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A case study of evolutionary computation of biochemical adaptation

Paul François and Eric D Siggia

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Simulations 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.


PACS

87.14.E- Proteins

87.15.K- Molecular interactions; membrane-protein interactions

87.23.Kg Dynamics of evolution

87.15.N- Properties of solutions of macromolecules

Subjects

Biological physics

Environmental and Earth science

Dates

Issue 2 (June 2008)

Received 11 April 2008, accepted for publication 2 June 2008

Published 24 June 2008

 
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