Physical Model for the Evolution of the Genetic Code

TL;DR

This paper introduces a physical model for the evolution of the genetic code, explaining mechanisms of codon capture and ambiguous intermediate scenarios through a minimal model based on codon levels, supported by simulations.

Contribution

It presents a novel physical framework and minimal model to unify and simulate two major genetic code evolution scenarios.

Findings

Rapid transition of code change in ambiguous intermediate scenario

Reduction of non-uniqueness issues during code evolution

Hierarchical structure explains different evolutionary routes

Abstract

We propose a physical model to describe the mechanisms of two major scenarios of the genetic code evolution, the codon capture and ambiguous intermediate scenarios, in a consistent manner. We sketch the lowest dimensional version of our model, a minimal model, by introducing a physical quantity, codon level. On the basis of the hierarchical structure of the codon levels two scenarios are classified into two different routes of the evolutional process. In the case of the ambiguous intermediate scenario we perform a simulation implemented cost selection of amino acids and confirm a rapid transition of the code change. Such rapidness reduces uncomfortableness of the non-unique translation of the code at intermediate state that is the weakness of the scenario.