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

1. The Origins of Life

Matange, Kavita, et al. Biological Polymers: Evolution, Function, and Significance. Accounts of Chemical Research. February 5, 2025. NASA Center for Integration of the Origins of Life, Atlanta and Georgis Tech bioscientists including Loren Dean Williams describe a more complete precursor trajectory whereof these prebiotic compounds are seen to make a significant contribution.

A holistic description of biopolymers and their evolution will contribute to our understanding of biochemistry and the origins of life. While biopolymer sequences evolve through Darwinian processes, how the backbones of polypeptides, polynucleotides, and polyglycans came to be is less certain.? To address this, we distinguished chemical species produced by evolutionary mechanisms from those formed by physical, chemical, or geological processes. Biopolymers display homo- and hetero- complementarity, enabling atomic-level control of structure and function. We argue that evolved biopolymer backbones then facilitated a seamless transition from chemical to Darwinian evolution. (Excerpt)

In sum, we present a model in which life on Earth was preceded by sustained chemical evolution. We propose that the chemical evolutionary process that led to biology is a special case of a general phenomenon. This model opens the possibility of applications of directed chemical evolution to a broad range from pharmaceuticals to material sciences. If an evolutionary process produced incredible molecules such as RNA and protein, then humankind can gain advantage by understanding and redirecting that process. (10)

Matange, Kavita, et al.. Evolution of complex chemical mixtures reveals combinatorial compression and population synchronicity. Nature Chemistry. February, 2025. In a news worthy paper, NASA Center for Integration of the Origins of Life, Atlanta and Georgis Tech bioscientists including Loren Williams and Jessica Bowman add a new dimension to origin studies by an emphasis on generic processes such as Wet-Dry Cycling, Complex Libraries of Condensable Components, Population Synchronicity, Energy Harvesting and Selective Fitness. As a result, a pre-existent self-organizing fertility can become evident before complex biochemicals began to form. As a planatural note, here is one more sophisticated advance as many prebiotic aspects just now reveal a phenomenal integrity from the uniVerse to an evolutionary gestation to our curious selves.

Many open questions about the origins of life involve the generation of complex chemical species. Here we propose to investigate general processes by which chemical systems continuously change with water as a medium. Our system (1) transitions to new chemical spaces; (2) demonstrates combinatorial compression with stringent selection; and (3) displays synchronicity of molecular populations. Our results suggest that chemical complexity can be observed in organic mixtures and might produce a broad array of molecules with novel structures and functions. (Excerpt)

Future Prospects. Our focus here is early-stage chemical evolution, rather than the production of highly evolved biopolymers such as RNA or protein. As noted by François Jacob, “the really creative part in biochemistry must have occurred very early.”
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The Center for Integration of the Origins of Life (iCOOL) seeks to integrate chemical sciences with evolutionary theory. We are developing conceptual and experimental models of chemical evolution focusing on selection, exaptations, mutualisms, and creativity. We believe that humankind will learn to understand, recapitulate, and avail chemical progressions analogous to those that led to the formation of biopolymers on ancient Earth.

Mathis, Cole, et al. Prebiotic RNA Network Formation: A Taxonomy of Molecular Cooperation. Life. Online October, 2017. Mathis, Sanjay Ramprasad, and Sara Imari Walker, Arizona State University, with Niles Lehman, Portland State University, find that nature’s network topologies and dynamics are in effect even at this early nucleotide phase because they provide cooperative benefits. The entry is for The RNA World and the Origin of Life issue, see also Evolutionary Conflict Leads to Innovation (Paulien Hogeweg) and The Role of Templating in the Emergence of RNA from the Prebiotic Chemical Mixture (Paul Higgs). In further regard, see Topological and Thermodynamic Factors that Influence the Evolution of Small Networks of Catalytic RNA Species by Niles Lehman, et al in the journal RNA (23/7, 2017).

