PLoS Biology has an interesting essay out that’s worth mentioning: Evolution, Interactions, and Biological Networks. Personally, my interest is in better describing the evolution of complex signal transduction networks, or as the essay describes them, regulatory networks. To wit (emphasis mine):
If we are to develop an evolutionary ecology of networks then we should: (i) improve classification schemes for describing the microstates of networks; (ii) develop a more rigorous, and perhaps, system-specific understanding of permitted moves and trade-offs between networks; and (iii) use the principles of game theory and adaptive dynamics to consider how networks interact via their emergent properties. For regulatory networks, do features emerge primarily through gene duplication with subsequent neofunctionalization, what are the fitness and energetic costs of such duplication events, or are there other more complex processes at work [26,27]?
That is an excellent cluster of questions.
Do features emerge primarily through gene duplication with subsequent neofunctionalization? Well, I’ve made that argument before, and I still think that that is the parsimonious explanation.
What are the fitness and energetic costs of such duplication events? The costs of such events are probably negligible – they happen often enough in biology, and with little impact either way. Even in simple unicellular organisms, gene duplication is commonly observed across genomes.
Or are there more complex processes at work? That’s the 64,000-dollar question, isn’t it? But as you can tell by now, my hunch is that the answer is no. The parsimonious explanation is that it’s all “simple” biochemical processes (but even simple biochemical processes can be difficult to wrap your head around sometimes) – it’s just that there are very very many such simple processes going on in any given network. This creates many constraints, but also many opportunities for change to occur and take hold, and it feeds into the observed roles for a robust array of options for such changes, and modularity in many instances, among other themes of molecular evolution.
It’s this sheer volume of processes in any given network, I think, that makes it difficult to clearly describe the evolution of networks to neophytes.
Additional Reading (references 26-27 from quote):