But humans—and most other vertebrates for that matter—do not "begin development looking like embryonic fish" and second humans do not have gill slits at any embryonic stage.
The Coyne apologist objected because Coyne is well aware that those "gill slits" are not literally slits. Rather, they are grooves between the branchial arches which Coyne simply refers to as gill slits. The apologist writes:
He [Coyne] introduces branchial arches starting on p. 78: "Perhaps the most striking fish-like feature is a series of five to seven pouches, seperated by grooves, that lie on each side of the embryo near its future head. These pouches are called branchial arches, but we'll call them "arches" for short. [...] As fish and shark embryos develop, the first arch becomes a jaw and the rest become gill structures: the clefts between the pouches open up to become the gill slits, [...]. But in other vertebrates that don't have gills as adults, these arches turn into very different structures - structures that make up the head." And there's a figure with a shark and a human embryo, with an arrow pointing at the pouches of both embryos labelled "branchial arches".
In other words, Coyne is not so uninformed as to think that this stage of human development sports actual slits. Of course, but that was not my point. I have no doubt Coyne is a smart person and knows his biology. The problem is he is an evolutionist and as a consequence he makes a mockery of science. The problem, in this case, is not so much with his use of the word "slit" but with his use of the word "gill." More on this below, but first, the apologist concludes:
In my opinion, if you actually read the book instead of looking for a quote that can be misrepresented, than there's no way in which you can claim that Coyne actually means that human embryos have gill slits like those in adult fish. Even embryonic fish do not have open gill slits like an adult fish.
If evolutionists are searching for misrepresentations they should look closer to home. As usual, evolution is guilty of what it accuses others of doing. Coyne and evolutionists misrepresent science when they contort the embryonic evidence in an attempt to find support for their absurd ideas. And yes, I did read Coyne's book. It is the apologist who apparently has not read it since he quotes from the Google books version. Here is what I wrote in an earlier blog:
Some books are difficult to read because they are not well written while others are difficult to read because the ideas don't make sense. There is turgid prose and then there is turgid logic. I have finally finished Jerry Coyne's Why Evolution is True which, if Coyne was not a leading evolutionist of international repute, I would have dismissed after the first chapter. Coyne is an excellent writer but Why Evolution is True is a laborious read because it doesn't make much sense. Thumbing through my copy, I see page after page with margin notes indicating various fallacies and inconsistencies. More later on this, but for now here are some aggregate statistics.
By my count Coyne affirms the consequent 21 times throughout Why Evolution is True. He begs the question 33 times and makes 35 theological claims. Coyne fails to mention important scientific problems that bear on his points 31 times.
I finally tired of counting but the volume is a veritable treasure trove of evolutionary thought. There are the usual just-so stories, unfalsifiable claims, presumptuous statements, ad hominem criticisms and so forth. In the evolution genre you can hope for quality writing but it seems there is no escaping problems with the content of that writing.
Yes, I read the book.
Now what's wrong with Coyne's description of vertebrate development? First, vertebrates simply do not begin development looking like embryonic fish. This is what evolutionary theory predicts, and what evolutionists want to see. Yes there are similarities, but this is yet another case of theory-driven, rather than data-driven, thinking.
Also, Coyne describes development as the usual just-add-water process so typical in evolutionary thought. Life just happened to arise, so evolutionists view it as simple. Coyne writes:
In fish and sharks, then, the development of gills from the embryonic arches is more or less direct: these embryonic features simply enlarge without much change to form the adult breathing apparatus. 
Sure, just add a few nerves, blood vessels, bone and cartilage and poof, there you have gills.
Next, Coyne begins immediately to refer to the grooves between the branchial arches, in human embryos, as gill slits. But humans don't have gills as adults. Humans never have gills at any stage. So there is no basis for referring to the grooves as "gill slits" aside from the silly evolutionary mandate that the branchial arches are an evolutionary leftover that today just happen to form structures such as the middle ear, larynx, Eustachian tube, and arteries and nerves.
So Coyne interprets the evidence according to the theory he thinks is true, and then presents the ludicrous interpretation as powerful evidence for the theory. I would have been astonished if I hadn't seen such circular reasoning so many times before in the evolution genre. There are other problems with this section, which I describe here. Once again evolution makes a mockery of science.