Evolving Biological Clocks using Genetic Regulatory Networks

@inproceedings{citeulike:1069994, abstract = {We study the evolvability and dynamics of artificial genetic regulatory networks (GRNs), as active control systems, realizing simple models of biological clocks that have evolved to respond to periodic environmental stimuli of various kinds with appropriate periodic behaviors. GRN models may differ in the evolvability of expressive regulatory dynamics. A new class of artificial GRNs with an evolvable number of complex cis-regulatory control sites - each involving a finite number of inhibitory and excitatory binding factors - is introduced, allowing realization of complex regulatory logic. Previous work on biological clocks in nature has noted the capacity of clocks to oscillate in the absence of environmental stimuli, putting forth several candidate explanations for their observed behavior, related to anticipation of environmental conditions, compartmentation of activities in time, and robustness to perturbations of various kinds, or unselected accidents of neutral selection. Several of these hypotheses are explored by evolving GRNs with and without (gaussian) noise and "black out periods" for environmental stimulation. Robustness to environmental perturbation experienced by the lineage appears to account for some, but not all, dynamical properties of the evolved networks including unselected abilities such as capacity to adapt to shift in phase or frequency of environmental stimulus.}, author = {Knabe, Johannes F. and Nehaniv, Chrystpoher L. and Schilstra, Maria J. and Quick, Tom }, booktitle = {Artificial Life X : Proceedings of the Tenth International Conference on the Simulation and Synthesis of Living Systems}, citeulike-article-id = {1069994}, editor = {Rocha, Luis M. and Yaeger, Larry S. and Bedau, Mark A. and Floreano, Dario and Goldstone, Robert L. and Vespignani, Alessandro }, keywords = {alife, evolution, genetic\_regulatory\_networks, modelling}, month = {August}, organization = {International Society for Artificial Life}, pages = {15--21}, posted-at = {2007-01-26 22:43:34}, priority = {0}, publisher = {The MIT Press (Bradford Books)}, title = {Evolving Biological Clocks using Genetic Regulatory Networks}, url = {http://panmental.de/GRNclocks/}, year = {2006} }

TY - CONF ID - citeulike:1069994 L3 - citeulike-article-id:1069994 TI - Evolving Biological Clocks using Genetic Regulatory Networks T2 - Artificial Life X : Proceedings of the Tenth International Conference on the Simulation and Synthesis of Living Systems SP - 15 EP - 21 OR - International Society for Artificial Life PB - The MIT Press (Bradford Books) N2 - We study the evolvability and dynamics of artificial genetic regulatory networks (GRNs), as active control systems, realizing simple models of biological clocks that have evolved to respond to periodic environmental stimuli of various kinds with appropriate periodic behaviors. GRN models may differ in the evolvability of expressive regulatory dynamics. A new class of artificial GRNs with an evolvable number of complex cis-regulatory control sites - each involving a finite number of inhibitory and excitatory binding factors - is introduced, allowing realization of complex regulatory logic. Previous work on biological clocks in nature has noted the capacity of clocks to oscillate in the absence of environmental stimuli, putting forth several candidate explanations for their observed behavior, related to anticipation of environmental conditions, compartmentation of activities in time, and robustness to perturbations of various kinds, or unselected accidents of neutral selection. Several of these hypotheses are explored by evolving GRNs with and without (gaussian) noise and "black out periods" for environmental stimulation. Robustness to environmental perturbation experienced by the lineage appears to account for some, but not all, dynamical properties of the evolved networks including unselected abilities such as capacity to adapt to shift in phase or frequency of environmental stimulus. KW - alife KW - evolution KW - genetic_regulatory_networks KW - modelling AU - Knabe, Johannes AU - Nehaniv, Chrystpoher AU - Schilstra, Maria AU - Quick, Tom A2 - Rocha, Luis A2 - Yaeger, Larry A2 - Bedau, Mark A2 - Floreano, Dario A2 - Goldstone, Robert A2 - Vespignani, Alessandro PY - 2006/08/01/ UR - http://panmental.de/GRNclocks/ ER -