Charles Darwin once said that he thought the evidence from the comparative anatomy of embryos was “by far the strongest single class of facts” in favor of common descent (Darwin, 1860) and while it has since been eclipsed by genetics, it remains one of most compelling subsets of evidence for evolution. And perhaps the single most striking detail in the comparative embryology of vertebrates, are the structures colloquially known as “gill slits”.  

Embryonic “gill slits” or “branchial clefts” (branchia is Greek for gill) or more properly pharyngeal clefts (grooves, folds, etc.) are part of what is called the “pharyngeal apparatus” found in front (ventral) and sides (lateral) of the head/neck region of all vertebrates in the “pharyngula stage” of development. In “fish”, and the larva of amphibians, these develop into respiratory organs used to extract oxygen from water while in amniotes (“reptiles”, birds and mammals) they are modified into other structures.

Before I go on, a brief digression about “fish”. Throughout this article I will often use “fish” in the generic sense; but it should be noted that the term as it is commonly used—to refer to any vertebrate that swims in the water, has fins and gills—is not a valid scientific classification. This is because the three main types of animals commonly called “fish” —the Chondrichthyes (sharks, rays, skates and chimaeras), the Actinopterygii (ray fined fish, which constitutes the majority of living fishes), and the Sarcopterygii (lobe fined fish, the group from which four legged land animals, i.e. tetrapods, evolved)—are not a monophyletic group. That is they are not very closely related to each other despite some of their outward similarities (like gills). For example the living Sarcopterygii, lung fish and coelacanths share a more recent common ancestor with us (and all tetrapods) than with the other “fishes”.

OK, so the “pharyngeal apparatus” consists of a series of paired pharyngeal arches and fissures which develop on the exterior with a corresponding set of pharyngeal pouches on the inside of the throat, separated from the external fissures by a thin membrane (more on the details in a moment). And in fact the possession of these structures at some point in development, along with a hollow dorsal nerve cord, a notochord and a post anal tail, are the defining characteristics of the phylum chordata to which we and all other vertebrates belong.

Please note that the above illustration is diagrammatic and not intended to be photographically accurate (I have to say that lest I be accused by creationists of conveying a fraud). Below are actual photographs of both a skate embryo and a human embryo for comparison. Also note: the gill structures in the embryos of Elasmobranch fishes—the subdivision of Chondrichthyes which contains sharks, rays and skates—are much less derived than in other “fishes” and therefore generally more similar to those of amniote embryos than the corresponding structures in the bony “fishes” (which are significantly modified).

The first of the arches, the mandibular arch, forms the jaw in all jawed vertebrates (Gnathostomes). Most vertebrates develop a total of six arches but the full complement is usually only retained into adulthood by hexanchiform sharks. Hexanchiformes are very plesiomorphic which means that they are more like earlier types of sharks.  Some species of hexanchiformes even develop a seventh arch. Likewise the extant jaw-less vertebrate, the lamprey, also have seven gill openings.

In human embryos the four arches are visible and take shape at around 4th week of development; the 5th arch is transitory while the 4th and 6th fuse in to one.  And as with most terrestrial vertebrates they are modified during embryological development into non-gill related structures in the adult.

The standard evolutionary explanation the formation of the pharyngeal apparatus in the embryos of amniotes is of course that their distant ancestors were in fact aquatic, gill bearing, organisms and that the remnants of embryonic gill-like structures have been preserved in their embryological development. And though these structures in the embryos of amniotes never develop into, actual gills, they have historically been informally referred to as “gill slits” due to their overall anatomical agreement with the corresponding structures of aquatic vertebrates which do develop into gills.

As you might imagine the fact that so called “gill slits” are found in amniotes embryos has been a big bugaboo for creationists, driving them to put a lot of effort over the years into minimizing the similarity of these structures (Price, 1924), and into denouncing any scientist who talks about them.

This has led to the development of a fairly standard boilerplate on the subject among creationists. Here are several prime examples, the first being from Drs. Elisabeth & Tommy Mitchell who are from the young Earth creationist organization Answers in Genesis and are both ostensibly medical doctors (one is even supposed to be an obstetrician):

The so-called gill slits of a human embryo have nothing to do with gills, and the human embryo does not pass through a fish stage or any other evolutionary stage. The development of the human embryo reveals steady progress toward a fully functional human body. Never in the course of development does a human embryo absorb oxygen from water as fish do with gills. (The human embryo is fully supplied with oxygen through the umbilical cord.) In fact, these “gill slits” are not even slits.

