“Gill slits” by any other name…

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.

Copyright © 1999 McGraw-Hill Companies, Inc.

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).

(Gillis et al 2009, p.5721)

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:


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?

kiwi wing

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.

Copyright 2006, Dr. J.G.M. Thewissen

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:

Source bionalogy.com, with modifications.

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.

Cut-away diagram of the human ear structures including the tympanic membrane and eustachian tube.

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:

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.

(Stansfield 1977)


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

(Shubin 2009, p.92)

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).

Coyne 2009, p.83

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 3rd and/or 4th embryonic pharyngeal pouches (Okabe & Graham 2004).

For more see:

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

Kuratani 2004, p. 337 (fig. 3)

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).
  • Basal amniotes (Anapsid “reptiles”)
  • Basal Synapsids (the ancestors of mammals) and Diapsids (the ancestors of “reptiles” and birds).
  • Basal mammals & birds.

[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 19th century.


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.


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.


* 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.


Agassiz, Louis (1849) Twelve lectures on comparative embryology: delivered before the Lowell institute, in Boston, December and January, 1848-9, Redding & Co.

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

Ascherson, Ferdinand Mauritius (1848) “On Congenital Fistulæ of the Neck with a Succinct History of the Branchial Fissures in Mammals and in Birds” in Clay, Charles (1849) The British Record of Obstetric Medicine and Surgery for 1849, Vol. II

Butt, Kyle 2010 “Shubin’s Subtly Deceptive “Gill Arches”“, Apologetics Press (website) downloaded on 5-29-2012

Carpenter, William Benjamin (1839) Principles of comparative physiology, Intended as an Introduction to the Study of Human Physiology and as a Guide to the Philosophical Pursuit of Natural History, John Churchill, Soho

Coyne, Jerry A. (2009) Why Evolution is True, Viking

Darwin, Charles (1860) in a Sept. 10 letter to Asa Gray, published in Darwin, Francis (editor) (1896) The Life and Letters of Charles Darwin, Vol. II, New York: D. Appleton and Company, p 131.

Gillis, Andrew J., et al. (2009)”Shared developmental mechanisms pattern the vertebrate gill arch and paired fin skeletons“, Proceedings of the National Academy of Sciences, 106(14):5720–5724

Grigg, Russel (1996) “Ernst Haeckel: Evangelist for evolution and apostle of deceit“, Creation, 18(2):33-36

Haeckel, Ernst (1902) The History of Creation Vol. II (4th Edition), D. Appleton and Co.

Harrub, Brad (2001) “Haeckel’s Hoax—CONTINUED!“, Apologetics Press (website) downloaded on 5-29-2012

Hunt, Paul et al. (1991) “The branchial Hox code and its implications for gene regulation, patterning of the nervous system and head evolution”, Development; Supplement 2:63-77

Hunter, Cornelius (2010) “Why Coyne is False“, Darwin’s God (Blog), downloaded on 5-28-2012

Kardong, Kenneth (2009) Vertebrates: Comparative anatomy, function, evolution (5th ed.), McGraw-Hill, New York, NY

Kuratani, Shigeru (2004) “Evolution of the vertebrate jaw: comparative embryology and molecular developmental biology reveal the factors behind evolutionary novelty“, Journal of Anatomy 205(5): 335–347

MacDonald, R. B. et al. (2010) “Regulation of Dlx gene expression in the zebrafish pharyngeal arches: from conserved enhancer sequences to conserved activity”, Journal of Applied Ichthyology 26:187-191

Menton, David N. (1991) “Human Embryo “Gill Slits” During Development“, bestbiblescience.org (web page), downloaded on 5-28-2012

Mitchell, Tommy & Mitchell, Elizabeth (2007) “Something fishy about gill slits!“, Answers in Genesis; website

Morris, John (1989) “Does the Human Embryo Go through Animal Stages?Acts & Facts 18(8)

Okabe, Masataka & Graham, Anthony (2004) “The origin of the parathyroid gland“, Proceedings of the National Academy of Science 101(51):17716-17719

Price, George McCready (1924) The Phantom of Organic Evolution, pp. 157-159

Prince, Victoria E. et al. (1998) “Zebrafish hox genes: expression in the hindbrain region of wild-type and

mutants of the segmentation gene, valentine”, Development 125:393-406

Rathke, Martin Heinrich (1825a) “Kiemen bei Säugetier,” Isis(1825), 747-749;

Rathke, Martin Heinrich (1825b) “Kiemen bei Vögeln,” Isis(1825), 1100-1101.

