Michael Lynch in Nature Reviews Genetics, The evolution of genetic networks by non-adaptive processes:
Although numerous investigators assume that the global features of genetic networks are moulded by natural selection, there has been no formal demonstration of the adaptive origin of any genetic network. This Analysis shows that many of the qualitative features of known transcriptional networks can arise readily through the non-adaptive processes of genetic drift, mutation and recombination, raising questions about whether natural selection is necessary or even sufficient for the origin of many aspects of gene-network topologies. The widespread reliance on computational procedures that are devoid of population-genetic details to generate hypotheses for the evolution of network configurations seems to be unjustified.
A richer exposition of the author's ideas can be found in The Origins of Genome Architecture. An early paper which shows the seeds of his thinking can be found over at Genetics, Preservation of Duplicate Genes by Complementary, Degenerative Mutations , while The origins of eukaryotic gene structure is a more recent piece. Both are now open access. Lynch has strong opinions, for example, see this volley launched against Sean Carroll (of evo-devo fame).