Skip to main content
Log in

Modularity in Biological Evolution and Evolutionary Computation

  • Published:
Biology Bulletin Reviews Aims and scope Submit manuscript

Abstract

The basic principles of selectionism were transferred in a simplified form from population genetics to the field of evolutionary computation in order to solve applied problems of optimization and adaptation. Considerable practical experience has been gained for the almost half a century of development in this field of computer science, and interesting theoretical results have been obtained. One of the main properties of biological systems is modularity, which manifests itself at all levels of their organization, starting with molecular genetics and ending with entire organisms and their communities. In this survey, the phenomena and patterns associated with modularity in genetics and evolutionary computation are compared. The similarities and differences in the results from these areas of research are analyzed from the point of view of modularity, and the possibilities for sharing knowledge between them are discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1.
Fig. 2.
Fig. 3.
Fig. 4.
Fig. 5.

Similar content being viewed by others

Notes

  1. The objective function in mathematical optimization is understood to be a function with real values defined on a set of solutions to the optimization problem. The latter consists in the search for a solution that achieves the maximum or minimum of the objective function.

  2. The salesman’s task is to find the shortest route through all of the given cities and then return to the original city.

REFERENCES

  1. Altukhov, Yu.P., Geneticheskie protsessy v populyatsiyakh (Genetic Processes in Populations), Moscow: Akademkniga, 2003.

  2. Banzhaf, W., Artificial regulatory networks and genetic programming, in Genetic Programming Theory and Practice, Riolo, R.L. and Worzel, B., Eds., Dordrecht: Springer-Verlag, 2003, pp. 43–62.

    Google Scholar 

  3. Barabasi, A. and Oltvai, Z.N., Network biology: understanding the cells' functional organization, Nat. Rev. Genet., 2004, vol. 5, no. 2, pp. 101–113.

    CAS  PubMed  Google Scholar 

  4. Behe, M. and Snoke, D., Simulating evolution by gene duplication of protein features that require multiple amino acid residues, Protein Sci., 2004, vol. 13, no. 10, pp. 2651–2664.

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Bork, P., Shuffled domains in extracellular proteins, FEBS Lett., 1991, vol. 286, nos. 1–2, pp. 47–54.

    CAS  PubMed  Google Scholar 

  6. Bork, P., Sander, C., and Valencia, A., An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins, Proc. Natl. Acad. Sci. U.S.A., 1992, vol. 89, no. 16, pp. 7290–7294. https://doi.org/10.1073/pnas.89.16.7290

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Bornberg-Bauer, E. and Albà, M.M., Dynamics and adaptive benefits of modular protein evolution, Curr. Opin. Struct. Biol., 2013, vol. 23, pp. 459–466.

    CAS  PubMed  Google Scholar 

  8. Burke, D.H. and Willis, J.H., Recombination, RNA evolution, and bifunctional RNA molecules isolated through chimeric SELEX, RNA, 1998, vol. 4, pp. 1165–1175.

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Callebaut, W., The ubiquity of modularity, in Modularity: Understanding the Development and Evolution of Natural Complex Systems, Callebaut, W. and Rasskin-Gutman, D., Eds., Cambridge, MA: MIT Press, 2005, pp. 3–28.

    Google Scholar 

  10. Carson, H.L., The genetics of speciation at the diploid level, Am. Nat., 1975, vol. 109, no. 965, pp. 83–92.

    Google Scholar 

  11. Cavalli, L.L. and Maccacaro, G.A., Polygenic inheritance of drug-resistance in the bacterium escherichia coli, Heredity, 1952, vol. 6, pp. 311–331.

    Google Scholar 

  12. Chai, C., Xie, Z., and Grotewold, E., SELEX (Systematic Evolution of Ligands by EXponential Enrichment), as a powerful tool for deciphering the protein-DNA interaction space, Methods Mol. Biol., 2011, vol. 754, pp. 249–258.

    CAS  PubMed  Google Scholar 

  13. Chothia, C., Proteins. One thousand families for the molecular biologist, Nature, 1992, vol. 357, no. 6379, pp. 543–544.

    CAS  PubMed  Google Scholar 

  14. Ciliberti, S., Martin, O.C., and Wagner, A., Innovation and robustness in complex regulatory gene networks, Proc. Natl. Acad. Sci. U.S.A., 2007, vol. 104, pp. 13591–13596.