Roget, Peter Mark (1834) Animal and Vegetable Physiology Considered with Reference to Natural Theology, Vol. II (Treatise V of The Bridgewater Treatise on the Power Wisdom and Goodness of God as Manifested in the Creation), William Pickering, London

Schilling, T. (2003) “Making Jaws“, Heredity, 90:3-5

Sherwin, Frank (2011) “Design of Man: No Evolutionary Evidences“, Acts & Facts 40(1):16

Shubin, Neil (2009) Your Inner Fish: A journey into the 3.5 billion year history of the human body, Vintage Books, New York, NY

Stansfield, William D. (1977) The Science of Evolution, MacMillan Publishing Company, Inc., p.110

Takezaki, Naoko et al. (2004) “The Phylogenetic Relationship of Tetrapod, Coelacanth, and Lungfish Revealed by the Sequences of Forty-Four Nuclear Genes“, Molecular Biology and Evolution 21(8):1512-1524

Tuttle, Albert H. (1884) “The Relation of the External Meatus, Tympanum, and Eustachian Tube to the First Visceral Cleft“, Proceedings of the American Academy of Arts and Sciences, New Series Vol. XI, Whole Series Vol. xix, pp. 111-132 + plates

Venkatesh, Byrappa et al. (2001) “Molecular synapomorphies resolve evolutionary relationships of extant jawed vertebrates“, Proceedings of the National Academy of Science 98(20):11382-11387

Wagner, Rudolph (1844) Elements of Physiology, Sherwood, Gilbert, & Piper, Paternoster Row, London (translated from the German by Robert Willis).

Wells, Jonathan (2000) Icons Of Evolution: Science Or Myth?: Why much of what we teach about evolution is wrong, Regnery Publishing Inc.



92 thoughts on ““Gill slits” by any other name…

  1. Thank you for a well done article.

    Ive known for many years creationism is B.S. It is information like this that is one of many nails in the coffin.

    The only option they have is to lie, obfuscate, deny, mislead, and cling to their imaginary friend like a life preserver, as the ship goes down.

    ..or the sometimes preferred method of fingers in ears, chanting “la la la la la”…pausing occasionally to proclaim “its magic..all the way down”

    Liked by 1 person

  2. Troy, this is magnificent. I’m going to ask my editor if we can make a link to this in the next edition of “Vertebrate Life” (but they might think it inappropriate, we’ll see).

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  4. Very good article that managed to cover, in an easily accessible form, both the history and the mechanisms of “gill slits”. Now how to get this into wider circulation…? (But of course the ones who need to read and understand it will either ignore it or proclaim that it’s the work of the debil.)

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  7. Really informative article. I enjoyed it thoroughly, and am pleased to see that it is going to get wider distribution as it deserves. One quibble- it’s ‘innervates’ not ‘enervates.’ Thanks for your efforts.

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  8. Troy,
    What a fine article.

    You quote from the 1902 American edition of The History of Creation shows that Haeckel recognized the non-functionality of embryonic gill slits of amniotes. Lankester’s earlier (1876) English translation (also from the 1873 4th German edition) has the same affirmation (vol.2, p.220). It seems to be absent from the 1868 first German edition. Pending verification, the explicit statement that embryonic gill slits are definitely not functional seems to have originated, or been most forcefully and unambiguously expressed by Haeckel in 1873.

    Going a little off topic, it is instructive how your findings depart so markedly from the way Stephen Jay Gould depicted Haeckel in his highly regarded Ontogeny and Phylogeny (1977). Gould’s introductory chapter accuses Haeckel – and tarring Haeckel seems to have been a central goal of the book – of divining embryos as miniature adults. Saying this once didn´t suffice: Gould used the word “adult” no fewer than 18 times in his first 7 pages to suggest that Haeckel was a self-deluded extremist. However, Gould did not document his charge, and my word searches of Haeckel’s major works have failed to turn up a single case of either ‘adult’ or ‘mature’ used to characterize embryos or embryonic character states in the way told by Gould. It may be that it is Gould who best deserves the title of not-entirely-honest ideologue.

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    • Hello Woody!

