# data[].attributes.body
"Mi poesía tiene un compromiso social y político, mejor dicho, revolucionario. He sido poeta, sacerdote y revolucionario "

# data[].attributes.attachment_link.readable_text
Father Cardenal defied the Roman Catholic Church in the 1980s by serving as a minister in the revolutionary government of Nicaragua.

Ernesto Cardenal at a reading of his poems in Mexico City in 2014. Fascinated by evolution and its lessons for politics, he began to incorporate science into his poetry in the 1980s. Credit... Adriana Zehbrauskas for The New York Times

The Rev. Ernesto Cardenal, one of Latin America's most admired poets and priests, who defied the Roman Catholic Church in the 1980s by serving in the revolutionary Sandinista government of Nicaragua, died on Sunday in Managua, Nicaragua. He was 95.

His personal assistant, Luz Marina Acosta, confirmed his death to The Associated Press.

Born to a wealthy Nicaraguan family, Father Cardenal became a prominent intellectual voice of the Nicaraguan revolution and an ardent proponent of liberation theology, a Christian movement rooted in Marxist principles and committed to social justice and uplifting the poor. He was appointed Nicaragua's first minister of culture after the Sandinistas overthrew the dictator Gen. Anastasio Somoza Debayle in 1979.

As the Vatican's opposition to liberation theology intensified in the 1980s under Pope John Paul II, Father Cardenal became a focal point. Before a scheduled visit to Nicaragua in 1983, the pope publicly demanded that Father Cardenal and four other priests who had actively supported the revolution resign their government positions. The Sandinista government refused the demand to replace them, but said its invitation to the pope still stood.

After months of public arguing, the pope accepted the invitation and landed in Managua, Nicaragua's capital. As he walked along a receiving line on the tarmac shaking hands, the pope seemed taken aback to see Father Cardenal among the dignitaries.

While other priests were in clerical garb, Father Cardenal had shown up wearing a collarless white shirt, slacks and his signature black beret over his thick white hair. When he knelt to kiss the pope's ring, the pope withheld his hand and wagged his finger at him as he spoke to him, apparently sternly. According to a Vatican official, the pope told Father Cardenal, "You must straighten out your position with the church," The Associated Press reported.

Videotape of the scolding, though not audible, was broadcast around the world.

"Christ led me to Marx," Father Cardenal said in an interview in 1984. "I don't think the pope understands Marxism. For me, the four gospels are all equally communist. I'm a Marxist who believes in God, follows Christ, and is a revolutionary for the sake of his kingdom."

His priestly authority was revoked by Nicaragua's bishops that same year. (Three other priests were also disciplined.) Father Cardenal's suspension was lifted in February 2019, when Pope Francis granted him absolution from "all canonical censorships," the Vatican News reported.

Father Cardenal began writing poetry as a young man, tracing the tormented history of Nicaragua and Latin America as epics in blank verse.

Much of his poetry, though, was intimate: love poems that recalled the longings of his youth, finely wrought images of city lights at dusk or his famous "Prayer for Marilyn Monroe," in which he describes how Monroe was found on her deathbed in 1962, "like someone wounded by gangsters/stretching out his hand to a disconnected telephone."

Fascinated by evolution and its lessons for politics, Father Cardenal began to incorporate science into his poetry in the 1980s. He developed the theme until the end of his life, marveling at the origins of the universe and the mysteries of DNA - sources of awe that in his vision brought people closer to God.

"In this monumental vision, everything merges and condenses," the Nicaraguan writer Sergio Ramírez wrote in the introduction to Father Cardenal's anthology "Ninety at Ninety,"which was published in Spanish in 2014. "Not only do the poet's intimate personal experience and the scientific exploration of the heavens enter into the mystical, so do the memories of his own past."

The most recent complete collection of Father Cardenal's poetry published in English was "Pluriverse: New and Selected Poems," (2009, edited and translated in part by Jonathan Cohen).

Closing the volume was the poem "Stardust," Father Cardenal's meditation on death. It concludes:
And the galaxy was taking the shape of a flower the way it looks now on a starry night. Our flesh and our bones come from other stars and perhaps even from other galaxies, we are universal, and after death we will help to form other stars

and other galaxies. We come from the stars, and to them we shall return.
Ernesto Cardenal Martínez was born on Jan. 20, 1925, to an upper-class family in Granada, a city on Lake Nicaragua. He studied literature in Managua and at Columbia University in New York City, where he read Walt Whitman, Emily Dickinson and Ezra Pound.

