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

1. The Origins of Life

Wills, Peter, et al. Emergence of Coding and its Specificity as a Physico-Informatic Problem. Origins of Life and Evolution of Biospheres. Online March, 2015. Into the 2010s, scientists are increasingly realizing and articulating a physical cosmos that is becoming alive and fertile as it develops by way of an informational, genetic like, inherency. Search Mathis, Aguirre, Falkenberg, for further entries. In this paper, Wills, University of Auckland, Kay Nieselt, Integrative Transcriptomics, University of Tubingen, and John McCaskill, Ruhr Universitat Bochum, continue their version whence an active materiality, by virtue of innate procreative properties, proceeds to compute and self-organize an embryonic evolution of living systems.

We explore the origin-of-life consequences of the view that biological systems are demarcated from inanimate matter by their possession of referential information, which is processed computationally to control choices of specific physico-chemical events. Cells are cybernetic: they use genetic information in processes of communication and control, subjecting physical events to a system of integrated governance. The genetic code is the most obvious example of how cells use information computationally, but the historical origin of the usefulness of molecular information is not well understood. Genetic coding made information useful because it imposed a modular metric on the evolutionary search and thereby offered a general solution to the problem of finding catalysts of any specificity. We use the term “quasispecies symmetry breaking” to describe the iterated process of self-organisation whereby the alphabets of distinguishable codons and amino acids increased, step by step. (Abstract)

Yeates, Jessica, et al. Dynamics of Prebiotic RNA Reproduction Illuminated by Chemical Game Theory. Proceedings of the National Academy of Sciences. 113/5030, 2016. Yeates, with Miles Lehman and Martin Zwick, Portland State University, and Martin Nowak and Christian Hilbe, Harvard university, attest to processes of competition and cooperation in effect even at life’s nucleotide origins. These molecular interactions are seen to take on network topologies as these contests play out at this rudimentary stage. Companion 2016 articles that use this approach are Evolutionary Game Theory: Molecules (Katrin Bohl) and Evolutionary Game Theory: Cells as Players (Sabine Hummert) in Molecular Biosystems.

Many origins-of-life scenarios depict a situation in which there are common and potentially scarce resources needed by molecules that compete for survival and reproduction. The dynamics of RNA assembly in a complex mixture of sequences is a frequency-dependent process and mimics such scenarios. Pairwise interplays between RNAs involve both cooperation and selfishness, quantifiable in a 2 × 2 payoff matrix. We show that a simple model of differential equations based on chemical kinetics accurately predicts the outcomes of these molecular competitions using simple rate inputs into these matrices. In some cases, we find that mixtures of different RNAs reproduce much better than each RNA type alone, reflecting a molecular form of reciprocal cooperation. Our experiments suggest a new type of evolutionary game dynamics, called prelife game dynamics or chemical game dynamics. These operate without template-directed replication, illustrating how small networks of RNAs could have developed and evolved in an RNA world. (Abstract)

The origins of life required a means for information-containing molecules to compete with one another for survival and reproduction. Using an analysis based on game theory, we can predict the situations in which cooperation, selfishness, or a mixture of the two is beneficial to the future evolutionary success of RNAs. (Significance)

Yu, Jinhan, et al. Prebiotic access to enantioenriched amino acids via peptide-mediated transamination reactions.. PNAS. 121/7, 2024. As life origin retro-studies continue to gain a finer focus, Scripps Research, La Jolla, CA biochemists including Donna Blackmond report how these appropriate metabolic biomaterials played their vital role early on. And once again, the whole animate process seems to be unfolding by its own innate merits.

The kinetic resolution of racemic amino acids mediated by dipeptides and pyridoxal provides a prebiotically plausible route to enantioenriched proteinogenic amino acids. The enzymatic transamination cycles that are key to modern biochemical formation of enantiopure amino acids may have evolved from this half of the reversible reaction couple. Kinetic resolution of racemic precursors emerges as a general route to enantioenrichment under prebiotic conditions. (Abstract)

Transamination is the process by which amino groups are removed from amino acids and transferred to acceptor keto-acids to generate the amino acid version of the keto-acid and the keto-acid version of the original amino acid.

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