Cooperation is essential for evolution of biological complexity. Recent work has shown game theoretic arguments, commonly used to model biological cooperation, can also illuminate the dynamics of chemical systems. Here we investigate the types of cooperation possible in a real RNA system based on the Azoarcus ribozyme, by constructing a taxonomy of possible cooperative groups. We construct a computational model of this system to investigate the features of the real system promoting cooperation. We find triplet interactions among genotypes are intrinsically biased towards cooperation due to the particular distribution of catalytic rate constants measured empirically in the real system. For other distributions cooperation is less favored. We discuss implications for understanding cooperation as a driver of complexification in the origin of life. (Abstract)

Mathis, Cole, et al. Self-Organization in Computation & Chemistry: A Return to AlChemy. arXiv:2408.12137. Arizona State University, University of Michigan, and Santa Fe Institute complexity theorists including Stephanie Forrest provide a 30 year update to an original attempt to inform reaction networks with novel computational aspects. As the Abstract says, the approach can presently yield new insights into nature’s seemingly innate propensity to engender complex, viable, evolving entities.

How do complex adaptive systems such as life emerge from constituent parts? In the 1990s Walter Fontana and Leo Buss proposed an approach based on a computation model known as λ calculus whereby simple rules within in large space of possibilities could yield complex, dynamic stable biochemical reaction networks. Here, we revisit this classic model, called AlChemy, to study those results using current computing resources. Our analysis now reveals that complex, stable organizations emerge more frequently than expected, and are robust against collapse. We conclude with applications of AlChemy to self-organization in programming languages and to the origin of life.

Mathis, Cole, et al. The Emergence of Life as a First Order Phase Transition.. arXiv:1503.02776. Astrophysicists Mathis, ASU, Tanmoy Bhattacharya, SFI, and Sara Imari Walker, ASU, assume an inherently organic cosmos whereof “life is a phase of matter.” By this frontier scientific view, a non-equilibrium universe is seen to spontaneously evolve and develop by way of information and replication. Again in 2015, we move closer to a revolutionary natural genesis as its genetic narrative begins to breakthrough unto its own recognition.

We demonstrate a phase transition from non-life to life, defined as non-replicating and replicating systems respectively, and characterize some of its dynamical properties. The transition is first order and demonstrates many characteristics one might expect from a newly emergent biosphere. During the phase transition the system experiences an explosive growth in diversity, with restructuring of both the extant replicator population and the environment. The observed dynamics have a natural information-theoretic interpretation, where the probability for the transition to occur depends on the mutual information shared between replicators and environment. Through the transition, the system undergoes a series of symmetry breaking transitions whereby the information content of replicators becomes increasingly distinct from that of their environment. Thus, the replicators that nucleate the transition in the non-life phase are often not those which are ultimately selected in the life phase. We discuss the implications of these results for understanding the emergence of life, and natural selection more broadly. (Abstract)

Matsumara, Shigeyoshi, et al. Transient Compartmentalization of RNA Replicators Prevents Extinction Due to Parasites. Science. 354/1293, 2016. Ten researchers from Japan, France, Germany, and Hungary, including Eors Szathmary, Faith Coldren, and Phillippe Nghe, explain how original living systems were able to evolve in spite of contrary conditions, which the quotes detail. A natural propensity seem to be the formation of bounded cellular forms, which as primordial communities fostered their survival. See also, for example, How Life Can Arise from Chemistry by Michael Gross in Current Biology (26/R1247, 2016). A philosophical view of these many reports implies an innately conducive biocosmos from which our late collaborative quantification is meant to appear, discovery and affirm.

The evolution of molecular replicators was a critical step in the origin of life. Such replicators would have suffered from faster-replicating “molecular parasites” outcompeting the parental replicator. Compartmentalization of replicators inside protocells would have helped ameliorate the effect of parasites. Matsumura et al. show that transient compartmentalization in nonbiological materials is sufficient to tame the problem of parasite takeover. They analyzed viral replication in a droplet-based microfluidic system, which revealed that as long as there is selection for a functional replicator, the population is not overwhelmed by the faster-replicating parasite genomes. (Editorial Summary)

The appearance of molecular replicators (molecules that can be copied) was probably a critical step in the origin of life. However, parasitic replicators would take over and would have prevented life from taking off unless the replicators were compartmentalized in reproducing protocells. Paradoxically, control of protocell reproduction would seem to require evolved replicators. We show here that a simpler population structure, based on cycles of transient compartmentalization (TC) and mixing of RNA replicators, is sufficient to prevent takeover by parasitic mutants. TC tends to select for ensembles of replicators that replicate at a similar rate, including a diversity of parasites that could serve as a source of opportunistic functionality. Thus, TC in natural, abiological compartments could have allowed life to take hold. (Abstract)

Mauro, Ernesto, ed.. The First Steps of Life. Wiley Online, 2023. This edited, authoritative collection is published as an ebook edition. Typical chapters are The Emergence of Life-Nurturing Conditions in the Universe by Juan Vladilo, The Role of Formamide in Prebiotic Chemistry (Raffaele Saladino), A Praise of Imperfection: Emergence and Evolution of Metabolism (Juli Pereto), and Making Biochemistry-Free Life in a Test Tube by Juan Perez-Mercader (see review). Here again, a dozen diverse chapters convey and integrate strong evidence that a veritable proof an in fact confirm a revolutionary ecosmic procreation.