He returned to Nicaragua in the 1950s, but after a failed coup against the Somoza family, he fled and joined the Trappist monastery Gethsemani, in Kentucky, where he befriended the American monk and writer Thomas Merton. He was ordained a priest after his subsequent return to Nicaragua.

Father Cardenal was an early supporter of the Sandinista National Liberation Front, which was founded in the early 1960s, named after Augusto César Sandino, the revolutionary who had led a guerrilla campaign against the American occupation of Nicaragua in the 1920s and '30s and was assassinated in 1934.

Father Cardenal furthered the cause after settling on an island in the Solentinamearchipelago, in vast Lake Nicaragua near the southern border, in the 1960s. He built a chapel, founded an artists colony, and taught literature and painting to local residents.

His poetry began to gain recognition. He became known for what he called his "Epigrams" - lyrical bursts about love and longing mixed with political and social commentary against the Somoza regime. In one, he wrote:
I've handed out clandestine pamphlets, yelling: VIVA LA LIBERTAD! In the middle of the street defying armed guards. I participated in the April rebellion: but I grow pale when I pass by your house and one look from you makes me tremble.
His sermons, too, were political, full of denunciations of the Somoza regime. Some of his young parishioners became "guerrilleros," and the island became a central military training ground for the Sandinista movement. After the Sandinistas came to power in 1979, after a bloody period of rioting, guerrilla resistance and a mass kidnapping operation in the capital, Father Cardenal was named minister of culture by the junta leader, Daniel Ortega.

As a government minister, Father Cardenal sought what he called the "democratization of culture." He created poetry workshops around the country, tapping into Nicaragua's rich poetic tradition, embodied in part by Ruben Dario, who spearheaded a Latin American modernist literary movement in the late 19th century.

But Father Cardenal's critics said the ministry was imposing ideological uniformity by pressuring new writers to produce propaganda, particularly during the Sandinistas' long guerrilla war against an American-backed counterrevolutionary force, known as the contras.

No immediate family members survive. His brother, the Rev. Fernando Cardenal, died in 2016.

Father Cardenal remained culture minister until 1987, when the ministry was dissolved and merged with another government agency. In the 1990s he distanced himself from the Sandinista government and in recent years criticized what he called the increasingly authoritarian style of Mr. Ortega, who became president in 2007. For Father Cardenal, the Sandinista revolution had failed.

But he remained committed to his Marxist ideals.

"I am a revolutionary," Father Cardenal said in an interview with The New York Times published in January 2015. "Revolutionary means that I want to change the world."

He added: "The Bible is full of revolutions. The prophets are people with a message of revolution. Jesus of Nazareth takes the revolutionary message of the prophets. And we also will continue trying to change the world and make revolution. Those revolutions failed, but others will come."

Elisabeth Malkin contributed reporting.

# data[].attributes.attachment_link.title
Ernesto Cardenal, Nicaraguan Priest, Poet and Revolutionary, Dies at 95

# data[].attributes.attachment_link.description
Father Cardenal defied the Roman Catholic Church in the 1980s by serving as a minister in the revolutionary government of Nicaragua. The Rev. Ernesto Cardenal, one of Latin America's most admired poets and priests, who defied the Roman Catholic Church in the 1980s by serving in the revolutionary Sandinista government of Nicaragua, died on Sunday in Managua, Nicaragua.

# data[].attributes.attachment_link.readable_text
Several years ago, I was given as a gift a remote session with a bibliotherapist at the London headquarters of the School of Life, which offers innovative courses to help people deal with the daily emotional challenges of existence. I have to admit that at first I didn't really like the idea of being given a reading "prescription." I've generally preferred to mimic Virginia Woolf's passionate commitment to serendipity in my personal reading discoveries, delighting not only in the books themselves but in the randomly meaningful nature of how I came upon them (on the bus after a breakup, in a backpackers' hostel in Damascus, or in the dark library stacks at graduate school, while browsing instead of studying). I've long been wary of the peculiar evangelism of certain readers: You must read this, they say, thrusting a book into your hands with a beatific gleam in their eyes, with no allowance for the fact that books mean different things to people-or different things to the same person-at various points in our lives. I loved John Updike's stories about the Maples in my twenties, for example, and hate them in my thirties, and I'm not even exactly sure why.

