# data[].attributes.body
Plato was not a naturalist (Ernst Mayr, page 89).  In “Timaeus,” Plato presented a cosmogony that involved a divine craftsman or Demiurge who shaped the material world based on eternal Forms.  Nor was Plato a physicalist.  Plato’s philosophical views, as exemplified in his dialogues “Phaedo” and “Timaeus,” firmly established his rejection of physicalism and his belief in the existence of non-material entities.  For example, in “Phaedo,” Plato argued for the soul’s immortality, asserting its separateness from the body and the soul’s continuation beyond death.  Additionally, in Plato’s “Allegory of the Cave,” the material world is described as secondary to the realm of the ideal Forms and as mere reflection or shadow of the true reality found outside of the cave.  This dualistic perspective contradicts physicalism’s assertion that everything can be reduced to physical entities.

Plato’s theory of Forms provides additional support for my contention.  According to Plato, abstract and universal forms such as justice, beauty, and equality exist independently and transcend the material realm.  These Forms are non-material and possess an eternal quality, challenging the physicalist notion that all phenomena can be exclusively explained in terms of physical substances.

Aristotle, not Plato, believed in a “thing” ontology.  Aristotle’s ontology centered on the concept of “substances,” defined as that which exists independently and is not predicated upon anything else.   In his work “Metaphysics,” Aristotle categorized existence into different substance types, suggesting that ultimate reality could be defined in terms of its constituent substances, and everything else, including qualities and quantities, depended on or was predicated upon these substances.

In contrast, although Plato’s ontology begins with the eternal and unchanging Forms, at the emanative level of his “Receptacle,” I have argued that his philosophy can be reasonably described as processual.  See: “On the Socratic Cosmos.”

# data[].attributes.headline
Abiogenesis is more than a “qualitatively new form of motion.” 

# data[].attributes.subject
Abiogenesis is more than a “qualitatively new form of motion.” 

# data[].attributes.body
Describing the origin of life as a “qualitatively new form of motion” (Oparin, page 72) might be excused as a poetic or metaphorical expression.  However, it fails to communicate the scientific complexities and nuances of the topic.

The theory of abiogenesis, which suggests the natural origin of life on Earth, encompasses several complex stages.  The most critical of these is the transition from chemistry to biology, which involves the evolution of simple chemical reactions into entities with metabolic and reproductive capabilities.  Abiogenesis begins with the formation of simple organic molecules, such as amino acids and nucleotides, from inorganic compounds.  Various energy sources on early Earth, including UV radiation, heat, and electrical discharges, could have facilitated this process.  These simple organic molecules must then be transformed into more complex biomolecules.  The resulting biomolecules must then self-organize into metabolic and reproductive pathways and be protected from environmental degradation as the energy sources useful to the formation of complex biomolecules can also cause them to break down.

Metabolism is believed to involve a self-organized “patchwork” of diverse chemical reactions that sequentially transform environmentally available molecules into forms useful to the biological entity.  Primitive enzymes, capable of catalyzing reactions with a wide range of chemical substrates, are thought to have been assembled through the environmental forces and conditions prevailing at that time.  This assembly formed a patchwork of different catalytic functions that eventually self-organized to become a metabolic pathway for the developing entity.

The final challenge for the ultimate emergence of self-replicating entities with metabolic activity involves the intricate development of systems and structures for reproduction.  This process requires the integration of molecular processes, including the synthesis and faithful transmission of the information required for the entity to at least catalyze copies of itself, to eventually include the formation of protective cellular structures and the orchestration of biochemical pathways providing the energy and resources required for replication.

Chirality is a property of asymmetry in molecules.  A molecule is considered chiral if it cannot be superimposed onto its mirror image.  Homochirality is the tendency of living organisms to predominantly exhibit biological molecules with only one chiral form.  As early life processes typically yield a mixture of both chiral forms, biological homochirality in an abiogenic context involves additional perplexing unknowns as to the selective forces or processes that caused a specific chiral orientation to dominate among biological entities.

