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Evolutionary Constraint in Artificial Gene Regulatory Networks

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Advances in Computational Intelligence Systems (UKCI 2018)

Abstract

Evolutionary processes such as convergent evolution and rapid adaptation suggest that there are constraints on how organisms evolve. Without constraint, such processes would most likely not be possible in the time frame in which they are seen. This paper investigates how artificial gene regulatory networks (GRNs), a connectionist architecture designed for computational problem solving may too be constrained in its evolutionary pathway. To understand this further, GRNs are applied to two different computational tasks and the way their underlying genes evolve over time is observed. From this, rules about how often genes are evolved and how this correlates with their connectivity within the GRN are deduced. By generating and applying these rules, we can build an understanding of how GRNs are constrained in their evolutionary path, and build measures to exploit this to improve evolutionary performance and speed.

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References

  1. Pigliucci, M.: Is evolvability evolvable? Nat. Rev. Genet. 9(1), 75–82 (2008)

    Article  Google Scholar 

  2. Li, J., Yuan, Z., Zhang, Z.: The cellular robustness by genetic redundancy in budding yeast. PLoS Genet. 6(11), e1001187 (2010)

    Article  Google Scholar 

  3. Tokuriki, N., Tawfik, D.S.: Protein dynamism and evolvability. Science 324(5924), 203–207 (2009)

    Article  Google Scholar 

  4. Pavlicev, M., Wagner, G.P.: A model of developmental evolution: selection, pleiotropy and compensation. Trends Ecol. Evol. 27(6), 316–322 (2012)

    Google Scholar 

  5. Graves, C.J., Ros, V.I., Stevenson, B., Sniegowski, P.D., Brisson, D.: Natural selection promotes antigenic evolvability. PLoS Pathog 9(11), e1003766 (2013)

    Article  Google Scholar 

  6. Mitchell, M.: An Introduction to Genetic Algorithms. MIT Press, Cambridge (1998)

    Google Scholar 

  7. Michalewicz, Z.: Genetic Algorithms + Data Structures = Evolution Programs. Springer, Heidelberg (2013)

    MATH  Google Scholar 

  8. Droste, S., Jansen, T., Wegener, I.: On the analysis of the (1+1) evolutionary algorithm. Theor. Comput. Sci. 276(1–2), 51–81 (2002)

    Article  MathSciNet  Google Scholar 

  9. LeCun, Y., Bengio, Y., Hinton, G.: Deep learning. Nature 521(7553), 436–444 (2015)

    Article  Google Scholar 

  10. Hamann, H., Schmickl, T., Crailsheim, K.: Coupled inverted pendulums: a benchmark for evolving decentral controllers in modular robotics. In: Proceedings of the 13th Annual Conference on Genetic and Evolutionary Computation, pp. 195–202. ACM (2011)

    Google Scholar 

  11. Dowsland, K.A., Thompson, J.M.: Simulated annealing. In: Handbook of Natural Computing, pp. 1623–1655. Springer (2012)

    Google Scholar 

  12. Castro, L.N.D., Timmis, J.: Artificial Immune Systems: A New Computational Intelligence Approach. Springer Science & Business Media (2002)

    Google Scholar 

  13. Schwab, J.D., Siegle, L., Kühlwein, S.D., Kühl, M., Kestler, H.A.: Stability of signaling pathways during aging-a boolean network approach. Biology 6(4), 46 (2017)

    Google Scholar 

  14. Turner, A.P., Caves, L.S., Stepney, S., Tyrrell, A.M., Lones, M.A.: Artificial epigenetic networks: Automatic decomposition of dynamical control tasks using topological self-modification (2016)

    Google Scholar 

  15. Ribba, B., Grimm, H.P., Agoram, B., Davies, M.R., Gadkar, K., Niederer, S., van Riel, N., Timmis, J., van der Graaf, P.H.: Methodologies for quantitative systems pharmacology (QSP) models: design and estimation. CPT Pharmacometrics Syst. Pharmacol. 6(8), 496–498 (2017)

    Google Scholar 

  16. Kirschner, M.: Beyond Darwin: evolvability and the generation of novelty. BMC Biol. 11(1), 1 (2013)

    Article  Google Scholar 

  17. Kitano, H.: Biological robustness. Nat. Rev. Genet. 5(11), 826–837 (2004)

    Article  Google Scholar 

  18. Palazzo, A.F., Gregory, T.R.: The case for junk DNA. PLoS Genet. 10(5), e1004351 (2014)

    Article  Google Scholar 

  19. Pennisi, E.: Encode project writes eulogy for junk DNA (2012)

    Google Scholar 

  20. Zotenko, E., Mestre, J., O’Leary, D.P., Przytycka, T.M.: Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. PLoS Comput. Biol. 4(8), e1000140 (2008)

    Article  MathSciNet  Google Scholar 

  21. Silva, F., Duarte, M., Correia, L., Oliveira, S.M., Christensen, A.L.: Open issues in evolutionary robotics. Evol. Comput. 24(2), 205–236 (2016)

    Article  Google Scholar 

  22. Valero, K.W.: Aligning functional network constraint to evolutionary outcomes. bioRxiv (2018)

    Google Scholar 

  23. Pervouchine, D.D., Djebali, S., Breschi, A., Davis, C.A., Barja, P.P., Dobin, A., Tanzer, A., Lagarde, J., Zaleski, C., See, L.-H., et al.: Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression. Nat. Commun. 6, 5903 (2015)

    Article  Google Scholar 

  24. Foote, A.D., Liu, Y., Thomas, G.W.C., Vinař, T., Alföldi, J., Deng, J., Dugan, S., van Elk, C.E., Hunter, M.E., Joshi, V., et al.: Convergent evolution of the genomes of marine mammals. Nat. Genet. 47(3), 272 (2015)

    Article  Google Scholar 

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Correspondence to Alexander P. Turner .

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Turner, A.P., Lacey, G., Schoene, A., Dethlefs, N. (2019). Evolutionary Constraint in Artificial Gene Regulatory Networks. In: Lotfi, A., Bouchachia, H., Gegov, A., Langensiepen, C., McGinnity, M. (eds) Advances in Computational Intelligence Systems. UKCI 2018. Advances in Intelligent Systems and Computing, vol 840. Springer, Cham. https://doi.org/10.1007/978-3-319-97982-3_3

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