So what are these misnamed structures? Actually, they are nothing more than folds in the region of the tiny embryo’s throat. By the 28th day of life, the embryo’s brain and spinal cord seem to be racing ahead of the rest of the body in growth. Therefore, for a time, the spinal cord is actually longer than the body, forcing the body to curl and flexing the neck area forward. (This curled embryo with the long spinal cord is mistakenly accused by some people of having a tail.) Just as many people develop a double chin when bending the neck forward, so the embryo has folds in its neck area due to this flexing.

[…] The outer and middle ear as well as the bones, muscles, nerves, and glands of the neck develop from these folds. Only superficially do these important folds ever resemble gills; the pharyngeal arches are no more related to gills than stars are to streetlights. (Mitchell & Mitchell 2007, emphasis mine)

Here we have “creationist anatomist” and veteran antievolution warrior, Dr. David Menton, also from Answers in Genesis:

HUMAN EMBRYOS HAVE “GILL SLITS” AT ONE STAGE OF THEIR DEVELOPMENT PROVING THAT MAN EVOLVED FROM AQUATIC, FISH AND AMPHIBIAN, ANCESTORS.

You can hardly attend high school or college now days with out hearing or reading this “whopper”. In fact, neither gills nor their slits are found  at  any  stage  in  the  embryological development of any mammal including man. The folds in the neck region of the mammalian embryo, that are erroneously called “gills”, are not gills in any sense of the word and never have anything to do with breathing. They are merely flexion folds, or wrinkles, in the neck region resulting from the sharply down turned head and protruding heart of the developing embryo. These folds eventually develop into a portion of the face, inner ear, tonsils, parathyroid and thymus. No reputable medical embryology text claims that there are “gill slits” in mammals.

Still, the gill slit myth is perpetuated in many high school and college biology text books as “scientific evidence” for evolution. Even Dr. Spock in his book ‘Baby and Child Care’ claims that “as the baby lies in the amniotic fluid of the womb, he has gills like a fish.” Perhaps the “gill slit” myth continues to be taught because there is no better  “evidence” for evolution. How many of you were taught the gill slit myth in school?? (Menton 1991, emphasis mine)

Next we have intelligent design creationist Dr. Cornelius Hunter, a biophysicists and Fellow at the Discovery Institute’s Center for the Renewal of Science and Culture:

Now what’s wrong with Coyne’s [biologist Jerry Coyne (2009)] 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.

[…] 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. (Hunter 2010, emphasis mine)

Finally we have another intelligent design creationist, Dr. Jonathan Wells a Senior Fellow of the Discovery Institute’s Center for the Renewal of Science and Culture, and ostensibly a developmental biologist:

Midway through development, all vertebrate embryos posses a series of folds in the neck region, or pharynx. The convex parts are called pharyngeal “arches” or “ridges,” and the concave parts are called pharyngeal “clefts” or “pouches.” But pharyngeal folds are not gills. They’re not even gills in pharyngula-stage fish embryos.

In a fish, pharyngeal folds later develop into gills, but in a reptile, mammal, or bird they develop into other structures entirely (such as the inner ear and parathyroid gland). In reptiles, mammals, and birds, pharyngeal folds are never even rudimentary gills; they are never “gill-like” except in the superficial sense that they form a series of parallel lines in the neck region.

[…] In other words, there is no embryological reason to call pharyngeal pouches “gill-like.” The only justification for that term is the theoretical claim that mammals evolved from fish-like ancestors.

[…] The only way to see “gill-like” structures in human embryos is to read evolution into development. (Wells 2000, pp.105-106, emphasis mine)

So,  there are apparently at least three main points the creationists want to make:

1. Pharyngeal structures of amniote embryos never function as gills and therefore should not be referred to as “gill slits”.
2.  Whatever resemblance to the gills of aquatic vertebrates the pharyngeal structures of amniotes has, it is superficial.
3. Seeing the pharyngeal structures of amniote embryos as being gill-like and calling them gill-slits despite their not functioning as gills is “reading evolution into development”.

Obviously there is some overlap there but let us examine each in turn.

Number 1: Gill slits by any other name…

This is essentially a semantic argument about what we call these structures in vertebrate embryos combined with a straw man argument and this combination is far from being new.

If you were only to read creationist sources on this subject you would come away with the strong impression that the controversial mid-19th century German biologist Ernst Haeckel (1834–1919), fabricated the idea that amniote embryos have “gill slits” out of whole cloth, sometime in the 1860’s in order to prop up Darwin’s failing and unfounded idea of evolution (Morris 1989)(Grigg 1996)(Harrub 2001)(Butt 2010)(Sherwin 2011).

