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

1. The Origins of Life

Derr, Julien, et al. Prebiotically Plausible Mechanisms Increase Compositional Diversity of Nucleic Acid Sequences. Nucleic Acids Research. 40/10, 2012. By way of sophisticated theory and experiment, Harvard University biosystem scientists including Irene Chen and Martin Nowak, engage the deepest issue of whether the appearance of such viable replicative biomolecules happened by capriciousness or was due to some innate, independent â€œpredispositionâ€ at work. Indeed, this ultimate â€œto be or not to beâ€ question is just lately becoming answerable in actual favor of a primal propensity to cause and give rise to complexifying life and its evolutionary ascent.

During the origin of life, the biological information of nucleic acid polymers must have increased to encode functional molecules (the RNA world). Ribozymes tend to be compositionally unbiased, as is the vast majority of possible sequence space. However, ribonucleotides vary greatly in synthetic yield, reactivity and degradation rate, and their non-enzymatic polymerization results in compositionally biased sequences. While natural selection could lead to complex sequences, molecules with some activity are required to begin this process. Was the emergence of compositionally diverse sequences a matter of chance, or could prebiotically plausible reactions counter chemical biases to increase the probability of finding a ribozyme?

Our in silico simulations using a two-letter alphabet show that template-directed ligation and high concatenation rates counter compositional bias and shift the pool toward longer sequences, permitting greater exploration of sequence space and stable folding. We verified experimentally that unbiased DNA sequences are more efficient templates for ligation, thus increasing the compositional diversity of the pool. Our work suggests that prebiotically plausible chemical mechanisms of nucleic acid polymerization and ligation could predispose toward a diverse pool of longer, potentially structured molecules. Such mechanisms could have set the stage for the appearance of functional activity very early in the emergence of life. (Abstract)

Dokholyan, Nikolay, et al. Expanding Protein Universe and Its Origin from the Biological Big Bang. Proceedings of the National Academy of Sciences. 99/14132, 2002. The microcosm of macromolecular proteins is found to exhibit a universal similarity at different levels of complexity.

With the large number of protein structures identified in the past decades, we have discovered peculiar patterns that nature imprints on protein structural space in the course of evolution. In particular, we have discovered that the universe of protein structures is organized hierarchically into a scale-free network. (14132)

Douglas, Jordan, et al. Douglas, Jordan, et al. Enzymic recognition of amino acids drove the evolution of primordial genetic codes. Nucleic Acids Research. 52/2, 2024. Into this late year, University of Auckland and University of North Carolina paleobiologists including Peter Wills and Charles Carter (search each) are able todelve deeper to reach better quantified reasons of how and why prebiotic precursors and reactions formed biomolecular systems that could replicate themselves. And as one reads along, an impression grows that our Earthuman retrospective has indeed come upon a preordained ecosmic fertility as it proceeds to complexify, reproduce, develop and evolve.

How genetic information gained its control over chemical processes which build living cells remains to be understood. Today, the aminoacyl-tRNA synthetases (AARS) are known to foster the genetic codes in all living systems. A phylogenetic reconstruction of extant AARS genes, enhanced by modular acquisitions, reveals six AARS with distinct bacterial, archaeal, eukaryotic, or organellar clades. The resulting model shows a tendency for less elaborate enzymes, with simpler catalytic domains, to activate amino acids that did not appear until later. A probable evolutionary route for an amino acid type to find a place in the code was by recruiting older, less specific AARS. (excerpt)

