Christopher Hitchens was impressed by the existence of blind cave organisms, and wrote that they argue against a linear progression in evolution. He's quite right; creationism doesn't explain why their god tossed in to salamanders and fish a collection of complex developmental mechanisms that the animals simply throw away and do not use. Evolution does — descent from a sighted ancestor explains how blind cave animals can still possess the machinery for a lost organ.
Do you think the Discovery Institute would let this challenge pass by? Of course not. They put their top man on the job, so Casey Luskin wrote a rebuttal. After a long weekend and before a busy day of work, it always makes me happy to find a new Luskin screed — they're so dang easy to shred. Here's his devastating critique:
Hitchens, Dawkins and Carroll can have all the evidence they want that the neo-Darwinian mechanism can mess things up, turn genes off, and cause "loss-of-function." No one on any side of this debate doubts that random mutations are quite good at destroying complex features. Us folks on the ID side suspect that random mutation and natural selection aren’t good at doing very much more than that. And the constant citations by Darwinists of "loss of function" examples as alleged refutations of ID only strengthens our argument.
The claim that evolution can't create new features is one of the oldest and most tired fables in the creationist playbook — note that that link cites the Watchtower Bible and Tract Society and Henry Morris. It's false. In this case, their superficial knowledge also trips them up. The loss of eyes seems like a clear-cut case of degeneration…but when you look deeper, it's not.
The best studied case is the comparison of blind and sighted forms of Astyanax, a fish that has species that live in surface waters and have eyes, and others that live in caves and have lost them.
The Jeffery lab has worked out the molecular details of eye loss, and it isn't as simple as messing things up, turning genes off, and causing loss-of-function mutations. To the contrary, all the genes for eyes are there and functional in the blind species. Simply transplanting small bits of organizing tissue from species with eyes to embryos of the blind forms can recruit host tissue to build a complete functional eye — that tells you the genes are still there. A comparison of gene expression patterns between the two also reveals that the blind species actually upregulates a majority of its developmental genes. Contrary to what Luskin claims, this is a positive change in development, not a loss, but an active suppression of eye expression.
What's actually going on is that there is an increased expression of a gene called Sonic hedgehog, which causes an expansion of jaw tissue, including both the bones of the jaw and the array of sensory structures on the ventral surface — this is an adaptation that produces stronger jaws and more sensitive skin, what the fish finds useful when rooting about in the dark at the bottom of underground rivers to find food. The expansion of Shh has a side effect of inhibiting expression of another gene, Pax-6, which is the master regulator of eye development. Loss of eyes is a harmless (if you're living in the dark) consequence of selection for better tactile reception.
Pathetic, isn't it, how abysmally wrong Luskin can be? His conclusion is even sillier.
Meanwhile, ID proponents seek to explain a far more interesting aspect of biological history: the origin of new complex biological features. Despite his quotation of Michael Shermer on the evolution of the eye, Hitchens has yet to do that.
Actually, despite claiming that ID proponents are trying to explain the origin of biological features, Luskin hasn't used this opportunity to even try. He can't; "Designer did it" is not an explanation.