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

1. The Origins of Life

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)

Ogata, Norichika. Quantitative Measurement of Heritability in the Pre-RNA World. arXiv:1901.07400. We cite this entry by a Nihon BioData Corp., Japan researcher, formerly at Kawasaki Medical University, as a 2019 example of how origin of life studies have moved beyond biomolecules (RNA) or metabolism alone to include the generative presence of nature’s universal independent generative propensities.

Before assembly with nucleotides, in the pre-RNA era, what system dominated heredity? Self-organized complex systems are hypothesized to be a primary factor of the origin of life and to dominate heritability, mediating the partitioning of an equal distribution of structures and molecules at cell division. The degree of strength of self-organization would correlate with heritability; self-organization is known to be a physical basis of hysteresis phenomena, and the degree of hysteresis is quantifiable. However, there is no argument corroborating the relationship between heritability and hysteresis. Here, we show that the degree of cellular hysteresis indicates its heritability and daughter equivalence at cell division. Our results demonstrate that self-organized complex systems contribute to heredity and are still important in mammalian cells. Discovering ancient and hidden heredity systems enables us to study our own origin, to predict cell features and to manage them in the bio-economy. (Abstract excerpt)

Pargellis, Andrew. Self-organizing Genetic Codes and the Emergence of Digital Life. Complexity. 8/4, 2003. Computer-based studies illuminate the role of complex system dynamics at life’s origin which served to organize the various molecular and protocell components.

A major observation is that self-organization of the genetic code can greatly increase the probability of emergence of self-replicators from the primordial soup. (69)

Pascal, Robert. A Possible Non-Biological Reaction Framework for Metabolic Processes on Early Earth. Nature. 569/47, 2019. The University of Montpellier biochemist comments on a paper, Synthesis and Breakdown of Universal Metabolic Precursors Promoted by Iron, in the same issue (569/104) by Kamila Muchowaka, et al (University of Strasbourg) which reports how a network of reactions for converting carbon dioxide into organic compounds could have fostered the advent and advance of original life.

Pascal, Robert, et al. Towards an Evolutionary Theory of the Origin of Life Based on Kinetics and Thermodynamics. Open Biology. Online November, 2013. In this new Royal Society web journal, prime theorists Pascal, Institut des Biomolecules, Montpellier, France, with Addy Pross, Ben-Gurion University of the Negev, and John Sutherland, MRC Laboratory of Molecular Biology, Cambridge, combine their prebiotic chemistry and energetic drive studies to achieve a unitary synthesis of regnant living systems with a conducive cosmos. On page 2, per the quote, the issue of whether life’s occasion is an improbable rarity, or arises due to intrinsic properties is put To wit, in addition to biochemical pathways, there must be some nonequilibrium creative force, which much evidence now implicates. See also The Nature and Mathematical Basis for Material Stability in the Chemical and Biological Worlds by Pascal and Pross in the Journal of Systems Chemistry, online March 2014. This work is a significant coalescence and contribution to explain a natural organic genesis.

A sudden transition in a system from an inanimate state to the living state — defined on the basis of present day living organisms — would constitute a highly unlikely event hardly predictable from physical laws. From this uncontroversial idea, a self-consistent representation of the origin of life process is built up, which is based on the possibility of a series of intermediate stages. This approach requires a particular kind of stability for these stages — dynamic kinetic stability (DKS) — which is not usually observed in regular chemistry, and which is reflected in the persistence of entities capable of self-reproduction. The necessary connection of this kinetic behaviour with far-from-equilibrium thermodynamic conditions is emphasized and this leads to an evolutionary view for the origin of life in which multiplying entities must be associated with the dissipation of free energy. Any kind of entity involved in this process has to pay the energetic cost of irreversibility, but, by doing so, the contingent emergence of new functions is made feasible. The consequences of these views on the studies of processes by which life can emerge are inferred. (Abstract)

We thus face a dilemma; either Monod was right, life emerged as a consequence of an event that had almost no chance to occur during the lifetime of the universe, or the emergence of life is not a mere question of the probability of a single event, but a driving force exists—and can thus be discovered—to drive this process through its various stages. So the second possibility — the existence of some driving force governing the evolutionary process—needs to be investigated. (2)