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Clune, J., Pennock, R.T., Ofria, C., and Lenski, R.E., Ontogeny tends to recapitulate phylogeny in digital organisms, Am. Nat., 2012, vol. 180, pp. E54–E63.

    PubMed  Google Scholar 

  16. Clune, J., Mouret, J.-B., and Lipson, H., The evolutionary origins of modularity, Proc. R. Soc. B, 2013, vol. 280, no. 1755, art. ID 20122863.

  17. Colombo, M., Moving forward (and beyond) the modularity debate: a network perspective, Philos. Sci., 2013, vol. 80, pp. 356–377.

    Google Scholar 

  18. Cooper, M.B., Brookfield, J.F.Y., and Loose, M., Evolutionary modeling of feed forward loops in gene regulatory networks, Biosystems, 2008, vol. 91, pp. 231–244.

    CAS  PubMed  Google Scholar 

  19. Corus, D., Dang, D.-C., Eremeev, A.V., and Lehre, P.K., Level-based analysis of genetic algorithms and other search processes, IEEE Trans. Evol. Comput., 2018, vol. 22, no. 5, pp. 707–719. https://doi.org/10.1109/TEVC.2017.2753538

    Article  Google Scholar 

  20. Crow, J.F. and Kimura, M., Evolution in sexual and asexual populations, Am. Nat., 1965, vol. 99, pp. 439–450.

    Google Scholar 

  21. Davidson, J.N., Chen, K.C., Jamison, R.S., et al., The evolutionary history of the first three enzymes in pyrimidine biosynthesis, BioEssays, 1993, vol. 15, no. 3, pp. 157–164.

    CAS  PubMed  Google Scholar 

  22. Dawkins, R., Universal Darwinism, in Evolution from Molecules to Man, Bendall, D.S., Ed., Cambridge: Cambridge Univ. Press, 1983, pp. 403–428.

    Google Scholar 

  23. De Jong, K.A., Evolutionary Computation: A Unified Approach, Cambridge, MA: MIT Press, 2006.

    Google Scholar 

  24. Doerr, B., Doerr, C., and Ebel, F., From black-box complexity to designing new genetic algorithms, Theor. Comp. Sci., 2015, vol. 567, pp. 87–104.

    Google Scholar 

  25. Doerr, B., Johannsen, D., Kötzing, T., Neumann, F., and Theile, M., More effective crossover operators for the all-pairs shortest path problem, Theor. Comput. Sci., 2013, vol. 471, pp. 12–26.

    Google Scholar 

  26. Draghi, J.A. and Plotkin, J.B., Selection biases the prevalence and type of epistasis among beneficial substitutions, Evolution, 2013, vol. 67, pp. 3120–3131.

    PubMed  Google Scholar 

  27. Eble, G.J., Morphological modularity and macroevolution: conceptual and empirical aspects, in Modularity: Understanding the Development and Evolution of Natural Complex Systems, Callebaut, W. and Rasskin-Gutman, D., Eds., Cambridge, MA: MIT Press, 2005, pp. 221–238.

    Google Scholar 

  28. El-Mihoub, T.A., Hopgood, A.A., Nolle, L., and Battersby, A., Hybrid genetic algorithms: a review, Eng. Lett., 2006, vol. 13, no. 2, art. ID EL_13_2_11.

  29. Elena, S.F., Cooper, V.S., and Lenski, R.E., Punctuated evolution caused by selection of rare beneficial mutations, Science, 1996, vol. 272, pp. 1802–1804.

    CAS  PubMed  Google Scholar 

  30. Eremeev, A.V. and Kolokolov, A.A., On some genetic and L-class enumeration algorithms in integer programming, Proc. First Int. Conf. on Evolutionary Computation and its Applications, Moscow, 1996, pp. 297–303.

  31. Eremeev, A.V. and Kovalenko, J.V., Experimental evaluation of two approaches to optimal recombination for permutation problems, in Evolutionary Computation in Combinatorial Optimization, Lecture Notes in Computer Science vol. 9595, Chicano, F., Hu, B., and Garcia-Sanchez, P., Eds., New York: Springer-Verlag, 2016, pp. 138–153.