# data[].attributes.body
Mayr’s description of “integrons” in the context of emergence (pages 96-97) seems to be inaccurate to the extent a reader infers the section applies to the genetic diversity in mammals.  Integrons are genetic elements that play a role in the acquisition, rearrangement, and expression of genes in bacteria.  They consist of distinct components, including a gene cassette array and an integrase enzyme.  The gene cassette array is composed of individual gene cassettes, each containing a specific genetic element or a combination of elements.  The integrase enzyme is responsible for the site-specific recombination that allows the integration and rearrangement of these gene cassettes.  Integrons facilitate horizontal gene transfer, allowing bacteria to acquire and incorporate gene cassettes from other bacteria or the environment and, as such, contribute to the adaptability and evolution of bacterial populations.

Integrons are not naturally present in the mammalian genome.  Except for bacteria, it does not play a role in broadening an organism’s genetic diversity or changing the organism’s survival capacity.  Mayr claimed that “[a]n integron is formed by assembling integrons of the level below it” and “it takes part in the construction of the integron of the level above.” However, this doesn’t align with the typical understanding of integron biology in bacteria.  Integrons are usually seen as discrete genetic elements within bacterial genomes, not as hierarchical structures formed by the assembly of smaller integrons.

While integrase enzymes in the context of integrons are likely nonexistent in eukaryotic organisms, there are instances where eukaryotes possess their own versions of integrase-like enzymes that are involved in various cellular processes, such as DNA repair, recombination (the genetic reshuffling during meiosis), and transposition (the relocation of gene segments, called transposons, within the genome).

# data[].attributes.headline
Can Quantum Mechanics Help Resolve the Origin of Life Mystery?

# data[].attributes.subject
Can Quantum Mechanics Help Resolve the Origin of Life Mystery?

# data[].attributes.body
Abiogenesis  is the theory that life emerged from non-living matter through a series of natural processes.  These biological processes are believed to have caused the complex biomolecules and structures necessary for life to arise and spontaneously self-organize from simpler organic compounds. The theory, however, involves many issues that have not yet been overcome.

“The point is that for even a single protein to be successfully expressed in the cell, a huge number of molecules need to interact with one another in exactly the right way, at exactly the right time, and in exactly the right order.  And it should not be surprising that the likelihood that all of this happens in a perfectly efficient and precisely timed fashion (as one would expect of the programmatic execution of an algorithmic sequence of coded instructions) is virtually zero once we take into account the random and ferocious buffeting that all molecules are subject to inside the cell by virtue of their size.” Daniel J. Nicholson, On being the right size, revisited:  The problem with engineering metaphors in molecular biology  page 46

Organicism is a theoretical model within biology that studies living organisms as unified entities, emphasizing the organicism’s functional interactions, integration, coherence, and purpose of the organism’s parts.  The theory suggests that the combined interactions of cells, tissues, organs, and organ systems contribute to the organism’s overall functioning and flourishing and that the organism’s survival needs have caused novel properties and functions that are transcendent to the organism’s isolated components to evolve at every biological level.  Organicism argues that these evolutionary forces have impelled the “adaptation” of new functions and capacities that appear purposeful and goal-directed.
Teleological explanations may be divided into two categories: “intentional teleology,” which requires the intervention of a conscious agent to achieve a final state, and “constraint teleology,” where a teleological-like attractor is innate within biological laws.  The biologist Colin Pittendrigh coined the term teleonomy to release biology’s goal-directed processes and purposes from the encumbrances of teleological explanation.

“…Darwin gave a rational, materialistic explanation of the way in which this “purposiveness” arose in higher organisms by means of natural selection.  “Purposiveness” of structure does not, however, manifest itself solely in the more highly organized creatures, it pervades the whole living world from the top to the bottom, right down to the most elementary forms of life.  It is necessary to every living body but in the absence of the living body there would be no “purposiveness” under natural conditions.  It would therefore be fruitless for us to seek its explanation simply in terms of the laws of the inorganic world, i.e., the laws of physics and chemistry.”  Alexander Oparin, The Nature of Life, Session #1 Reading Pack - The Nature of Life, Pages 75-76

Although it may be difficult to imagine how Pittendrigh’s teleonomy might operate without the “agency” that pre-existing organisms provide, when time-symmetry, reverse causality, and attractors are embraced within physics’ laws, I argue in “Can Quantum Mechanics Help Resolve the Origin of Life Mystery?” that the problems Dr. Nicholson has brought to our attention can be overcome.

NOTE that this a draft paper.
Your comments and suggestions will be valued.

https://wordpress.com/post/jontrevathan.wordpress.com/309