Section: New Results

CRN design by artificial evolution

Participants : Elisabeth Degrand, François Fages, Mathieu Hemery, Sylvain Soliman.

In [4], [12], we study an alternative method based on artificial evolution to build a CRN that approximates a real function given on finite sets of input values. We present a nested search algorithm that evolves the structure of the CRN and optimizes the kinetic parameters at each generation. We evaluate this algorithm on the Heaviside and Cosine functions both as functions of time and functions of input molecular species. We then compare the CRN obtained by artificial evolution both to the CRN generated by the numerical method from a PIVP definition of the function, and to the natural CRN found in the BioModels repository for switches and oscillators.

On a Heaviside function of time, the results obtained by artificial evolution lead to a remarkably simple CRN of 3 molecular species and 5 reactions with double catalysts which provide a very stiff transition although using mass action law kinetics. This solution is more economical than the CRN generated by the PIVP method for sigmoid functions. On a Heaviside function of input, the CRN found by evolution are slightly more complicated than the bistable switch found in cell cycle CRN for instance, but much less complex than the MAPK signaling network that plays a similar role.

On the cosine function of time, the best CRN found by evolution contains an annihilation reaction similar to the CRN generated by the numerical method for positive and negative variables, but one less reaction thanks to an intriguing non symmetric use of the two variables which preserves the limit cycle. Interestingly, the evolved and the PIVP generated structures could be compared to prokaryote and eukaryote models of the circadian clock found in BioModels.

On the cosine function of input, a CRN surprisingly emerges with the structure of the CRN for cosine function of time, using the same trick as for PIVP compilation to stop time at the desired input value.

In [2], we use a genetic algorithm to evolve biochemical networks displaying a direct logarithmic response. Numerous biological systems are known to harbour a form of logarithmic behaviour, from Weber's law to bacterial chemotaxis. Working on a logarithmic scale allows the organism to respond appropriately to large variations in a given input at a modest cost in terms of metabolism. Interestingly, a quasi-perfect log-response implemented by the same simple core network evolves in a convergent way across our different replications. The best network is able to fit a logarithm over 4 order of magnitude with an accuracy of the order of 1%. At the heart of this network, we show that a logarithmic approximation may be implemented with one single non-linear interaction, that can be interpreted either as a phosphorylation or as a ligand induced multimerization and provide an analytical explanation of the effect. Biological log-response might thus be easier to implement than usually assumed.