From a reader:
I'm the TA for an Intro to Philosophy course. This week, we're discussing Paley's Design Argument, Darwin's argument(s), and the evidence that favors Darwin's arguments over Paley's.
Here's my question: I had heard that mammals during early stages of development have vestigial gill slits. But I'm having a hard time finding legitimate documentation of this. Do you know either way? If not, do you know of any other good cases of vestigial traits in humans? Unfortunately, as I'm sure you realize, there are people whose brains simply cannot process evidence for common ancestry, so I try to make the examples as anthropocentric as possible, figuring those examples have at least some shot of convincing.
The "gill slits" in a human embryo are the pharyngeal arches and clefts, which ultimately develop into many different tissues of the head and neck. They are homologous to pharyngeal arches at the same embryonic stage in other vertebrates, but they do not have any role in respiration and do not include any true gill-like tissue. P.Z. Myers has written an accessible account of the history and current understanding of the gill slits (http://www.talkorigins.org/faqs/wells/haeckel.html). They are misleading as an example of evolution because they are not vestigial gills, however, the occurrence of the same structures in embryos of all vertebrates does reflect their common descent.
The wiki page on "human vestigiality" is not bad as a summary of traits that humans have in common with other animals but are basically useless in us. (http://en.wikipedia.org/wiki/Human_vestigiality) For me, the clearest and best examples of common descent are pseudogenes (example: GULOP, which makes vitamin C in most mammals, in anthropoid primates and tarsiers the gene still exists but is nonfunctional, broken). Also, LINE insertions -- a kind of retrotransposon that makes up a large fraction of junk DNA, humans share many nonfunctional insertions with chimpanzees, gorillas, etc., even though they have no function.
Also, a better anatomical example is the recurrent laryngeal nerve -- which takes a path that doesn't make any anatomical sense, except when you consider our ancestry in animals with very different configurations of head and neck: (described well by Jerry Coyne http://geophagus.wordpress.com/2009/07/11/why-evolution-is-true/) It originates in the sixth branchial arch of the embryo, which makes this a natural example to follow up the "gill slit" argument -- a real homology that is not a superficial similarity.
Hope that helps you. The classic response to the Paleyan argument in evolutionary biology is the long list of examples of poor design. Of course, a clever person can often argue that something that works badly is nevertheless well-suited for a vestigial purpose. That makes the DNA comparisons often much more persuasive.