But the session was a gift, and I found myself unexpectedly enjoying the initial questionnaire about my reading habits that the bibliotherapist, Ella Berthoud, sent me. Nobody had ever asked me these questions before, even though reading fiction is and always has been essential to my life. I love to gorge on books over long breaks-I'll pack more books than clothes, I told Berthoud. I confided my dirty little secret, which is that I don't like buying or owning books, and always prefer to get them from the library (which, as I am a writer, does not bring me very good book-sales karma). In response to the question "What is preoccupying you at the moment?," I was surprised by what I wanted to confess: I am worried about having no spiritual resources to shore myself up against the inevitable future grief of losing somebody I love, I wrote. I'm not religious, and I don't particularly want to be, but I'd like to read more about other people's reflections on coming to some sort of early, weird form of faith in a "higher being" as an emotional survival tactic. Simply answering the questions made me feel better, lighter.

We had some satisfying back-and-forths over e-mail, with Berthoud digging deeper, asking about my family's history and my fear of grief, and when she sent the final reading prescription it was filled with gems, none of which I'd previously read. Among the recommendations was "The Guide," by R. K. Narayan. Berthoud wrote that it was "a lovely story about a man who starts his working life as a tourist guide at a train station in Malgudi, India, but then goes through many other occupations before finding his unexpected destiny as a spiritual guide." She had picked it because she hoped it might leave me feeling "strangely enlightened." Another was "The Gospel According to Jesus Christ," by José Saramago: "Saramago doesn't reveal his own spiritual stance here but portrays a vivid and compelling version of the story we know so well." "Henderson the Rain King," by Saul Bellow, and "Siddhartha," by Hermann Hesse, were among other prescribed works of fiction, and she included some nonfiction, too, such as "The Case for God," by Karen Armstrong, and "Sum," by the neuroscientist David Eagleman, a "short and wonderful book about possible afterlives."

I worked my way through the books on the list over the next couple of years, at my own pace-interspersed with my own "discoveries"-and while I am fortunate enough to have my ability to withstand terrible grief untested, thus far, some of the insights I gleaned from these books helped me through something entirely different, when, over several months, I endured acute physical pain. The insights themselves are still nebulous, as learning gained through reading fiction often is-but therein lies its power. In a secular age, I suspect that reading fiction is one of the few remaining paths to transcendence, that elusive state in which the distance between the self and the universe shrinks. Reading fiction makes me lose all sense of self, but at the same time makes me feel most uniquely myself. As Woolf, the most fervent of readers, wrote, a book "splits us into two parts as we read," for "the state of reading consists in the complete elimination of the ego," while promising "perpetual union" with another mind.

Bibliotherapy is a very broad term for the ancient practice of encouraging reading for therapeutic effect. The first use of the term is usually dated to a jaunty 1916 article in The Atlantic Monthly, "A Literary Clinic." In it, the author describes stumbling upon a "bibliopathic institute" run by an acquaintance, Bagster, in the basement of his church, from where he dispenses reading recommendations with healing value. "Bibliotherapy is...a new science," Bagster explains. "A book may be a stimulant or a sedative or an irritant or a soporific. The point is that it must do something to you, and you ought to know what it is. A book may be of the nature of a soothing syrup or it may be of the nature of a mustard plaster." To a middle-aged client with "opinions partially ossified," Bagster gives the following prescription: "You must read more novels. Not pleasant stories that make you forget yourself. They must be searching, drastic, stinging, relentless novels." (George Bernard Shaw is at the top of the list.) Bagster is finally called away to deal with a patient who has "taken an overdose of war literature," leaving the author to think about the books that "put new life into us and then set the life pulse strong but slow."

Today, bibliotherapy takes many different forms, from literature courses run for prison inmates to reading circles for elderly people suffering from dementia. Sometimes it can simply mean one-on-one or group sessions for "lapsed" readers who want to find their way back to an enjoyment of books. Berthoud and her longtime friend and fellow bibliotherapist Susan Elderkin mostly practice "affective" bibliotherapy, advocating the restorative power of reading fiction. The two met at Cambridge University as undergraduates, more than twenty years ago, and bonded immediately over the shared contents of their bookshelves, in particular Italo Calvino's novel "If on a Winter's Night a Traveller," which is itself about the nature of reading. As their friendship developed, they began prescribing novels to cure each other's ailments, such as a broken heart or career uncertainty. "When Suse was having a crisis about her profession-she wanted to be a writer, but was wondering if she could cope with the inevitable rejection-I gave her Don Marquis's 'Archy and Mehitabel' poems," Berthoud told me. "If Archy the cockroach could be so dedicated to his art as to jump on the typewriter keys in order to write his free-verse poems every night in the New York offices of the Evening Sun, then surely she should be prepared to suffer for her art, too." Years later, Elderkin gave Berthoud,who wanted to figure out how to balance being a painter and a mother, Patrick Gale's novel "Notes from an Exhibition," about a successful but troubled female artist.