However the truth is these structures were originally described in birds and mammal embryos in 1825 by German anatomist/embryologist Martin Heinrich Rathke (1793-1860) (Rathke 1825a & 1825b). Rathke referred to them both as “Schlundspalten” (“throat clefts”) and “Kiemenspalten” (“gill clefts”), meaning that, by modern creationist estimation, they have been mislabeled from very moment of their discovery (Tuttle 1884, pp.111-112) (see also Ascherson 1848). And modern creationists were not the first to raise such semantic objections:

The discovery and true interpretation of the branchial fissures in the embryo of the higher vertebrata belongs to Rathke, […] Shortly after this, Huschke illustrated the matter particularly in the chick […]. Very recently Reichert has pursued the subject deeply; he calls the branchial arches visceral arches―Müller’s Archiv für 1837. His assertion, that these are not branchial arches, is a mere dispute about a word; it was never imagined that the parts in question were proper gills; but they are vascular arches, which are in every respect analogous to the vascular arches of the gills of fishes, only not branching like these. (Wagner 1844, p. 111, emphasis mine)

What Rudolf Wagner said 166 years ago (please note the date) holds just as true today; no one is claiming that ‘gill slits’ ever function as gills in amniotes. That creationists continually harp on this is simple straw man bashing as no scientist, that I am aware of, save one—and I will discuss him later—has since Wagner wrote that statement, claimed that they do.

So that leaves us with the semantic objection to the informal use of the term gill slits to refer to these structures, which is a bit like getting worked up over calling the human coccyx a ‘tailbone’ because it never functions as a proper tail in humans.

Oh wait, they probably don’t like that either.

A bit more seriously, how about the tiny vestigial wing buds of kiwis (genus Apteryx, a flightless birds found in New Zealand)? They are clearly not used for flight at any point in the life of a kiwi. Is it inappropriate to refer to them as wings?

Or how about something a little closer to the subject at hand, the hind limb buds in the embryos of cetaceans (whales & dolphins)? In cetaceans they normally do not develop into hind limbs and are simply reabsorbed into the body. Occasionally whales and dolphins are born with external hind limb structures however these are not usually paired, symmetrical, and well formed. But they occur and they develop right were they should be if whales were to grow hind legs.

These structures will never be used to walk or even swim, so should comparative developmental biology texts be forbidden to use the term ‘hind limb bud’ when referring to these structures in cetaceans?

Of course not.

We can, informally, call pharyngeal clefts “gill slits” in the same way we call kiwi ‘wings’, wings, or cetacean “limb buds”, limb buds, because despite the fact they no longer develop into functioning wings, limbs, or gills, in the organisms that bear them, they are clearly homologous to those characters in organisms were they do retain those functions.

The creationist objection that referring to pharyngeal structures as gill slits assumes evolution (point #3), if valid, would apply equally to kiwi wings and whale hind limb buds since the major distinction between these various homologous structures, from an evolutionary point of view, is merely time.  However one will search in vain to find websites angrily denouncing the use of the term “wings” or “limb buds” to describe those structures. [Of course now some joker will spend an hour Google-mining just to find the one tin-foil hat wearer out there that has made this objection just so they can throw it in my face.]

I would suggest that the reason we don’t see creationists making a stink about these other terms is that they don’t touch on humans the way the presence of “gill slits” in amniote embryos does (given that we are amniotes) and the preservation of humans as special divine creations is their primary (theological) concern.

“Wait a minute!”, object the creationists, “You’ve been doing number three this whole time!”.

Have patience, I’ll get to that.

Number 2: Are “gill slits”, slits? And are the similarities between gill slits and pharyngeal structures superficial?

Regardless of what we call these pharyngeal structures in amniote embryos, do they in fact bear any similarities to the gills of “fish”, or at least the pharyngeal structures in “fish” embryos that become gills? Statements from creationists like those quoted above give the impression that pharyngeal arches and clefts were little more than “flexion  folds” or “parallel lines” in the ectoderm (what becomes the skin amongst other things) of the embryo; like the ridges you might get in a garden hose that has been sharply bent.

But ask yourself this, if that is all they were, if they were really just like a kinked hose or a double chin, is it probable that biologists would have been so impressed by these structures that they would consider them one of the defining characteristics of the phylum chordata? As usual, the story is a lot more complex than creationists let on.

The fact is, when we look at the details of these structures, we find not a mere superficial resemblance but rather a collection of anatomical similarities between the gill arches of “fish” and the embryonic pharyngeal structures of amniotes.

The pharyngeal arches, which precede  each of the cleft/pouches, are quite a bit more than simple fold ridges in skin as they contain a whole set of elements; skeletal, muscular, neural, and circulatory. At core of each of the arches is a cartilaginous element which is flanked by an aortic arch (blood vessel), cranial nerves and muscle elements.