A true understanding of biology must include knowledge of its chemical origins, and comprehending the chemical events that gave biology its foundations – cellular format, the central dogma, the genetic code – is therefore a fundamental aspect of natural science. Furthermore, understanding the way in which extant biology arose can inform the design of 'synthetic' biologies. We are interested in uncovering prebiotically plausible syntheses of the informational, catalytic and compartment–forming molecules necessary for the emergence of life. We have previously demonstrated the constitutional self-assembly of pyrimidine ribonucleotides from mixtures of simple building blocks, and we are now exploring similar 'systems chemistry' approaches to the purine ribonucleotides, and ways of assembling RNA from these ribonucleotides with regiocontrol of the internucleotide phosphodiester linkage. (JS, Chemical Origins of Molecular Biology site)

Patel, Bhavesh, et al. Common Origins of RNA, Protein and Lipid Precursors in a Cyanosulfidic Protometabolism. Nature Chemistry. 7/4, 2015. A team from John Sutherland’s (coauthor) laboratory at the MRC Laboratory of Molecular Biology, Cambridge describe for the first time how the essential classes of nucleic acids, amino acids, and lipids could have all formed at once. The work is noted as a breakthrough in an editorial A Primordial Soup that Cooks Itself, and by the Nobel chemist and origin of life researcher Jack Szostak in the journal Science (347/1298). As a result of this advance, it is said a singular environment can be identified which gave rise to diverse molecules that could store information, administer metabolism, and form bounded units, the three prime traits of life.

A minimal cell can be thought of as comprising informational, compartment-forming and metabolic subsystems. To imagine the abiotic assembly of such an overall system, however, places great demands on hypothetical prebiotic chemistry. The perceived differences and incompatibilities between these subsystems have led to the widely held assumption that one or other subsystem must have preceded the others. Here we experimentally investigate the validity of this assumption by examining the assembly of various biomolecular building blocks from prebiotically plausible intermediates and one-carbon feedstock molecules. We show that precursors of ribonucleotides, amino acids and lipids can all be derived by the reductive homologation of hydrogen cyanide and some of its derivatives, and thus that all the cellular subsystems could have arisen simultaneously through common chemistry. The key reaction steps are driven by ultraviolet light, use hydrogen sulfide as the reductant and can be accelerated by Cu(I)–Cu(II) photoredox cycling. (Abstract)

Pearce, Ben, et al. Origin of the RNA World: The Fate of Nucleobases in Warm Little Ponds. Proceedings of the National Academy of Sciences. 114/11327, 2017. Origins Institute, McMaster University and MPI Astronomy astrophysicists expand considerations of how living systems came to form on Earth, quite akin to Charles Darwin’s imagination of conducive baths. A commentary by David Deamer, Darwin’s Prescient Guess, in this issue commends their 2010s insight into life’s watery, and astral occasion.

There are currently two competing hypotheses for the site at which an RNA world emerged: hydrothermal vents in the deep ocean and warm little ponds. Because the former lacks wet and dry cycles, which are well known to promote polymerization (in this case, of nucleotides into RNA), we construct a comprehensive model for the origin of RNA in the latter sites. Our model advances the story and timeline of the RNA world by constraining the source of biomolecules, the environmental conditions, the timescales of reaction, and the emergence of first RNA polymers. (Significance)

Pearce et al. (1) have made a bold and challenging attempt to provide a quantitative estimate for the accumulation of nucleobases, like adenine, on the Hadean Earth some 4 billion y ago, before life began. Why bold? There must have been a source of organic compounds for life to begin, and they chose an extraterrestrial source—carbonaceous meteorites—rather than the geochemical source more commonly assumed in origins of life research. Why challenging? The authors chose to model the origin of life in fresh-water ponds on volcanic land masses emerging from a global ocean, in direct contrast to the current paradigm that life originated in sea water using chemical energy associated with hydrothermal vents. (Deamer, 11264)

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