  32. Eremeev, A. and Spirov, A., Estimates from evolutionary algorithms theory applied to gene design, Proc. 11th Int. Multiconf. “Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS\SB),” Novosibirsk, 2018, pp. 33–38. https://doi.org/10.1109/CSGB.2018.8544837

  33. Espinosa-Soto, C. and Wagner, A., Specialization can drive the evolution of modularity, PLoS Comput. Biol., 2010, vol. 6, p. e1000719. https://doi.org/10.1371/journal.pcbi.1000719

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Finn, R.D., Coggill, P., Eberhardt, R.Y., et al., The Pfam protein families database: towards a more sustainable future, Nucleic Acids Res., 2016, vol. 44, no. 1, pp. D279–D285.

    CAS  PubMed  Google Scholar 

  35. Fogel, L.J., Owens, A.J., and Walsh, M.J., Artificial Intelligence through Simulated Evolution, New York: Wiley, 1966.

    Google Scholar 

  36. Francois, P. and Hakim, V., Design of genetic networks with specified functions by evolution in silico, Proc. Natl. Acad. Sci. U.S.A., 2004, vol. 101, no. 2, pp. 580–585.

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Francois, P. and Siggia, E.D., Predicting embryonic patterning using mutual entropy fitness and in silico evolution, Development, 2010, vol. 137, no. 14, pp. 2385–2395.

    PubMed  Google Scholar 

  38. Francois, P., Hakim, V., and Siggia, E.D., Deriving structure from evolution: metazoan segmentation, Mol. Syst. Biol., 2007, vol. 3, no. 1. https://doi.org/10.1038/msb4100192

  39. Gary, M. and Johnson, D., Computers and Intractability: A Guide to NP-Completeness, New York, NY: W.H. Freeman, 1979.

    Google Scholar 

  40. Geary, C., Chworos, A., Verzemnieks, E., et al., Composing RNA nanostructures from a syntax of RNA structural modules, Nano Lett., 2017, vol. 17, no. 11, pp. 7095–7101.

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Gilbert, W., Origin of life: the RNA world, Nature, 1986, vol. 319, p. 618.

    Google Scholar 

  42. Goldberg, D.E., Genetic Algorithms in Search, Optimization and Machine Learning, Reading, MA: Addison-Wesley, 1989.

    Google Scholar 

  43. Gopinath, S.C., Methods developed for SELEX, Anal. Bioanal. Chem., 2007, vol. 387, no. 1, pp. 171–182.

    CAS  PubMed  Google Scholar 

  44. Grabow, W. and Jaeger, L., RNA modularity for synthetic biology, F1000 Prime Rep., 2013, vol. 5, pp. 46.

    Google Scholar 

  45. Grabow, W.W., Zhuang, Z., Shea, J.E., and Jaeger, L., The GA-minor submotif as a case study of RNA modularity, prediction, and design, Wiley Interdiscip. Rev.: RNA, 2013, vol. 4, no. 2, pp. 181–203.

    CAS  PubMed  Google Scholar 

  46. Gyorgy, A. and Del Vecchio, D., Modular composition of gene transcription networks, PLoS Comput. Biol., 2014, vol. 10, no. 3, p. e1003486.

    PubMed  PubMed Central  Google Scholar 

  47. Hartwell, L.H., Hopfield, J.J., Leibler, S., and Murray, A.W., From molecular to modular cell biology, Nature, 1999, vol. 402, no. 6761, pp. C47–C52.

    CAS  PubMed  Google Scholar 

  48. Hendrix, D.K., Brenner, S.E., and Holbrook, S.R., RNA structural motifs: building blocks of a modular biomolecule, Q. Rev. Biophys., 2005, vol. 38, no. 3, pp. 221–243.

    CAS  PubMed  Google Scholar 

  49. Henikoff, S., Greene, E.A., Pietrokovski, S., et al., Gene families: the taxonomy of protein paralogs and chimeras, Science, 1997, vol. 278, no. 5338, pp. 609–614.

    CAS  PubMed  Google Scholar 

  50. Holland, J.H., Adaptation in Natural and Artificial Systems, Ann Arbor, MI: Univ. of Michigan Press, 1975.

    Google Scholar 

  51. Hong, J.W., Hendrix, D.A., and Levine, M.S., Shadow enhancers as a source of evolutionary novelty, Science, 2008, vol. 321, p. 1314.

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Hu, T. and Banzhaf, W., Evolvability and speed of evolutionary algorithms in light of recent developments in biology, J. Artif. Evol. Appl., 2010, vol. 2010, art. ID 568375.