Here is an illustration that I grabbed off the ‘interwebs’ and modified to show the relationships of the different elements found in the pharyngeal structures of vertebrate embryos:

Clefts & Pouches

Creationists are fond of repeating that in amniotes, “gill slits” are not only not gills, they’re not even slits. And they are partly correct if by “slit” one means an unobstructed opening from the outside of the neck region to the inside the of throat of mammal embryos. That is, they are technically correct as far as normal mammal development goes, however this is not the case with all non-“fish” vertebrates, nor is it always the case with mammals including humans.

In most ‘normal’ amniotes, including we humans, the only thing keeping us from having at least one open ‘slit’ in our first pharyngeal clefts are the thin membranes of skin, the tympanic membranes, or ear drums. Without your ear drums you would have open channels from your outer ears, through your middle ears and Eustachian tubes, into your throat.

As for other pharyngeal clefts, some of these do open completely in the larva of some amphibians who breathe via gills just as “fish” do. Furthermore the “post ear” pharyngeal clefts also open temporarily in some “reptiles” and birds only to re-close in the course of normal development.

So in the case of some amphibian they are gill slits and in some “reptiles” and birds they are actual slits (openings into the throat).

And while it is true that mammals (including humans) do not normally possess literal ‘slits’ (openings) in the neck region, occasionally individuals with abnormal development do. There have been cases where individuals have been born where, for example, one or both of their second pharyngeal clefts perforates and remains open after their birth (see examples here, here and here). This phenomenon (atavism), is similar to the cases where whales born with hind limbs.

Pharyngeal arches

Each pharyngeal arch sports a cartilaginous bar, the first (mandibular) arch, as was noted earlier, develops into the jaw bones of all jawed vertebrates. In “reptiles” and birds this constitutes multiple bones of the lower jaw; while in mammals it develops into the singular lower jaw bone (the mandible) and two of the bones of the middle ear (the incus and the malleus). See: “Evolution of mammalian auditory ossicles“

For more on the evolution of the mammalian jaw and ear bones, see:

• “An Earful of Jaw” (1990) by Stephen Jay Gould
•  “Intermediate and transitional forms – Reptile-mammals” (1999-2012) by Douglas Theobald
• “Evolution of mammalian auditory ossicles” (Wikipedia)

In “fish” the other arches support the gills while in amniote they become modified into other structures in the neck. For example the second arch develops into the hyoid bone in the throat and the stapes in the ear of mammals.

Arches color legend: 1st = I, 2nd = II, 3rd = III, 4th = IV, 6th = VI

Aortic arches

Running parallel to each cartilaginous bar in the pharyngeal arches are arteries called the aortic arches. In “fish” and amphibian larva they route blood coming from the heart through the gills (where it dumps CO₂ and pick up O₂) and out to the dorsal aorta.

Likewise the aortic arches of amniote embryos route blood coming from the heart around the neck region through to the dorsal aorta. However unlike “fish” and amphibians they never develop the fine capillaries and gill filaments of proper gills. Instead they are modified during development to other purposes. For example in tetrapods (amphibians, “reptiles”, birds & mammals) the 6th aortic arch develops into the pulmonary artery that connects to the lungs. Interestingly, this same arrangement is just happens to be found in the aortic arches of extant lungfish (dipnoans)(Kardong 2009, p.456) which based upon comparative anatomy and genetics (Venkatesh et al. 2001) (Takezaki et al. 2004) are part of the group of “fish”, Sarcopterygii, which, as I explained at the beginning, is the group of “fish” most closely related to tetrapods.

From Eastern Kentucky University BIO 342 Comparative Vertebrate Anatomy site, with modifications (I colored and labeled the hearts).

Note the relative position of the heart to the pharyngeal arches in the diagram of amniote embryo shown above; just below and to the rear of the aortic arches. In “fish” development the heart maintains this relative position to the pharyngeal structures—just below (ventral) and to the rear (posterior) of the gills. In amniotes though, the pharyngeal structures of amniote embryos develop into the jaw and neck and the heart becomes separated from neck region of the body in the adult (this will be of significance when we next look at nerves), moving down into the chest.

Nerves

The first pharyngeal arch, which as already stated, develops into the jaw bones in all gnathostomes (jawed vertebrates) which is innervated by the 5^th cranial nerve (the trigeminal) which connects the brain to the jaws and parts of the face.

Another nerve of interest is 10th cranial or vagus nerve. In “fish” this comes out of the base of the brain and connects to various organs in the body occasionally sending off branches along the way.  One of these branches, the 4th, innervates the gills of the 6th pharyngeal arch in “fish”; which is a pretty straight path from the top (dorsal) part of the “fish” to the bottom (ventral) part (see the picture below).

