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

1. The Origins of Life

Siebert, Charles. The Genesis Project. New York Times Sunday Magazine. September 26, 2004. The author notes that at the same time earth is beset by violent fundamentalisms, a concerted global effort, especially by NASA’s Astrobiology Institute, is revealing the true creation of life both here and in the universe. A good current summary of the collaborative enterprise.

Silke, Asche, et al. What it takes to solve the Origin(s) of Life: An integrated review of techniques.. arXiv:2308.11665. As a good example of a 2020s spiral turn to a global research endeavor, over forty authors who make up an “Origin of Life Early-career Network” from across Europe, the USA, Japan and China, such as Martina Preiner, Stuart Harrison and Joanna Xavier scope a most comprehensive agenda from quantum chemistry and genetic replicators onto an evolutionary course. Topical aspects include Network Autocatalysis, Metagenomics, Information Theory, Synthetic Biology, Protocells for some 109 pages and backed by 680 references. A billion years or so later, just now a superorganic knowsphere can begin to achieve its retrospective observance.

Understanding the origin(s) of life (OoL) is a fundamental challenge for science in the 21st century. Research on OoL spans many disciplines from chemistry and physics to biology, planetary sciences, computer science, mathematics and philosophy. These diverse aspects has so far involved a contrast of techniques, data, and software in the field. Here, we hope to scope out and provide a common consolidation toward a unifying view on how life emerges and ultimately to empower a new generation of OoL scientists. (Excerpt)

Modeling Chemical Systems Both equilibrium and nonequilibrium approaches to modelling chemical systems are common in OoL studies. The nonequilibrium approach is based on chemical kinetic theory as well as the growing field of nonequilibrium thermodynamics, and it is used in environments that are driven out of equilibrium such as terrestrial atmospheres, protoplanetary disks, and biological enzyme catalysis. Finally, many biochemical and biological systems are modelled using the principles of chemical reaction networks - which share a framework with classical chemical kinetic theory. (37-38)

Smokers, Iris, et al. Complex Coacervation and Compartmentalizes Conversion of Prebiotically Relevant Metabolites. ChemSystemsChem. June, 2022. In this new Chemistry Europe journal, Radboud biochemists along with lab director Evan Spruijt contribute another 2020s instance whereby synthetic ideas can be fed back to help illume what went on long ago as life first came into being and on its cellular way to our curious selves.

Metabolism and compartmentalization are two of life’s most central elements. Constructing
synthetic assemblies based on prebiotically relevant molecules that combine these elements can provide insight into the formation of life-like protocells from abiotic building blocks. In this work, we show that a wide variety of anionic metabolites interact with oligoarginine to form coacervate protocells through liquid-liquid phase separation. We show that these metabolites remain reactive in compartmentalized systems. These results reveal the intricate interplay between (proto)metabolic reactions and coacervate compartments. (Abstract excerpt)

Stankiewicz, Johanna and Lars Henning Eckardt. Chemobiogenesis 2005 and Systems Chemistry Workshop. Angewandte Chemie. 45/342, 2006. Frontier insights into an innately dynamic materiality which leads on to biological precursors are arising in central Europe as evidenced by this conference report. Leading researchers such as Peter Schuster, Eors Szathmary, Antonia Lazcano, Reza Ghadiri, and Steen Rasmussen were in attendance. A “prebiotic robustness” via the spontaneous coevolution of peptides and chemical energetics is seen to cause the emergence of homochirality (molecules of similar handedness) and nucleotides. Self-organizing catalytic networks will spawn non-Brownian self-reproducing vesicles. Such protocells can then be seen as a “supersystem” phase of a complex nonlinear chemistry. Chembiogenesis 2007 is to be held in Dubrovnik, Croatia in May.

Stubbs, Trent, et al. A Plausible Metal-free Ancestral Analogue of the Krebs cycle Composed Entirely of Alpha-ketoacids. Nature Chemistry. October, 2020. NSF-NASA Center for Chemical Evolution (Google) researchers including Greg Springsteen (Furman University) delve deeper into early biochemical phases so to reconstruct endemic ways that life’s emergent course could have plausibly taken place. Our late observance and accomplishment again implies a phenomenal fertility of an organically procreative ecosmos.

Efforts to decipher the prebiotic roots of metabolic pathways have focused on recapitulating modern biological transformations, with metals serving in place of cofactors and enzymes. Here we show that the reaction of glyoxylate with pyruvate under mild aqueous conditions produces a series of α-ketoacid analogues of the reductive citric acid cycle without the need for metals or enzyme catalysts. The transformations proceed in the same sequence as the reverse Krebs cycle, resembling a protometabolic pathway, with glyoxylate acting as both the carbon source and reducing agent. (Abstract excerpt)

Subramanian, Hemachander and Robert Gatenby. Evolutionary Advantage of a Broken Symmetry in Autocatalytic Polymers Explains Fundamental Properties of DNA. arXiv:1605.00748. Moffitt Cancer Center and Research Institute, Tampa, FL physicians appear to describe an inherent, primordial propensity for a fertile nature to live, evolve, and learn so that one fine day cognizant peoples might be able to self-realize, heal, save, select, and enhance.