    Google Scholar 

  53. Hu, T., Banzhaf, W., and Moore, J.H., Population exploration on genotype networks in genetic programming, Proc. 13th Int. Conf. “Parallel Problem Solving from Nature—PPSN XIII,” Ljubljana, Slovenia, September 13–17,2014, Lecture Notes in Computer Science Series vol. 8672, Bartz-Beielstein, T., Branke, J., Filipic, B., and Smith, J., Eds., New York: Springer-Verlag, 2014, pp. 424–433.

  54. Ivakhnenko, A.G., Sistemy evristicheskoi samoorganizatsii v tekhnicheskoi kibernetike (The System of Heuristic Self-Organization in Engineering Cybernetics), Kiev: Tekhnika, 1971.

  55. Jaeger, L., Verzemnieks, E.J., and Geary, C., The UA_handle: a versatile submotif in stable RNA architectures, Nucleic Acids Res., 2009, vol. 37, pp. 215–230.

    CAS  PubMed  Google Scholar 

  56. Jansen, T. and Wegener, I., Real royal road functions—where crossover provably is essential, Dis. Appl. Math., 2005, vol. 149, nos. 1–3, pp. 111–125.

    Google Scholar 

  57. Jeong, S., Rebeiz, M., Andolfatto, P., et al., The evolution of gene regulation underlies a morphological difference between two Drosophila sister species, Cell, 2008, vol. 132, pp. 783–793.

    CAS  PubMed  Google Scholar 

  58. Jostins, L. and Jaeger, J., Reverse engineering a gene network using an asynchronous parallel evolution strategy, BMC Syst. Biol., 2010, vol. 4, p. 17. https://doi.org/10.1038/ng1165

    Article  PubMed  PubMed Central  Google Scholar 

  59. Joyce, G.F., The antiquity of RNA-based evolution, Nature, 2002, vol. 418, pp. 214–221.

    CAS  PubMed  Google Scholar 

  60. Kameya, Y. and Prayoonsri, C., Pattern-based preservation of building blocks in genetic algorithms, Proc. IEEE Congr. on Evolutionary Computation, CEC’2011, New Orleans, Piscataway, NJ: Inst. Electr. Electron. Eng., 2011, pp. 2578–2585.

  61. Kashtan, N. and Alon, U., Spontaneous evolution of modularity and network motifs, Proc. Natl. Acad. Sci. U.S.A., 2005, vol. 102, pp. 13773–13778.

    CAS  PubMed  PubMed Central  Google Scholar 

  62. Kim, J., He, X., and Sinha, S., Evolution of regulatory sequences in 12 Drosophila species, PLoS Genet., 2009, vol. 5, p. e1000330.

    PubMed  PubMed Central  Google Scholar 

  63. King, J.C. and Somme, L., Chromosomal analysis of the genetic factors for resistance to DDT in two resistant lines of Drosophila melanogaster,Genetics, 1958, vol. 43, pp. 577–593.

    CAS  PubMed  PubMed Central  Google Scholar 

  64. Koza, J.R., Bennett, F.H., Andre, D., and Keane, M.A., Genetic Programming III: Darwinian Invention and Problem Solving, San Francisco, CA: Morgan Kaufmann, 1999.

    Google Scholar 

  65. Koza, J. R., Lanza, G., Mydlowec, W., et al., Automated reverse engineering of metabolic pathways from observed data using genetic programming, in Foundations of Systems Biology, Kitano, H., Ed., Cambridge, MA: MIT Press, 2001, pp. 95–117.

    Google Scholar 

  66. Kouchakpour, P., Zaknich, A., and Braunl, T., A survey and taxonomy of performance improvement of canonical genetic programming, Knowl. Inf. Syst., 2009, vol. 21, no. 1, pp. 1–39. https://doi.org/10.1007/s10115-008-0184-9

    Article  Google Scholar 

  67. Leontis, N.B., Lescoute, A., and Westhof, E., The building blocks and motifs of RNA architecture, Curr. Opin. Struct. Biol., 2006, vol. 16, no. 3, pp. 279–287.