However, as we saw earlier the in mammals the 4th and 6th pharyngeal arches fuse—after the transitory 5th arch is reabsorbed. The 4th/6th arch, modified by development then contributes to the formation of the larynx. The trick is that when the extended neck evolved in amniotes and the 4th branch of the vagus nerve—now called the recurrent laryngeal nerve—got hooked by the 6th aortic arch and dragged down into the chest, changing what was a fairly straight shot along the 6th gill arch in “fish”, into a circuitous route wherein the vagus nerve come out of the base of the brain travels down into the chest, loops around the pulmonary artery and then goes back up the neck into the larynx.

This has led to a laryngeal nerve of comic proportions in giraffes.

If you’re not squeamish and you’d like to see this for yourself, the excellent British television show Inside Nature’s Giants did a dissection of a giraffe in their 4th episode, highlighting its recurrent laryngeal nerve (at 16:38); I cannot recommend this program highly enough.

Perhaps it’s not surprising then, that giraffes don’t vocalize very much. By the time the signal to make a noise travels from their brains down their necks and back up again they’ve forgotten what they were making noises about!

In any case, there is no obvious sense to this state of affairs from a designed from scratch, engineering point of view, but it makes perfect sense if amniotes are opportunistically modified “fish”.

Physiology, Genetics

Comparisons between pharyngeal arches in “fish” and amniotes extend beyond their gross anatomy; there are also shared physiological and genetic similarities.

For example, while it is universally admitted that amniote embryos don’t use their “gill slits” to breath, there is at least one other physiological function originating in the pharyngeal apparatus that is conserved between “fish” and amniotes; regulating calcium salts (a major component of vertebrate bones). “Fish” regulate the amount of calcium in their bodies using their gills. Amniotes do this by secreting hormones from their parathyroid glands which just happens to develop from the 3^rd and/or 4^th embryonic pharyngeal pouches (Okabe & Graham 2004).

For more see:

• Deep homologies in the pharyngeal arches on Pharyngula

• Human parathyroid probably evolved from gills on biochemist.org

At the genetic level there are two significant families of genes (Hox & Dlx) which control the development of the pharyngeal region of all vertebrates.

A nested set of Hox genes control the development of the pharyngeal structures head to tail (anterior to posterior) from just after the first pharyngeal arch (Hunt et al. 1991) (Prince et al. 1998) (Kuratani 2004). And likewise a nested set of Dlx gene are expressed in the development of the pharyngeal structures in the front to back (ventral/dorsal) direction (Schilling 2003) (MacDonald et al., 2010).

Paleontology bonus section

It addition to all the interesting stuff above, the pattern of vertebrate embryological development—wherein an aquatic body plan is modified into one better adapted to a terrestrial environment—roughly matches that of the fossil record (“fish” first, amphibians and amniotes later).

The first chordates to appear in the fossil record were the cephalochordates, small fish-like organisms that lacked both jaws and true head; much like the living Branchiostoma which feeds by filtering water through its gills. Thereafter chordates appear in the fossil record in a definite pattern (please note that this is highly simplified):

• Chordates with true heads (Craniates) but remained jaw-less similar to the living hagfish.
• Basal jawless vertebrates (Agnathans) similar to the living lamprey.
  • • The larvae of lamprey (ammocoetes) physically resemble Branchiostoma and filter feed via their gills in a similar manner.
• Various “fishes” with jaws (Gnathostomes).
  • • The jaws of some early Gnathostomes (Acanthodians) resemble enlarged gill arches.
• Tetrapod like fish (Tetrapodomorpha, a sub group of the Sarcopterygii mentioned earlier).
• Basal tetrapods (amphibian-like animals).
  • • Some early tetrapods retained internal gills like those of Tetrapodomorpha fish.
• Basal amniotes (Anapsid “reptiles”)
• Basal Synapsids (the ancestors of mammals) and Diapsids (the ancestors of “reptiles” and birds).
• Basal mammals & birds.
  • • Basal mammals layed eggs much like those of diapsids; monotreme mammals still do.

[Please note that the time ordered pattern of change in the fossil record, i.e. faunal succession, was a well established fact before Darwin published On the Origin of Species (1859). A fact established by geologists who were primarily creationist in their outlook.]

At this point, I hope, I have demonstrated the creationist characterization of the pharyngeal structures of amniote embryos as being only superficially gill-like “folds” or “grooves”, is beyond misleading. There are a host of anatomical similarities: at least one shared physiological process (that is not respiration), and a detailed underlying genetic similarity as well; none of which creationists even attempt to give a coherent explanation for.

