Sidney Markowitz’s PhD research proposal

Simulation Models of Prebiotic Evolution of Genetic Coding (106KB PDF)

Abstract

Common to all life on Earth are the mechanisms of genetic encoding, in which specific trinucleotide sequences in DNA and RNA map to specific amino acids in synthesized proteins. The proteins which catalyse the coding are themselves products of that synthesis, posing the question of how the system bootstrapped itself and how it maintains stability. Mechanistic models based on chemical associations between groups of nucleotides and amino acids, or stochastic theories of a random frozen accident have not fully explained the emergence of the genetic code. The proposed thesis project considers the genetic code and protein synthesis as a molecular information processing system with mutually catalytic information storage and functional components, using simulation to investigate feasible models of the emergence of genetic encoding from an initially random population of proteins. The focus of the research is on developing an abstract framework that does not depend on explicit molecular details while demonstrating a plausible mechanism of self-organisation. It is hoped that an understanding of the conditions under which such a system self-organises will make it possible to build a complete model of the stages of emergence of the genetic code from the prebiotic environment.