They kept recommending novels to each other, and to friends and family, for many years, and, in 2007, when the philosopher Alain de Botton, a fellow Cambridge classmate, was thinking about starting the School of Life, they pitched to him the idea of running a bibliotherapy clinic. "As far as we knew, nobody was doing it in that form at the time," Berthoud said. "Bibliotherapy, if it existed at all, tended to be based within a more medical context, with an emphasis on self-help books. But we were dedicated to fiction as the ultimate cure because it gives readers a transformational experience."

Berthoud and Elderkin trace the method of bibliotherapy all the way back to the Ancient Greeks, "who inscribed above the entrance to a library in Thebes that this was a 'healing place for the soul.' " The practice came into its own at the end of the nineteenth century, when Sigmund Freud began using literature during psychoanalysis sessions. After the First World War, traumatized soldiers returning home from the front were often prescribed a course of reading. "Librarians in the States were given training on how to give books to WWI vets, and there's a nice story about Jane Austen's novels being used for bibliotherapeutic purposes at the same time in the U.K.," Elderkin says. Later in the century, bibliotherapy was used in varying ways in hospitals and libraries, and has more recently been taken up by psychologists, social and aged-care workers, and doctors as a viable mode of therapy.

There is now a network of bibliotherapists selected and trained by Berthoud and Elderkin, and affiliated with the School of Life, working around the world, from New York to Melbourne. The most common ailments people tend to bring to them are the life-juncture transitions, Berthoud says: being stuck in a rut in your career, feeling depressed in your relationship, or suffering bereavement. The bibliotherapists see a lot of retirees, too, who know that they have twenty years of reading ahead of them but perhaps have only previously read crime thrillers, and want to find something new to sustain them. Many seek help adjusting to becoming a parent. "I had a client in New York, a man who was having his first child, and was worried about being responsible for another tiny being," Berthoud says. "I recommended 'Room Temperature,' by Nicholson Baker, which is about a man feeding his baby a bottle and having these meditative thoughts about being a father. And of course 'To Kill a Mockingbird,' because Atticus Finch is the ideal father in literature."

Berthoud and Elderkin are also the authors of "The Novel Cure: An A-Z of Literary Remedies," which is written in the style of a medical dictionary and matches ailments ("failure, feeling like a") with suggested reading cures ("The History of Mr. Polly," by H. G. Wells). First released in the U.K. in 2013, it is now being published in eighteen countries, and, in an interesting twist, the contract allows for a local editor and reading specialist to adapt up to twenty-five per cent of the ailments and reading recommendations to fit each particular country's readership and include more native writers. The new, adapted ailments are culturally revealing. In the Dutch edition, one of the adapted ailments is "having too high an opinion of your own child"; in the Indian edition, "public urination" and "cricket, obsession with" are included; the Italians introduced "impotence," "fear of motorways," and "desire to embalm"; and the Germans added "hating the world" and "hating parties." Berthoud and Elderkin are now working on a children's-literature version, "A Spoonful of Stories," due out in 2016.

For all avid readers who have been self-medicating with great books their entire lives, it comes as no surprise that reading books can be good for your mental health and your relationships with others, but exactly why and how is now becoming clearer, thanks to new research on reading's effects on the brain. Since the discovery, in the mid-nineties, of "mirror neurons"-neurons that fire in our brains both when we perform an action ourselves and when we see an action performed by someone else-the neuroscience of empathy has become clearer. A 2011 study published in the Annual Review of Psychology, based on analysis of fMRI brain scans of participants, showed that, when people read about an experience, they display stimulation within the same neurological regions as when they go through that experience themselves. We draw on the same brain networks when we're reading stories and when we're trying to guess at another person's feelings.

Other studies published in 2006 and 2009 showed something similar-that people who read a lot of fiction tend to be better at empathizing with others (even after the researchers had accounted for the potential bias that people with greater empathetic tendencies may prefer to read novels). And, in 2013, an influential study published in Science found that reading literary fiction (rather than popular fiction or literary nonfiction) improved participants' results on tests that measured social perception and empathy, which are crucial to "theory of mind": the ability to guess with accuracy what another human being might be thinking or feeling, a skill humans only start to develop around the age of four.