At least three of the five creationists (Elizabeth Mitchell, Menton and Wells) quoted above should have been, based on their education (an obstetrician, an anatomist and a developmental biologist), aware of the anatomical/embryological facts I documented above. Yet rather than relate any of this information to their readers they instead chose to tell them that pharyngeal clefts in amniote embryos are just superficial parallel lines in the neck or like the multiple chins a heavy set person might exhibit by tilting their head forward. Is this incompetence or dishonesty?

Setting aside the apparent creationist propensity to mislead by omission, what is their explanation for this pattern of embryological similarities amongst vertebrates that develop into very different adults?

When it comes to shared characteristics between different groups of organisms creationists are fond of drawing (deeply flawed) analogies between living things and manufactured items like automobiles. They argue that the reason organism A and organism B share a characteristic is not due to common ancestry, but rather common design in the same way cars produced by two different car companies both have four wheels and pistons etc. Of course if we take that analogy seriously the question that immediately comes to mind is that if amniotes are like automobiles, then why do they begin life by developing an embryonic form that more resembles a submarine?

In reality their use of the term “common design” does nothing but relabel our ignorance. Worse it creates whole new sets of unanswerable questions. Designed by whom? Was it one designer or many (as in car companies)? How did he/she/it/they implement their design? Why did they design things the way they did? Why did they implement their designs in the timetable that they did? And on and on.

It gets worse if the “designer” is transcendent and omnipotent. This makes the concept completely untestable (and therefore unscientific) as such a creator could create anything, in any way, for reasons known only to itself. It could create a world populated by evolutionarily impossible organisms like griffins and centaurs, or it could create a world that looks exactly as if it had evolved naturally without divine intervention (which is what appears to be the case with our world). There is no conceivable observation that could falsify “God did it”.

Contrast this with the theory of common descent. Under evolution these sorts of oddly cobbled together, jerry-rigged, structures, where things are modified from available materials to serve entirely different functions, are not just explicable, but demanded by the theory.

In other words, if evolution is true then we must find things like this.

Number 3: The only reason you’re calling them gill slits is because you’re presupposing evolution.

As for evolutionists supposedly seeing what they want to see, this argument is, falsified by the historical record. As noted earlier pharyngeal clefts in amniote embryos were called “Kiemenspalten” (gill clefts) by their discoverer, Rathke, in the 1820’s many decades before Charles Darwin brought evolution into the scientific mainstream.  And until 1859 the predominantly creationist scientists who studied these structures followed Rathke’s lead (* see footnote)(see also my friend Don Frack’s comment below):

However different the conformations of the Fish, the Reptile, the Bird, and the Warm blooded Quadruped, may be at the period of their maturity, they are scarcely distinguishable from one another in their embryonic state; and their early developement proceeds for some time in the same manner. They all possess at first the characters of aquatic animals; and the Frog even retains this form for a considerable period after it has left the egg. The young tadpole is in truth a fish, whether we regard the form and actions of its instruments of progressive motion, the arrangement of its organs of circulation and of respiration, or the condition of the central organs of its nervous system.

[…] Birds, though destined to a very different sphere of action from either fishes or reptiles, are yet observed to pass, in the embryonic stage of their existence, through forms of transition, which successively resemble these inferior classes. The brain presents, in its earliest formation, a series of tubercles, placed longitudinally, like those of fishes, and only assuming its proper character at a later period. The respiratory organs are at first branchiæ, placed like those of fishes, in the neck, where there are also found branchial apertures similar to those of the lamprey and the shark; and the heart and great vessels are constructed like those of the tadpole, with reference to a branchial circulation. In their conversion to the purposes of aerial respiration, they undergo a series of changes precisely analogous to those of the tadpole.

Mammalia, during the early periods of their developement, are subjected to all the transformations which have been now described; commencing with an organization corresponding to that of the aquatic tribes; exhibiting not only branchiæ, supported on branchial arches, but also branchial apertures in the neck; and thence passing quickly to the conditions of structure adapted to a terrestrial existence. The developement of various parts of the system, more especially of the brain, the ear, the mouth, and the extremities, is carried still farther than in birds. Nor is the human embryo exempt from the same metamorphoses; possessing at one period branchiæ and branchial apertures similar to those of the cartilaginous fishes,* a heart with a single set of cavities, and a brain consisting of a longitudinal series of tubercles; next losing its branchiæ, and acquiring lungs, while the circulation is yet single, and thus imitating the condition of the reptile; then acquiring a double circulation, but an incomplete diaphragm, like birds; afterwards, appearing like a quadruped, with a caudal prolongation of the sacrum, and an intermaxillary bone; and lastly, changing its structure to one adapted to the erect position, accompanied by a great expansion of the cerebral hemispheres, which extend backwards so as completely to cover the cerebellum. (Roget 1834, pp. 631-635, emphasis mine)

Please note that the above quote is from Animal and Vegetable Physiology Considered with Reference to Natural Theology, Vol. II of Treatise V of: The Bridgewater Treatise on the Power Wisdom and Goodness of God as Manifested in the Creation. As you might imagine, this was absolutely not a tome of atheistic evolution.

