V. Life's Corporeal Evolution Develops, Encodes and Organizes Itself: An Earthtwinian Genesis Synthesis

1. The Origins of Life

Kosc, Thomas, et al. Thermodynamic consistency of autocatalytic cycles. PNAS. 122/18, 2025. Laboratoire de Biométrie & Biologie Evolutive, Université Lyon and École Normale Supérieure Lyon, CNRS bioresearchers enter a strong, quantified, endorsement of how profligate these innate, spontaneous, precursor self-making reactions are as living systems complexified itself on the way to an emergent evolution,

Autocatalysis is seen as a potential key player in the origin of life, and more generally in the emergence of Darwinian dynamics. Here we tackle the computational task of detecting minimal autocatalytic cycles in reaction networks. Overall, by better characterizing the conditions of autocatalysis in biochemical reactions, this work brings us closer to appreciating the collective behavior on the path to the emergence of natural selection. (Abstract excerpt)

Kuhn, Hans. Is the Transition from Chemistry to Biology a Mystery? Journal of Systems Chemistry. 1/3, 2010. The emeritus director of the Max Planck Institute for Biophysical Chemistry, renowned chemist, author, and nonagenarian, in this new online edition strongly states that evolutionary life appears to be inexorably written into the physical universe, yet couches this in such machine terminology as per the long Abstract.

Today most chemists think that the answer to how life on earth emerged is still unknown. They assume a gap between chemistry and biology that is still unbridged. For chemists, understanding the origin of life requires the experimental modeling of a process that bridges this gap. They will not consider the problem solved before they are able to perform such tasks. No gap appears when we are pursuing a less ambitious goal, namely, to present a sequence of hypothetical processes that lead to an apparatus with the basic structure and fundamental feature of the genetic apparatus of biosystems but strongly simplified. The modeled apparatus has the basic machinery of living entities. Its fundamental feature is Darwinian behavior. Living individuals have the power to evolve toward ever increasing complexity and intricacy if appropriate conditions are given. The task to understand life’s origin as a rational process is closely related to the earlier attempts of the present author to design and construct supra-molecular machines.

The essence of what happens is inevitable, not accidental. Thus the emergence of life is assumed to be described by a distinct theory. Today’s great challenge is experimentally investigating chemical systems with the goal of creating artificial chemical life and the given theory provides a powerful stimulus. Life, from the perspective of physics, is the living state of matter and this view calls for a theory describing the fundamental requirements for the appearance of such a living state of matter (on the early earth and in the universe). The approach given here is an attempt in this direction. According to that approach the appearance of an entity with Darwinian behavior is instantaneous and linked with the creation of matter that carries information. Thus, Information (measured in bits according to Shannon) takes a meaning with that instant, the appearance of the first entity that evolves by multiplication, variation, selection and keeps that meaning during the entire evolution of the living (Information carrying) state of matter. (1)

Kuppers, Bernd-Olaf. The Nucleation of Semantic Information in Prebiotic Matter. Current Topics in Microbiology and Immunology. Volume 392, 2016. The University of Jena natural philosopher continues his endeavor (search) to explain how a newly fertile physics, vital biochemicals, an informed, encoded biology and more can engender life’s emergent evolution. Into the mid 2010s, the presence of nonlinear, complex, “structural systems,” along with a deep propensity for an informative, genetic-like basis, are being factored into the discussion.

The analysis of the inherent context-dependence of genetic information suggests that there are evolutionary mechanisms which are independent of environmental adaptation and yet are able to push prebiotic matter towards functional complexity. In regard, the extension of information space by random prolongation of biological macromolecules must have played a decisive role in the origin of life. The extension of information space can lead to an increase in the syntactic complexity of potential information carriers, and in turn to the evolution of semantic information. The increase in the dimensionality of information space expands the number of pathways for evolutionary optimisation and thereby improves the choices that can be made by progressive evolution. In addition, there are principles of evolutionary dynamics that direct the formation of functional order in prebiotic matter. Since these principles are constitutive for the proto-semantics of genetic information, they may be regarded as the elements of the semantic code of evolution. (Abstract)

Lahav, Noam. Biogenesis. New York: Oxford University Press, 1999. A proficient technical survey of the state of life’s biomolecular, genetic and protocellular origin.

