title: Hierarchical coordinate systems for understanding complexity and its evolution, with applications to genetic regulatory networks.
abstract: Beyond complexity measures, sometimes it is worthwhile in addition to investigate how complexity changes structurally, especially in artificial systems where we have complete knowledge about the evolutionary process. Hierarchical decomposition is a useful way of assessing structural complexity changes of organisms modeled as automata, and we show how recently developed computational tools can be used for this purpose, by computing holonomy decompositions and holonomy complexity. To gain insight into the evolution of complexity, we investigate the smoothness of the landscape structure of complexity under minimal transitions. As a proof of concept, we illustrate how the hierarchical complexity analysis reveals symmetries and irreversible structure in biological networks by applying the methods to the lac operon mechanism in the genetic regulatory network of Escherichia coli.
authors.affiliation: School of Computer Science, University of Hertfordshire, Hatfield, Hertfordshire, United Kingdom. A.Egri-Nagy@herts.ac.uk
authors.forename: Attila
authors.initials: A
authors.lastname: Egri-Nagy
authors.forename: Chrystopher L
authors.initials: CL
authors.lastname: Nehaniv
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D005075:Biological Evolution; D019295:Computational Biology; D003198:Computer Simulation; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry; D019143:Evolution, Molecular; D053263:Gene Regulatory Networks; D005796:Genes; D007763:Lac Operon; D008954:Models, Biological; D008957:Models, Genetic; D008962:Models, Theoretical; D049490:Systems Biology
chemical_list: D029968:Escherichia coli Proteins