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

1. The Origins of Life

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.

Morowitz, Harold. The Beginnings of Cellular Life. New Haven: Yale University Press, 1992. The veteran biochemist contends that rudimentary cells arose when membrane enclosed vesicles were formed by complexifying, clumping biochemicals. This original “biogenesis” is then found to be recapitulated in the metabolism of organisms by their universality of network reactions.

Nakashima, Satoru, et al. Geochemistry and the Origin of Life. Life. 8/4, 2018. Japanese system scientists from Osaka, Yokohama, Tokyo and Kanagawa contribute to this active research subject of especial interest amongst their Earth-Life Science institutes. The authors have engaged this project into the 21st century and present a topical review and preview which hones in on five prime facets: extraterrestrial biochemicals, prebiotic chemistry, first photosynthetic metabolism, “fossil” records, and hydrogen water bonds.

In 2001, the first author (S.N.) led the publication of a book entitled “Geochemistry and the Origin of Life” in collaboration with Dr. Andre Brack aiming to figure out geo- and astro-chemical processes essential for the emergence of life. Since then, much research progress has been achieved in relevant topics from our group and others, ranging from the extraterrestrial inputs of life’s building blocks, the chemical evolution on Earth with the aid of mineral catalysts, to the fossilized records of ancient microorganisms. In addition to summarizing these findings, here we propose a new hypothesis for the generation and co-evolution of photosynthesis with the redox and photochemical conditions on the Earth’s surface. Further spectroscopic studies on the hydrogen bonding behaviors of water molecules in living cells will provide important clues to solve the complex nature of life. (Abstract edits)

Life is generally characterized by the following three functions: (1) metabolism: the ability to capture energy and material resources, staying away from thermodynamic equilibrium, (2) replication: the ability to process and transmit heritable information to progeny, and (3) compartmentalization: the ability to keep its components together and distinguish itself from the environment. These functions are operated by biopolymers such as proteins, DNAs, RNAs, and phospholipids. Proteins are made of amino acids linked together by peptide bonds. DNAs and RNAs are made of nucleotides (composed of (deoxy)ribose and nucleobases) bound by phosphodiester linkages. (1)

Nghe, Philippe, et al. Prebiotic Network Evolution. Molecular BioSystems. 11/3206, 2015. In a Royal Society of Chemistry journal, after decades of origin of life studies to identify many relevant components, this premier paper with eight authors including Stuart Kauffman, Sara Walker, Wim Hordijk, and Niles Lehman can now aver an equally important presence of interconnective dynamics which altogether initiate the cellular ascent of organisms. “Collective autocatalytic sets” as an independent source prior to biochemistry, composed of characteristic “entity nodes and relational edges,” are seen to empower a “self-sustaining” vital organization. Six parameters can then be gleaned: viable cores, connectivity kinetics, information control (RNA), scalability, resource availability, and compartmentalization (vesicles). Three features follow to aid a lower entropy path from random to scale-free topologies: preferential attachment, limited homology, and a criticality phase. Along with other 2015 reports such as Quantum Criticality at the Origin of Life (arXiv:1502.06880) that find quantum phenomena and inorganic matter to exemplify these qualities, at last life’s advent and advance is found to be graced by the one same complementary, genomic program.

The origins of life likely required the cooperation among a set of molecular species interacting in a network. If so, then the earliest modes of evolutionary change would have been governed by the manners and mechanisms by which networks change their compositions over time. For molecular events, especially those in a pre-biological setting, these mechanisms have rarely been considered. We are only recently learning to apply the results of mathematical analyses of network dynamics to prebiotic events. Here, we attempt to forge connections between such analyses and the current state of knowledge in prebiotic chemistry. Of the many possible influences that could direct primordial network, six parameters emerge as the most influential when one considers the molecular characteristics of the best candidates for the emergence of biological information: polypeptides, RNA-like polymers, and lipids. These parameters are viable cores, connectivity kinetics, information control, scalability, resource availability, and compartmentalization. These parameters, both individually and jointly, guide the aggregate evolution of collectively autocatalytic sets. We are now in a position to translate these conclusions into a laboratory setting and test empirically the dynamics of prebiotic network evolution. (Abstract)

Nitash, C. G., et al. Origin of Life in a Digital Microcosm. arXiv:1701.03993. BEACON Center for the Study of Evolution in Action, Michigan State University, researchers Nitash, Thomas LeBar, Arend Hintze and Christoph Adami continue their project to apply computational analyses to life’s occasion and development so as to reach novel findings. The guiding premise, as the BEACON home page defines, is a view of evolution as arising from algorithmic processes. While they may disagree, such studies would seem to imply that emergent organisms are naturally written into an organic cosmos.

