Beyond networks: mechanism and process in evo-devo

Explanation in terms of gene regulatory networks (GRNs) has become standard practice in evolutionary developmental biology (evo-devo). In this paper, we argue that GRNs fail to provide a robust, mechanistic, and dynamic understanding of the developmental processes underlying the genotype-phenotype map. Explanations based on GRNs are limited by three main problems: (1) the problem of genetic determinism, (2) the problem of correspondence between network structure and function, and (3) the problem of diachronicity, as in the unfolding of causal interactions over time. Overcoming these problems requires dynamic mechanistic explanations, which rely not only on mechanistic decomposition, but also on dynamic modeling to reconstitute the causal chain of events underlying the process of development. We illustrate the power and potential of this type of explanation with a number of biological case studies that integrate empirical investigations with mathematical modeling and analysis. We conclude with general considerations on the relation between mechanism and process in evo-devo.