Egbert, Matthew, et al. Behavior and the Origin of Organisms. Origins of Life and Evolution of Biospheres. May, 2023. A nine person international effort by ME and Emily Parke, University of Auckland, Martin Hanczyc, University of Trento, Inman Harvey, University of Sussex, Nathaniel Virgo, Earth-Life Science Institute, Tokyo, Hiroki Sayama, SUNY Binghamton, Tom Froese, Okinawa Institute of Science and Technology, Alexandera Penn, University of Surrey, and Stuart Bartlett, Cal Tech (search each) draw on years of empirical and theoretic research, a good part their own, to quantify how prebiotic environs are suffused by an innately conducive viability. Typical sections include Behavior that Responds to Viability: A Common Structure Underlying the Self-Perserving Behaviors of Ante-Organisms; A Platform of Opportunity for Organismic Functional Diversity. Just as the JWST can hark back to the earliest galaxies, so a deeply rooted fertility can be found long before. Here is a prime 2023 advance as biology and physics come together within a phenomenal natural genesis. See also How Prebiotic Complexity Increases through Darwinian Evolution by Kohtoh Yukawa, et al in Current Opinion in Systems Biology (June 2023) for another deeper rooting.

It is common in origins of life research to view the first stages of life as the passive result of particular environmental conditions. This paper considers the alternative possibility: that the antecedents of life were already actively regulating their environment to maintain the conditions necessary for their own persistence. In support of this proposal, we describe ‘viability-based behaviour’: a way that simple entities can adaptively regulate their environment in response to their health, and in so doing, increase the likelihood of their survival. Drawing on empirical investigations of simple self-preserving abiological systems, we argue that these viability-based behaviours are simple enough to precede neo-Darwinian evolution. We also explain how their operation can reduce the demanding requirements that mainstream theories place upon the environment(s) in which life emerged. (Abstract)
Along the way, four ante-organism (ancestor) modes are reaction-diffusion spots, motile oil droplets, charge transportation networks, and Bénard convection cells which share a basic essential form: their activities occur in response to a systemic liveliness. To explain, each is a far-from-equilibrium dissipative structure (Nicolis and Prigogine 1989) whose ‘metabolism’ (i.e., energy-dissipating, structure-producing processes of self-construction) is distributed spatially. (10)

Egel, Richard. Eukaryogenesis: On the Communal Nature of Precellular States, Ancestral to Modern Life. Life. Online January, 2012. For a special, on-going issue of this online journal on the Origin of Life, a University of Copenhagen Biocenter researcher provides a 50 page contribution that stresses an inherent proclivity of biomatter toward such social assemblies. One might imagine that prokaryotes, eukaryotes, and precursor vesicles are moved and guided by these independent, genetic-like forces. See also the author’s chapter “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth” in Egel, et al, eds. Origins of Life (Springer, 2011 herein).

This problem-oriented, exploratory and hypothesis-driven discourse toward the unknown combines several basic tenets: (i) a photo-active metal sulfide scenario of primal biogenesis in the porespace of shallow sedimentary flats, in contrast to hot deep-sea hydrothermal vent conditions; (ii) an inherently complex communal system at the common root of present life forms; (iii) a high degree of internal compartmentalization at this communal root, progressively resembling coenocytic (syncytial) super-cells; (iv) a direct connection from such communal super-cells to proto-eukaryotic macro-cell organization; and (v) multiple rounds of micro-cellular escape with streamlined reductive evolution—leading to the major prokaryotic cell lines, as well as to megaviruses and other viral lineages. Hopefully, such nontraditional concepts and approaches will contribute to coherent and plausible views about the origins and early life on Earth. In particular, the coevolutionary emergence from a communal system at the common root can most naturally explain the vast discrepancy in subcellular organization between modern eukaryotes on the one hand and both archaea and bacteria on the other. (Abstract, 170)

Egel, Richard. Origins and Emergent Evolution of Life. Origins of Life and Evolution of Biospheres. Online September, 2014. The emeritus University of Copenhagen systems biologist continues his project to integrate many diverse approaches, theories, and aspects of this early occasion of proto-organic molecules, assemblies, cellular complexities, and so on into a succinct synthesis. He has schooled himself, as a long bibliography reflects, in contributions from Alexander Oparin in the 1930s to Sidney Fox and Freeman Dyson in the 1970s and 1980s to everyone today. Here the “colloid microsphere hypothesis” is revisited. A companion paper as humankind now learns altogether is The Origin and Spread of a Cooperative Replicase in a Prebiotic Chemical System by Julie Shay, Chris Huynh and Paul Higgs in the Journal of Theoretical Biology (Online September 2014).

