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

1. The Origins of Life

Fry, Iris. The Role of Natural Selection in the Origin of Life. Origins of Life and Evolution of Biospheres. 41/1, 2011. The author of a 2000 review, The Emergence of Life on Earth, noted above, can a decade on report significant advances as researchers now mostly divide into two camps or persuasions. As the quote avers, an iconic sorting has arisen between an emphasis on discrete nucleotide molecules – ‘gene-first’, or in favor of primal autocatalytic, self-organizational processes – ‘metabolism first.’ A necessity for the gene group is the formation of membrane enclosed compartments or proto-cells to house such RNA informants. This feature, posed early on by Alexander Oparin and Sidney Fox, is seen to bridge into the equally real and vital realm of dynamic “metabolic” hypercycles.

Working back then from evolutionary selection, a further sorting occurs over “digital genetic polymers” and a (prebiotic) “analog metabolic system.” From here Preparatory Metabolism gets into the act, much due to Christian de Duve, as a “protometabolic chemistry” that led to enzyme and ribozyme gene precursors. Iris Fry surveys the major players and aspects, such as Michael Russell’s hydrothermal vents, Gunther Wachtershauser’s ferrous substrates, along with the work of Leslie Orgel, Robert Shapiro, and many others. So from any worldwide vista today, viewing this common project over the years and schools, it begs a synthesis of both modes, which could then be readily seen as the paternal and maternal evidences of a cosmos to child genetic code.

It is commonly accepted among origin-of-life scientists that the emergence of life was an evolutionary process involving at one stage or other the working of natural selection. Researchers disagree, however, on the nature of the chemical infrastructure that could have formed prebiotically, enabling the evolutionary process. The division of the origin-of-life research community into `geneticists' and `metabolists' usually revolves around the issue whether the first to arise prebiotically was a genetic polymer or a primitive metabolic system. In this paper I offer an alternative classification based on the attitude to the onset of natural selection. From this perspective I add to the conventional division between gene-first and metabolism-first groups a position I call "preparatory metabolism". (Abstract, 3)

To recapitulate, according to the prevailing thesis the emergence of life, entailing the development of complex organization, depended on a process of evolution by natural selection. Fro such a gradual process to succeed, any advantage feature achieved at one state had to be handed over, or memorized from one generation to the next. This is why the unique chemical properties of nucleic acids: their ability to form specific hydrogen bonds between their bases that enable their faithful copying, are so attractive and so difficult of give up even as the earliest genetic systems. A central debate in the context of evolution and development is the question of digital versus analog information. (9)

Garcia, Adrien, et al. The Astrophysical Formation of Asymmetric Molecules and the Emergence of a Chiral Bias. Life. 9/1, 2019. Université Côte d’Azur, CNRS, France, and Aarhus University, Denmark scientists report a persistent proclivity of cosmic nature to form a rich variety of precursor complex biochemicals.

The biomolecular homochirality in living organisms has been investigated for decades, but its origin remains poorly understood. It has been shown that circular polarized light and other energy sources are capable of inducing small enantiomeric excesses in primary biomolecules such as amino acids or sugars. Since the first findings of amino acids in carbonaceous meteorites, a scenario in which essential chiral biomolecules originate in space and are delivered by celestial bodies has arisen. In this review we summarize the discoveries in amino acids, sugars, and organophosphorus compounds in meteorites, comets, and laboratory-simulated interstellar ices. (Abstract excerpt)

Goldenfeld, Nigel, et al. Universal Biology and the Statistical Mechanics of Early Life. Philosophical Transactions of the Royal Society A. Vol. 375/Iss. 2109, 2017. A paper by University of Illinois systems biophysicists for this Origins of Life issue which delves into the rootings and continuity that organic/genetic entities ought to have with an abiding physical cosmos. As the Abstract cites, an array of material tendencies (see second quote) seem to portend precursor biomolecular forms. Again, as living systems become known to inhere natural, dynamic principles, they can better merge with a physical ground which is in turn becoming more animate and fecund.

