Robustness and evolvability: Revisited, redefined and applied

Building on and extending existing definitions of robustness and evolvability, we propose and utilize new formal definitions, with matching measures, of robustness and evolvability of systems with genotypes and corresponding phenotypes. We explain and show how these measures are more general and more representative of the concepts they stand for, than the commonly used/referenced measures originally proposed by Wagner. Further, a versatile digital modeling approach (BNK) is proposed that is inspired by NK systems. However, unlike NK systems, BNK incorporates a genotype and a phenotype, in addition to fitness. We develop and apply an Evolutionary Algorithm to a BNK-modeled system to find different types of perfect oscillators. We then map the resulting oscillating systems to possible genetic circuit realizations. Continuing with the synthetic biology theme, we also investigate the effect of noise in DNA synthesis on the predicted functionality of a DNA-based biosensor (i.e., its robustness), and we carry out a theoretical assessment of the evolvability of different types of ribozymes, undergoing directed evolution.