa, which we call sequence biodiversity (or genomic biodiversity in the case of complete organelle or nuclear genomes) analysis in order to distinguish it from genomic diversity studies that focus on intraspecific variation (usually in humans). While a great deal of biodiversity is currently being explored at deep taxonomic levels with the sequencing of complete bacterial genomes, these taxa are generally too divergent to be useful in evaluating many important evolutionary processes which occur on a much shorter timescale. Even with the current array of complete genomes, it is expected that around half of the genes in the human genome will be so diverged that they will not be obviously homologous to any genes of known function. Thus, what is clearly needed is greater focus on sequence biodiversity among taxa much more closely related to humans, that is, on the near-human evolutionary environment.

Areas of Impact

The primary products of a large-scale approach to evolutionary genomics are listed in table 1 . The immediate products are sequences of large regions from many genomes. While there are many areas of research that would benefit from large-scale sequencing of diverse biota, we briefly describe here the possible impact on several of the most important: phylogenetics, the study of patterns and processes of sequence evolution, functional and structural genomics, and quantitative and population genetics.

Phylogenetics

Pattern and Processes of Sequence Evolution

The study of patterns and processes of genome and sequence evolution will benefit significantly from evolutionary genomics. Currently, it is difficult to obtain suitable data sets that cover large amounts of sequence from different genes and common divergent biota. Without such data sets, one cannot do more than estimate gross differences in overall rates between sites or between subsections of phylogenetic trees, and the sensitivity of coevolutionary analysis is limited. The large increase in homologous sequences from a broad range of taxa will lead to more accurate estimation of evolutionary dynamics at individual nucleotide and amino acid positions, which is essential to detailed understanding of the forces of molecular evolution and their relationship to structure and function. These improvements in accuracy will come from the diversity of taxa directly, from the improved accuracy in topological inference, and from having abundant sequences from identical taxa for comparison. Recent progress has been made in analyzing evolutionary behavior at individual sites, both by limiting the parameters to the equilibrium amino acid frequencies ( Bruno 1996 ) and by optimizing functions of underlying physicochemical properties ( Koshi, Mindell, and Goldstein 1999 ; Yang 2000 ). These techniques are limited, however, by the paucity of data sets that are sufficiently large for the analysis of accurate site-specific information. Likewise, analysis of the interaction between sites, or coevolution, has recently progressed to incorporate a wider diversity of coevolutionary maximum-likelihood models with reliable statistics ( Pollock and Taylor 1997 ; Pollock, Taylor, and Goldman 1999 ; W. J. Bruno, personal communication). In each case, accurate inferences about the patterns and processes of sequence evolution are limited by the amount of available data. Evolutionary genomics will also provide site-specific information on nucleotide and codon usage bias, insertion and deletion processes, and selective processes such as adaptation, coevolution, and functional divergence.

Functional and Structural Genomics

Functionally conserved regions of regulatory and coding regions of genes can also be efficiently identified by comparing sequences from divergent taxa, a process called evolutionary filtering ( Zurawski and Clegg 1987 ). As with other evolutionary analyses, the power of evolutionary filtering increases rapidly with the number of related sequences examined. In the protein structural realm, it is common practice to infer the functional importance of structural regions from the sequence conservation in that region, and internalization of conserved hydrophobic regions is one of the strongest components of successful structure prediction ( Livingstone and Barton 1996 ; Thompson and Goldstein 1996 ). The functional importance of structural regions can also be inferred from sequence hypervariability, as with the antigen recognition sites of HLA, plant disease resistance genes, fertilization genes, and surface antigens on viruses such as HIV and influenza. Recent work has also linked changes in evolutionary conservation and variability to functional divergence between duplicated paralogs ( Zhang and Gu 1998 ; Gu 1999 ). Thus, even simple models defining differences in evolutionary rate alone, focusing on extremes of the distribution, are extremely important.

More detailed phylogenetic analyses have correlated finer structural details (such as positions of catalytic and ligand-binding sites, secondary structure features, and subunit interaction surfaces) to differences in the rate and pattern of evolutionary substitution ( Goldman, Thorne, and Jones 1996, 1998 ; Koshi and Goldstein 1996 ; Thompson and Goldstein 1996, 1997 ; Thorne, Goldman, and Jones 1996 ; Koshi, Mindell, and Goldstein 1999 ; Dean and Golding 2000 ). There is every reason to believe that as the amount of evolutionary information increases dramatically, so will the accuracy in predicting structural and functional features.

The potential importance of these predictions to functional genomics cannot be understated. When the human genome is completely annotated, it can be expected that up to half of the genes will not be homologous to any genes of known function, and that many of the genes which are homologous to known genes will be far enough diverged that their exact function will be ambiguous. Large-scale analysis of expression patterns will aid in functional prediction in an efficient manner, but expensive and time-consuming experiments will eventually need to be performed. Predictions based on evolutionary genomics will provide a means of narrowing experimental possibilities to a feasible number and will allow better prediction of the possible effects of substitutions on structure and function, even when the exact structure is unknown or the gene is only remotely related to a gene of known structure.

Quantitative and Population Genetics

The inclusion of multiple individuals of the same species can provide information on the distributions and patterns of genetic polymorphisms. The simultaneous sequencing of multiple individuals has been discussed in the context of human genome research ( Weber and Myers 1997 ), and sample pooling strategies for mutation detection have been explored (Amos, Frazier, and Wang 2000). Quantitative trait locus mapping, marker-assisted breeding, and other research using polymorphic genetic markers (i.e., single-nucleotide polymorphisms, simple sequence repeats, microsatellites, etc.) benefit from an increase in density of polymorphic markers that come from evolutionary genomics. These additional markers can be incorporated in the design of genome scanning for mapping studies, resulting in increased statistical power.

A Strategy for Moving from Small-Scale to Large-Scale Surveys of Sequence Biodiversity

The current research design model in molecular-based studies of evolution can be described as a gene-based strategy characterized by low-throughput sequencing of one or a few short regions at a time. This approach is inherently limited and does not take full advantage of developments in high-throughput technologies and associated cost efficiencies. Some principal characteristics of gene-based and genome-based strategies are compared in table 2 . There are a number of procedural steps in any genomic study. These can be viewed as problems or challenges to be overcome, the solutions of which should be optimized to minimize cost without sacrificing accuracy. Analogous to arguments for whole-genome shotgun sequencing ( Fleischmann et al. 1995 ; Venter, Smith, and Hood 1996 ; Weber and Myers 1997 ; Venter et al. 1998 ), we describe, in general terms, some major problems associated with moving from gene-based to genome-based research, and we discuss their solutions. We briefly describe a strategy for evolutionary genomic sequencing ( fig. 1 ) and argue that this approach is less costly and will result in more rapid acquisition of useful information than the gene-based strategies currently dominating evolutionary studies.

Acquisition and Preparation of Samples

In contrast to typical single-taxon genomic projects, which generally require a single sample of a common and readily available species, evolutionary genomics requires multiple samples, often from a wide diversity of taxa, some of which may not be readily available. While DNA purification using CsCl density gradient centrifugation or differential lysis may be preferable for organelle genomes when sufficient tissue is available, PCR amplification can be applied more generally and can be used when tissue samples from particular taxa are rare or expensive to collect. PCR amplification of mitochondrial genomes or large regions of nuclear DNA in a single large piece or a few smaller pieces has already been well demonstrated ( Chang, Huang, and Lo 1994 ; ; Nelson, Prodohl, and Avise 1996 ; Mindell et al. 1999 ; Miya and Nishida 1999 ), and these long-PCR techniques can be applied to tissues in a wide variety of preservation states. Curators and staff at several natural history museums and zoological parks (e.g., Louisiana State University, the University of California at Berkeley, the University of New Mexico, and San Diego Zoological Park) have well-documented frozen tissue collections that are sources of samples suitable for evolutionary studies.

