Genetic Regulatory Network Models of Biological Clocks: Evolutionary History Matters

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 activatory 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 to unselected accidents of neutral selection. Several of these hypotheses are explored by evolving GRNs with and without (Gaussian) noise and blackout periods for environmental stimulation. Robustness to certain types of perturbation appears to account for some, but not all, dynamical properties of the evolved networks. Unselected abilities, also observed for biological clocks, include the capacity to adapt to change in wavelength of environmental stimulus and to clock resetting.

[1]  A. Telser.  Molecular Biology of the Cell, 4th Edition , 2002 .

[2]  Eörs Szathmáry,et al.  The Major Transitions in Evolution , 1997 .

[3]  Chrystopher L. Nehaniv.  Self-replication, Evolvability and Asynchronicity in Stochastic Worlds , 2005, SAGA.

[4]  Chrystopher L. Nehaniv,et al.  Hierarchical Coordinate Systems for Understanding Complexity and its Evolution, with Applications to Genetic Regulatory Networks , 2008, Artificial Life.

[5]  Chrystopher L. Nehaniv,et al.  Evolving Biological Clocks using Genetic Regulatory Networks , 2005 .

[6]  Peter J. Bentley,et al.  Biologically Inspired Evolutionary Development , 2003, ICES.

[7]  J. Raes,et al.  Small-scale gene duplications , 2005 .

[8]  Arthur T. Winfree,et al.  The timing of biological clocks , 1986 .

[9]  Stuart A. Kauffman,et al.  The origins of order , 1993 .

[10]  W. Arthur,et al.  The Origin of Animal Body Plans , 1997 .

[11]  E. Davidson.  Genomic Regulatory Systems: Development and Evolution , 2005 .

[12]  Albert,et al.  Emergence of scaling in random networks , 1999, Science.

[13]  Peter J. Bentley,et al.  Adaptive Fractal Gene Reguatory Networks for Robot Control , 2005 .

[14]  A. Winfree.  The geometry of biological time , 1991 .

[15]  Wolfgang Banzhaf.  On the Dynamics of an Artificial Regulatory Network , 2003, ECAL.

[16]  Torsten Reil,et al.  Dynamics of Gene Expression in an Artificial Genome - Implications for Biological and Artificial Ontogeny , 1999, ECAL.

[17]  Chrystopher L. Nehaniv,et al.  Evolving Embodied Genetic Regulatory Network-Driven Control Systems , 2003, ECAL.

[18]  Tim Taylor.  A Genetic Regulatory Network-Inspired Real-Time Controller for a Group of Underwater Robots , 2005 .

[19]  S. Gould,et al.  Ontogeny and Phylogeny , 1978 .

[20]  Lev Muchnik,et al.  Bioinformatics Original Paper Copying Nodes versus Editing Links: the Source of the Difference between Genetic Regulatory Networks and the Www , 2022 .

[21]  P. Callaerts,et al.  Induction of ectopic eyes by targeted expression of the eyeless gene in Drosophila. , 1995, Science.

[22]  Dr. Susumu Ohno.  Evolution by Gene Duplication , 1970, Springer Berlin Heidelberg.

[23]  S. Kauffman.  Metabolic stability and epigenesis in randomly constructed genetic nets. , 1969, Journal of theoretical biology.

[24]  Chrystopher L. Nehaniv,et al.  The Evolution and Understanding of Hierarchical Complexity in Biology from an Algebraic Perspective , 1999, Artificial Life.

[25]  J. Baldwin.  A New Factor in Evolution , 1896, The American Naturalist.

[26]  R. Gregory.  The evolution of the genome , 2005 .

[27]  M. West-Eberhard.  Developmental plasticity and evolution , 2003 .

[28]  Arantxa Etxeverria.  The Origins of Order , 1993 .

[29]  Chrystopher L. Nehaniv,et al.  Evolutionary robustness of differentiation in genetic regulatory networks , 2006 .

[30]  M. Schilstra,et al.  Modelling the Regulation of Gene Expression in Genetic Regulatory Networks , 2005 .

[31]  L. Buss,et al.  The evolution of individuality , 1987 .