Paul François and Eric D Siggia 2008 Phys. Biol. 5 026009 doi:10.1088/1478-3975/5/2/026009
Paul François and Eric D Siggia
Show affiliationsSimulations of evolution have a long history, but their relation to biology is questioned because of the perceived contingency of evolution. Here we provide an example of a biological process, adaptation, where simulations are argued to approach closer to biology. Adaptation is a common feature of sensory systems, and a plausible component of other biochemical networks because it rescales upstream signals to facilitate downstream processing. We create random gene networks numerically, by linking genes with interactions that model transcription, phosphorylation and protein–protein association. We define a fitness function for adaptation in terms of two functional metrics, and show that any reasonable combination of them will yield the same adaptive networks after repeated rounds of mutation and selection. Convergence to these networks is driven by positive selection and thus fast. There is always a path in parameter space of continuously improving fitness that leads to perfect adaptation, implying that the actual mutation rates we use in the simulation do not bias the results. Our results imply a kinetic view of evolution, i.e., it favors gene networks that can be learned quickly from the random examples supplied by mutation. This formulation allows for deductive predictions of the networks realized in nature.
87.15.K- Molecular interactions; membrane-protein interactions
Issue 2 (June 2008)
Received 11 April 2008, accepted for publication 2 June 2008
Published 24 June 2008
Paul François and Eric D Siggia 2008 Phys. Biol. 5 026009
Xiaofeng Gong et al 2008 EPL 83 28001
C. B. Korn and U. S. Schwarz 2008 EPL 83 28007
Xiao-Pu Han et al 2008 EPL 83 28003
T. Das and S. Chakraborty 2008 EPL 83 48003
Vesselin Petkov 1999 Nonlinearity 12 1663
Gemma De las Cuevas et al J. Stat. Mech. (2009) P07001
Jianjun Yang et al 2010 J. Phys.: Condens. Matter 22 095503
Caterina-E Mora et al 2008 New J. Phys. 10 083027
Ben-Hwa Jang et al 2008 J. Micromech. Microeng. 18 055020