The aromatase family offers an example where a combination of phylogenetic analysis, molecular evolutionary analysis, and chemical analysis set within the context of the paleontological and geological records, and supported by contemporary bioinformatics and molecular modeling tools, permits a higher order level of hypothesis generation concerning the function of proteins. Rather than simply an Enzyme Commission number (E.C. 126.96.36.199 for aromatase), a description of catalytic activity (the enzyme oxidizes testosterone), or a description of the regulatory pattern (the protein expressed between day 10 and 13), this type of analysis can generate a truly functional hypothesis: that the embryonic enzyme oxidizes testosterone as a way of managing the larger litter sizes that emerged in the Suoidea during a time of dramatic planetary cooling (ca. 35 Ma).
Such hypotheses set a higher bar, and a more useful standard, for the field of systems biology. Evolutionary theory holds that the only mechanism for obtaining functional behavior in a biological system is natural selection. Selection, based on a frequently poorly defined concept of "fitness", is determined by a context that not only includes the cell and tissue, but also the organism, the ecosystem, and a changing planet . One cannot expect a collection of expression data with a mathematical model, by themselves, to provide this type of functional information unless it is set in the organismic, ecosystem, and planetary context. The historical view, of the type outlined here, becomes a critical tool for constructing this setting (Supplementary Figure [see Additional File 1]).
Humans have evidently exploited the molecular biology of larger litters to select for pigs that have truly large litters (as many as 14) following their domestication. Evidence for ancient domestication of pigs comes, inter alia, from a study of Indo-European languages. Proto-Indo-European (PIE) language had words for "pig" (PIE su-, compared with Tocharian B suwo, Latin sus, Greek us, Sanskrit sukara, Church Slavic svinija, Old High German swin, and English sow; also compare PIE porko-, with Latin porcus, Church Slavic prase, Old High German farah, etc. ), indicating that the pig has been under human domestication for at least 6000 years, enough time to have suffered a significant impact on its genotype through husbandry. We are unable, at this time, to exploit complete genome sequences of pigs or other closely related taxa to discuss the impact of domestication on aromatase, steroid receptors, amphiregulins, or other proteins that appear to be associated with uterine capacity and large litter sizes in the domesticated pig . With the anticipated complete genome sequences of representatives of various mammal orders, including artiodactyls, it should be possible to extend this planetary biology approach.