On the evolution and dynamics of biological networks

Large numbers of interacting non-genic molecules regulate metabolism and embryonic morphogenesis through often unspecific mechanisms. This lack of specificity suggests that the prevailing viewpoint, that such ordered processes result from the direct control of genes and their products irrespective of local molecular dynamics, is incomplete. Proposed here is a hypothetical type of control dynamics, called indirect, that is exhibited in natural biological networks of interacting and adapting elements. Evidence in the literature suggests that ordinary interactions among such elements - including organisms, cells and molecules - produce six network phenomena that can be attributed to indirect-control dynamics. Although these hypotheses can be disproved, including by showing that the phenomena can be accounted for by an alternative process, the set of ecological dynamics argued to underlie the phenomena is observable, biologically consistent and universal. In contrast, the direct-control dynamics required by the modern synthesis likely is biologically disadvantageous. This biological view of networks suggests new areas of research.