Agent-based model of genotype editing

Authored by Chien-Feng Huang, Jasleen Kaur, Ana Maguitman, Luis M. Rocha

DOI: 10.1162/evco.2007.15.3.253

Sponsors: United States National Science Foundation (NSF)

Platforms: No platforms listed

Model Documentation: Other Narrative Mathematical description

Model Code URLs: Model code not found

Abstract

Evolutionary algorithms rarely deal with ontogenetic, non-inherited alteration of genetic information because they are based on a direct genotype-phenotype mapping. In contrast, several processes have been discovered in nature which alter genetic information encoded in DNA before it is translated into amino-acid chains. Ontogenetically altered genetic information is not inherited but extensively used in regulation and development of phenotypes, giving organisms the ability to, in a sense, re-program their genotypes according to environmental cues. An example of post-transcriptional alteration of gene-encoding sequences is the process of RNA. Editing. Here we introduce a novel Agent-based model of genotype editing and a computational study of its evolutionary performance in static and dynamic environments. This model builds on our previous Genetic Algorithm with Editing, but presents a fundamentally novel architecture in which coding and non-coding genetic components are allowed to co-evolve. Our goals are: (1) to study the role of RNA Editing regulation in the evolutionary process, (2) to understand how genotype editing leads to a different, and novel evolutionary search algorithm, and (3) the conditions under which genotype editing improves the optimization performance of traditional evolutionary algorithms. We show that genotype editing allows evolving agents to perform better in several classes of fitness functions, both in static and dynamic environments. We also present evidence that the indirect genotype/phenotype mapping resulting from genotype editing leads to a better exploration/ exploitation compromise of the search process. Therefore, we show that our biologically-inspired model of genotype editing can be used to both facilitate understanding of the evolutionary role of RNA regulation based on genotype editing in biology, and advance the current state of research in Evolutionary Computation.

Tags

Genetic Algorithms Agent-based modeling Coevolution Genotype Editing RNA Editing biologically-inspired computing dynamic environments indirect genotype/phenotype mapping