Cloning and Sequencing Template Preparation

One factor that distinguishes a gene-based program from a genomics-based program is the size of the DNA sequence region that is examined at one time. A principal challenge is to take advantage of genomic approaches when the sequence region from any single taxon is relatively short. One way to overcome this challenge is to pool sequence regions across individuals or taxa so that the aggregate sequence corresponds to amounts well suited to genomic methods. For example, pooling 10-20 animal mitochondrial genomes, typically each about 16 kb in length, would yield an aggregate sequence comparable to a BAC, or about 0.1-0.2 the size of many bacterial genomes. Pooling ratios should be based on estimates of the number of molecules rather than DNA concentration in order to keep the concentration of each site constant in the face of length variation (e.g., differences in intron length or hypervariable regions). Pooling samples reduces the number of times labor-intensive steps involved in cloning (fractionation, size selection, ligation, transformation, etc.) have to be performed and allows for larger numbers of templates to be processed simultaneously without the need to track individuals or taxa during the sequencing phase. Pooling samples itself presents challenges with respect to sequence assembly and assignment of a specific sequence to a specific taxon or haplotype. These challenges are readily dealt with through proper taxon sampling and direct PCR of the original samples.

Sequencing

The standard procedures of genomic sequencing, including large-scale automatic sequencing of random shotgun clones, are utilized in evolutionary genomic research. Specific details such as the appropriate mixture of single- and double-ended sequencing, insert size, amount of coverage, gap closure methods, and association of contigs with taxa may vary from project to project and can be optimized to minimize cost. Our experience and limited simulation studies have indicated, however, that cost savings associated with optimizing these details are small and may be offset by costs associated with tracking clones and modifying protocols already in place at genome centers. Thus, our preferred strategy, in line with current protocols at many genomic centers, is to randomly clone inserts of 2-3 kb in length and sequence them automatically at both ends to an average redundancy of sevenfold coverage of each genomic region. This strategy minimizes costs associated with steps requiring human thought and labor, particularly the choice of clone-specific primers and final gap closure.

A critical consideration is that of identifying and minimizing the effects of sequencing errors, since they will bias estimates of variation and potentially create problems in assembly and annotation. There are several distinct sources of sequence error, depending on the source of DNA. Simply, these can be divided into error from PCR in those cases where PCR is used to generate material for cloning, and error typically associated with DNA sequencing itself. The error associated with DNA sequencing is reduced by multiple coverage of all regions sequenced. This multiple coverage for most sequence regions, sevenfold on average, is an inherent aspect of the sequencing of random shotgun clones. Furthermore, sequencing errors generally result in lower confidence in the sequencing calls (i.e., lower quality values) compared with correctly called bases, and standard assembly programs use this quality information from redundantly sequenced bases to reduce error propagation in the assembly process ( Weber and Myers 1997 ).

PCR error due to the misincorporation of nucleotides during polymerization is expected to be similar in distribution to sequencing error. In contrast to sequencing error, however, the quality values associated with PCR errors will be indistinguishable from correct sequence, since incorrect bases will be incorporated prior to cloning. Given a large number of initial starting templates, most misincorporated bases will be of low frequency and, thus, distinguishable from the majority of authentic variation at most sites. In projects with one individual per species, there will be little natural variation (none in the case of mitochondria in the absence of heteroplasmy), and these cases can be used to obtain an accurate estimate of PCR error in the system. This estimate can then be used to correct estimates of sequence variation (particularly important in the low-frequency range) in projects with multiple individuals per species, and to calculate the probability that any given variant is real as opposed to an artifact of PCR. For heterozygotes, both nucleotides segregating at a site should be well represented in the raw sequences and mostly distinguishable from PCR error.

Postsequencing Data Processing

The task of sequence annotation is greatly simplified for evolutionary genomics projects compared to standard genomics projects because a great deal of information is available a priori with respect to the gene content and other features of the sequences being examined. This prior knowledge and availability of comparative data makes evolutionary genomics extremely well suited for annotation using case-based reasoning ( Overton and Haas 1998 ), since there will already be a moderate number of homologous sequences available. Although appropriate software is not currently available, this prior knowledge can theoretically be used to guide sequence assembly, allowing for the ordering and linking of contigs with extremely short overlaps and thus reducing the amount of sequencing redundancy required for a minimal final gap closure effort. Subsequent steps, such as data preparation for GenBank submission, can be accomplished using available tools.

Evolutionary data analysis for inferring phylogenetic relationships, characterizing patterns of sequence evolution, and estimating population genetic parameters can also be accomplished using standard methods and available software. The only difference will be an increase in the numbers and lengths of sequences analyzed. Faster computers, improvements in algorithms (e.g., Lewis 1998 ), and parallel computing implementation of algorithms will continue to decrease the real time of analysis. With a rapid increase in evolutionary genomics data, there will be, however, a qualitative change in the analytical potential of the data that should spur development of novel analytical approaches.

The Case for an Examination of Vertebrate Mitochondrial Genomes

In order to give a concrete demonstration of our approach and the potential benefit for functional genomic analysis, we are implementing a pilot project to simultaneously sequence large numbers of vertebrate mitochondrial genomes. Mitochondrial genes and genomes have long been a major focus in molecular evolution, and these genomes are an excellent candidate for working out the details and demonstrating the power of evolutionary genomics. They have the advantage that they are present in high concentrations in many tissues, they are reliably amplified by PCR, and they can easily be enriched by purification of the mitochondria prior to DNA extraction (e.g., Dowling et al. 1996 ). The vertebrate focus of our model experiment is of rare benefit in that, unlike many primarily bacterial data sets, proteins within the vertebrate mitochondria are unlikely to have diverged to such an extent that the structural context has dramatically altered over the data set ( Lesk and Chothia 1980 ; Chothia and Lesk 1987 ; Orengo et al. 1999 ). Thus, evolutionary analysis will not be blurred by mixing sites with widely diverged evolutionary and coevolutionary dynamics. In addition, the relatively high degree of amino acid conservation will reduce the amount of ambiguous sequence alignment, thus reducing the probability of incorrectly inferring stationary evolutionary processes for nonhomologous sites.

Mitochondrial genomes also have a strong advantage over nuclear genes in that they are unlikely to have experienced many intraspecific recombination events (but see recent controversy; Arctander 1999 ; Awadalla, Eyre-Walker, and Smith 1999 ; Merriweather and Kaestle 1999 ; Awadalla, Eyre-Walker, and Maynard Smith 2000 ; Kivisild et al. 2000 ). Thus, there is more likely to be a single mitochondrial phylogeny, as opposed to nuclear gene or gene segment phylogenies, which may be composites of different phylogenies. Within the vertebrates, there are few known rearrangements of genes, and none of protein-coding genes ( Curole and Kocher 1999 ), so phylogenies are also unlikely to be confounded by inaccurate reconstruction of those events.

A detailed review concerning the effects of the current set of complete mitochondrial genomes on questions in vertebrate phylogenetics has been written ( Curole and Kocher 1999 ), but in summary, as of March 2000, there were 69 complete vertebrate mitochondrial genomes publicly available, with slightly more than half coming from mammals ( fig. 2 ). While many phylogenetic questions have been resolved with complete vertebrate mitochondrial genomes, many more are currently ambiguous or directly at odds with morphological and other sequence data. Thus, increasing the vertebrate mitochondrial genome data set, particularly by breaking up many of the long unbroken branches (e.g., within the rodents, bats, marsupials, snakes, lizards, turtles, and amphibia), is likely to have a large impact on confidence in the resolution of the tree structure.

The genomes of vertebrate mitochondria are also appropriate in that they contain a diversity of genes with different amounts of structural and functional information available, and with segments experiencing different structural and functional contexts and, thus, different types of selective pressure. With the cloning and sequencing of the first few mitochondrial genomes ( Anderson et al. 1981, 1982a, 1982b ; Bibb et al. 1981 ; Roe et al. 1985 ; Gadaleta et al. 1989 ; Desjardins and Morais 1990 ; Arnason, Gullberg, and Widegren 1991 ; Arnason and Johnsson 1992 ; Tzeng et al. 1992 ), it became clear that in addition to a control region, the vertebrate mitochondrial genome generally contains 12S and 16S ribosomal RNAs, 22 transfer RNAs, and 13 protein-coding genes that vary in length and average rate of evolution. These proteins are subunits of four different molecular complexes involved in oxidative phosphorylation and ATP synthesis: NADH reductase (NAD), cytochrome oxidase (CO), cytochrome bc ₁ (CYTB), and ATP synthase (ATP). These complexes are large and have many nuclear-encoded subunits in addition to the mitochondrion-encoded proteins. Three of them, CO, CYTB, and ATP, are complete or have had many subunits crystallized, although the mitochondrion-encoded subunits of ATP (subunits a and b; ATP6 and ATP8) are the two major proteins in the complex which remain to be crystallized ( Abrahams et al. 1994 ; Takeyasu et al. 1996 ; Tsukihara et al. 1996 ; Yoshikawa, Tsukhihara, and Shinzawa-Itoh 1996 ; Shirakihara et al. 1997 ; Uhlin, Cox, and Guss 1997 ; Iwata et al. 1998 ; Yoshikawa, Shinzawa-Itoh, and Tsukihara 1998 ; Vik et al. 2000 ). These protein subunits thus represent a wide variety of evolutionary rates, structural and functional contexts (including alpha helices, beta sheets, turns, random coils, and transmembrane regions), and examples of interaction between positions within and between protein domains and subunits. Defects in these genes have also been linked to neurological diseases, aging, and cell death, and thus there is potential to accurately relate genomic biodiversity to both normal and disease-related intraspecific genomic diversity in humans ( Wallace et al. 1995 ).

