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Heuristic algorithms in evolutionary computation and modular organization of biological macromolecules: Applications to in vitro evolution

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  • Alexander V Spirov
  • Ekaterina M Myasnikova

Abstract

Evolutionary computing (EC) is an area of computer sciences and applied mathematics covering heuristic optimization algorithms inspired by evolution in Nature. EC extensively study all the variety of methods which were originally based on the principles of selectionism. As a result, many new algorithms and approaches, significantly more efficient than classical selectionist schemes, were found. This is especially true for some families of special problems. There are strong arguments to believe that EC approaches are quite suitable for modeling and numerical analysis of those methods of synthetic biology and biotechnology that are known as in vitro evolution. Therefore, it is natural to expect that the new algorithms and approaches developed in EC can be effectively applied in experiments on the directed evolution of biological macromolecules. According to the John Holland’s Schema theorem, the effective evolutionary search in genetic algorithms (GA) is provided by identifying short schemata of high fitness which in the further search recombine into the larger building blocks (BBs) with higher and higher fitness. The multimodularity of functional biological macromolecules and the preservation of already found modules in the evolutionary search have a clear analogy with the BBs in EC. It seems reasonable to try to transfer and introduce the methods of EC, preserving BBs and essentially accelerating the search, into experiments on in vitro evolution. We extend the key instrument of the Holland’s theory, the Royal Roads fitness function, to problems of the in vitro evolution (Biological Royal Staircase, BioRS, functions). The specific version of BioRS developed in this publication arises from the realities of experimental evolutionary search for (DNA-) RNA-devices (aptazymes). Our numerical tests showed that for problems with the BioRS functions, simple heuristic algorithms, which turned out to be very effective for preserving BBs in GA, can be very effective in in vitro evolution approaches. We are convinced that such algorithms can be implemented in modern methods of in vitro evolution to achieve significant savings in time and resources and a significant increase in the efficiency of evolutionary search.

Suggested Citation

  • Alexander V Spirov & Ekaterina M Myasnikova, 2022. "Heuristic algorithms in evolutionary computation and modular organization of biological macromolecules: Applications to in vitro evolution," PLOS ONE, Public Library of Science, vol. 17(1), pages 1-42, January.
  • Handle: RePEc:plo:pone00:0260497
    DOI: 10.1371/journal.pone.0260497
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    References listed on IDEAS

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    1. Melanie Mitchell & John H. Holland, 1993. "When Will a Genetic Algorithm Outperform Hill-Climbing?," Working Papers 93-06-037, Santa Fe Institute.
    2. Steve O'Hagan & Joshua Knowles & Douglas B Kell, 2012. "Exploiting Genomic Knowledge in Optimising Molecular Breeding Programmes: Algorithms from Evolutionary Computing," PLOS ONE, Public Library of Science, vol. 7(11), pages 1-14, November.
    3. Chalermsub Sangkavichitr & Prabhas Chongstitvatana, 2016. "The use of explicit building blocks in evolutionary computation," International Journal of Systems Science, Taylor & Francis Journals, vol. 47(3), pages 691-706, February.
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