Blind salamanders and natural selection

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Christopher Hitchens has a "Eureka!" moment.

But what of the creatures who turned around and headed back in the opposite direction, from complex to primitive in point of eyesight, and ended up losing even the eyes they did have?

Whoever benefits from this inquiry, it cannot possibly be Coulter or her patrons at the creationist Discovery Institute. The most they can do is to intone that "the Lord giveth and the Lord taketh away." Whereas the likelihood that the post-ocular blindness of underground salamanders is another aspect of evolution by natural selection seems, when you think about it at all, so overwhelmingly probable as to constitute a near certainty.
Hitchens is right that the presence of vestigial organs is compelling evidence for evolution. As Dawkins put it, "Why on earth would God create a salamander with vestiges of eyes?" But natural selection may not be the mechanism responsible for the change.
Eyes are complicated organs. The correct expression of many genes is required for them to develop and function properly. If a mutation occurs in one of those genes in a salamander living in absolute darkness, it's not likely to affect its ability to survive or reproduce. Such a mutation is selectively neutral.

Most mutations are lost quickly after they occur, but for a neutral mutation, there's a chance that it will sweep through the population so that all individuals will carry it.1 Given that there are a lot of different ways that eyesight could be impaired, given that natural selection isn't acting to eliminate mutations that impair eyesight for salamanders living in absolute darkness (as it is for those living above ground), and given that the blind salamanders have been living deep in caves for a very long time, it's not at all surprising they have only vestigial eyes. We don't have to postulate that there's an advantage to blindness, only that there's no disadvantage.

Bottom line, though. Vestigial organs are evidence for evolution, specifically that present day organisms have the features they do, in part, because they inherited them from their ancestors.2

1There's even a chance that a mutation that is disfavored by natural selection will become fixed, but it's smaller than the chance that a neutral mutation will be fixed.
2Thanks to Panda's Thumb for the link.

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