Theory and practice of optimal mutation rate control in Hamming spaces of DNA sequences

Belavkin, Roman V. and Channon, Alastair and Aston, Elizabeth and Aston, John and Knight, Christopher (2011) Theory and practice of optimal mutation rate control in Hamming spaces of DNA sequences. In: Advances in artificial life, ECAL 2011: proceedings of the Eleventh European Conference on the Synthesis and Simulation of Living Systems. Lenaerts, Tom and Giacobini, Mario and Bersini, Hugues and Bourgine, Paul and Dorigo, Marco and Doursat, René, eds. MIT Press, pp. 85-92. ISBN 9780262297141

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Abstract

We investigate the problem of optimal control of mutation by asexual self-replicating organisms represented by points in a metric space. We introduce the notion of a relatively monotonic fitness landscape and consider a generalisation of Fisher's geometric model of adaptation for such spaces. Using a Hamming space as a prime example, we derive the probability of adaptation as a function of reproduction parameters (e.g. mutation size or rate). Optimal control rules for the parameters are derived explicitly for some relatively monotonic landscapes, and then a general information-based heuristic is introduced. We then evaluate our theoretical control functions against optimal mutation functions evolved from a random population of functions using a meta genetic algorithm. Our experimental results show a close match between theory and experiment. We demonstrate this result both in artificial fitness landscapes, defined by a Hamming distance, and a natural landscape, where fitness is defined by a DNA-protein affinity. We discuss how a control of mutation rate could occur and evolve in natural organisms. We also outline future directions of this work.

Item Type:Book Section
Research Areas:School of Science and Technology > Computer and Communications Engineering
School of Science and Technology > Science & Technology
School of Science and Technology > Natural Sciences
ID Code:8399
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Deposited On:17 Feb 2012 05:41
Last Modified:22 Jul 2014 12:34

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