Assessing the Feasibility of the Evolutionary Genomics Strategy: Experiments with Existing Mitochondrial Genomes

The potential assembly problems with our evolutionary genomics strategy are different from those of standard genomic projects in that misleading regions of identity in the sequence data arise not from repetitive elements, but from homologous regions in divergent taxa. The nature of the problem is very similar, however, in that these regions can lead to misassembling of contigs if they are not accounted for. In order to assess the feasibility of an evolutionary genomics strategy, computer simulations were conducted.

We tested our ability to assemble real sequences by resampling from known genomes. Sequences of 10 complete mitochondrial genomes available in GenBank were sampled following the protocol outlined above. These mitochondrial genomes were those of the human ( H. sapiens; Anderson et al. 1981 ), the mouse ( Mus musculus; Bibb et al. 1981 ), the cow ( Bos taurus; Anderson et al. 1982b ), the gorilla ( Gorilla gorilla; Horai et al. 1995 ), the rat ( Rattus norvegicus; Gadaleta et al. 1989 ), the finback whale ( Balaenoptera physalus; Arnason, Gullberg, and Widegren 1991 ), the horse ( Equus caballus; Xu and Arnason 1994 ), the domestic cat ( Felis catus; Lopez, Cevario, and O'Brien 1996 ), the armadillo ( Dasypus novemcinctus; Arnason, Gullberg, and Janke 1999 ), and the white rhinoceros ( Ceratotherium simum; Xu and Arnason 1997 ), for a total of 183,298 bp.

To simulate the cloning process, insert size and raw sequence reads from both ends were sampled uniformly within a small range of length (2,000 kb ± 15% for insert length, 500 bp ± 5% for sequence read length) and a small range of relative concentrations of samples (plus or minus 15%). These distributions do not reflect the exact distributions of read lengths and insert sizes in genomic cloning, but they are roughly compatible with ranges observed (unpublished data); these parameters have been shown in previous simulations not to have a strong effect on simulated assembly results ( Weber and Myers 1997 ). Standard genome projects do not have to deal with mixing of samples, so we do not have data on what the range of relative concentrations of samples will be, but the range used was intended to reasonably incorporate the variability that might be expected from DNA concentration estimates. The expected effect of a large underestimate of DNA concentration in a particular sample is that that sample will be sequenced at lower-than-optimal redundancy, and it will not be possible to fully assemble that genome. It is entirely feasible, however, that such a sample could be added at an appropriate concentration to a subsequent round for completion, while the first round could be terminated early on completion of the other genomes, thus only minimally affecting the overall cost of sequencing. Overestimates of DNA concentration in a single sample would have to be very large to dramatically affect the sequencing strategy and would generally simply lead to wasted sequence effort in direct proportion to the percentage of the overestimate. In extreme cases, sequencing would be terminated after assembly of the high-concentration sample, and the lower-concentration samples would then be recloned without that sample.

In our simulation experiment, we were able to reassemble 6 of the 10 genomes (human, cow, armadillo, whale, mouse, and horse) correctly with no gaps after sampling at 7.0-fold average coverage. There were single gaps in the rat, cat, gorilla, and rhinoceros sequences of lengths 118, 56, 63, and 90 bp, respectively, for a mean gap probability of 0.4 and a mean size of 81.5. The rhinoceros sequence was divided into two contigs, the smaller of which was 1,560 bp and bounded by the gap on one side and a 13 bp overlap on the other which was not sufficiently long to join it with the larger contig. This result is in line with expectations of this experiment for random DNA sequences, and the gaps are of a sufficient size that they could easily be closed by short PCR amplification and sequencing. Thus, the assembly was not adversely affected by the relatedness of these sequences or variation in sample concentrations, nor was it dramatically affected by substantial repetitive elements in the control regions of the horse, the rhinoceros, the cat, and the armadillo.

The taxa in this experiment were chosen to be representative of how each round in an evolutionary genomics-based vertebrate mitochondrial sequencing project might be chosen. All taxa were from separate genera, but some taxon pairs, particularly the human and the gorilla, are relatively close. Are these taxa in fact representative? In order to answer this, we determined the length distribution of regions of identity for mitochondrial genomes from taxon pairs over a range of genetic distances ( fig. 3 ). These ranged from an interclass comparison of a mammal ( H. sapiens) and a bird ( Gallus gallus), to the closest interspecies comparison available from the 69 taxa in figure 2 , which involves Equus asinus (donkey) and E. caballus. In intragenomic comparisons within the human, gorilla, cat, and mouse genomes, identical stretches have a maximum between 14 and 17, with the exception of some repetitive expansions in the control region of the cat ( Felis catus; data not shown). Thus, for pairwise intergenomic comparisons ( fig. 3 ), the stretches of length 15 or more are of the greatest interest.

As expected, the most divergent comparison, that between the chicken and the human, tapered off most quickly, and there were no identical stretches longer than 35 nt ( fig. 3 ). More closely related taxonomic pairs had more identical segments of all lengths, with the largest numbers coming from the intraequine comparison. No comparisons other than those of the intraequine (horse-donkey) and the great ape (human-gorilla) pairs had identical segments longer than 78 nt; the intraequine comparison had another 13 regions of identity of up to 93 nt, and 6 that were longer than 93 nt (lengths 97, 108, 116, 127, 128, and 205 nt), while the great ape comparison had only four regions of identity longer than 78 nt (lengths 85, 97, 127, and 164). These distributions do not theoretically present a great challenge for existing assemblers, which are designed to deal with much longer repeat sequences. Even the longest identical segment in the closest taxon pair was somewhat less than half the length of a sequence read, and less than one-tenth the length of the average cloned insert size.

Since there are roughly 4,000 species of mammals, 7,000 birds, 20,000 fish, and thousands of reptiles and amphibians, the possibilities for sampling sufficiently distinct taxa within the vertebrates are not limited; it seems feasible to avoid combining species as close as the human-gorilla pair or the horse-donkey pair, meaning that identical segments longer than 80 bp would be unlikely. Furthermore, samples from many thousands of these species are available from museums for PCR sampling, if not mitochondrial purification. A pilot project is now underway to implement the procedures we have outlined.

Evolutionary Genomics Is Cost-Effective

Any efficient method of sequencing can be used to generate the approximately 2.2 million nucleotides of raw sequence necessary in a typical experiment to simultaneously complete 20 mitochondrial genomes, and multiple laboratories worldwide could contribute to both the DNA purification and the sequencing stages. The key to cost savings is that once the cloning is done, all sequencing can be done automatically with the same two primers per clone, and there is no need to track clones. Thus, costs per individual genome are limited to sample acquisition, PCR (if applicable), and DNA purification. Assembly, filling of gaps, and verification of ambiguous organism assignment would probably be performed most efficiently at one central laboratory. Sequence can initially be assembled automatically using existing assembly programs, although this may be done more efficiently with yet-to-be-written specialty programs. A focused, large-scale evolutionary genomics effort will also avoid excess costs caused by piecemeal and sometimes redundant noncollaborative efforts in multiple laboratories.