    CAS  PubMed  PubMed Central  Google Scholar 

  68. Leier, A., Kuo, P.D., Banzhaf, W., and Burrage, K., Evolving noisy oscillatory dynamics in genetic regulatory networks, Proc. European Conf. on Genetic Programming, Lecture Notes in Computer Science Series vol. 3905, Collet, P., Tomassini, M., Ebner, M., Gustafson, S., and Ekart, A., Eds., Berlin: Springer-Verlag, 2006, pp. 290–299. https://doi.org/10.1007/11729976_26

  69. Li, F., Liu, Q.H., Min, F., and Yang, G.W., A new adaptive crossover operator for the preservation of useful schemata, in Advances in Machine Learning and Cybernetics, Lecture Notes in Artificial Intelligence Series vol. 3930, Yeung, D.S., Liu, Z.Q., Wang, X.Z., and Yan, H., Eds., Berlin: Springer-Verlag, 2006, pp. 507–516. https://doi.org/10.1007/11739685_53

  70. Livnat, A., Papadimitriou, C., Dusho, J., and Feldman, M.W., A mixability theory of the role of sex in evolution, Proc. Natl. Acad. Sci. U.S.A., 2008, vol. 105, no. 50, pp. 19803–19808.

    CAS  PubMed  PubMed Central  Google Scholar 

  71. Lorenz, D.M., Jeng, A., and Deem, M.W., The emergence of modularity in biological systems, Phys. Life Rev., 2011, vol. 8, pp. 129–160. https://doi.org/10.1016/j.plrev.2011.02.003

    Article  PubMed  PubMed Central  Google Scholar 

  72. Lu, Z., Whalen, I., Boddeti, V., et al., NSGA-Net: neural architecture search using multi-objective genetic algorithm, Proc. Genetic and Evolutionary Computation Conf. (GECCO 2019), Prague, New York, NY: Assoc. Comput. Mach., 2019, pp. 419–427. https://doi.org/10.1145/3321707.3321729

  73. Lutz, S. and Benkovk, S.J., Protein engineering by evolutionary methods, in Directed Molecular Evolution of Proteins: Or How to Improve Enzymes for Biocatalysis, Brakmann, S. and Johnsson, K., Eds., Weinheim: Wiley, 2002, pp. 177–213.

    Google Scholar 

  74. Manrubia, S.C. and Briones, C., Modular evolution and increase of functional complexity in replicating RNA molecules, RNA, 2007, vol. 13, pp. 97–107.

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Masquida, B., Beckert, B., and Jossinet, F., Exploring RNA structure by integrative molecular modeling, New Biotechnol., 2010, vol. 27, pp. 170–183.

    CAS  Google Scholar 

  76. Mitchell, M., Forrest, S., and Holland, J.H., When will a genetic algorithm outperform hill climbing? in Advances in Neural Information Processing Systems, San Mateo, CA: Morgan Kaufmann, 1994, pp. 51–58.

  77. Müller, G.B. and Wagner, G.P., Homology, Hox genes, and developmental integration, Am. Zool., 1996, vol. 36, pp. 4–13.

    Google Scholar 

  78. Neumann, F. and Witt, C., Bioinspired Computation in Combinatorial Optimization: Algorithms and Their Computational Complexity, Berlin: Springer-Verlag, 2010.

    Google Scholar 

  79. Neduva, V. and Russell, R.B., Linear motifs: evolutionary interaction switches, FEBS Lett., 2005, vol. 579, no. 15, pp. 3342–3345.

    CAS  PubMed  Google Scholar 

  80. Nimwegen van, E. and Crutchfield, J.P., Optimizing epochal evolutionary search population-size dependent theory, Mach. Learn. J., 2001, vol. 45, pp. 77–114.

    Google Scholar 

  81. Nimwegen van, E., Crutchfield, J.P., and Mitchell, M., Statistical dynamics of the Royal Road genetic algorithm, Theor. Comp. Sci., 1999, vol. 229, no. 1, pp. 41–102.

    Google Scholar 

  82. Nordin, P., Banzhaf, W., and Francone, F., Introns in nature and in simulated structure evolution, in Bio-Computation and Emergent Computation, Lundh, D., Olsson, B., and Narayanan, A., Eds., Singapore: World Scientific, 1997, pp. 22–35.

    Google Scholar 

  83. Ohno, S., Evolution by Gene Duplication, New York: Springer-Verlag, 1970.

    Google Scholar 

  84. Paixão, T., Badkobeh, G., Barton, N., et al., Toward a unifying framework for evolutionary processes, J. Theor. Biol., 2015, vol. 383, pp. 28–43.