Origin of Life studies have a retrospective goal: understanding nature through the comprehension of its origins and its complexities. This book proposes both an overview of this large area and an in-depth look at the opinions and results obtained by some of the active contributors. The topics occur a bottom-up order from the habitability of the universe to a meaningful prebiotic chemistry, the problem of chirality, and on through the role of minerals in biogenesis, fertile environments, cellular vesicles, replicative codes, the structure of LUCA and on their way to the evolution of information and complexity. (EDM)

Ernesto Di Mauro is a Molecular Biology professor and vice-president of the Académie Européenne Interdisciplinaire des Sciences, France. His research focuses on structural codes for complex molecular interactions in DNA topology, RNA-polymerases and DNA-topoisomerases.

McFarland, Ben. A World From Dust: How the Periodic Table Shaped Life. New York: Oxford University Press, 2016. In the main lecture hall of the new Integrated Sciences Building at UM Amherst hangs an iconic, 12’X16’ periodic table. By any stretch the millions of compounds which those 100 elements can form so that we peoples can write and observe it cannot be an accident. In this volume, a Seattle Pacific University biochemist draws on the latest advances to trace and document an oriented evolutionary universe to human scenario. Surely contingencies abound, with dead ends along the way, but it is not a random, blind passage. Akin to a physical basis, chemical structures and reactions serve to constrain and guide the course of complex organisms. By these lights, it is pointedly put that Stephen Jay Gould’s 1980s claim that earth life’s tape is so chancy it would not run again can be refuted. Here is another glimpse that a Ptolemaic pointless, accidental, nature from nothing is seriously wrong, and need be set aside for intimations of a phenomenal genesis cosmos from which entailed, intended persons can so witness, and creatively continue.

Therefore, the story of chemical life must start, as chemists do, with the periodic table itself. If life is built from the periodic table, then what is the periodic table built from? Like physics itself (and to tell the truth, this is physics itself), the answer would make Plato proud. The rows and columns of the periodic table are built from Platonic ideals, from the abstract combinations and logical consistencies of mathematics. (39) If we do find conditions that could have built life on the early Earth, say with (John) Sutherland’s light driven reactions, then that would argue against (Stephen Jay) Gould’s “tape of life” thought experiment at the molecular level. Such a result would mean that, despite a vast distance of time, early-Earth chemistry could be deduced and repeated in a modern lab. This first song on the tape of life would be rewound, replayed, and recapitulated, even 4 billion years later. Life’s most fundamental biochemistry would be explained by and predicted from the chemistry of the periodic table. (109)

Gould’s tape of life was a story that was too simple. It assumed that genetic changes were largely independent of other events, when in fact they were hemmed in by the biology of other species in the ecological network, by the chemistry available in the environment, and by the physics of energy efficiency. Gould’s assertion that the tape of life is unrepeatable requires a type of evolution that can solve hard problems only once, rather than a tape that converges on repeated and efficient solutions. Gould’s evolution is weak tea compared to a chemically driven and convergent evolution. (264)

Melendez-Hevia, Enrique, et al. From Prebiotic Chemistry to Cellular Metabolism: The Chemical Evolution of Metabolism before Darwinian Natural Selection. Journal of Theoretical Biology. 252/505, 2008. Biologists at the Institute of Cell Metabolism, Canary Islands, and the Universidad Complutense de Madrid, Spain present a detailed case for life’s inexorable occasion, for which we cite the full article abstract.