It is our intention that assembled sequence should be made available in a dedicated phylogeny-oriented database, in addition to deposition in GenBank, in order to give added value in the form of comparative functional annotation, phylogenetic filtering, and easier access to mitochondrial-specific features. Again, a coordinated and centralized data-processing effort will avoid wasting resources through redundant efforts in multiple laboratories processing data to a point where it can be analyzed. Another large benefit of a centralized effort will be that all sequences can be tightly linked to some form of museum-deposited voucher as a matter of course, and DNA samples can also be regularly deposited with museums. Thus, one important function of a dedicated phylogenetic database will be to link directly back to the original museum information on all taxa included. This aspect of genomic analysis is often neglected by molecular biologists (few of the current complete mitochondrial genomes cite deposition of a voucher specimen), but it is extremely important to taxonomists and conservation biologists. Such linkage to original sources may not appear central to the techniques of evolutionary genomics, but it is central to creating and maintaining the resources used and to adding the full potential value of the sequence products.

Summary

We have demonstrated here that the strategy we have outlined for evolutionary genomics is theoretically viable, practical, and likely to be cost-effective. We have focused on the sampling of sequence and genomic biodiversity because the potential of these data for phylogenetics, molecular evolution, and functional genomics is compelling. At a small marginal cost increase, samples from multiple individuals in each species can also be pooled, and the intraspecific variation data obtained will then produce a large benefit for population genetics analyses. Likewise, rather than restrict the possibilities, our example of the vertebrate mitochondrial genome is intended to show the feasibility of the strategy in a specific context. The work with mitochondria is relatively straightforward, and there are fewer interpretational problems with the lack of recombination and heteroplasmy. Using the methods we have outlined here, the number of vertebrate mitochondrial genomes sequenced could easily be increased from the nearly one hundred today to thousands or more.

Given moderate funding, we believe that those thousands of taxa could be sequenced rapidly at roughly one-fifth the cost of conventional approaches. By comparison, the human genome involves about 130 times the sequencing effort with 10-fold coverage (ignoring preliminary mapping costs and duplication of efforts by noncooperating ventures). In order to put this into perspective, a single ABI 3700 automatic DNA sequencer running at full capacity could sequence 23 mitochondrial genomes per week and complete 2,000 genomes in 20 months. Thus, the full capacity of the DOE Joint Genome Institute could complete 2,000 vertebrate mitochondrial genomes in about a week, and Celera Corporation or the Human Genome Project could complete them in a matter of days. Considering this, we suggest that a moderate-sized program be initiated to sequence 2,000 or more complete genomes from vertebrate mitochondria to fully demonstrate the potential benefits of evolutionary genomics and genomic biodiversity. This would include perhaps 800, or one-fifth, of the mammals in order to focus more on the human evolutionary environment, and the remainder would be from birds, reptiles, amphibians, and fish. Ideally, such a sequencing effort would be conducted in conjunction with a dedicated collaborative bioinformatics program and would itself be viewed as a pilot for continuing communitywide large-scale nuclear evolutionary genomics and sequence biodiversity projects.

Simon Easteal, Reviewing Editor

Keywords: evolutionary genomics genomic biodiversity functional genomics comparative genomics molecular evolution phylogenetics

Address for correspondence and reprints: David D. Pollock, Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803. E-mail: daviddpollock@yahoo.com.

Natural history museums at Louisiana State University and the University of New Mexico contributed invaluable cooperation in making available the details of their frozen tissue collections for our analyses. C.-B. Stewart and D. Mindell both contributed expert consultation in mtDNA analysis, and we thank S. Easteal and an anonymous reviewer for helpful and insightful comments on the manuscript. D.D.P. was funded by a Director's Fellowship from Los Alamos National Laboratory. M.P.C. was funded by grants from NASA, NSF, and the Alfred P. Sloan Foundation.

literature cited

# data[].attributes.attachment_link.title
Case for Evolutionary Genomics and the Comprehensive Examination of Sequence Biodiversity

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Comparative analysis is one of the most powerful methods available for understanding the diverse and complex systems found in biology, but it is often limited by a lack of comprehensive taxonomic sampling.

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A step closer to understanding evolution: Mitochondrial division conserved across species

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A step closer to understanding evolution: Mitochondrial division conserved across species

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Exciting new research describes how mitochondrial replication is similar in the simplest to most complex organisms, shedding light on its origin. Credit: Tokyo University of Science

Cellular origin is well explained by the "endosymbiotic theory," which famously states that higher organisms called "eukaryotes" have evolved from more primitive single-celled organisms called "prokaryotes." This theory also explains that mitochondria-energy-producing factories of the cell-are actually derived from prokaryotic bacteria, as part of a process called "endosymbiosis." Biologists believe that their common ancestry is why the structure of mitochondria is "conserved" in eukaryotes, meaning that it is very similar across different species-from the simplest to most complex organisms.

Now, it is known that as cells divide, so do mitochondria, but exactly how mitochondrial division takes place remains a mystery. Is it possible that mitochondria across different multicellular organisms-owing to their shared ancestry-divide in an identical manner? Considering that mitochondria are involved in some of the most crucial processes in the cell, including the maintenance of cellular metabolism, finding the answer to exactly how they replicate could spur further advancements in cell biology research.

In a new study published in Communications Biology, a group of scientists at Tokyo University of Science, led by Prof Sachihiro Matsunaga, wanted to find answers related to the origin of mitochondrial division. For their research, Prof Matsunaga and his team chose to study a type of red alga-the simplest form of a eukaryote, containing only one mitochondrion.

Specifically, they wanted to observe whether the machinery involved in mitochondrial replication is conserved across different species and, if so, why. Talking about the motivation for this study, Prof Matsunaga says, "Mitochondria are important to cellular processes, as they supply energy for vital activities. It is established that cell division is accompanied by mitochondrial division; however, many points regarding its molecular mechanism are unclear."

The scientists first focused on an enzyme called Aurora kinase, which is known to activate several proteins involved in cell division by "phosphorylating" them (a well-known process in which phosphate groups are added to proteins to regulate their functions). By using techniques such as immunoblotting and kinase assays, they showed that the Aurora kinase in red algae phosphorylates a protein called dynamin, which is involved in mitochondrial division.

Excited about these findings, Prof Matsunaga and his team wanted to take their research to the next level by identifying the exact sites where Aurora kinase phosphorylates dynamin, and using mass spectrometric experiments, they succeeded in identifying four such sites. Prof Matsunaga says, "When we looked for proteins phosphorylated by Aurora kinase, we were surprised to find dynamin, a protein that constricts mitochondria and promotes mitochondrial division."

Having gained a little more insight into how mitochondria divide in red algae, the scientists then wondered if the process could be similar in more evolved eukaryotes, such as humans. Prof Matsunaga and his team then used a human version of Aurora kinase to see if it phosphorylates human dynamin-and just as they predicted, it did. This led them to conclude that the process by which mitochondria replicate is very similar in different eukaryotic organisms.

Prof Matsunaga elaborates on the findings by saying, "Using biochemical in vitro assays, we showed that Aurora kinase phosphorylates dynamin in human cells. In other words, it was found that the mechanism by which Aurora kinase phosphorylates dynamin in the mitochondrion is preserved from primitive algae to humans."

Scientists have long pondered over the idea of mitochondrial division being conserved in eukaryotes. This study is the first to show not only the role of a new enzyme in mitochondrial replication but also that this process is similar in both algae and humans, hinting towards the fact that their common ancestry might have something to do with this.

Prof Matsunaga concludes by talking about the potential implications of this study: "Since the mitochondrial fission system found in primitive algae may be preserved in all living organisms including humans, the development of this method can make it easier to manipulate cellular activities of various organisms, as and when required."

As it turns out, we have much more in common with other species than we thought, and part of the evidence lies in our mitochondria!

More information: Shoichi Kato et al, Cyanidioschyzon merolae aurora kinase phosphorylates evolutionarily conserved sites on its target to regulate mitochondrial division, Communications Biology (2019). DOI: 10.1038/s42003-019-0714-x

# data[].attributes.attachment_link.title
A step closer to understanding evolution: Mitochondrial division conserved across species

# data[].attributes.attachment_link.description
Cellular origin is well explained by the "endosymbiotic theory," which famously states that higher organisms called "eukaryotes" have evolved from more primitive single-celled organisms called "prokaryotes." This theory also explains that mitochondria-energy-producing factories of the cell-are actually derived from prokaryotic bacteria, as part of a process called "endosymbiosis."

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The social coevolution hypothesis for the origin of enzymatic cooperation | Nature Ecology & Evolution

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The social coevolution hypothesis for the origin of enzymatic cooperation | Nature Ecology & Evolution

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There are no data to report.

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All code has been made available, along with an implementation of the calculations, in Supplementary Software 1, and is available on GitHub at https://github.com/srlevin/sticky.git.

