Excerpt: “…structural properties of regulatory networks are remarkably conserved and that orthologous regulatory factor families recognize similar binding motifs in vivo and show some similar co-associations.”
My comment: The co-associations of structure and function in the context of across species comparison are best explained in the context of what is currently known about how the epigenetic landscape becomes the physical landscape of DNA in the organized genomes of species from microbes to man.
If mutations and natural selection led to similarities in structure and function, the Laws of Physics, which biophysically constrain mutation-driven evolution, would need to be abandoned by evolutionary theorists.
If nutrient-dependent pheromone-controlled cell type differentiation via amino acid substitutions led to similarities in structure and function and to differences in structure and function, a single nutrient-dependent base pair change could conceivably lead from atom-level changes to ecological speciation without the pseudoscientific nonsense of population genetics.
See for instance: “We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms.”
Ask a social scientist whether pattern recognition of similarities makes more sense than recognition of differences in morphological and behavioral phenotypes to determine whether he or she is more like a bird-watcher or butterfly-collector than a serious scientist who has learned about biologically-based cause and effect.