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Artificial Life

Winter 2016, Vol. 22, No. 1, Pages 76-111
(doi: 10.1162/ARTL_a_00191)
© 2016 Massachusetts Institute of Technology
Evolutionary Growth of Genome Representations on Artificial Cellular Organisms with Indirect Encodings
Article PDF (2.51 MB)

Evolutionary design targets systems of continuously increasing complexity. Thus, indirect developmental mappings are often a necessity. Varying the amount of genotype information changes the cardinality of the mapping, which in turn affects the developmental process. An open question is how to find the genotype size and representation in which a developmental solution would fit. A restricted pool of genes may not be large enough to encode a solution or may need complex heuristics to find a realistic size. On the other hand, using the whole set of possible regulatory combinations may be intractable. In nature, the genomes of biological organisms are not fixed in size; they slowly evolve and acquire new genes by random gene duplications. Such incremental growth of genome information can be beneficial also in the artificial domain. For an evolutionary and developmental (evo-devo) system based on cellular automata, we investigate an incremental evolutionary growth of genomes without any a priori knowledge on the necessary genotype size. Evolution starts with simple solutions in a low-dimensional space and incrementally increases the genotype complexity by means of gene duplication, allowing the evolution of scalable genomes that are able to adapt genetic information content while compactness and efficiency are retained. The results are consistent when the target phenotypic complexity, the geometry size, and the number of cell states are scaled up.