It seems that Intelligent Design advocates have challenged PZ Myers to answer '10+1' questions about evolutionary biology, while he's on an upcoming visit to Glasgow. PZ's published the list here. One in particular caught my eye, because it mentioned lungs (the subject of a recent post of my own), so I thought I'd have a crack at answering it myself.
9) If, as is often claimed by Darwinists, the pharyngeal pouches and ridges are indeed accurately thought of as vestigial gill slits (thus demonstrating our shared ancestry with fish), then why is it that the ‘gill-slit’ region in humans does not contain even partly developing slits or gills, and has no respiratory function? In fish, these structures are, quite literally, slits that form openings to allow water in and out of the internal gills that remove oxygen from the water. In human embryos, however, the pharyngeal pouches do not appear to be ‘old structures’ which have been reworked into ‘new structures’ (they do not develop into homologous structures such as lungs). Instead, the developmental fate of these locations includes a wide variety of structures which become part of the face, bones associated with the ear, facial expression muscles, the thymus, thyroid, and parathyroid glands (e.g. Manley and Capecchi, 1998).
Let's get the really glaring error out of the way first. Our questioner says that pharyngeal pouches "do not develop into homologous structures such as lungs." Bzzzzzzzt! Wrong! Lungs are not homologous to gill slits - they do not have anything approaching a common evolutionary history. I guess you could describe lungs & gills as analogous, because they are both involved in gas exchange, but that's as far as it goes. Lungs formed as outpocketings from the gut, not from the pharynx.
Down to the meatier stuff. The questioner is happily conflating pharyngeal pouches with gill slits, presumably so that s/he can set up that 'gills -> lungs' strawman. Pharyngeal pouches are found in some form in all chordates, even if only during embryonic development. As the name suggests, they are outpocketings from the pharynx. But not all of them pierce the body wall, or function in gas exchange. In cephalochordates like Branchiostoma (personally I find the old name Amphioxus more euphonious), the pouches become slits that pass through the pharynx wall & open into the surrounding body cavity (the coelom). These structures do not function in gas exchange - this takes place across the thin epidermis that covers the animal's body & lines its coelom (which is open to the sea). Instead, the pharyngeal slits act as a filter-feeding mechanism, trapping food particles from the current of water flowing over them. The same is true for sea squirts.
Yes, in fish the pharyngeal pouches go on to push through to the outside of the body, and the tissues between the 'slits' develop into the gill bars of bone or cartilage that support the delicate filaments of the gils themselves. Those gill bars are important, because we can trace their developmental fate, not just in fish but in frogs, reptiles, birds and mammals. And what do we find?
Jawless fish, aka agnathans - like lampreys - have mouths but (rather counterintuitively) no jaws. Juveniles are filter-feeders, just like Branchiostoma, but adult lampreys show vampiric tendences, latching onto passing fish with their toothy lips and rasping at the prey with a tooth-bearing tongue until they can suck at its blood. But embryological studies show that the first two sets of gill-bars in agnathans are homologous to the jaws of all other fish - they were co-opted for another function, a very long time ago indeed. The first set formed the 'mandibular' bones of the jaw, while the second is called the hyo-mandibular arch & helps to link a fish's jaw to its skull. One explanation for this co-option is that it involved a change in Hox gene switching, opening up new ways of getting food. (A mutation, in other words. Which pretty much negates the tired old contention, revived in another of those 10+1 questions, that mutations are always harmful.)
And we can trace the fate of other sets of gill bars - and the associated circulatory loops - in frogs and reptiles, birds and mammals. The pharyngeal pouches are homologous to the various small glands that you find in the neck (thymus, thyroid, and parathyroid glands). The cartilage of trachea and larynx are ultimately derived from the gill bar tissues. And remember the hyomandibular arch in fish? It's ended up as the stapes in your middle ear.
Oh yes, I mentioned the plumbing. In fish, each gill slit has an accompanying set of blood vessels (5 in most sharks - at Massey we used to dissect them out as part of first-year bio labs). Lewis Held (2009) comments that
Human embryos go to the trouble of making five pairs of aortic arches (which once sent blood to five pairs of gills) but then destroy two of them completely**. This Sisyphean stupidity only makes sense as a historical constraint: it must have been genetically easier to reconfigure the existing plumbing than to scrap it altogether and start afresh.
(** The remaining aortic arches become the vessels that take oxygenated blood to the lungs, head, and body.)
Lewis Held (2009) Quirks of human anatomy: an evo-devo look at the human body. Cambridge University Press. ISBN 978-0-511-59384-0 (e-book, Kindle edition)