We shall now briefly trace the evolution of the respiratory apparatus in the embryo of the higher Vertebrata. […] At about the third day of the development of the chick, four pairs of clefts or transverse slits are observable behind the mouth, in the situation of the branchial apertures of fishes; and at the same time, the branchial vessels are developed from the aorta, as already described (§325). One of the apertures is intermediate between each pair of vascular arches just as in the gills of fishes and tadpoles. Nothing like branchial tufts, however, are developed; and the appearance described is very transitory, the vessels changing their direction and condition within two days. The development of perfect gills would have been useless, as the animal has not to maintain its own existence like the tadpole, but subsists, until the time of the perfect evolution of its respiratory system, upon the store of aliment furnished by the parent. It is evident, however, that the history of this evolution is so far the same as in Reptiles and Fishes. The lung first appears as a simple closed sac lying at the posterior and lowest part of the thorax; it soon becomes bifid, and presents a cavity, which does not, however, for some time communicate with the intestinal tube, the trachea and bronchi being last developed. The history of the evolution of these organs in the Mammalia is precisely analogous. It is usually at about the sixth of the period of uterine gestation that the rudiments of the branchial apparatus are seen, as marked by the shortness and thickness of the neck, the penetration of the sides of the pharynx by the branchial clefts, and the division of the aorta into vessels corresponding in number and distribution with the branchial arteries of fishes. These general features have been observed in the embryos of most orders of Mammalia, not excepting man himself; and they are probably common to all. A few days after the appearance of the fifth arch, which is the last developed, the neck begins to elongate, the apertures are closed gradually on the outside, while the vascular arches undergo those changes by which the permanent arterial branches arising from the heart are formed. The lungs in Mammalia are developed touch in the same manner as in Birds. They are not discernible before the period when the branchial apertures begin to close; a single mass is first perceived, which is soon divided into the rudiments of a right and left lung by a longitudinal groove; and the trachea and bronchi are subsequently developed as in birds. Scarcely a more beautiful illustration of the Unity of Design manifested in the creation of different classes of animals could be adduced than this hidden but not obscured correspondence… (Carpenter 1839, pp. 320-321, emphasis mine)

Please note that Carpenter’s repeated use of the term “evolution” here has nothing to do with evolutionary theory but rather is being used in the original sense of an “unfolding process”, as in embryological development. And of course as with Roget, Carpenter viewed these structures as an illustration of the “unity of design manifested in creation”. There is no reading evolution (in the modern sense) into the evidence there.

Perhaps the best example would be the zoologist/paleontologist Louis Agassiz (1807-1873) of Harvard University. Agassiz was a hard core (progressive) creationist who essentially believed that God specially created each species as they are (or were) throughout geologic time. However, despite his inveterate creationism he recognized the similarities between “fish” gills and the pharyngeal apparatus of amniote embryos. In fact Agassiz, a creationist, is the only scientist I have ever read that actually claimed that the embryos of amniotes have functional gills!

It may therefore be said with perfect propriety, that the higher Vertebrates undergo changes through which in different periods of their life, they resemble the lower ones; that there is a period when the young bird has the structure, not only the form, but the structure, and even the fins, which characterize the Fish. And of the young Mammals the same may be said. There is a period in the structure of the young Rabbit, (in which the investigations have been traced more extensively than in any other species,) when the young Rabbit resembles so closely the Fish, that it even has gills, living in a sac full of water breathing as Fishes do. (Agassiz 1849, p. 96, emphasis mine)

Again, Agassiz utterly rejected Darwin’s theory. For example at the conclusion of his review of Darwin’s On the Origin of Species he wrote that he considered the “transmutation theory” (evolution) to be “…a scientific mistake, untrue in its facts, unscientific in its method, and mischievous in its tendency.” (Agassiz 1860, p.154)

He never wavered from this position; nor did he apparently ever waver from his position regarding functional gills in amniote embryos:

I have myself watched carefully all the successive changes of development in the North American Axolotl, whose recently discovered metamorphoses have led to much discussion in connection with the modem doctrine of evolution. I can see no difference between this and other instances of metamorphosis. Certain organs, conspicuous in one phase of the animal’s life, are resorbed and disappear in a succeeding phase. But this does not differ at all from like processes in the toads and frogs, for instance; nor does it even differ essentially from like processes in the ordinary growth of all animals. The higher Vertebrates, including man himself, breathe through gill-like organs in the early part of their life.  These gills disappear and give place to lungs only in a later phase of their existence. Metamorphoses have all the constancy and invariability of other modes of embryonic growth, and have never been known to lead to any transition of one species into another. (Agassiz 1874, p. 9, emphasis mine)

The careful reader will note that in this quote Agassiz is actually calling these structures “gill-like” in the midst of denying that such things might be evidence for evolution!