Self-replicating molecules, in particular RNA, have long been assumed as key to origins of life on Earth. This notion, however, is not very secure since the reduction of life’s complexity to self-replication alone relies on thermodynamically untenable assumptions. Alternative, earlier hypotheses about peptide-dominated colloid self-assembly should be revived. Such macromolecular conglomerates presumably existed in a dynamic equilibrium between confluent growth in sessile films and microspheres detached in turbulent suspension. The first organic syntheses may have been driven by mineral-assisted photoactivation at terrestrial geothermal fields, allowing photo-dependent heterotrophic origins of life. Inherently endowed with rudimentary catalyst activities, mineral-associated organic microstructures can have evolved adaptively toward cooperative ‘protolife’ communities, in which ‘protoplasmic continuity’ was maintained throughout a graded series of ‘proto-biofilms’, ‘protoorganisms’ and ‘protocells’ toward modern life. Eventually, Darwinian speciation of cell-like lineages commenced after minimal gene sets had been bundled in transmissible genomes from multigenomic protoorganisms. (Abstract excerpts)

Egel, Richard, et al, eds. Origins of Life: The Primal Self-Organization. Heidelberg: Springer, 2011. With coeditors Dirk-Henner Lankenau and Armen Mulkidjanian, a large volume with these sections: Energetics of the First Life, Primeval Syntheses, Facets of an Ancestral Peptide World, and RNA Worlds – Ancestral and Contemporary. And might one wonder what kind of cosmos strives by way of us late collaborative creatures over a noosphere world, many billion years on, to reconstruct how life and mind came to be. Could such an apparent self-learning, observing, and selecting universal emergence be meant to engender the beginning of a second, intentional genesis?

If theoretical physicists can seriously entertain canonical “standard models” even for the big-bang generation of the entire universe, why cannot life scientists reach a consensus on how life has emerged and settled on this planet? Scientists are hindered by conceptual gaps between bottom-up inferences (from early Earth geological conditions) and top-down extrapolations (from modern life forms to common ancestral states). This book challenges several widely held assumptions and argues for alternative approaches instead. Primal syntheses (literally or figuratively speaking) are called for in at least five major areas. (1) The first RNA-like molecules may have been selected by solar light as being exceptionally photostable. (2) Photosynthetically active minerals and reduced phosphorus compounds could have efficiently coupled the persistent natural energy flows to the primordial metabolism. (3) Stochastic, uncoded peptides may have kick-started an ever-tightening co-evolution of proteins and nucleic acids. (4) The living fossils from the primeval RNA World thrive within modern cells. (5) From the inherently complex protocellular associations preceding the consolidation of integral genomes, eukaryotic cell organization may have evolved more naturally than simple prokaryote-like life forms. – If this book can motivate dedicated researchers to further explore the alternative mechanisms presented, it will have served its purpose well. (Publisher)

Fahrenbach, Albert and Quoc Phuong Tran. Prebiotic Metabolism gets a Boost. Nature Chemsitry. 12/11, 2020. University of New South Wales biochemists introduce a special issue on the latest research with entries such as: A Metal-free Ancestral Analogue of the Krebs cycle Composed of Alpha-ketoacids by Trent Stubbs, et al. and Harnessing Chemical Free Energy for Activation and Joining of Prebiotic Building Block by Ziwei Liu, et al.

It’s generally assumed that primitive forms of cellular life arose from nucleic acids and peptides compartmentalized within vesicles, along with a non-enzymatic protometabolism. So then how could this complex chemistry arise in the first place? To address this question, prebiotic chemists have explored non-enzymatic pathways for production of these biomolecules under conditions that are consistent with an early-Earth environment, and represent various stages along the progression from non-life to protolife amd to life as we recognize it today. In this issue of Nature Chemistry, three studies demonstrate such non-enzymatic chemistry that can point towards possible mechanisms,at life’s progressive emergence. (982)

Fairchild, Jaspar, et al. Prebiotically plausible chemoselective pantetheine synthesis in water. Science. 383/911, 2024. In a paper that made science news, University College London biochemists including Matthew Powner report that they were able to explain how this unique intermediary compound came into existence on cue so as to complement a vital biochemical regimen so that protocellular metabolisms could proceed on their lively way.