The macromolecules that encode and translate information in living systems, DNA and RNA, exhibit distinctive structural asymmetries, including homochirality or mirror image asymmetry and 3'-5' directionality, that are invariant across all life forms. Here we construct a simple model of hypothetical self-replicating polymers to show that asymmetric autocatalytic polymers are more successful in self-replication compared to their symmetric counterparts in the Darwinian competition for space and common substrates. This broken-symmetry property, called asymmetric cooperativity, arises when the catalytic influence of inter-strand bonds on their left and right neighbors is unequal. Asymmetric cooperativity also leads to simple evolution-based explanations for a number of other properties of DNA that include four nucleotide alphabet, three nucleotide codons, circular genomes, helicity, anti-parallel double-strand orientation, heteromolecular base-pairing, asymmetric base compositions, and palindromic instability, apart from the structural asymmetries mentioned above. (Abstract excerpts)

Living systems, uniquely in nature, acquire, store and use information autonomously. The molecular carriers of information, DNA and RNA, exhibit a number of distinctive physico-chemical properties that are optimal for information storage and transfer. This suggests that significant prebiotic evolutionary optimization preceded and resulted in RNA and DNA, and that the nucleotide properties are not simply random. (1)

Szathmary, Eors. Coevolution of Metabolic Networks and Membranes: the Scenario of Progressive Sequestration. Philosophical Transactions of the Royal Society B. 362/1781, 2007. As the extended Abstract notes, the Eotvos University, Budapest, biologist presses the view that enclosed proto-vesicles was a crucial feature of life’s original advance. Evolution is then a story of their sequential ramification via hierarchies of wholes nested within wholes, lately a worldwide humankind. See also in the same issue Tristan Rocheleau, et al. Emergence of Protocellular Growth Laws.

Many regard metabolism as one of the central phenomena (or criteria) of life. Yet, the earliest infrabiological systems may have been devoid of metabolism: such systems would have been extreme heterotrophs. We do not know what level of complexity is attainable for chemical systems without enzymatic aid. Lack of template-instructed enzymatic catalysis may put a ceiling on complexity owing to inevitable spontaneous decay and wear and tear of chemodynamical machines. Views on the origin of metabolism critically depend on the assumptions concerning the sites of synthesis and consumption of organic compounds. If these sites are different, non-enzymatic origin of autotrophy is excluded. Whether autotrophy is secondary or not, it seems that protocell boundaries may have become more selective with time, concurrent with the enzymatization of the metabolic network. Primary heterotrophy and autotrophy imply pathway innovation and retention, respectively. The idea of metabolism–membrane coevolution leads to a scenario of progressive sequestration of the emerging living system from its exterior milieu. Comparative data on current protein enzymes may shed some light on such a primeval process by analogy, since two main ideas about enzymatization (the retroevolution and the patchwork scenarios) may not necessarily be mutually exclusive and the earliest enzymatic system may have used ribozymes rather than proteins. (1781)

Szostak, Jack. Systems Chemistry on Early Earth. Nature. 459/171, 2009. A commentary on the paper “Synthesis of Activated Pyrimidine Ribonucleotides in Prebiotically Plausible Conditions” in the same issue by University of Manchester chemists Matthew Powner, Beatrice Gerland and John Sutherland which is seen as a breakthrough in being able to explain how RNA “informational polymers” first formed via phosphate reactants and catalysts. Its importance was also noted by Nicholas Wade in “Chemist Shows How RNA Can Be the Starting Point for Life” in the N. Y. Times for May 14, 2009. But even more significance might accrue because nature’s primordial chemistry then seems primed for such “spontaneous assembly,” as the quote avers with British understatement. See also a later article by Wade in the NYT for June 16, 2009 on this and other Origin of Life advances.

Our findings suggest that the prebiotic synthesis of activated pyrimidine nucleotides should be viewed as predisposed. This predisposition would have allowed the synthesis to operate on the early Earth under geochemical conditions suitable for the assembly sequence. (Powner, et al 242)

Szostak, Jack. The Narrow Road to the Deep Past: In Search of the Chemistry of the Origin of Life. Angewandte Chemie International. 56/37, 2017. The Nobel chemist (2009) at the Howard Hughes Medical Institute, Center for Computational and Integrative Biology, Boston writes a popular update on his own work and on the long project to recover and quantify how living, evolving systems came to be. A salient aspect is the appearance of membrane-bounded protocell vesicles, which then play a role in forming vital RNA polymerase replicators. Once life got going, other catalytic biochemicals could complexify toward enzymes, metabolisms all the way to we curious curators.

