The Dark Proteome and Dark Evolution

Evolution Did It

A new PNAS paper published 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” 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, “dark proteins may be newly evolved proteins or rare proteins adapted to specific functional niches.”

We might call this dark evolution. Once again, the pattern is not one of common descent, but of unique structures.

The results also have implications for the so-called orphans, open reading frames found only in a particular species. Such genetic sequences contradict evolution and when they were first discovered evolutionists predicted they would be found in other species as more genomes were decoded. Instead the number of orphans just continued to grow.

Evolutionists next predicted that orphan sequences were probably not part of a mature protein coding gene and did not form functional proteins. That has not been found to be true, and this new survey provides further evidence for this. As the authors conclude, “Thus, our results suggest that many of the uncharacterized orphan sequences … are indeed real proteins.”

Protein science, however, is clear that blind mutations cannot form real proteins this fast from scratch (or at all for that matter). Hence we must believe that built-in cellular processes must have created these proteins—processes that are complex and require, among other things, proteins.

Real ones.