Coenzyme A (CoA) is essential to life and its functional subunit, pantetheine, is vital to origin-of-life scenarios, but how pantetheine (a cysteamine amide analog of pantothenic acid = vitamin B5) emerged on the early Earth remains a mystery. In this work, we report high-yielding and selective prebiotic syntheses of pantetheine in water. Chemoselective multicomponent aldol, iminolactone, and aminonitrile reactions delivered spontaneous differentiation of pantoic acid and proteinogenic amino acid syntheses. Our results are consistent with a role for canonical pantetheine at the outset of life on Earth. (Excerpt)

Fishkis, Maya. Emergence of Self-Reproduction in Cooperative Chemical Evolution of Prebiological Molecules. Origins of Life and Evolution of Biospheres. Online September, 2010. A Canadian systems biologist proposes that the complexity sciences via agent-based modeling, aka artificial chemistry, can be extended to prebiotic material realms. The implication then arises that primordial matter appears so composed that life’s origin is a non-random probability.

Flack, Jessica. Coarse-Graining as a Downward Causation Mechanism. Philosophical Transactions of the Royal Society A. Vol. 375/Iss. 2109, 2017. In this Origins issue, the Santa Fe Institute professor of Collective Computation continues her project (search) to discern and express life’s apparent ascent from earlier upward forces of some kind to later, emergent realms which can then proceed in an intentional, formative way to act upon lower levels so as to facilitate higher phases going forward. As the Abstract says, a salient feature seems to be regular, iterative motifs that a knowledge-gaining evolution consistently employs. Again neural networks are availed as an iconic model.

Downward causation is the controversial idea that ‘higher’ levels of organization can causally influence behaviour at ‘lower’ levels of organization. Here I propose that we can gain traction on downward causation by being operational and examining how adaptive systems identify regularities in evolutionary or learning time and use these regularities to guide behaviour. I suggest that in many adaptive systems components collectively compute their macroscopic worlds through coarse-graining. I further suggest we move from simple feedback to downward causation when components tune behaviour in response to estimates of collectively computed macroscopic properties. I introduce a weak and strong notion of downward causation and discuss the role the strong form plays in the origins of new organizational levels. I illustrate these points with examples from the study of biological and social systems and deep neural networks. (Abstract)

Froese, Tom, et al. Horizontal Transfer of Code Fragments between Protocells can Explain the Origins of the Genetic Code without Vertical Descent. Nature Scientific Reports. 8/3532, 2018. As the Abstract notes, TF and Jorge Campos, National Autonomous University of Mexico, Kosuke Fujishima and Nathaniel Virgo, Earth-Life Science Institute, Tokyo Institute of Technology, and Daisuke Kiga, Waseda University, Tokyo achieve a robust proof of Carl Woese’s integral evolutionary synthesis (search CW, Sarkar) about how early dynamic genome cross-transmissions served life’s initial development.

Theories of the origin of the genetic code typically appeal to natural selection and/or mutation of hereditable traits to explain its regularities and error robustness, yet the present translation system presupposes high-fidelity replication. (Carl) Woese’s solution to this bootstrapping problem was to assume that code optimization had played a key role in reducing the effect of errors caused by the early translation system. He further conjectured that initially evolution was dominated by horizontal exchange of cellular components among loosely organized protocells, rather than by vertical transmission of genes. Here we simulated such communal evolution based on horizontal transfer of code fragments, possibly involving pairs of tRNAs and their cognate aminoacyl tRNA synthetases or a precursor tRNA ribozyme capable of catalysing its own aminoacylation, by using an iterated learning model. This is the first model to confirm Woese’s conjecture that regularity, optimality, and (near) universality could have emerged via horizontal interactions alone. (Abstract)

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