Dynamics of genetic code evolution: The emergence of universality

We study the dynamics of genetic code evolution. The model of Vetsigian et al. [Proc. Natl. Acad. Sci. USA 103, 10696 (2006)] and Vetsigian [Collective evolution of biological and physical systems, Ph.D. thesis, 2005] uses the mechanism of horizontal gene transfer to demonstrate convergence of the genetic code to a near universal solution. We reproduce and analyze the algorithm as a dynamical system. All the parameters used in the model are varied to assess their impact on convergence and optimality score. We show that by allowing specific parameters to vary with time, the solution exhibits attractor dynamics. Finally, we study automorphisms of the genetic code arising due to this model. We use this to examine the scaling of the solutions to re-examine universality and find that there is a direct link to mutation rate.

Automated summary

The study focuses on the dynamics of genetic code evolution, using a model that demonstrates convergence to a near universal solution through horizontal gene transfer mechanism. Analysis of varying parameters shows impact on convergence and optimality score, with attractor dynamics observed in the solution by allowing specific parameters to vary with time. Investigation of genetic code automorphisms due to the model reveals a direct link to mutation rate for re-examining universality.