References

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Maynard Smith, J. & Szathmary, E. The Major Transitions in Evolution (Oxford Univ. Press, 1995).

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Bourke, A. F. Principles of Social Evolution (Oxford Univ. Press, 2011).

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Frank, S. A. Foundations of Social Evolution (Princeton Univ. Press, 1998).

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Acknowledgements

We thank G. Cooper and S. Frank for helpful comments on the manuscript. S.R.L. is supported by The Clarendon Fund, Hertford College and NERC. S.G. is supported by the Leverhulme Trust (visiting professorship grant).

Author information

Affiliations

1. Department of Zoology, University of Oxford, Oxford, UK

Samuel R. Levin & Stuart A. West

2. CEFE UMR 5175, CNRS, Université de Montpellier, Montpellier, France

Sylvain Gandon

Contributions

S.R.L. and S.A.W. conceived of the manuscript. The modelling was carried out by S.R.L. and S.G. All authors contributed equally to the final presentation of the manuscript.

Corresponding author

Correspondence to Samuel R. Levin.

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The authors declare no competing interests.

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Supplementary information

Supplementary Figs. 1 and 2, Table 1, discussion, models and references.

Mathematica notebook containing all of the numerical calculations and code for generating the figures.

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Levin, S.R., Gandon, S. & West, S.A. The social coevolution hypothesis for the origin of enzymatic cooperation. Nat Ecol Evol 4, 132-137 (2020). https://doi.org/10.1038/s41559-019-1039-3
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Paul Adamski

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, Ádám Kun

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Nature Reviews Chemistry (2020)

Mohamed Khadar Abdi

, Ian C W Hardy

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& Daniela Lupi

Biological Journal of the Linnean Society (2020)

Nature Ecology & Evolution (2020)

# data[].attributes.attachment_link.title
The social coevolution hypothesis for the origin of enzymatic cooperation

# data[].attributes.attachment_link.description
At the start of life, the origin of a primitive genome required individual replicators, or genes, to act like enzymes and cooperatively copy each other. The evolutionary stability of such enzymatic cooperation poses a problem, because it would have been susceptible to parasitic replicators that did not act like enzymes but could still benefit from the enzymatic behaviour of other replicators.

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Large multiple sequence alignments with a root-to-leaf regressive method | Nature Biotechnology

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Large multiple sequence alignments with a root-to-leaf regressive method | Nature Biotechnology

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All data, analyses and results are available from Zenodo ( https://doi.org/10.5281/zenodo.3271452).

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The regressive alignment algorithm has been implemented in T-Coffee and is available at the T-Coffee website ( http://www.tcoffee.org) and on GitHub ( https://github.com/cbcrg/tcoffee). A GitHub repository containing the Nextflow workflow25 and Jupyter notebooks26 to replicate the analysis are available at https://github.com/cbcrg/dpa-analysis (release v.1.2).

References

1. 20.
Greenacre, M. J. Biplots in Practice (Fundacion BBVA, 2010).

2. 22.
Herlihy, M. & Shavit, N. The Art of Multiprocessor Programming 1st edn (Morgan Kaufmann, 2012).

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Acknowledgements

We thank G. Riddihough for revisions and comments on the manuscript and O. Gascuel for suggestions. This project was supported by the Centre for Genomic Regulation, the Spanish Plan Nacional, the Spanish Ministry of Economy and Competitiveness, 'Centro de Excelencia Severo Ochoa' (E.G., P.T., C.M., I.E., L.M., A.B., F.K., E.F. and C.N.) and an ERC Consolidator Grant from the European Commission, grant agreement no. 771209 ChrFL (F.K.).

Author information

Affiliations

1. Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain

Edgar Garriga, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Evan Floden & Cedric Notredame

2. Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain

Hafid Laayouni

3. Bioinformatics Studies, ESCI-UPF, Barcelona, Spain

Hafid Laayouni

4. Institute of Science and Technology, Klosterneuburg, Austria

Fyodor Kondrashov

5. Universitat Pompeu Fabra (UPF), Barcelona, Spain

Cedric Notredame

Contributions

C.N. designed and implemented the algorithm. E.F., E.G., L.M., A.B. and P.D.T designed the validation procedure and carried out the validation. I.E. performed statistical and CCA analyses. E.F., C.N., E.G., C.M., L.M., A.B., P.D.T., I.E., F.K. and H.L. wrote and edited the manuscript.

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Correspondence to Evan Floden or Cedric Notredame.

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Garriga, E., Di Tommaso, P., Magis, C. et al. Large multiple sequence alignments with a root-to-leaf regressive method. Nat Biotechnol 37, 1466-1470 (2019). https://doi.org/10.1038/s41587-019-0333-6
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, Tandy Warnow

& Olivier Gascuel

Systematic Biology (2020)

Cory D. Dunn

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& Vivek Sharma

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# data[].attributes.attachment_link.title
Large multiple sequence alignments with a root-to-leaf regressive method

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Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary predictions1,2, but the complexity of aligning large datasets requires the use of approximate solutions3, including the progressive algorithm4. Progressive MSA methods start by aligning the most similar sequences and subsequently incorporate the remaining sequences, from leaf to root, based on a guide tree.

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New artificial evolution research could finally prove Darwin was right

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New artificial evolution research could finally prove Darwin was right

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An international team of researchers may have just figured out why single-celled organisms such as the AIDS virus and cancer cells manage to be so incredibly successful. And, in doing so, they may also have unraveled the mystery behind the origin of life. Hooray for science!

Life on Earth emerged as the result of a bunch of chemicals swirling around in a primordial ooze until they turned into amino acids, then proteins, and eventually cells. The spark of life happened at some point and those non-living cells and clusters went through an evolutionary transition into living organisms.

Here we are 3.5 billion years later and we don't know much else about the process. We know that evolution plays a major role, but exactly what causes the evolutionary transition has eluded scientists so far.

Researchers from the ESPCI Paris, France, and Max Planck Institute for Evolutionary Biology, Plön, Germany, and Andrew Black at University of Adelaide, Australia and Pierrick Bourrat, at Macquarie University, Australia hope to remedy that. They recently conducted an experiment involving "free-living" bacteria - single-celled organisms that live alone in nature - that shows "ecology" may be the missing the link responsible for the spark of life.

The bacteria the team used reproduces by a process called binary fission. Basically, they split into two identical halves. Logically, this means that evolution can't advance bacteria because no matter what happens the offspring have no variance from their parents.

However, when the team forced something called "ecological scaffolding" on large groups of bacteria they found evolutionary behavior similar to that exhibited by groups of multi-celled species. In other words: by forcing nomadic bacteria into groups, they exhibited behavior that placed the well-being of the entire collective over the survival of each individual cell.

Viruses and bacteria may follow this form of evolution by spreading themselves out thin enough to make it from one patch of resources to another, in essence prioritizing the species over the individual cells. This could explain why pathogens sourced from a single cell, such as HIV and cancer, are so successful.

Lead researcher Paul Rainey told Phys.Org:

Not only did groups become more successful, but they even evolved traits that underpinned a developmental program fueling a multi-cellular life cycle.

In essence, we have produced an ecological recipe that, if followed, will result in the affected entities participating in the process of evolution by natural selection, with the outcome being some kind of Darwinian machine.

A Darwin Machine is a construct by which a non-living entity - in this case a bunch of living cells clustered together as a community that, itself, is not a single living organism - can produce a result with greater viability than its contents currently have. Basically, the bacteria in groups "evolved" to be better at dealing with their environment than those that continued to live on their own.

Rainey compares this event - the entire community working together to send a single cell off towards a new resource - like a complex organism reproducing. Per Phys.Org, he says:

For pathogens, such as HIV, the human host is a patch of resource. Transmission of the virus to new hosts via a single cell is akin to a group-level reproductive event.

When this occurs the virus will experience selective conditions as if it were part of a multicellular organism. Our theory thus predicts that HIV populations should be composed of cells that perform different functions-some soma-like and others germ line-like.

According to recent HIV research, this is exactly what's happening.

While the team's results will require further research, they're significant enough to warrant a large measure of optimism. We've struggled to explain how a bunch of protein-based cells swirling around in the primordial soup could "magically" become a living organism, but adding "ecological scaffolding" into the mix as an underpinning factor could provide the math we need to shape our understanding of what "the spark of life" actually entails.