While all organisms on Earth descend from a common ancestor, there is no consensus on whether the origin of this ancestral self-replicator was a one-off event or whether it was only the final survivor of multiple origins. Here we use the digital evolution system Avida to study the origin of self-replicating computer programs. By using a computational system, we avoid many of the uncertainties inherent in any biochemical system of self-replicators. We generated the exhaustive set of minimal-genome self-replicators and analyzed the network structure of this fitness landscape. We studied the differential ability of replicators to take over the population when competed against each other (akin to a primordial-soup model of biogenesis) and found that the probability of a self-replicator out-competing the others is not uniform. Instead, progenitor (most-recent common ancestor) genotypes are clustered in a small region of the replicator space. Our results demonstrate how computational systems can be used as test systems for hypotheses concerning the origin of life. (Abstract)

In this work we have performed the first complete mapping of a primordial sequence landscape in which replicators are extremely rare (about one replicator per 200 million sequences) and found two functionally inequivalent classes of replicators that differ in their fitness as well as evolvability, and that form distinct (mutationally disconnected) clusters in sequence space. In direct evolutionary competition, only the highest-fitness sequences manage to repeatedly become the common ancestor of all life in this microcosm, showing that despite significant diversity of replicators, historical contingency plays only a minor role during early evolution. (14)

Norris, Vic, et al. How did Metabolism and Genetic Replication Get Married. Origins of Life and Evolution of Biospheres. 45/2, 2013. Norris, with Corinne Loutelier-Bourhis, University of Rouen, and Alain Thierry, Sysdiag UMR, Montpelier, France advance a number of concepts, as noted in the Abstract, whence these “either/or” modes can be seen to proceed in mutual concert. This unification is informed by pre-existing tendencies to form viable vesicular whole that balance element and unit, persistence and evolability.

In addressing the question of the origins of the relationship between metabolism and genetic replication, we consider the implications of a prebiotic, fission-fusion, ecology of composomes. We emphasise the importance of structures and non-specific catalysis on interfaces created by structures. From the assumption that the bells of the metabolism-replication wedding still echo in modern cells, we argue that the functional assemblies of macromolecules that constitute hyperstructures in modern bacteria are the descendants of composomes and that interactions at the hyperstructure level control the cell cycle. A better understanding of the cell cycle should help understand the original metabolism-replication marriage. This understanding requires new concepts such as metabolic signalling, metabolic sensing and Dualism, which entails the cells in a population varying the ratios of equilibrium to non-equilibrium hyperstructures so as to maximise the chances of both survival and growth. A deeper understanding of the coupling between metabolism and replication may also require a new view of cell cycle functions in creating a coherent diversity of phenotypes and in narrowing the combinatorial catalytic space. (Abstract)

Nowak, Martin and Hisashi Ohtsuki. Prevolutionary Dynamics and the Origin of Evolution. Proceedings of the National Academy of Sciences. 105/14924, 2008. We enter a paper by Harvard biologists referenced in Walker and Mathis 2018 as an example of how a much decade of global collaboration can advance scientific studies from patchy rudiments to a robust integral finding.

Life is that which replicates and evolves. A fundamental question is when do chemical kinetics become evolutionary dynamics? Here we formulate a general mathematical theory for the origin of evolution. All known life on earth is based on biological polymers, which act as information carriers and catalysts. We describe prelife as an alphabet of active monomers that form random polymers. Prelife is a generative system that can produce information. Prevolutionary dynamics have selection and mutation, but no replication. Life marches in with the ability of replication as polymers act as templates for their own reproduction. Prelife is a scaffold that builds life. (Abstract)

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