It is generally assumed that the complex map of metabolism is a result of natural selection working at the molecular level. However, natural selection can only work on entities that have three basic features: information, metabolism and membrane. Metabolism must include the capability of producing all cellular structures, as well as energy (ATP), from external sources; information must be established on a material that allows its perpetuity, in order to safeguard the goals achieved; and membranes must be able to preserve the internal material, determining a selective exchange with external material in order to ensure that both metabolism and information can be individualized. It is not difficult to understand that protocellular entities that boast these three qualities can evolve through natural selection. The problem is rather to explain the origin of such features under conditions where natural selection could not work. In the present work we propose that these protocells could be built by chemical evolution, starting from the prebiotic primordial soup, by means of chemical selection. This consists of selective increases of the rates of certain specific reactions because of the kinetic or thermodynamic features of the process, such as stoichiometric catalysis or autocatalysis, cooperativity and others, thereby promoting their prevalence among the whole set of chemical possibilities. Our results show that all chemical processes necessary for yielding the basic materials that natural selection needs to work may be achieved through chemical selection, thus suggesting a way for life to begin. (505)

Menor-Salvan, Cesar. ed. Prebiotic Chemistry and Chemical Evolution of Nucleic Acids. International: Springer, 2018. A Universidad de Alcala, Spain astrobiologist assembles ten authoritative chapters which provide strong evidence for an innate natural occasion and forward progress of living, evolving complex entities. We note Mineral-Organic Interactions in Prebiotic Synthesis by Stephen Benner, et al, Nucleobases on the Primitive Earth by James Cleaves, and Self-Assembly Hypothesis for the Origin of Proto-RNA by Brian Cafferty, et al. Of especial import is Network Theory in Prebiotic Evolution by Sara Imari Walker and Cole Mathis which is reviewed below for its inclusion of this essential feature.

Chemical evolution encompasses the processes and interactions conducive to self-assembly and supramolecular organization, leading to an increase of complexity and the emergence of life. The book starts with the pioneering work of Stanley Miller and Jeffrey Bada on the Chemistry of Origins of Life and how the development of organic chemistry beginning in the 19th century led to the emergence of the field of prebiotic chemistry, situated between organic, geo- and biochemistry. It continues with current central topics regarding the organization of nucleic acids: the origin of nucleobases and nucleosides, their phosphorylation and polymerization and ultimately, their self-assembly and supramolecular organization at the inception of life. (Publisher)

Moi, David, et al. Archaeal Origins of Gamete Fusion. bioRxiv. October 13, 2021. We cite this entry by a 16 member international team (Argentina, Uruguay, Israel, Sweden, the UK, France, Switzerland) as an example of a global retrospective which can now gain a deeper degree of whole scale analysis of how living systems formed, developed, and gave rise to us. See also the report A Billion Years before Sex, Ancient Cells were Equipped for It by Jake Buehler Quanta Magazine (Feb. 2022). A philoSophia approach might view all this phenomena – bigender identities and issue – as inherent features of a true greater genesis.

Sexual reproduction in Eukarya consists of genome reduction by meiosis and gamete fusion. The presence of meiotic genes in Archaea and Bacteria suggests that prokaryotic DNA repair mechanisms evolved towards meiotic recombination.. The evolutionary origin of gamete fusion is less clear because fusogenic proteins have not been identified in prokaryotes. Here, using bioinformatics, we identified archaeal genes as a superfamily of fusogens mediating somatic and gamete fusion in multiple eukaryotic lineages. We thus propose a new hypothesis on the origins of eukaryotic sex where an archaeal fusexin used by selfish elements for horizontal transmission, was repurposed to enable gamete fusion. (Abstract excerpt)

The archaeal fusexins we identified reveal a broader presence of fusogens in yet another domain of life. We also unveil a wider physicochemical landscape for this protein superfamily, from cold hypersaline lakes to hot springs and hydrothermal vents. Discovery of the Asgard superphylum and the recent cultivation of one of its members have lent weight to eukaryogenesis models where heterogeneous populations of bacteria and archaea lived in syntrophy by transferring metabolites and genetic information. Our findings suggest that today's eukaryotic sexual reproduction is the result of over two billion years of evolution of this ancient archaeal cell fusion machine. (8-9)

Monnard, Pierre-Alain and Peter Walde. Current Ideas about Prebiological Compartmentalization. Life. Online April, 2015. University of Southern Denmark, Odense, and ETH-Zurich systems chemists describe how precursor chemicals and minerals organized themselves into bounded units on the prebiotic early earth. These formations rose from simpler, inorganic agglomerates onto complex vesicular forms. A threshold to a “living form of matter” was passed when these vital compartments could be called “protocells.” By this view, life’s evolution from its origins is seen to involve and proceed by a nested formation of whole cellular entities.

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