Keith Oatley, a novelist and emeritus professor of cognitive psychology at the University of Toronto, has for many years run a research group interested in the psychology of fiction. "We have started to show how identification with fictional characters occurs, how literary art can improve social abilities, how it can move us emotionally, and can prompt changes of selfhood," he wrote in his 2011 book, "Such Stuff as Dreams: The Psychology of Fiction." "Fiction is a kind of simulation, one that runs not on computers but on minds: a simulation of selves in their interactions with others in the social world...based in experience, and involving being able to think of possible futures." This idea echoes a long-held belief among both writers and readers that books are the best kinds of friends; they give us a chance to rehearse for interactions with others in the world, without doing any lasting damage. In his 1905 essay "On Reading," Marcel Proust puts it nicely: "With books there is no forced sociability. If we pass the evening with those friends-books-it's because we really want to. When we leave them, we do so with regret and, when we have left them, there are none of those thoughts that spoil friendship: 'What did they think of us?'-'Did we make a mistake and say something tactless?'-'Did they like us?'-nor is there the anxiety of being forgotten because of displacement by someone else."

George Eliot, who is rumored to have overcome her grief at losing her life partner through a program of guided reading with a young man who went on to become her husband, believed that "art is the nearest thing to life; it is a mode of amplifying experience and extending our contact with our fellow-men beyond the bounds of our personal lot." But not everybody agrees with this characterization of fiction reading as having the ability to make us behave better in real life. In her 2007 book, "Empathy and the Novel," Suzanne Keen takes issue with this "empathy-altruism hypothesis," and is skeptical about whether empathetic connections made while reading fiction really translate into altruistic, prosocial behavior in the world. She also points out how hard it is to really prove such a hypothesis. "Books can't make change by themselves-and not everyone feels certain that they ought to," Keen writes. "As any bookworm knows, readers can also seem antisocial and indolent. Novel reading is not a team sport." Instead, she urges, we should enjoy what fiction does give us, which is a release from the moral obligation to feel something for invented characters-as you would for a real, live human being in pain or suffering-which paradoxically means readers sometimes "respond with greater empathy to an unreal situation and characters because of the protective fictionality." And she wholeheartedly supports the personal health benefits of an immersive experience like reading, which "allows a refreshing escape from ordinary, everyday pressures."

So even if you don't agree that reading fiction makes us treat others better, it is a way of treating ourselves better. Reading has been shown to put our brains into a pleasurable trance-like state, similar to meditation, and it brings the same health benefits of deep relaxation and inner calm. Regular readers sleep better, have lower stress levels, higher self-esteem, and lower rates of depression than non-readers. "Fiction and poetry are doses, medicines," the author Jeanette Winterson has written. "What they heal is the rupture reality makes on the imagination."

One of Berthoud's clients described to me how the group and individual sessions she has had with Berthoud have helped her cope with the fallout from a series of calamities, including losing her husband, the end of a five-year engagement, and a heart attack. "I felt my life was without purpose," she says. "I felt a failure as a woman." Among the books Berthoud initially prescribed was John Irving's novel "The Hotel New Hampshire." "He was a favorite writer of my husband, [whom] I had felt unable to attempt for sentimental reasons." She was "astounded and very moved" to see it on the list, and though she had avoided reading her husband's books up until then, she found reading it to be "a very rewarding emotional experience, both in the literature itself and ridding myself of demons." She also greatly appreciated Berthoud guiding her to Tom Robbins's novel "Jitterbug Perfume," which was "a real learning curve for me about prejudice and experimentation."

One of the ailments listed in "The Novel Cure" is "overwhelmed by the number of books in the world," and it's one I suffer from frequently. Elderkin says this is one of the most common woes of modern readers, and that it remains a major motivation for her and Berthoud's work as bibliotherapists. "We feel that though more books are being published than ever before, people are in fact selecting from a smaller and smaller pool. Look at the reading lists of most book clubs, and you'll see all the same books, the ones that have been shouted about in the press. If you actually calculate how many books you read in a year-and how many that means you're likely to read before you die-you'll start to realize that you need to be highly selective in order to make the most of your reading time." And the best way to do that? See a bibliotherapist, as soon as you can, and take them up on their invitation, to borrow some lines from Shakespeare's "Titus Andronicus": "Come, and take choice of all my library/And so beguile thy sorrow..."

# data[].attributes.attachment_link.description
Several years ago, I was given as a gift a remote session with a bibliotherapist at the London headquarters of the School of Life, which offers innovative courses to help people deal with the daily emotional challenges of existence. I have to admit that at first I didn't really like the idea of being given a reading "prescription."

# data[].attributes.body
Lemur yoga is a thing.

# data[].attributes.attachment_link.readable_text
Downward facing lemur is the new go-to yoga pose

We have had goat, puppy and even hedgehog yoga, but now lemoga is a thing: a British hotel has launched yoga classes with a troop of lemurs.

