Abstract
The EvoEvo project was a 2013–2017 FP7 European project aiming at developing new evolutionary approaches in information science and producing novel algorithms based on the current understanding of molecular and evolutionary biology, with the ultimate goals of addressing open-ended problems in which the specifications are either unknown or too complicated to express, and of producing software able to operate even in unpredictable, varying conditions. Here we present the main rationals of the EvoEvo project and propose a set of design rules to evolve adaptive software systems.
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Notes
- 1.
The following text is massively derived from the EvoEvo project documents. In particular, many paragraphs are derived from the EvoEvo Description of Work (DoW) and from the project Final Report (EvoEvo Deliverable 6.8), available at www.evoevo.eu.
- 2.
ICT-2013.9.6 – FET Proactive: Evolving Living Technologies (EVLIT).
- 3.
Clustering is a data-mining task that aims to group objects sharing similar characteristics into a same cluster over the whole data space. Subspace clustering similarly aims at identifying groups of similar objects, but it also aims at detecting the subspaces where similarity occurs. Hence it can be conceived as “similarity examined under different representations” [23]. Subspace clustering is recognized as a more complicated and general task than standard clustering. Moreover, retrieving meaningful subspaces is particularly useful when dealing with high dimensional data [21].
References
Abernot, J., Beslon, G., Hickinbotham, S., Peignier, S., Rigotti, C.: Evolving instrument based on symbiont-host metaphor: a commensal computation. J. Creative Music Syst. 2(1), 1–10 (2017)
Banzhaf, W., et al.: Defining and simulating open-ended novelty: requirements, guidelines, and challenges. Theory Biosci. 135(3), 131–161 (2016)
Batut, B., Parsons, D.P., Fischer, S., Beslon, G., Knibbe, C.: In silico experimental evolution: a tool to test evolutionary scenarios. In: BMC Bioinformatics, vol. 14, no. 15, p. S11 (2013)
Beslon, G., Liard, V., Elena, S.F.: Evolvability drives innovation in viral genomes. In: 2nd EvoEvo Workshop, Satellite Workshop of CCS2016, Amsterdam, September 2016, 6 p. (2016)
Brooks, R.A.: Elephants don’t play chess. Rob. Auton. Syst. 6(1–2), 3–15 (1990)
Chatterjee, K., Pavlogiannis, A., Adlam, B., Nowak, M.A.: The time scale of evolutionary innovation. PLoS Comput. Biol. 10(9), e1003818 (2014)
Clark, E.B., Hickinbotham, S.J., Stepney, S.: Semantic closure demonstrated by the evolution of a universal constructor architecture in an artificial chemistry. J. R. Soc. Interface 14, 20161033 (2017)
Colizzi, E.S., Hogeweg, P.: Evolution of functional diversification within quasispecies. Genome Biol. Evol. 6(8), 1990–2007 (2014)
Colizzi, E.S., Hogeweg, P.: High cost enhances cooperation through the interplay between evolution and self-organisation. BMC Evol. Biol. 16(1), 31 (2016)
Cuypers, T.D., Hogeweg, P.: Virtual genomes in flux: an interplay of neutrality and adaptability explains genome expansion and streamlining. Genome Biol. Evol. 4(3), 212–229 (2012)
de Boer, F.K., Hogeweg, P.: Co-evolution and ecosystem based problem solving. Ecol. Inform. 9, 47–58 (2012)
Fischer, S., Bernard, S., Beslon, G., Knibbe, C.: A model for genome size evolution. Bull. Math. Biol. 76(9), 2249–2291 (2014)
Hickinbotham, S., Stepney, S.: Bio-reflective architectures for evolutionary innovation. In: A Life 2016, Cancun, Mexico, pp. 192–199. MIT Press (2016)
Hickinbotham, S., Stepney, S.: Augmenting live coding with evolved patterns. In: Johnson, C., Ciesielski, V., Correia, J., Machado, P. (eds.) EvoMUSART 2016. LNCS, vol. 9596, pp. 31–46. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-31008-4_3
Hindré, T., Knibbe, C., Beslon, G., Schneider, D.: New insights into bacterial adaptation through in vivo and in silico experimental evolution. Nat. Rev. Microbiol. 10, 352–365 (2012)
Hooper, L.V., Gordon, J.I.: Commensal host-bacterial relationships in the gut. Science 292, 1115–1118 (2001)
Hooper, L.V., Midtvedt, T., Gordon, J.I.: How host-microbial interactions shape the nutrient environment of the mammalian intestine. Ann. Rev. Nutr. 22(1), 283–307 (2002)
Hoverd, T., Stepney, S.: EvoMachina: a novel evolutionary algorithm inspired by bacterial genome reorganisation. In: 2nd EvoEvo Workshop, CCS 2016, Amsterdam, Netherlands (2016)
Kimura, M.: Evolutionary rate at the molecular level. Nature 217, 624–626 (1968)
Kriegel, H.-P., Kröger, P., Zimek, A.: Clustering highdimensional data: a survey on subspace clustering, pattern-based clustering, and correlation clustering. ACM Trans. Knowl. Discov. Data 3(1), 1–58 (2009)
Pagie, L., Hogeweg, P.: Evolutionary consequences of coevolving targets. Evol. Comput. 5(4), 401–418 (1997)
Patrikainen, A., Meila, M.: Comparing subspace clusterings. IEEE Trans. Knowl. Data Eng. 18(7), 902–916 (2006)
Peignier, S., Rigotti, C., Beslon, G.: Subspace clustering using evolvable genome structure. In: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, pp. 575–582 (2015)
Peignier, S., Abernot, J., Rigotti, C., Beslon, G.: EvoMove: evolutionary-based living musical companion. In European Conference on Artificial Life (ECAL), pp. 340–347 (2017)
Peignier, S., Rigotti, C., Rossi, A., Beslon, G.: Weight-based search to find clusters around medians in subspaces. In: ACM Symposium on Applied Computing, p. 10 (2018)
Plucain, J., et al.: Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli. Science 343, 1366–1369 (2014)
Rocabert, C., Knibbe, C., Consuegra, J., Schneider, D., Beslon, G.: Beware batch culture: seasonality and niche construction predicted to favor bacterial adaptive diversification. PLoS Comput. Biol. 13(3), e1005459 (2017)
Rutten, J., Hogeweg, P., Beslon, G.: (in prep) Adapting the engine to the fuel: mutator populations can reduce the mutational load by reorganizing their genome structure. in prep
Szathmáry, E., Maynard-Smith, J.: The major evolutionary transitions. Nature 374(6519), 227–232 (1997)
van Dijk, B., Hogeweg, P.: In silico gene-level evolution explains microbial population diversity through differential gene mobility. Genome Biol. Evol. 8(1), 176–188 (2016)
Acknowledgments
This work was supported by the European Commission \(7^{th}\) Framework Program (FP7-ICT-2013.9.6 FET Proactive: Evolving Living Technologies) EvoEvo project (ICT- 610427, http://www.evovo.eu/). The authors thank all the partners of the EvoEvo project for fruitful discussions.
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Beslon, G., Elena, S.F., Hogeweg, P., Schneider, D., Stepney, S. (2018). Evolving Living Technologies—Insights from the EvoEvo Project. In: Colanzi, T., McMinn, P. (eds) Search-Based Software Engineering. SSBSE 2018. Lecture Notes in Computer Science(), vol 11036. Springer, Cham. https://doi.org/10.1007/978-3-319-99241-9_2
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