Topological, statistical, and dynamical origins of genetic code: Comment on “A colorful origin for the genetic code: Information theory, statistical mechanics and the emergence of molecular codes” by T. Tlusty

Abstract

How has the genetic code evolved to link genetic sequences to corresponding amino acids? Why are only 20 amino acids used from 64 possible triplet codes when forming proteins? Since the discovery of codons, these two questions have been integral to evolutionary biology, and addressed by distinguished biologists. For example, a beautiful theory by Crick et al. [1] to explain the number 20 from the optimal code without stopping symbol (comma) was selected as the most elegant ‘wrong’ theory ever to be proposed in science by Maynard-Smith [2]. Later on, Crick himself described the ‘universal’ genetic code as luck with the ‘frozen accident’ in the common ancestor of living organisms [3]. In the present paper [4], the author presented a statistical-physics based explanation for the evolution of the genetic code by using a more sophisticated mathematical theory than that of Crick et al. Topological and information-theoretic approaches were adopted by imposing the optimization of a certain quantity that consists of diverse amino acids, errortolerance and minimal energy cost. A second-order phase transition from random to non-random mapping between codons and amino acids was found to coincide with changes in this quantity. This resembles known behavior in magnetic spin systems, which is analogous to the error-catastrophe seen in chemical evolutions [5]. Furthermore, the author introduced the topology of the codon graph determining the lowest modes of the graph-Laplacian and related it to the mathematical map coloring problem. By removing the ambiguity in the third position of the codon and considering the optimization process under this topological constraint, the maximum number of amino acids to be coded is predicted to be 25. This is an elegant theory that can be experimentally verified.