Armathwaite Hall, a hotel in the Lake District in the north of England, has introduced "lemoga" to its selection of wellness services as part of its Meet the Wildlife wellness programme.

According to the hotel, the mammals' "friendly, outgoing personalities and love for human contact make them the perfect yoga buddies, helping people to laugh, unwind and stretch away their troubles".

Lemurs are native to Madagascar, there are 105 varieties of lemur, but the Cumbrian hotel is home to ring-tailed lemurs, which weigh between 2.2 kilograms and 3.4kg.

Richard Robinson, manager of the adjoining wildlife park, said of the mammals: "When you watch lemurs they do some form of the poses naturally - that typical pose warming their bellies in the sunshine ... It seemed to be a really good combination to encourage people to have a go and spend time with a lemur."

Carolyn Graves, the owner the rural hotel adds that the sessions make a perfect escape for people with busy city lives: "Lemoga offers our guests the chance to feel at one with nature, at the same time joining in with the lemurs' playtime."

The hotel's Meet the Wildlife programme also includes walks with alpacas, a chance to meet meerkats and apprentice keeper sessions.

"I don't think you ever see an unhappy zoo keeper. We spend all our time with animals," Robinson adds. "We know how it makes us feel and if we can give a little piece of that to people then great."

Ring-tailed lemurs are currently listed as endangered by the International Union for Conservation of Nature.

Other varieties of animal yoga

It seems as though there is no animal humans won't practice yoga around. Here are a few more animal yoga sessions made popular by Instagram:

Dog yoga

Hedgehog yoga

Goat yoga

Cow yoga

Cat yoga

Horse yoga

Alpaca yoga

Elephant yoga

# data[].attributes.attachment_link.description
Downward facing lemur is the new go-to yoga pose We have had goat, puppy and even hedgehog yoga, but now lemoga is a thing: a British hotel has launched yoga classes with a troop of lemurs.

# data[].attributes.body
This sense that the world can be reinvented [evokes] the Sixties in this country, those years when no one at all seemed to have any memory or mooring...

I never learned the answer, nor did the answer matter, for one of the eerie and liberating aspects of broadcast discourse is that nothing one says will alter in the slightest either the form or the length of the conversation.

J.D.

# data[].attributes.headline
The adventures and sartorial splendor of an orphaned, gray squirrel in the 1940s.

# data[].attributes.subject
The adventures and sartorial splendor of an orphaned, gray squirrel in the 1940s.

# data[].attributes.body
https://www.google.com/amp/amp.timeinc.net/time/3517606/a-squirrels-guide-to-fashion

# data[].attributes.body
Self portraits from a past life?

# data[].attributes.body
What if you are one of them now, young, and you go out there really living whatever you are doing?

# data[].attributes.attachment_link.readable_text
These days, new genomes of different types of organisms are being sequenced and published on a regular basis. When some new genome is sequenced, evolutionary biologists expect that it will be highly similar to the genomes of other organisms that are assumed to be closely related.

As ENV already noted, the latest organism to have its genome sequenced has confounded that expectation: the octopus, whose genome was recently reported in Nature. It turns out to be so unlike other mollusks and other invertebrates that it's being called "alien" by the scientists who worked on that project.

One article on the subject was titled " Don't freak out, but scientists think octopuses 'might be aliens' after DNA study ":

Not to send you into a meltdown or anything but octopuses are basically 'aliens' - according to scientists.

Researchers have found a new map of the octopus genetic code that is so strange that it could be actually be an "alien".

[...]

"The octopus appears to be utterly different from all other animals, even other molluscs, with its eight prehensile arms, its large brain and its clever problem-solving abilities," said US researcher Dr Clifton Ragsdale, from the University of Chicago.

[...]

Analysis of 12 different tissues revealed hundreds of octopus-specific genes found in no other animal, many of them highly active in structures such as the brain, skin and suckers.

Obviously no one thinks the octopus is an "alien" from another planet. ( Nature News quotes one co-author of the paper on the genome noting that the alien quip is a "joke.") But it certainly is alien to standard evolutionary expectations that genomes of related species ought to be highly similar. Thus, Nature points out the large number of unique genes found in the octopus genome:

Surprisingly, the octopus genome turned out to be almost as large as a human's and to contain a greater number of protein-coding genes - some 33,000, compared with fewer than 25,000 in Homo sapiens.

