The gorilla's genome says . . .

The full genome of the last of the great ape species has been sequenced at last, and the results have been the cause of great excitement among the 'Intelligent Design' community. The gorilla genome is about the 50th to be completed, and it turns out that it has taken quite a while, partly because it is a great deal larger than our own.

The surprise is the finding that about 15% of the genes of gorillas are shared with humans and a different 15% with chimpanzees.  On the face of it, ID's proponents would appear to have a good point when they claim that this calls the family tree of the great apes/hominids into question.   They claim (e.g. here if you can read the words of Casey Luskin without imagining his whining voice) that 'neo-Darwinian evolution' has now been shown to have failed - yet again!

Just a few observations about Luskin's technique before attempting any analysis of the science.  In only the second paragraph he had to launch into an 'ad hominem' attack on Eugenie Scott.  Given that his argument might have had some face-value scientific merit, I think I can be forgiven for finding this approach to be unnecessarily confrontational and defensive.  But evidently he thought that it strengthened his argument.  I don't agree but I'm interested (and proud) to see that Eugenie has got him on the run like that.

I am much more interested in his 'reasoning'.  He says:

"The standard evolutionary phylogeny of primates holds that humans and chimps are more closely related to one-another than to other great apes like gorillas. In practice, all that really means is that when we sequence human, chimp, and gorilla genes, human and chimp genes have a DNA sequence that is more similar to one-another's genes than to the gorilla's genes."

Indeed that is what we might have expected, but the fact that the data seem to show something different is interesting isn't it?  I would also have expected Luskin to 'muddy the waters' for a non-specialist audience by using words like 'phylogeny'.  Why use a small word when a big one can be used instead.

I like to hone my arguments by listening to this sort of rhetorical tosh and trying to spot the logical fallacies.  My first thought on the topic was that the process of speciation must have been slow enough to allow a degree of gene transfer between the sub-species that later divided into the current completely separate species. We know that Neanderthals interbred with our ancestors to some degree.

Indeed, it turns out that this has been offered as an argument, but being a relatively weak one, this was the one that Luskin proceeded to attack.

"Called incomplete lineage sorting, it provides a convenient after-the-fact explanation for why different genes carry different phylogenetic signals. Of course, this is merely an ad hoc hypothesis invoked to explain away inconvenient data which contradicts the standard phylogeny."

That sounds reasonable until you discover that 'incomplete lineage sorting' is not quite what he describes.  Fortunately, proper specialists in genetics have come to the rescue.

In his slightly technical but manageable post Chimps are our closest relatives… but not for all of our genes, David Winter describes much more clearly how different variants of genes (called alleles) can be spread exactly as has been observed.  It turns out that it is perfectly understandable how the gene tree can be different from the species tree.

The gene tree can be different from the species tree. 
From an excellent article by David Winter

As David Winter says:

"For recent or repeated and rapid speciation processes there might not be time for the genetic lineages to sort. The gene tree can be different from the species tree"

and he then goes on to explain that this very observation can probably tell science something useful:

"Although we’ve always known this problem existed, we’ve only recently been able to extend population genetics theory to actually infer the history of species for gene trees even when those gene trees are unsorted."

So now you can decide for yourself who to side with - since we are 'teaching the controversy' as the ID community likes to say.  Do we believe a real geneticist who has a real explanation (or was it only an ad hoc hypothesis that we have always known about?).  Or do we believe someone who goes for ad hominem attacks on respectable and rational scientists, then uses 2 dimensional analogies that fail to prove anything because of their simplistic nature and merely rhetorical value?

I would still go for a strong adherence to the belief that chimps are our nearest cousins (speaking as a species of course).

ID might still be one of the strongest lines of evidence for the existence of a god, but let's face it, it doesn't have much competition!  Nor does it imply which of the current catalogue of 3000+ gods might have been responsible for the design, or why he did such a poor job of it.

Small note: Of course this very post could be said to be an 'ad hominem' attack but I trust you to judge that for yourself.