V. Life's Corporeal Evolution Encodes and Organizes Itself: An EarthWinian Genesis Synthesis

1. The Origins of Life

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.

Malaterre, Christophe, et al. The Origin of Life: What is the Question? Astrobiology. May, 2022. Astroscholars in Montreal and Paris including Philip Nghe post a somewhat procedural review as a way to identify and integrate several schools of studies from early biochemistry to synthetic biology aspects.

Markovitch, Omer, et al. Chemical Heredity as Group Selection at the Molecular Level. arXiv:1802.08024. As many similar studies nowadays, systems biochemists OM, University of Groningen with Olaf Witkowski and Nathaniel Virgo, Earth-Life Science Institute, Tokyo, proceed to root life’s multilevel evolutionary phenomena such as selection, replication, autocatalysis, and especially cooperative groups deeply and firmly into fertile, active physical matter. In one more way, the extant natural cosmos is becoming wholly organic in kind.

Many examples of cooperation exist in biology. In chemical systems however we do not appear to observe intricate cooperative interactions. A key question for the origin of life, is how can molecular cooperation first arise in an abiotic system prior to the emergence of biological replication. We postulate that selection at the molecular level is a driving force behind the complexification of chemical systems. In the theory of multilevel selection the two selective forces are: within-group and between-group, where the former tends to favor "selfish" replication of individuals and the latter favor cooperation between individuals enhancing the replication of the group as a whole. Our central claim is that replication and heredity in chemical systems are subject to selection, and quantifiable using the multilevel Price equation. The biological relation of parent-progeny is proposed to be analogue to the reactant-product relation in chemistry, thus allowing for tools from evolutionary biology to be applied to chemistry and would deepen the connection between chemistry and biology. (Abstract excerpts)

Arguing that it is possible to apply biology tools on chemical systems, together with the present example help portray a route to further deepen the connections between chemistry
and biology, as much as such connections exist. For the origins of life, this supports a view of a continuous transition from the prebiotic chemistry towards present-day biology. The picture we imagine is that selection on ensembles of molecules gives rise to cooperative processes between molecules; this provides a starting point from which the complexity of biology can develop. (15)

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. 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)

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.

Morowitz, Harold. A Theory of Biochemical Organization, Metabolic Pathways, and Evolution. Complexity. 4/6, 1999. An update review wherein the emergence of life is seen to be facilitated by hierarchical circuits of biomolecule reactions.

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