Moreover, this research could have huge implications for the field of artificial intelligence. A successful artificial evolution paradigm could result in a Darwin Machine-based neural network capable of better emulating the natural selection process and, possibly, the human brain's own organic neural network.

Check out the full research paper here on Nature.
ou're here because you want to learn more about artificial intelligence. So do we. So this summer, we're bringing Neural to TNW Conference 2020, where we will host a vibrant program dedicated exclusively to AI. With keynotes by experts from companies like Spotify, RSA, and Medium, our Neural track will take a deep dive into new innovations, ethical problems, and how AI can transform businesses. Get your early bird ticket and check out the full Neural track .
Published February 17, 2020 - 21:46 UTC

# data[].attributes.attachment_link.title
New artificial evolution research could finally prove Darwin was right

# data[].attributes.attachment_link.description
An international team of researchers may have just figured out why single-celled organisms such as the AIDS virus and cancer cells manage to be so incredibly successful. And, in doing so, they may also have unraveled the mystery behind the origin of life. Hooray for science!

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Ecological scaffolding and the evolution of individuality | Nature Ecology & Evolution

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Ecological scaffolding and the evolution of individuality | Nature Ecology & Evolution

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All data are available within the manuscript.

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Simulation codes for the models presented in this paper are available at the GitHub repository https://github.com/andxblack/eco-scaff-paper-code under an MIT licence.

References

1. 15.
Hanschen, E. R. et al. The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity. Nat. Commun. 7, 11370 (2016).

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Gallie, J. et al. Bistability in a metabolic network underpins the de novo evolution of colony switching in Pseudomonas fluorescens. PLoS Biol. 13, e1002109 (2015).

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Gallie, J. et al. Repeated phenotypic evolution by different genetic routes in Pseudomonas fluorescens SBW25. Mol. Biol. Evol. 36, 1071-1085 (2019).

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Acknowledgements

We thank J. Wietz for critical review of the manuscript and valuable comment. We thank S. De Monte, G. Doulcier, M. Diard and members of our respective teams for lively discussion. A.J.B. acknowledges an Australian Research Council (ARC) DECRA fellowship (grant no. DE160100690) and support from both the ARC Centre of Excellence for Mathematical and Statistical Frontiers (CoE ACEMS) and the Australian Government NHMRC Centre for Research Excellence in Policy Relevant Infectious diseases Simulation and Mathematical Modelling (CRE PRISM2). P.B. acknowledges a Macquarie University Research Fellowship and a grant from the John Templeton Foundation (grant no. ID 60811). P.B.R. acknowledges generous financial support from MPG core funding and previously from the Marsden Fund Council from New Zealand Government funding, administered by the Royal Society of New Zealand.

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Affiliations

1. School of Mathematical Sciences, University of Adelaide, Adelaide, South Australia, Australia

Andrew J. Black

2. Department of Philosophy, Macquarie University, Sydney, New South Wales, Australia

Pierrick Bourrat

3. Department of Philosophy & Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia

Pierrick Bourrat

4. Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany

Paul B. Rainey

5. Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI) UMR8231, ESPCI Paris, CNRS, PSL Research University, Paris, France

Paul B. Rainey

Contributions

P.B.R. and P.B. developed the main concepts. A.J.B. contributed the mathematical models and ran simulations to clarify initial ideas. All authors wrote and revised the manuscript.

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Correspondence to Andrew J. Black or Paul B. Rainey.

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Extended data

The simulations have only 10 patches and modified mutational parameters compared with those in Fig. 2 of the main text. This is to allow a clearer visualization of the process, which otherwise requires many more generations for change to be apparent. Video versions of these are also included in the supplementary material. As in Figs. 4 and 5 of the main text, the cell numbers in each patch are proportional to the area of the circles and the growth rates are indicated by the colours, as shown by the colour bar in Fig. 4 of the main text. The mutational parameters are larger for these simulations ( µ=0.05, p = 0.05) so evolution occurs on a quicker timescale as compared with the results shown in Fig. 3 of the main text.

The comparative slowness of this convergence, as well as the large fluctuations in the mean value of q for single realizations, can be attributed to the flatness of the fitness landscape about the equilibrium as shown in the Supplementary Information.

Fitness landscapes showing the effect of changes in the assistance, ρ, given to dispersing G cells by non-dispersing S cells on the equilibrium (*) relationship between cell growth rate, β, and the rate of production of S cells, q, under the slow ( T  = 30) dispersal regime.

Supplementary information

Supplementary Figs. 1-7, text and references.

Single realization of the model under the slow dispersal regime as shown in Fig 4A.

Single realization of the model under the fast dispersal regime as shown in Fig 4B.

Evolutionary fate of 10 lineages under the slow dispersal regime as shown in Extended Data 1A.

Evolutionary fate of 10 lineages under the fast dispersal regime as shown in Extended Data 1B.

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Black, A.J., Bourrat, P. & Rainey, P.B. Ecological scaffolding and the evolution of individuality . Nat Ecol Evol 4, 426-436 (2020). https://doi.org/10.1038/s41559-019-1086-9
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# data[].attributes.attachment_link.title
Ecological scaffolding and the evolution of individuality

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Evolutionary transitions in individuality are central to the emergence of biological complexity. Recent experiments provide glimpses of processes underpinning the transition from single cells to multicellular life and draw attention to the critical role of ecology. Here, we emphasize this ecological dimension and argue that its current absence from theoretical frameworks hampers development of general explanatory solutions.

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Brève | Une protéine d'origine extraterrestre découverte dans une météorite

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Brève | Une protéine d'origine extraterrestre découverte dans une météorite

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" C'est la première jamais découverte dans une extraterrestre ", s'enthousiasment les trois chercheurs qui viennent de publier leur trouvaille sur le site . Les scientifiques, de l'université Harvard, de la biotech Plex Corporation et de Bruker Scientific ont analysé la météorite Acfer 086, trouvée en Algérie il y a 30 ans, grâce à la spectrométrie de masse .

Ils ont identifié une comprenant des chaînes de et d'hydroxyglycine terminées par des de , d' et de . La molécule, que les chercheurs ont baptisée hémolithine, possède une structure semblable à d'autres protéines terrestres connues, avancent les chercheurs.

Des acides aminés ont déjà été découverts dans des météorites , mais n'ayant pas de chaîne suffisamment longue pour être considérés comme des protéines complètes. Les résultats, qui demandent encore à être confirmés, appuient la thèse de l'origine extraterrestre de la vie sur . Mais d'autres chercheurs penchent plutôt vers l'hypothèse de protéines formées à partir d'ARN et d'éléments organiques déjà présents sur Terre.

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Une protéine d'origine extraterrestre découverte dans une météorite

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" C'est la première jamais découverte dans une extraterrestre ", s'enthousiasment les trois cher­cheurs qui viennent de publier leur trouvaille sur le site . Les scientifiques, de l'uni­ver­sité Harvard, de la biotech Plex Corporation et de Bruker Scientific ont analysé la météo­rite Acfer 086, trouvée en Algérie il y a 30 ans, grâce à la spectrométrie de masse .

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New mathematical model reveals how major groups arise in evolution

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New mathematical model reveals how major groups arise in evolution

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Credit: CC0 Public Domain

Researchers at Uppsala University and the University of Leeds presents a new mathematical model of patterns of diversity in the fossil record, which offers a solution to Darwin's "abominable mystery" and strengthens our understanding of how modern groups originate. The research is published in the journal Science Advances.

The origins of many major groups of organisms in the fossil record seem to lie shrouded in obscurity. Indeed, one of the most famous examples, the flowering plants, was called "an abominable mystery" by Darwin. Many modern groups appear abruptly, and their predecessors-if there are any-tend to be few in number and vanish quickly from the fossil record shortly afterwards. Conversely, once groups are established, they tend to be dominant for long periods of time until interrupted by the so-called "mass extinctions" such as the one at the end of the Cretaceous period some 66 million years ago.

Such patterns appear surprising, and often seem to be contradicted by the results from " molecular clocks"-using calibrated rates of change of molecules found in living organisms to estimate when they started to diverge from each other. How can this conflict be resolved, and what can we learn from it?

