ABSTRACT
Optimality theory is based on the ability of natural selection to maximize fitness, and hence to converge on particular circuit designs and parameter values in a given environment. Thus, optimality theory aims to predict and understand which circuit and parameters will arise in each situation. This chapter considers optimality as an idealized assumption that is a good starting point for generating testable hypotheses. Optimality theory predicts that the protein expression level that is selected maximizes the fitness function. Analysis of the evolutionary dynamics indicated that the cells reached their optimal, adapted levels in each case by means of a mutation that changed the LacZ protein level. Cells evolve to the optimal value in evolutionary experiments in several hundred generations. The optimal delay for a feedforward loop in such an environment is equal to the duration of the short pulses. This delay filters out the non-beneficial pulses, with minimal negative impact on fitness during long pulses.