This excess results mostly from the expansion of a few specific gene families, Ragsdale says. One of the most remarkable gene groups is the protocadherins, which regulate the development of neurons and the short-range interactions between them. The octopus has 168 of these genes - more than twice as many as mammals. This resonates with the creature's unusually large brain and the organ's even-stranger anatomy. ...

A gene family that is involved in development, the zinc-finger transcription factors, is also highly expanded in octopuses. At around 1,800 genes, it is the second-largest gene family to be discovered in an animal, after the elephant's 2,000 olfactory-receptor genes.

The analysis also turned up hundreds of other genes that are specific to the octopus and highly expressed in particular tissues. The suckers, for example, express a curious set of genes that are similar to those that encode receptors for the neurotransmitter acetylcholine. The genes seem to enable the octopus's remarkable ability to taste with its suckers.

Scientists identified six genes for proteins called reflectins, which are expressed in an octopus's skin. These alter the way light reflects from the octopus, giving the appearance of a different colour - one of several ways that an octopus can disguise itself, along with changing its texture, pattern or brightness.

The technical paper explains that the octopus genome reveals "massive expansions in two gene families previously thought to be uniquely enlarged in vertebrates: the protocadherins, which regulate neuronal development, and the C2H2 superfamily of zinc-finger transcription factors." Moreover:

We identified hundreds of cephalopod-specific genes, many of which showed elevated expression levels in such specialized structures as the skin, the suckers and the nervous system.

They conclude: "Our analysis suggests that substantial expansion of a handful of gene families, along with extensive remodelling of genome linkage and repetitive content, played a critical role in the evolution of cephalopod morphological innovations, including their large and complex nervous systems." In other words, the cephalopod genome is unusual in many major respects, unlike other organisms we've sequenced.

Actually, that's not completely correct. There are some peculiar similarities between the cephalopod genome and something else they've seen - but they aren't the kind of similarities that were predicted by common descent. The technical papers notes that the cephalopod genome bears unexpected resemblance in certain respects to vertebrate genomes - and since these similarities aren't predicted by common descent, they predictably attribute them to convergent evolution:

the independent expansions and nervous system enrichment of protocadherins in coleoid cephalopods and vertebrates offers a striking example of convergent evolution between these clades at the molecular level.

Indeed, even within cephalopods they found evidence of convergent evolution (i.e., genetic similarity that didn't fit the expectations of common descent): "Surprisingly, our phylogenetic analyses suggest that the squid and octopus protocadherin arrays arose independently. Unlinked octopus protocadherins appear to have expanded ~135 Mya, after octopuses diverged from squid."

But the big story here is the large number of unique genes found in the octopus genome. The technical paper elaborates on one of these major gene groups:

The octopus genome encodes 168 multi-exonic protocadherin genes, nearly three-quarters of which are found in tandem clusters on the genome (Fig. 2b), a striking expansion relative to the 17-25 genes found in Lottia [a limpet], Crassostrea gigas (oyster) and Capitella [polychaete worm, and annelid] genomes.

The paper doesn't even try to speculate about how these unique cephalopod genes might have arisen. The standard view - that new genes originate via gene duplication - is hardly mentioned. But invoking gene duplication requires one to find another gene elsewhere that's similar. Given that cephalopods apparently have many unique genes not similar to genes found in other organisms, gene duplication might not be a candidate explanation in many of these cases. One wonders if future investigators will resort to " de novo " gene origin.

What's that? Stephen Meyer explains in Darwin's Doubt:

Remember: ORFans, by definition, have no homologs. These genes are unique - one of a kind - a fact tacitly acknowledged by the increasing number of evolutionary biologists who attempt to "explain" the origin of such genes through de novo ("out of nowhere") origination.

[...]

Many other papers invoke de novo origination of genes. Long mentions, for example, a study seeking to explain the origin of an antifreeze protein in an Antarctic fish that cites " de novo amplification of a short DNA sequence to spawn a novel protein with a new function." Likewise, Long cites an article in Science to explain the origin of two human genes involved in neurodevelopment that appealed to " de novo generation of building blocks - single genes or gene segments coding for protein domains," where an exon spontaneously "originated from a unique noncoding sequence." Other papers make similar appeals. A paper in 2009 reported "the de novo origin of at least three human protein- coding genes since the divergence with chimp[s]," where each of them "has no proteincoding homologs in any other genome." An even more recent paper in PLoS Genetics reported "60 new protein- coding genes that originated de novo on the human lineage since divergence from the chimpanzee," a finding that was called "a lot higher than a previous, admittedly conservative, estimate."