Larson, Brian, et al. The Chemical Origin of Behavior is Rooted in Abiogenesis. Life. Online November, 2012. An online definition of Abiogenesis is “a natural organic phenomenon by which living organisms spontaneously arose from nonliving matter.” Coauthor Niles Lehman, Portland State University Chemistry Chair, with grad students Larson and Paul Jensen, join the mission to extend life’s regnant activity ever deeper into a conducive fertile ground. In regard, as a precursor “informational” source becomes more evident, suitable molecules then seem to make relative “choices” such as better “folding pathways” within a variable environment. Such an appreciation of an “anthropomorphic” biochemical materiality then contributes to a deep, true continuity between human and universe. Might one surmise that a dynamic cosmos of contingency and choice, a self-creating and selecting procreative genesis, could soon be in the offing?

We describe the initial realization of behavior in the biosphere, which we term behavioral chemistry. If molecules are complex enough to attain a stochastic element to their structural conformation in such as a way as to radically affect their function in a biological (evolvable) setting, then they have the capacity to behave. This circumstance is described here as behavioral chemistry, unique in its definition from the colloquial chemical behavior. This transition between chemical behavior and behavioral chemistry need be explicit when discussing the root cause of behavior, which itself lies squarely at the origins of life and is the foundation of choice. RNA polymers of sufficient length meet the criteria for behavioral chemistry and therefore are capable of making a choice. (Abstract)

Once Nature had the capacity to synthesize information-bearing macromolecules though, the stochasticity of the system became embodied into the “behavior” of the molecules because now there was the possibility that a molecule was the system! In essence, a system requires both a genotype and a phenotype to be able to display behavior. The “self” is now clearly defined; however, it can be a single self-replicating molecule or a network of related cooperators. Here we are using the example of RNA as the informational polymer, but the same conclusions were to apply if other polymers, or even inorganic lattices or compositional sets of macromolecules such as lipids, were the ancestral genotypes. Clearly, the advent of compartmentalization (protocellular life) would further enhance the establishment of a bounded genotype, thereby firmly entrenching behavior. (315)

Lazcano, Antonio. The Origins of Life. Natural History. February, 2006. A popular glimpse of the “heterotrophic” theory whereby “the first living entities evolved “abiotically” from nonliving organic molecules on the primitive Earth.” In this primal phase, a prebiotic soup cooked complex molecules such as amino acids. Although self-catalyzing systems are mentioned, this approach seems to labor within an inorganic, inanimate universe. Protein synthesis is seen as “machinery” leading to an RNA world.

Letelier, Juan-Carlos, et al. From L'Homme Machine to Metabolic Closure: Steps Toward Understanding Life. Journal of Theoretical Biology. Online July, 2011. For a 50th Anniversary Review of this journal’s tenure, Universidad de Chile (Letelier), and CRNS, France (Maria Cardenas and Athel Cornish-Bowden), biologists provide a unique history of many efforts to define the phenomenon of life. Julien Offray de La Mettrie’s (1707-1751) title mechanical manifesto leads to Nicolas Rashevshy’s (1899-1972) relational biology, Robert Rosen’s (1934-1998) M,R systems, and onto cybernetics, chemotons, hypercycles, autocatalysis, autopoiesis, systems biology. From our late vantage, by a re-evaluation and synthesis of these precursors, the essence of life appears much to be a bounded metabolic organization, with a penchant for self-construction. The article wraps up with the quoted paragraph, for a definitive discovery still eludes.

As for whether biology really needs a theory of the living state, we conclude by quoting (Carl) Woese (2004, search), who wrote that “without an adequate technological advance (sequencers, etc.) the pathway of progress is blocked, and without an adequate guiding vision there is no pathway, there is no way ahead.” Of course we need the technological advances that we have seen in the past 60 years, bu we also need a guiding vision.

Li, Tao, et al. Synthesis and Stability of Biomolecules in C–H–O–N Fluids under Earth’s Upper Mantle Conditions. Journal of the American Chemical Society. 146/45, 2024. Hong Kong, USA, France, China biochemists and geologists are able to prove that prebiotic phenomena could naturally take place even in crustal depths. Into late this year as these many evidential findings come together, they make a strong case case that life’s occasion and ascent is a preordained, essential quality of an ecosmic orthogenesis.