    PubMed  PubMed Central  Google Scholar 

  85. Payne, J.L., Moore, J.H., and Wagner, A., Robustness, evolvability, and the logic of genetic regulation, Artif. Life, 2014, vol. 20, pp. 111–126.

    PubMed  Google Scholar 

  86. Radcliffe, N.J., Forma analysis and random respectful recombination, Proc. Fourth Int. Conf. on Genetic Algorithms, San Diego: Morgan Kaufmann, 1991, pp. 222–229.

  87. Ratner, V.A., Block-modular principle of organization and evolution of molecular genetic control systems (MGCS), Genetika, 1992, vol. 28, no. 2, pp. 5–23.

    PubMed  Google Scholar 

  88. Richardson, J.S., The anatomy and taxonomy of protein structure, Adv. Protein Chem., 1981, vol. 34, pp. 167–339.

    CAS  PubMed  Google Scholar 

  89. Rivas, E. and Eddy, S.R., The language of RNA: a formal grammar that includes pseudoknots, Bioinformatics, 2000, vol. 16, pp. 334–340.

    CAS  PubMed  Google Scholar 

  90. Rohlfshagen, P. and Bullinaria, J., Nature inspired genetic algorithms for hard packing problems, Ann. Oper. Res., 2010, vol. 179, pp. 393–419.

    Google Scholar 

  91. Rutkowska, D., Piliński, M., and Rutkowski, L., Sieci Neuronowe, Algorytmy Genetyczne i Systemy Rozmyte, Warsaw: Państwowe Wydawnictwo Naukowe, 1997.

    Google Scholar 

  92. Sanchez, D., Whitley, D., and Tinós, R., Building a better heuristic for the traveling salesman problem: combining edge assembly crossover and partition crossover, Proc. Genetic and Evolutionary Computation Conference (GECCO’2017), Berlin, New York, NY: Assoc. Comput. Mach., 2017, pp. 329–336.

  93. Sanjuan, R. and Nebot, M.R., A network model for the correlation between epistasis and genomic complexity, PLoS One, 2008, vol. 3, p. e2663.

    PubMed  PubMed Central  Google Scholar 

  94. Schlosser, G., The role of modules in development and evolution, in Modularity in Development and Evolution, Schlosser, G. and Wagner, G.P., Eds., Chicago: Univ. of Chicago Press, 2004, pp. 519–582.

    Google Scholar 

  95. Schlosser, G. and Wagner, G.P., Introduction: the modularity concept in development and evolutionary biology, in Modularity in Development and Evolution, Schlosser, G. and Wagner, G.P., Eds., Chicago: Univ. of Chicago Press, 2004, pp. 1–16.

    Google Scholar 

  96. Schmidt, D., Wilson, M.D., Ballester, B., et al., Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding, Science, 2010, vol. 328, pp. 1036–1040.

    CAS  PubMed  PubMed Central  Google Scholar 

  97. Segal, E., Shapira, M., Regev, A., et al., Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data, Nat. Genet., 2003, vol. 34, pp. 166–176. https://doi.org/10.1038/ng1165

    Article  PubMed  Google Scholar 

  98. Shabash, B. and Wiese, K.C., Diploidy in evolutionary algorithms for dynamic optimization problems: a best-chromosome-wins dominance mechanism, Int. J. Intell. Comput. Cybern., 2015, vol. 8, no. 4, pp. 312–329.

    Google Scholar 

  99. Simon-Loriere, E. and Holmes, E.C., Why do RNA viruses recombine? Nat. Rev. Microbiol., 2011, vol. 9, no. 8, pp. 617–626.

    CAS  PubMed  PubMed Central  Google Scholar 

  100. Simon-Loriere, E., Martin, D.P., Weeks, K.M., and Negroni, M., RNA structures facilitate recombination-mediated gene swapping in HIV-1, J. Virol., 2010, vol. 84, no. 24, pp. 12675–12682.

    CAS  PubMed  PubMed Central  Google Scholar 

  101. Sistemnaya komp’yuternaya biologiya (System Computer Biology), Kolchanov, N.A., Goncharov, S.S., Likhoshvai, V.A., and Ivanisenko, V.A., Eds., Novosibirsk: Sib. Otd., Ross. Akad. Nauk, 2008.

    Google Scholar 

  102. Skinner, C. and Riddle, P., Expected rates of building block discovery, retention and combination under 1-point and uniform crossover, Proc. 8th Int. Conf. on Parallel Problem Solving from Nature, Lecture Notes in Computer Science Series vol. 3242, Berlin: Springer-Verlag, 2004, pp. 121–130.