Now, while Agassiz was wrong about “higher vertebrates” breathing through their “gills” (and again, he is the only scientist I have ever seen make this claim), he clearly recognized the existence of these gill-like structures even though he was as far as one could be from being an evolutionist. This and the previous early 19th century quotes clearly illustrates the fact that recognition of these embryonic structures in amniotes as being gill-like, even to the point of referring to them as gill or branchial clefts, can be done independently of the acceptance of evolutionary theory. It therefor does not follow that informally calling them “gill slits” is necessarily reading evolution into the evidence.

Amusingly while the creationist, Agassiz, had mistakenly claimed that amniote embryos breathe through their “gills”, the much maligned evolutionist Ernst Haeckel had this to say on the subject:

In all Vertebrata already discussed [lampreys, sharks, bony fish] we found that they either always breathed through gills, or at least did so in early life, as in the case of Frogs and Salamanders. On the other hand, we never meet with a Reptile, Bird, or Mammal which at any period of its actual life breaths through gills, and the gill-arches and openings which do exist in the embryos are, during the course of their ontogeny, changed into entirely different structures, viz. into parts of the jaw-apparatus and the organ of hearing. (Haeckel 1902, p.302, emphasis mine)

So let’s look at the historical score card, with all the creationist caterwauling about how pharyngeal clefts never function as gills in amniotes and how calling them “gill slits” is an atheistic evolutionary deception hatched by Ernst Haeckel, in mind.

I. Pharyngeal clefts were discovered and described in amniote embryos almost a decade before Ernst Haeckel was even born (1825 vs. 1834).

II. They were referred to as “gill clefts” by their discoverer, Rathke.

III. They were regularly called “gill clefts” or “branchial clefts” by creationist scientists in the 34 years between their discovery and the publication of Darwin’s On the Origin of Species (1859), demonstrating that referring to them in this manner is not simply a matter of reading evolution into the evidence.

IV. While creationist scientists commonly referred to the pharyngeal clefts of amniote embryos as “gill” or “branchial” clefts, they generally understood that they never function as gills.

V. There was one noted exception to number IV and it was arch creationist (pun intended) Louis Agassiz, not the evolutionist Ernst Haeckel (or any other evolutionist).

One, two, three, four, five strikes, you’re out!

As is so often the case, the creationists apparent lack of curiosity about the natural world and ignorance about the history and philosophy of science, especially where it pertains to evolutionary theory, has led them up a blind alley.

As I’ve shown, by the time Darwin published On the Origin of Species, creationist biologists had for years been talking about these curious structures in amniote embryos that look a lot like the gills of fish and attempting to explain why they might be that way (“Unity of Design” etc.). The evidence from embryology was not something concocted after the fact by Darwin and his supporters to prop up an a priori belief in evolution (that’s how modern creationists work). Rather what Darwin did was take facts that were already known and gave them a logical, coherent explanation.

All Darwin essentially said was: “Hey you know those embryonic things you’ve been wondering about? I think I have a better explanation for why they exist.”

Just as the concept of the geologic column, and the pattern of fossil record upon which it is based, came to be part of the supporting evidence for evolution—even though its originators were creationists—so too did the recognized and established facts of embryology in the early 19^th century.

Conclusion

As with so many other things about the natural world, creationists are simply in denial about the evidence from comparative embryology. They have no coherent, testable, alternative explanation. And their “information” regarding the subject is a muddle of half-truths, misinformation and (willful) ignorance, relayed in a fashion that raises the question as to whether incompetence or dishonesty is to blame.

Update

Intelligent design creationist Dr. Cornelius Hunter (quoted above) has attacked me (a “NCSE member” with a “fancy new blog”), or rather biologist Jerry Coyne because of me [???], oh, I dunno, go try and figure it out for yourself.

Footnote

* A few people have pointed towards apparent misspellings of words in these 19th century quotes, however these are the spellings given in the originals and not the result (as is usually the case) of my lack of typing, English and/or proofreading skills.

References:

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Agassiz, Louis (1860) “Prof. Agassiz on the Origin of Species”, The American Journal of Science and Arts, 2nd Series, Vol. XXX, pp. 142-154

Agassiz, Louis (1874) Evolution and Permanence of Type, p. 9

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