Even Koonin nods

Classicists have a turn of phrase, "Even Homer Nods". The phrase originates from the Roman poet Horace (et idem indignor quandoque bonus dormitat Homerus) and has become a proverbial phrase not just for Homer's numerous continuity errors, but more generally to allow for slip-ups by someone of such high stature that the idea that they can make mistakes seems unthinkable. 

Eugene Koonin is a colossus in the application of bioinformatics to the study of evolution, with over 500 papers to his name. But I am afraid in a paper just published he suffers from his very own Homeric nod.

An abstract and link to the paper in question can be found here:

Koonin EV (2008). Evolution of genome architecture. Int J Biochem Cell Biol.

The offending phrase is the very first sentence of the abstract:

"Charles Darwin believed that all traits of organisms have been honed to near perfection by natural selection."

which elicits a roar in response: NO, HE DIDN'T!!

Eugene appears to have overlooked a whole section of Chapter XIII of the Origin of Species, entitled Rudimentary, atrophied, or aborted organs and starting off with:

Organs or parts in this strange condition, bearing the stamp of inutility, are extremely common throughout nature. For instance, rudimentary mammæ are very general in the males of mammals: I presume that the "bastard-wing" in birds may be safely considered as a digit in a rudimentary state: in very many snakes one lobe of the lungs is rudimentary; in other snakes there are rudiments of the pelvis and hind limbs. Some of the cases of rudimentary organs are extremely curious; for instance, the presence of teeth in fœtal whales, which when grown up have not a tooth in their heads; and the presence of teeth, which never cut through the gums, in the upper jaws of our unborn calves. It has even been stated on good authority that rudiments of teeth can be detected in the beaks of certain embryonic birds. Nothing can be plainer than that wings are formed for flight, yet in how many insects do we see wings so reduced in size as to be utterly incapable of flight, and not rarely lying under wing-cases, firmly soldered together!

And as Darwin himself recognised, such rudimentary features are not some throwaway feature under the Theory of Evolution, but a crucial pillar of support for it!

On the view of descent with modification, we may conclude that the existence of organs in a rudimentary, imperfect, and useless condition, or quite aborted, far from presenting a strange difficulty, as they assuredly do on the ordinary doctrine of creation, might even have been anticipated, and can be accounted for by the laws of inheritance.

And of course similar arguments apply at the level of genomes. No intelligent designer would ever leave such a mess of junk behind in the genomes of mammals like ourselves. And why would such a creator deliberately break the gene that allows us humans to make vitamin C?! Is scurvy a message from God telling us not to undertake long sea voyages of exploration? (here is an exercise for students on this issue)

But back to the offending paper. So, here we have a "Kooninian nod" equal to the resurrection of Pylaimenes. Even the "well-born" sometimes slip up!

PS. I am afraid that Eugene's outline of natural selection in the paper itself also strikes me as rather shaky, but as I am about to disappear off on vacation, I will leave it to the reader to work out why.