All known life on the Earth exhibits at least two non-trivial common features: the canonical genetic code and biological homochirality, both of which emerged prior to the Last Universal Common Ancestor state. This article describes recent efforts to provide a narrative of this epoch using tools from statistical mechanics. During the emergence of self-replicating life far from equilibrium in a period of chemical evolution, minimal models of autocatalysis show that homochirality would have necessarily co-evolved along with the efficiency of early-life self-replicators. Dynamical system models of the evolution of the genetic code must explain its universality and its highly refined error-minimization properties. These have both been accounted for in a scenario where life arose from a collective, networked phase where there was no notion of species and perhaps even individuality itself. We show how this phase ultimately terminated during an event sometimes known as the Darwinian transition, leading to the present epoch of tree-like vertical descent of organismal lineages. (Abstract)

Homochirality describes a geometric property of some materials that are composed of chiral units. Chiral bodies are objects which are non-superposable on their mirror images. For example, left and right hands are chiral. A substance is said to be homochiral if all the constituent units have the same chiral form (enantiomer). In biology, homochirality is a common property of amino acids and sugars; almost all biologically produced chiral amino acids are L-chiral, while sugars are D-chiral. (Wikipedia)

Greenwell, Chris and Peter Coveney. Layered Double Hydroxide Minerals as Possible Prebiotic Information Storage and Transfer Compounds. Origins of Life and Evolution of Biospheres. 36/1, 2006. This substrate is suggested as the necessary suitable matrix which not only had the capacity to replicate, but could undergo discrete inherited mutations.

Guttenberg, Nicholas, et al. Selection First Path to the Origin of Life. arXiv:1706.05831. As the quote details, with Nathaniel Virgo, Chris Butch, and Norman Packard, Earth-Life Science Institute, Tokyo Institute of Technology researchers propose a synthesis beyond present models as a better, more integral, way to reconstruct. By their perspective, an informational quality can now be attributed to self-amplifying populations.

We propose an alternative to the prevailing two origin of life narratives, one based on a replicator first hypothesis, and one based on a metabolism first hypothesis. Both hypotheses have known difficulties: All known evolvable molecular replicators such as RNA require complex chemical (enzymatic) machinery for the replication process. Likewise, contemporary cellular metabolisms require several enzymatically catalyzed steps, and it is difficult to identify a non-enzymatic path to their realization. We propose that there must have been precursors to both replication and metabolism that enable a form of selection to take place through action of simple chemical and physical processes. We model a concrete example of such a process, repeated sequestration of binary molecular combinations after exposure to an environment with a broad distribution of chemical components, as might be realized experimentally in a repeated wet-dry cycle. We show that the repeated sequestration dynamics results in a selective amplification of a very small subset of molecular species present in the environment, thus providing a candidate primordial selection process. (Abstract)

Hanczyc, Martin. Metabolism and Motility in Prebiotic Structures. Philosophical Transactions of the Royal Society B. 366/2885, 2011. A paper in an issue on The Chemical Origins of Life and its Early Evolution, see Lilley below. In a similar way as Leroy Cronin (search), a University of Southern Denmark, Center for Fundamental Living Technology, biochemist reports an inherent, persistent tendency of so-called “inorganic” materiality to congeal into vesicular droplets, in some guise as primordial protocells. May thus one add an even earlier stage to animate nature’s sequential nest of dolled-up compartmental cells and multicellular selves, lately reaching us writer and reader. Newly edified by this discovery, may we intentionally continue such communality as “social proto-cells,” of nominal 100 persons, the archetypal human grouping, as Sustainable Ecovillages herein personifies?

Easily accessible, primitive chemical structures produced by self-assembly of hydrophobic substances into oil droplets may result in self-moving agents able to sense their environment and move to avoid equilibrium. These structures would constitute very primitive examples of life on the Earth, even more primitive than simple bilayer vesicle structures. A few examples of simple chemical systems are presented that self-organize to produce oil droplets capable of movement, environment remodelling and primitive chemotaxis. Such motile agents would be capable of finding resources while escaping equilibrium and sustaining themselves through an internal metabolism, thus providing a working chemical model for a possible origin of life. (2885)

Hazen, Robert. Genesis: The Scientific Quest for Life’s Origin. Washington, DC: Joseph Henry Press, 2005. A synopsis of this premier perception of an innate gestation is cited in Current Vistas.