Another 2009 paper in the journal Genome Research was appropriately titled "Darwinian Alchemy: Human Genes from Noncoding RNA." It investigated the de novo origin of genes and acknowledged, "The emergence of complete, functional genes - with promoters, open reading frames (ORFs), and functional proteins - from 'junk' DNA would seem highly improbable, almost like the elusive transmutation of lead into gold that was sought by medieval alchemists." Nonetheless, the article asserted without saying how that: "evolution by natural selection can forge completely new functional elements from apparently nonfunctional DNA - the process by which molecular evolution turns lead into gold."

The presence of unique gene sequences forces researchers to invoke de novo origin of genes more often than they would like. After one study of fruit flies reported that "as many as ~12% of newly emerged genes in the Drosophila melanogaster subgroup may have arisen de novo from noncoding DNA," the author went on to acknowledge that invoking this "mechanism" poses a severe problem for evolutionary theory, since it doesn't really explain the origin of any of its "nontrivial requirements for functionality." The author proposes that "preadaptation" might have played some role. But that adds nothing by way of explanation, since it only specifies when (before selection played a role) and where (in noncoding DNA), not how the genes in question first arose. Details about how the gene became "preadapted" for some future function is never explained. Indeed, evolutionary biologists typically use the term " de novo origination" to describe unexplained increases in genetic information; it does not refer to any known mutational process. ( Darwin's Doubt, pp. 216, 220-221.)

In other words, de novo isn't an explanation at all. It's more like a magic wand to be invoked when evolutionary biologists encounter some unique gene and they have no way to explain its origin via duplication from a similar pre-existing gene. ( As an evolutionary mechanism, gene duplication has its own issues.)

Nonetheless, a recent article in Quanta Magazine points out just how many recent scientific studies have resorted to calling upon de novo origin of genes:

For most of the last 40 years, scientists thought that this was the primary way new genes were born - they simply arose from copies of existing genes. The old version went on doing its job, and the new copy became free to evolve novel functions.

Certain genes, however, seem to defy that origin story. They have no known relatives, and they bear no resemblance to any other gene. They're the molecular equivalent of a mysterious beast discovered in the depths of a remote rainforest, a biological enigma seemingly unrelated to anything else on earth.

The mystery of where these orphan genes came from has puzzled scientists for decades. But in the past few years, a once-heretical explanation has quickly gained momentum - that many of these orphans arose out of so-called junk DNA, or non-coding DNA, the mysterious stretches of DNA between genes. "Genetic function somehow springs into existence," said David Begun, a biologist at the University of California, Davis.

If the idea that "Genetic function somehow springs into existence" doesn't sound compelling to you, join the club. But that's about as much detail as you're likely to get from proponents of de novo gene origination. One proponent of this idea in the article is even quoted saying: "It's hard to see how to get a new protein out of random sequence when you expect random sequences to cause so much trouble." Unfortunately for evolutionists, this problem seems to be common among animals, as the Quanta article continues:

This metamorphosis was once considered to be impossible, but a growing number of examples in organisms ranging from yeast and flies to mice and humans has convinced most of the field that these de novo genes exist. Some scientists say they may even be common. Just last month, research presented at the Society for Molecular Biology and Evolution in Vienna identified 600 potentially new human genes. "The existence of de novo genes was supposed to be a rare thing," said Mar Albà, an evolutionary biologist at the Hospital del Mar Research Institute in Barcelona, who presented the research. "But people have started seeing it more and more."

Whenever you see " de novo" origin of a gene invoked, you know that evolutionary biologists lack any explanation for how that gene arose. Scientists haven't had much time yet to analyze the cephalopod genome, but given early reports of many unique genes, it will be interesting to learn to what extent they are forced to invoke these mysterious processes - what amounts to evolution ex nihilo - to explain how this "alien" genome arose.
Image: Minoan clay vase, c. 1500 BCE, by Wolfgang Sauber (Own work) [GFDL or CC BY-SA 3.0], via Wikimedia Commons.

# data[].attributes.attachment_link.title
The Octopus Genome: Not "Alien" but Still a Big Problem for Darwinism | Evolution News

# data[].attributes.attachment_link.description
These days, new genomes of different types of organisms are being sequenced and published on a regular basis. When some new genome is sequenced, evolutionary biologists expect that it will be highly similar to the genomes of other organisms that are assumed to be closely related.

# data[].attributes.body
Skills

# data[].attributes.attachment_link.description
GB synchronised swimmers Kate Shortman and Izzy Thorpe show off their underwater world.

# data[].attributes.body
Where am I? Do I need to know?

# data[].attributes.body
Blablabla

# data[].attributes.body
Oooohhh