A new PNAS paperpublished last week on the dark proteome has some interesting implications for the theory of evolution. The paper presents a survey of protein sequences, focusing on the many sequences for which the corresponding three dimensional protein structure is not known, and cannot be inferred from any remotely similar sequence. Why is this so-called “dark proteome” is so large? The survey finds that the various hypotheses to explain this—that the dark proteins are intrinsically disordered, or their sequences are compositionally biased, or they are transmembrane proteins, all reasons that can confound structure determination—don’t work very well. The paper concludes that “a surprisingly large fraction of dark proteins … cannot be easily accounted for by these conventional explanations.” And not surprisingly, these dark proteins are less common across the species. So where did all these dark protein sequences come from? Well evolution did it. As the paper explains … read more