Hazen, Robert. Geochemical Origins of Life. Knoll, Andrew, et al, eds. Fundamentals of Geobiology. New York: Wiley-Blackwell, 2012. In a volume reviewed more in A Living Planet, the Carnegie Institution of Washington geochemist and author proposes, from this vista, that a “progressive sequence” from physical matter to organic entities can be attributed to the innate action of self-organizing, complex adaptive systems. By these lights, the “emergence of natural selection” occurs quite after and ancillary to this vitalizing force. The chapter concludes by saying such an inclusive synthesis can settle the current metabolism or replication first argument, as the second quotes cites.

Emergence as a Unifying Concept in Origins Research Life’s origins can be modeled as a sequence of so-called ‘emergent’ events, each of which added new structure and chemical complexity to the prebiotic Earth. Observations of numerous everyday phenomena reveal that new patterns commonly emerge when energy flows through a collection of many interacting particles. (315) In the words of John Holland….emergent systems display three distinctive characteristics: they arise from the interactions of many ‘agents,’ energy flows through those systems, and they display new patterns or behaviors that are not manifest by the individual agents. (315)

3. Life began as a cooperative chemical phenomenon between metabolism and genetics: A third possible scenario rests on the possibility that neither primitive metabolic cycles (which lack the means of faithful self-replication) nor primitive genetic molecules (which are not very stable and lack a reliable source of chemical energy) could have progressed far by themselves. If, however, a crudely self-replication genetic molecule became attached to a crudely functioning surface-bound metabolic coating, then a kind of cooperative chemistry might have kicked in. (328)

Hazen, Robert. The Emergence of Patterning in Life’s Origin and Evolution. International Journal of Developmental Biology. 53/5-6, 2009. An update by a prime contributor to the revolution that the universe is not alien to or bereft of life, but rather an ordained nature seems made to generate complex viable systems. In so doing, generic complex, self-organizing, adaptive systems composed of many agents in informed interrelation are increasingly and robustly found everywhere.

Three principles guide natural pattern formation in both biological and non-living systems: (1) patterns form from interactions of numerous individual particles, or “agents,” such as sand grains, molecules, cells or organisms; (2) assemblages of agents can adopt combinatorially large numbers of different configurations; (3) observed patterns emerge through the selection of highly functional configurations. (683)

Complex patterning is a hallmark of biological systems at every scale, from molecules to cells to organisms to ecosystems. Life’s triumph of order over chaos is the epitome of the more general natural phenomenon of emergent systems, in which numerous components or “agents” respond to their local environments, thus interacting to produce patterns or behaviors not characteristic of individual agents. (683)

Helmbrecht, Vanessa, et al. White and green rust chimneys accumulate RNA in a ferruginous chemical garden. Geobiology. 21/6, 2023. Ludwig-Maximilians University paleo-geoscientists return to thermal vent environs with 2020s analytical techniques to be able to explain how they could be a plausible origin site.

Mechanisms of nucleic acid accumulation were likely critical to life's emergence in the ferruginous oceans of the early Earth. How prebiotic geological settings accumulated nucleic acids from dilute aqueous solutions is poorly understood. We, simulated low-temperature alkaline hydrothermal vents in co-precipitation experiments to investigate chemical gardens via sorption. RNA was only extractable from the ferruginous solution in the presence of a phosphate buffer, suggesting RNA in solution was bound to Fe2+ ions. This represents a new mechanism for nucleic acid accumulation in the ferruginous oceans of the early Earth and may have helped to concentrate RNA in a dilute prebiotic ocean.

Hengeveld, Rob, ed. Recent Work on the Origin of Life. Acta Biotheoretica. 55/2, 2007. A special issue of some 225 pages that contains substantial papers such as an “alkaline solution” to life’s start, and how this salient event was bootstrapped upon energy flows.

Herdewijn, Piet and M. Volkan Kisakurek, eds. Origin of Life: Chemical Approach. Weinheim: WILEY-VCH Verlag, 2008. A recent collection from Chemistry & Biodiversity with notable authors such as Christian de Duve and Antonio Lazcano. A good review by Harold Morowitz appears in the March 2009 issue of the Quarterly Review of Biology.

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