Quarterly (winter, spring, summer, fall)
128 pp. per issue
7 x 10, illustrated
ISSN
1064-5462
E-ISSN
1530-9185
2014 Impact factor:
1.39

Artificial Life

Fall 2011, Vol. 17, No. 4, Pages 353-364
(doi: 10.1162/artl_a_00043)
© 2011 Massachusetts Institute of Technology
Properties of Biological Mutation Networks and Their Implications for ALife
Article PDF (429.35 KB)
Abstract

We report a study of networks constructed from mutation patterns observed in biology. These networks form evolutionary trajectories, which allow for both frequent substitution of closely related structures, and a small evolutionary distance between any two structures. These two properties define the small-world phenomenon. The mutation behavior between tokens in an evolvable artificial chemistry determines its ability to explore evolutionary space. This concept is underrepresented in previous work on string-based chemistries. We argue that small-world mutation networks will confer better exploration of the evolutionary space than either random or fully regular mutation strategies. We calculate network statistics from two data sets: amino acid substitution matrices, and codon-level single point mutations. The first class are observed data from protein alignments; while the second class is defined by the standard genetic code that is used to translate RNA into amino acids. We report a methodology for creating small-world mutation networks for artificial chemistries with arbitrary node count and connectivity. We argue that ALife systems would benefit from this approach, as it delivers a more viable exploration of evolutionary space.