The analysis of complex molecular networks has become widespread in biology in recent years. The initiating event for this development was the publication of some landmark papers that argued for the ubiquity of so called “scale-free” networks in numerous biological systems and human communications networks (Barabasi and Albert, 1999; Jeong et al., 2000). Subsequent analysis (Doyle et al., 2005) has undermined the case for the near-universality of scale-free networks, but the general importance of networks as organizational devices is undisputed. In biology, an understanding of the structure and dynamics of genetic networks, in particular, is now widely viewed as crucial to understanding phenomena as diverse as metabolic systems, phage developmental switches, protein interaction systems, transcriptional controls, and complex developmental traits. Indeed, the study of molecular and genetic networks is central to the new field of systems biology (Strogatz, 2003).

The fundamental concept of genetic networks, however, is hardly new. A hint of the intricacy of the genetic architecture that underlies complex morphological traits, and of the complexity of the genetic interactions involved, can be found in a seminal paper on the gene by H. J. Muller (1922). Furthermore, the concept of genetic networks was implicit in much of C. H. Waddington’s work (1940, 1957), although he did not use the term. Most importantly, however, the structure of genetic networks (in particular, one class of genetic networks, those underlying the biochemistry of mammalian coat colors) was central to the work of S. Wright (1968, 1980). Beyond these three great pioneers of 20th century biology, S. Kauffman added a molecular dimension to network-thinking with an early, if necessarily rather abstract, exploration of the generic structural properties of regulatory genetic networks (Kauffman, 1971). Not least, R. H. Britten and E. Davidson produced some thought-provoking schemes of how transcriptional networks might operate (Britten and Davidson, 1969, 1971). These specific hypotheses have not held up, but the basic thinking was prescient. It was, however, only the confluence, more than two decades later, of advances in genetics and molecular techniques in the 1990s with the then-new graph theory analyses of various networks (Barabasi and Albert, 1999; Jeong et al., 2000) that launched the current wave of interest amongst biologists, in networks generally and, more specifically, in genetic networks (reviewed in Wilkins, 2007a).

An important part of this recent scientific development has been a focus on the evolutionary dynamics of networks (Dorogovtsev and Mendes, 2003; Barabasi and Oltvai, 2004; Berg et al., 2004; Manke et al., 2006). In principle, this theoretical work should provide a significant bridge between systems biology and evolutionary biology. In reality, however, there has remained a gap between the theoretical work on genetic network evolution and its application to understanding organismal evolution.