In a paper, Graham Budd, Uppsala University, and Richard Mann, University of Leeds, present a novel mathematical model for how the origin of modern groups based on a so-called "birth-death" process of speciation and extinction. Birth-death models show how random extinction and speciation events give rise to large-scale patterns of diversity through time. Budd and Mann show that the ancestral forms of modern groups are typically rather few in number, and once they give rise to the modern group, they can be expected to quickly go extinct. The modern group, conversely, tends to diversify very quickly and thus swamp out the ancestral forms. Thus, rather surprisingly, living organisms capture a great percentage of all the diversity there has ever been.

The only exceptions to these patterns are caused by the "mass extinctions," of which there have been at least five throughout history, which can massively delay the origin of the modern group, and thus extend the longevity and the diversity of the ancestral forms, called "stem groups." A good example of this is the enormous diversity of the dinosaurs, which properly considered are stem-group birds. The meteorite impact at the end of the Cretaceous some 66 million years ago killed off nearly all of them, apart from a tiny group that survived and flourished to give rise to the more than 10,000 species of living birds.

The new model explains many puzzling features about the fossil record and suggests that it often records a relatively accurate picture of the origin of major groups. This in turn suggests that increased scrutiny should be paid to molecular clock models when they significantly disagree with what the fossil record might be telling us.

More information: Graham Budd and Richard Mann. The dynamics of stem and crown groups. Science Advances (2020). DOI: 10.1126/sciadv.aaz1626 , advances.sciencemag.org/content/6/8/eaaz1626

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New mathematical model reveals how major groups arise in evolution

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Researchers at Uppsala University and the University of Leeds presents a new mathematical model of patterns of diversity in the fossil record, which offers a solution to Darwin's "abominable mystery" and strengthens our understanding of how modern groups originate. The research is published in the journal Science Advances.

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Species | The Smithsonian Institution's Human Origins Program

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Species | The Smithsonian Institution's Human Origins Program

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The Smithsonian Institution's Human Origins Program

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Smithsonian National Museum of Natural History

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Homosexualité : Quand Freud fait de la biologie – Le Carnet de l'Épervier

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Homosexualité : Quand Freud fait de la biologie – Le Carnet de l'Épervier

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Phylogénie et évolution moléculaires : Bio-informatique (5)

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Phylogénie et évolution moléculaires : Bio-informatique (5)

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Phylogénie et évolution moléculaires : Bio-informatique (5)

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Rapports d'expertise collective Les Cahiers du Comité pour l'histoire de l'Inserm Revue médecine/sciences Le magazine | Science&Santé Les Dossiers de la Mission Associations de l'Inserm

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Le lien entre diversité génétique et adaptation par sélection naturelle

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La diversité génétique des populations de plantes et d'animaux à l'échelle mondiale: mieux la comprendre pour mieux la conserver
La diversité génétique permet aux espèces de s'adapter face aux modifications de l' environnement (L'environnement est tout ce qui nous entoure. C'est l'ensemble des éléments naturels et...) . C'est un trésor façonné par l'évolution et la conserver efficacement à l'échelle du globe est devenu une priorité.

Dans un article paru dans Nature Communications le 22 janvier 2021, des scientifiques de la Station d'Ecologie Théorique et Expérimentale ( En art, il s'agit d'approches de création basées sur une remise en question des dogmes...) (SETE - CNRS), de l' Institut (Un institut est une organisation permanente créée dans un certain but. C'est...) de Systématique (En sciences de la vie et en histoire naturelle, la systématique est la science qui a pour...) , Evolution, Biodiversité (La biodiversité est la diversité naturelle des organismes vivants. Elle s'apprécie...) (ISYEB - MNHN / CNRS (Le Centre national de la recherche scientifique, plus connu sous son sigle CNRS, est le plus grand...) / Sorbonne (La Sorbonne est un complexe monumental du Quartier latin de Paris. Elle tire son nom du...) Université (Une université est un établissement d'enseignement supérieur dont l'objectif est la...) / EPHE / Université des Antilles) et de l'Université de Louvain analysent pour la première fois la distribution de la diversité génétique (La diversité génétique est une caractéristique décrivant le niveau de...) chez plus de 8000 populations de plantes et d'animaux à l'échelle du globe. Ils démontrent une distribution très hétérogène de cette diversité entre les espèces et les espaces, qui résulte de nombreux facteurs comme le climat (Le climat correspond à la distribution statistique des conditions atmosphériques dans une...) ou la longévité (La longévité d'un être vivant est la durée de vie pour laquelle il est...) des individus. Ces résultats ouvrent de nouvelles perspectives pour la conservation de la biodiversité à l'échelle du globe.

Face aux changements globaux comme le réchauffement climatique (Le réchauffement climatique, également appelé réchauffement planétaire, ou...) , la destruction des habitats ou la pollution (La pollution est définie comme ce qui rend un milieu malsain. La définition varie selon le...) , les espèces animales et végétales doivent s'adapter pour persister. La diversité génétique est l'essence qui permet aux espèces de s'adapter par sélection naturelle (En biologie, la sélection naturelle est l'un des mécanismes qui guident l'évolution...) ; plus elle est élevée, plus les capacités d'adaptation sont importantes. La conservation de cette facette de la biodiversité est donc essentielle. Toutefois, on sait encore mal comment elle est répartie sur Terre (La Terre est la troisième planète du Système solaire par ordre de distance...) ni quels sont les facteurs qui gouvernent sa distribution à une telle échelle. Ces connaissances sont requises pour développer des politiques de conservation qui soient pertinentes et durables.

Dans une récente étude parue dans Nature Communications, un groupe de chercheurs belges et français, issus de de la Station d'Ecologie Théorique et Expérimentale (SETE - CNRS), de l'Institut de Systématique, Evolution, Biodiversité (ISYEB - MNHN / CNRS / Sorbonne Université / EPHE / Université des Antilles) et de l'Université de Louvain, a synthétisé pour la première fois les données (Dans les technologies de l'information (TI), une donnée est une description élémentaire, souvent...) génétiques existantes dans la littérature pour plus de 8000 populations et plus de 700 espèces de plantes et d'animaux terrestres à l'échelle de la planète (Une planète est un corps céleste orbitant autour du Soleil ou d'une autre étoile de...) (Figure 1).

En collectant les données génétiques à l'échelle de la population, c'est à dire là où les contraintes environnementales agissent sur les organismes, les auteurs ont pu identifier les facteurs qui influencent la diversité génétique: des facteurs environnementaux (par exemple le climat actuel ou la variabilité climatique au cours des derniers millénaires), mais aussi des facteurs biologiques (les caractéristiques des individus comme leur taille, leur fécondité ou leur longévité) et biogéograhiques (la place de la population au sein de l'aire de répartition de l'espèce).

Leurs résultats indiquent que la diversité génétique est distribuée de façon très hétérogène à l'échelle de la planète, mais aussi entre les espèces (Figure 2). Par exemple, les plantes ont en moyenne (La moyenne est une mesure statistique caractérisant les éléments d'un ensemble de...) une diversité génétique beaucoup plus faible que les animaux. De la même façon, au sein des animaux, les amphibiens et les mollusques ont une diversité génétique particulièrement faible (Figure 2), ceci pouvant s'expliquer par la façon dont ces organismes se reproduisent. Certaines généralités ont par ailleurs émergé entre les espèces, comme par exemple l'impact consistant de facteurs climatiques contemporains comme le niveau de précipitation (En météorologie, le terme précipitation désigne des cristaux de glace ou des...) ou la température (La température est une grandeur physique mesurée à l'aide d'un thermomètre et...) , ou encore le rôle majeur de caractéristiques individuelles telles que la longévité (Figure 2).

Cette étude confirme par ailleurs l'hypothèse selon laquelle - de façon générale - la diversité génétique est plus forte au coeur de l'aire de répartition d'une espèce (Dans les sciences du vivant, l'espèce (du latin species, " type "...) plutôt qu'en périphérie (Le mot périphérie vient du grec peripheria qui signifie circonférence. Plus...) , même si des exceptions ont été identifiées, avec des implications importantes en matière (La matière est la substance qui compose tout corps ayant une réalité tangible. Ses...) de conservation. En revanche, et de façon très surprenante, les auteurs n'ont pas trouvé d'évidence que la diversité génétique était plus forte à l'équateur qu'aux pôles, ce qui remet en question l'idée reçue voulant que tous les niveaux de biodiversité soient plus riches à l'équateur. De manière générale, cette étude montre que la distribution de la diversité génétique est influencée par de nombreux facteurs qui parfois interagissent, ce qui implique que de nouvelles théories soient élaborées pour expliquer sa répartition à l'échelle du globe.