  103. Solé, R.V., Salazar, I., and Garcia-Fernandez, J., Common pattern formation, modularity and phase transitions in a gene network model of morphogenesis, Phys. A (Amsterdam), 2002, vol. 305, pp. 640–647.

    Google Scholar 

  104. Spirov, A. and Holloway, D., New approaches to designing genes by evolution in the computer, in Real-World Applications of Genetic Algorithms, Roeva, O., Ed., London: InTech Open, 2012, pp. 235–260. https://doi.org/10.5772/2674

  105. Spirov, A. and Holloway, D., Using evolutionary computation to understand the design and evolution of gene and cell regulatory networks, Methods, 2013, vol. 62, no. 1, pp. 39–55.

    CAS  PubMed  PubMed Central  Google Scholar 

  106. Spirov, A. and Holloway, D., Using evolutionary algorithms to study the evolution of gene regulatory networks controlling biological development, in Evolutionary Computation in Gene Regulatory Network Research, Iba, H. and Noman, N., Eds., Hoboken, NJ: Wiley, 2016. https://doi.org/10.1002/9781119079453.ch10

  107. Stebel, S.C., Gaida, A., Arndt, K.M., and Muller, K.M., Directed protein evolution, in Molecular Biomethods Handbook, Walker, J.M. and Rapley, R., Eds., Totowa, NJ: Humana, 2008, pp. 631–656.

    Google Scholar 

  108. Stemmer, W.P., Rapid evolution of a protein in vitro by DNA shuffling, Nature, 1994a, vol. 370, pp. 389–391.

    CAS  PubMed  Google Scholar 

  109. Stemmer, W.P.C., DNA shuffling by random fragmentation and reassembly—in vitro recombination for molecular evolution, Proc. Natl. Acad. Sci. U.S.A., 1994b, vol. 91, no. 22, pp. 10747–10751.

    CAS  PubMed  PubMed Central  Google Scholar 

  110. Umbarkar, A.J. and Sheth, P.D., Crossover operators in genetic algorithms: a review, ICTACT J. Soft Comp., 2015, vol. 6, no. 1, pp. 1083–1092.

    Google Scholar 

  111. Voigt, C.A., Martinez, C., Wang, Z.G., et al., Protein building blocks preserved by recombination, Nat. Struct. Biol., 2002, vol. 9, pp. 553–558.

    CAS  PubMed  Google Scholar 

  112. von Dassow, G. and Munro, E., Modularity in animal development and evolution: elements of a conceptual framework for EvoDevo, J. Exp. Zool., 1999, vol. 285, pp. 307–325.

    CAS  PubMed  Google Scholar 

  113. Vose, M.D., The Simple Genetic Algorithm: Foundations and Theory, Cambridge, MA: MIT Press, 1999.

    Google Scholar 

  114. Wagner, G.P. and Altenberg, L., Perspective: complex adaptations and the evolution of evolvability, Evolution, 1996, vol. 50, pp. 967–976.

    PubMed  Google Scholar 

  115. Watson, R.A. and Jansen, T., A building-block royal road where crossover is provably essential, Proc. 9th Annual Conf. on Genetic and Evolutionary Computation (GECCO’07), New York, NY: Assoc. Comput. Mach., 2007, pp. 1452–1459.

  116. Wetlaufer, D.B., Nucleation, rapid folding, and globular intrachain regions in proteins, Proc. Natl. Acad. Sci. U.S.A., 1973, vol. 70, no. 3, pp. 697–701.

    CAS  PubMed  PubMed Central  Google Scholar 

  117. Zaritsky, A. and Sipper, M., The preservation of favoured building blocks in the struggle for fitness: the puzzle algorithm, IEEE Trans. Evol. Comput., 2004, vol. 8, no. 5, pp. 443–455.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to A. V. Spirov or A. V. Eremeev.

Ethics declarations

Conflict of interests. The authors declare that they have no conflicts of interest.

Statement on the welfare of animals. This article does not contain any studies involving animals performed by any of the authors.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Spirov, A.V., Eremeev, A.V. Modularity in Biological Evolution and Evolutionary Computation. Biol Bull Rev 10, 308–323 (2020). https://doi.org/10.1134/S2079086420040076

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S2079086420040076

Keywords

Navigation