Theory and Practice of Optimal Mutation Rate Control in Hamming Spaces of DNA Sequences

Christopher Knight, T Lenaerts (Editor), M Giacobini (Editor), H Bersini (Editor), P Bourgine (Editor), M Dorigo (Editor), R Doursat (Editor)

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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. Us- ing a Hamming space as a prime example, we derive the prob- ability of adaptation as a function of reproduction parameters (e.g. mutation size or rate). Optimal control rules for the pa- rameters are derived explicitly for some relatively monotonic landscapes, and then a general information-based heuristic is introduced. We then evaluate our theoretical control func- tions against optimal mutation functions evolved from a ran- dom 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 artifi- cial 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 oc- cur and evolve in natural organisms. We also outline future directions of this work.
    Original languageEnglish
    Title of host publicationAdvances in Artificial Life, ECAL 2011
    EditorsT Lenaerts, M Giacobini, H Bersini, P Bourgine, M Dorigo, R Doursat
    PublisherMassachusetts Institute of Technology
    Pages85-92
    Number of pages8
    ISBN (Print)978-0-262-29714-1
    Publication statusPublished - 12 Aug 2011
    EventEuropean Conference on Artificial Life - Paris
    Duration: 8 Aug 201112 Aug 2011

    Conference

    ConferenceEuropean Conference on Artificial Life
    CityParis
    Period8/08/1112/08/11

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