VI. Earth Life Emergence: Development of Body, Brain, Selves and Societies
2. The Origins of Life
Wills, Peter and Charles Carter. Insuperable Problems of the Genetic Code Initially Emerging in an RNA World. Biosystems. Online September 7, 2017. The University of Auckland and UNC Chapel Hill biochemist team weighs in to say that a current origin of life fix on this primordial nucleotide is misplaced. While they are a factor, in a integral view many more facets and forces are in play such as dynamical self-assemblies. Once again, to comment, every project seems to divide into a particulate view (large colliders) and relational dynamics (neural nets) as equally in effect. An evident solution would be to join all the approaches, aspects, models into a composite synthesis as humankinder may reconstruct how Earth life came to form, arise, evolve unto our seemingly intended, worldwide retrospect. See also their concurrent paper Interdependence, Reflexivity, Fidelity, Impedance Matching, and the Evolution of Genetic Coding in Molecular Biology and Evolution (Online October 2017), along with a news review The End of the RNA World is Near, Biochemists Argue by Jordana Cepelewicz in Quanta Magazine (Online December 2017).
Differential equations for error-prone information transfer (template replication, transcription or translation) are developed in order to consider, within the theory of autocatalysis, the advent of coded protein synthesis. Variations of these equations furnish a basis for comparing the plausibility of contrasting scenarios for the emergence of specific tRNA aminoacylation, ultimately by enzymes, and the relationship of this process with the origin of the universal system of molecular biological information processing embodied in the Central Dogma. The hypothetical RNA World does not furnish an adequate basis for explaining how this system came into being, but principles of self-organisation that transcend Darwinian natural selection furnish an unexpectedly robust basis for a rapid, concerted transition to genetic coding from a peptide•RNA world. (Abstract)
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)