How life started on Earth is an on-going project. Here we apply molecular dynamics to study chemical reactions between NH3, H2O, H2, and CO at pressures (P) and temperatures (T) to mimic conditions of Earth’s upper mantle. Contrary to assumptions, we found that many organic compounds formed and persisted in C–H–O–N fluids under these extremes, including glycine, ribose, urea, and uracil-like molecules. We have thus uncovered a further domain where biomolecules could be synthesized from geofluids in the deep interior of Earth and other worlds. (Excerpt)

Lilley, David and John Sutherland. The Chemical Origins of Life and its Early Evolution. Philosophical Transactions of the Royal Society B. 366/2853, 2011. University of Dundee and MRC Laboratory of Molecular Biology researchers introduce a full issue on increasing accessible primeval seedings and stirrings of life’s earthly emergence, lately bent on reconstructing itself via our human phenomenon. In addition to Hanczyc above, “Prebiotic Chemistry: A New Modus Operandi” by Matthew Powner and John Sutherland cites an original “systems chemistry” that forms vesicular membranes, while Robert Pascal and Laurent Boiteau in “Energy Flows, Metabolism and Translation” continue their work on a thermodynamic basis for cellular compartments, information, and metabolism. And many authors and articles seem by inference to be on the verge of admitting an inherent cosmic and earthly predisposition for life to get going from nature’s deepest material recesses and ancient ages.

Can we look at contemporary biology and couple this with chemical insight to propose some plausible mechanisms for the origin of life on the planet? In what follows, we examine some promising chemical reactions by which the building blocks for nucleic acids might have been created about a billion years after the Earth formed. This could have led to self-assembling systems that were based on an all-RNA metabolism, where RNA is both catalytic and informational. (Abstract, 2853)

López-Díaz, Amahury Jafet , et al. The Origin of Information Handling. arXiv:2404.04374. Binghamton University, New York theorists including Hiroki Sayama and Carlos Gershenson consider and finesse another algorithm-like component as life gets its well proscribed act altogether. In regard, core guidance is provided by Howard Pattee, Juan Perez-Mercader, Chiara Marletto and Matthew Egbert. Once again something and someone seems in gestation, as long foreseen.

A major challenge when describing the origin of life is to explain how instructional information systems emerge naturally from mere molecular dynamics. Based on recent experimental results showing that chemical computations does not require a biological basis, we elucidate the origin and evolution of information processes by automata, computation and storage and transmission. In contrast to theories that assume initial complex structures, our narrative starts from early interactive self-replicators. By way of describing these primordial transitions, our metaphor can be translated to other models to explore biological phenomena at multiple spatial and temporal scales. (Excerpt)

We can imagine our planet as a big parallel, quasi-universal Turing machine capable of simulating a huge variety of functions (programs). Of course, natural resources are finite, and this is a limitation for life to emerge. Under this perspective, the first organisms on the planet could be described as some kind of automata which were running in these primitive environments. As a result of the geophysical and geochemical constraints, which we could call the primeval ecosystem language, elementary bimolecular reactions emerged. These chemical reactions are capable of recognizing regular languages, a task that does not involve counting or memory. (1, 2)

Lu, Heng, et al. Small-molecule autocatalysis drives compartment growth, competition and reproduction. Nature Chemistry. August 7, 2023. Fifteen investigators mainly at the Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, and Université PSL, Paris, France, along with Eors Szathmary (Centre for Ecological Research, Budapest) post novel insights into how a network of small-molecule autocatalytic reactions, without genetic material and enzymes, can foster and grow into protocellular compartments. The result is said to be fundamental to the experimental verification of the principles of systems chemistry and points the way forward in the study of the origin of life. So once more in a major study nature’s propensity to boot itself up through auto-spontaneous means is well quantified.

Sustained autocatalysis coupled to compartment growth and division is a key step in the origin of life, but an experimental demonstration of this phenomenon in an artificial system has proven elusive. We show that autocatalytic reactions within compartments drive osmosis and diffusion resulting in vesicle growth. Our work indicates how a combination of properties of living systems (growth, division, variation, competition, rudimentary heredity and selection) can arise from simple physical–chemical processes and may have paved the way for the emergence of evolution by natural selection. (Excerpt)

Lynn, David, et al. Origins of Chemical Evolution. Accounts of Chemical Research. 45/12, 2012. This significant topical issue is reviewed much more in Organic Universe, where several articles are also noted separately.

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