La plupart des plans internationaux de conservation de la biodiversité sont actuellement développés à l'échelle des espèces, avec comme principal enjeu le maintien de la diversité des espèces à l'échelle du globe. Néanmoins la diversité génétique propre aux espèces est essentielle car elle constitue le fondement de la biodiversité. Cette étude, en servant de de référence, est donc une première pierre à l'édification d'une politique globale de conservation de la biodiversité couvrant tous ses niveaux d' organisation (Une organisation est) , des gènes aux espèces et aux écosystèmes.

Ce travail contribue à comprendre la façon dont se répartit la biodiversité des plantes et des animaux à l'échelle du globe, et comment les activités humaines modifient cette répartition. En particulier, cette étude se concentre sur la diversité génétique des êtres vivants qui permet à ces derniers d'évoluer face aux nouvelles pressions comme le changement climatique.

Références:
De Kort H., Prunier J.G., Ducatez S., Honnay O., Baguette M., Stevens V.M., and Blanchet S. (2021). Life history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal (Un animal (du latin animus, esprit, ou principe vital) est, selon la classification classique, un...) populations. Nature Communications

Contact:
- Michel Baguette - Institut de Systématique, Evolution, Biodiversité (ISYEB - CNRS/Sorbonne Univ/MNHN/EPHE) - baguette at mnhn.fr
- Simon Blanchet - Station d'Ecologie Théorique et Expérimentale (SETE - CNRS) - Simon.blanchet at sete.cnrs.fr
- Hanne De Kort - Laboratory of Plant Conservation and Population Biology (KU Leuven) - hanne.dekort at kuleuven.be
- Olivier Guillaume (Guillaume est un prénom masculin d'origine germanique. Le nom vient de Wille, volonté et Helm,...) - Correspondant communication (La communication concerne aussi bien l'homme (communication intra-psychique, interpersonnelle,...) - Station d'Ecologie Théorique et Expérimentale (SETE - CNRS) - Olivier.GUILLAUME at sete.cnrs.fr
- Catherine Clerc - Correspondant communication - Station d'Ecologie Théorique et Expérimentale (SETE - CNRS) - catherine.clerc at sete.cnrs.fr

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📰 Le lien entre diversité génétique et adaptation par sélection naturelle

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La diversité génétique des populations de plantes et d'animaux à l'échelle mondiale: mieux la comprendre pour mieux la conserver La diversité génétique permet aux espèces de s'adapter face aux modifications de l' environnement (L'environnement est tout ce qui nous entoure. C'est l'ensemble des éléments naturels et...) .

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Un mystérieux microbe découvert dans les profondeurs de l'océan Pacifique pourrait détenir les secrets de l'évolution des premières formes de vie muticellulaires. En effet, selon une nouvelle étude, le petit " organisme à tentacules " pourrait nous renseigner sur ce qui a permis à la vie de se complexifier durant les premiers stades de l'évolution.
Bien avant l'existence d'êtres vivants complexes, le monde abritait de simples organismes unicellulaires, des archées et les bactéries. Il y a entre 2 et 1.8 milliard d'années, ces micro-organismes ont commencé à évoluer, conduisant à l'émergence de formes de vie plus complexes, appelées eucaryotes.

Le domaine des eucaryotes comprend aujourd'hui les humains, les animaux, les plantes et les champignons. Mais cette incroyable évolution de la vie aquatique à la vie hors de l'eau, puis à la marche - et pour les êtres les plus évolués, à la pensée et aux sentiments, est encore mal comprise par les scientifiques.

Les Asgard archaea, potentiels ancêtres des eucaryotes

Dans une précédente étude, des biologistes avaient émis l'hypothèse qu'un groupe d'archées appelé Asgard archaea (les archées d'Asgård) regroupait les ancêtres très recherchés des eucaryotes, car ils contiennent des gènes similaires à leurs homologues complexes.

Pour analyser à quoi ressemblaient ces microbes et comment cette transition aurait pu se produire, un groupe de chercheurs japonais a ensuite passé une décennie à collecter et analyser la boue du fond de la crête d'Omine, au large des côtes du Japon. Les résultats de l'étude ont été publiés le 15 janvier dans la revue Nature.

L'équipe a conservé les échantillons de boue (et les micro-organismes qui s'y trouvent) dans un bioréacteur spécial, dans un environnement de laboratoire qui imite les conditions de la mer profonde dans laquelle ils ont été trouvés.

Des années plus tard, ils ont commencé à isoler les micro-organismes dans des échantillons. Le but initial des chercheurs était de trouver des microbes consommant du méthane et qui pourraient être en mesure de nettoyer les eaux usées, selon le New York Times. Mais quand ils ont découvert que leurs échantillons contenaient une souche inconnue d'Asgard archaea, ils ont décidé de l'analyser et de la cultiver en laboratoire.

Prometheoarchaeum syntrophicum, une nouvelle souche d'Asgard archaea

Ils ont nommé la souche nouvellement trouvée d'Asgard archaea " Prometheoarchaeum syntrophicum " , d'après le dieu grec Prométhée, qui aurait créé des humains à partir de boue, selon la mythologie.

Les chercheurs ont constaté que ces archées se cultivaient relativement lentement, ne doublant que tous les 14 à 25 jours. Leur analyse a ensuite confirmé que P. syntrophicum avait un grand nombre de gènes similaires à ceux des eucaryotes. En effet, ces gènes détenaient les instructions pour créer certaines protéines présentes à l'intérieur de ces microbes. Cependant, comme prévu, les protéines n'ont pas créé de structures semblables à des organites, comme celles trouvées à l'intérieur des eucaryotes.

Ils ont également constaté que les microbes avaient de longues saillies ramifiées ressemblant à des tentacules, à l'extérieur, qui pourraient être utilisées pour attraper les bactéries de passage. En effet, l'équipe a découvert que les microbes avaient tendance à coller aux autres bactéries dans les boîtes de Petri.
Sur le même sujet : La vie sur Terre s'est-elle formée à partir d'un mélange d'RN et d'ADN ?
Une hypothèse élégante expliquant les changements chez P. syntrophicum

Les auteurs proposent une hypothèse intéressante pour ce qui s'est passé dans ces eaux anciennes, qu'ils expliquent dans une vidéo récemment publiée (disponible en fin d'article) : il y a environ 2.7 milliards d'années, l'oxygène a commencé à s'accumuler sur Terre. Mais ayant vécu si longtemps dans un monde sans oxygène, cet élément s'avérerait toxique pour P. syntrophicum.

Alors, P. syntrophicum peut avoir développé une nouvelle adaptation : une façon de former des liens avec des bactéries tolérantes à l'oxygène. Ces bactéries auraient procuré à P. syntrophicum les vitamines et les composés nécessaires pour survivre, tout en se nourrissant à leur tour des déchets des archées.

Alors que les niveaux d'oxygène augmentaient encore plus, P. syntrophicum aurait pu devenir plus agressif, arrachant des bactéries de passage avec ses longues structures ressemblant à des tentacules, et les intégrant. À l'intérieur de P. syntrophicum, cette bactérie aurait finalement évolué en une organite produisant de l'énergie, la clé de la survie des eucaryotes : la mitochondrie.

Le succès de l'équipe dans la culture de Prometheoarchaeum, après des efforts s'étalant sur plus d'une décennie, " représente une énorme percée pour la microbiologie ", écrivent dans un éditorial d'accompagnement Christa Schleper et Filipa L. Sousa, deux chercheuses de l'Université de Vienne, qui n'ont pas participé à l'étude. " Il ouvre la voie à l'utilisation de techniques moléculaires et d'imagerie pour élucider davantage le métabolisme des Prométhéoarché et le rôle des protéines de signature eucaryote en biologie des cellules archéennes " ajoutent-elles.

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Cet étrange organisme des profondeurs pourrait cacher des secrets sur les origines de la vie complexe sur Terre

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Un mystérieux microbe découvert dans les profondeurs de l'océan Pacifique pourrait détenir les secrets de l'évolution des premières formes de vie muticellulaires. En effet, selon une nouvelle étude, le petit " organisme à tentacules " pourrait nous renseigner sur ce qui a permis à la vie de se complexifier durant les premiers stades de l'évolution.