The sequence of events that gave rise to the first life on our planet took place in the Earth's deep past, seemingly beyond our reach. Understanding the processes that led to the chemical building blocks of biology and how these molecules self‐assembled into cells that could grow, divide and evolve, nurtured by a rich and complex environment, seems insurmountably difficult. And yet, to my own surprise, simple experiments have revealed robust processes that could have driven the growth and division of primitive cell membranes. Even our efforts to combine replicating compartments and genetic materials into a full protocell model have moved forward in unexpected ways. Fortunately, many challenges remain, so the future in this field is brighter than ever! (Abstract)

Takeuchi, Nobuto and Paulien Hogeweg. Multilevel Selection in Models of Prebiotic Evolution II: A Direct Comparison of Compartmentalization and Spatial Self-Organization. PLoS Computational Biology. 5/10, 2010. In a follow up to their 2003 paper herein, Utrecht University bioinformaticians offer new pathways to help perceive and factor in these real, prior, endemic dynamics and resultant nested emergences for the welling evolutionary revision to complement and augment post selection.

Takeuchi, Nobuto, et al. On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems. PLoS Computational Biology. Online March 24, 2011. As the extensive Abstract explains, bioinformatic researchers Nobuto, NIH, Paulien Hogeweg, Utrecht University, and Eugene Koonin, NIH, achieve notable insights into how life’s replication process initially got its evolving act together. We resultant people are just beginning to learn the rest of the story. And might one imagine that since material nature innately appears to develop this way, it might in fact be made for this purpose?

At the core of all biological systems lies the division of labor between the storage of genetic information and its phenotypic implementation, in other words, the functional differentiation between templates (DNA) and catalysts (proteins). This fundamental property of life is believed to have been absent at the earliest stages of evolution. The RNA world hypothesis, the most realistic current scenario for the origin of life, posits that, in primordial replicating systems, RNA functioned both as template and as catalyst. How would such division of labor emerge through Darwinian evolution? We investigated the evolution of DNA-like molecules in minimal computational models of RNA replicator systems. Two models were considered: one where molecules are adsorbed on surfaces and another one where molecules are compartmentalized by dividing cellular boundaries. Both models exhibit the evolution of DNA and the ensuing division of labor, revealing the simple governing principle of these processes: DNA releases RNA from the trade-off between template and catalyst that is inevitable in the RNA world and thereby enhances the system's resistance against parasitic templates. Hence, this study offers a novel insight into the evolutionary origin of the division of labor between templates and catalysts in the RNA world. (Abstract)

Takeuchi, Nobuto, et al. The Origin of a Primordial Genome through Spontaneous Symmetry Breaking. Nature Communications. 8/250, 2017. Veteran theoretical and experimental biologists NT and Kunihiko Kaneko, University of Tokyo and Paulien Hogeweg, Utrecht University go on to perceive a whole genomic complementarity amongst replicative nucleotides in rudimentary bounded cells and autocatalytic processes. As the Abstract notes, an efficient self-organized critical poise between these dual functional stages is then becoming apparent.

The paper is included in an Early Earth Collection on this site which has Nucleoside and Nucleotide, Early Cells, and Early Earth Conditions segments. See, e.g., Considering Planetary Environments in Origin of Life Studies by Laura Barge, Life as a Guide to Prebiotic Nucleotide Synthesis by Stuart Harrison and Nick Lane, and Prebiotic Plausibility and Networks of Paradox-Resolving Independent Models by Stephen Benner.

The heredity of a cell is provided by a small number of non-catalytic templates. How did these genomes originate? We demonstrate the possibility that genome-like molecules arise from symmetry breaking between complementary strands of self-replicating molecules. Our model assumes a population of protocells, each containing a population of self-replicating catalytic molecules. The protocells evolve towards maximising the catalytic activities of the molecules to increase their growth rates. Conversely, the molecules evolve towards minimising their catalytic activities to increase their intracellular relative fitness.

These conflicting tendencies induce the symmetry breaking, whereby one strand of the molecules remains catalytic and increases its copy number (enzyme-like molecules), whereas the other becomes non-catalytic and decreases its copy number (genome-like molecules). This asymmetry increases the equilibrium cellular fitness by decreasing mutation pressure and increasing intracellular genetic drift. These results implicate conflicting multilevel evolution as a key cause of the origin of genetic complexity. (Abstract)

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