      W.B.: You quote from the 1902 American edition of The History of Creation shows that Haeckel recognized the non-functionality of embryonic gill slits of amniotes. Lankester’s earlier (1876) English translation (also from the 1873 4th German edition) has the same affirmation (vol.2, p.220). It seems to be absent from the 1868 first German edition. Pending verification, the explicit statement that embryonic gill slits are definitely not functional seems to have originated, or been most forcefully and unambiguously expressed by Haeckel in 1873.

      Ah, interesting. Yeah, I went with what I personally had on the shelf (the 1902 version). There was also this on pgs. 352-352 of same edition:

      Every one surely knows the gill-arches of fish, those arched bones which lie behind one another, to the number of three or four, on each side of the neck, and which support the gills, the respiratory organs of the fish (double rows of red leaves, which are popularly called “fishes’ ears”). Now, these gill-¬arches originally exist exactly the same in man (D), in dogs (C), in fowls (B), and in tortoises (A), as well as in all other vertebrate animals. (In Fig. A―D the three gill-arches of the right side of the neck are marked k1 k2 k3.) Now, it is only in fishes that these remain in their original form, and develop into respiratory organs. In the other vertebrate animals they are partly employed in the formation of the face (especially the jaw apparatus), and partly in the forma¬tion of the organ of hearing. (emphasis mine)

      Though clearly his description of the pharyngeal apparatus as being “exactly the same” in man is a bit of an exaggeration (assuming the translation is correct).

      Then there is the following from his The Evolution of Man (Anthropogenie); mine is the English translation of the 3rd edition (1876):

      In the embryo of Man, as in that of all other Vertebrates, the very remarkable and important structures, which are called gill-arches and gill-openings, appear, at a very early period, on each side of the head (Plate I. Fig. 1, and Figs. 116, 118, f). These are among the characteristics and never-failing organs of the Vertebrates, for which reason we mentioned them in considering the typical primitive Vertebrate (Figs. 52, 53, p.256). On the right and left walls of the intestinal head-cavity, in the anterior portion, first one, and then several pairs of sac-like protuberances are formed, which break through the entire thickness of the side wall of the head. They thus become slits through which these is a free passage from without into the throat-cavity: these are the gill-openings the wall of the throat cavity grows thicker, and is changed into a bow-shaped or sickle-shaped ridge: these are the gill-arches; on their inner side a vascular arch afterwards arises (Fig. 101, p336). The number of the gill-arches, and of the gill-openings, which alternate with the former, amounts in higher Vertebrates to four or five on each side (Fig. 118, e, d, f, f, f’). The lower Vertebrates have a yet larger number. Originally these remarkable formations discharged the function of a breathing-apparatus – were gills. Even yet in Fishes generally, water, serving for respiration, and which is taken in through the mouth, passes out through the gill slits on the side of the gullet. In higher Vertebrates they afterwards close. The gill-arches are transformed partly into the jaws, partly into the tongue-bone and the bonelets of the ear (ossicula auditus). – Haeckel, Ernst (1876) The Evolution of Man Vol. I (3rd Edition), H. L. Fowle, pp.355-357 (emphasis mine)

      Here Haeckel is mistaken about the clefts (normally) perforating in humans but I don’t know if this was definitively known at that time.

      W.B.: Going a little off topic, it is instructive how your findings depart so markedly from the way Stephen Jay Gould depicted Haeckel in his highly regarded Ontogeny and Phylogeny (1977). Gould’s introductory chapter accuses Haeckel – and tarring Haeckel seems to have been a central goal of the book – of divining embryos as miniature adults. Saying this once didn´t suffice: Gould used the word “adult” no fewer than 18 times in his first 7 pages to suggest that Haeckel was a self-deluded extremist. However, Gould did not document his charge, and my word searches of Haeckel’s major works have failed to turn up a single case of either ‘adult’ or ‘mature’ used to characterize embryos or embryonic character states in the way told by Gould. It may be that it is Gould who best deserves the title of not-entirely-honest ideologue.

      Oh my! Someone else who has actually bothered to go back and read what Haeckel said rather than simply accepting the “common knowledge” about what he supposedly thought! Yes my friend Don (who will probably be jumping in here shortly) and I have been talking about this and other bits of misrepresentations and exaggerations of Haeckel’s ideas for many years now; Gould’s definitely being one of them (which is not to say there are no justifiable criticisms one can make of Haeckel).

      Yeah, you really have to read Haeckel “between the lines” to get whole “recapitulation of adult characters only” thing as Gould did. Don is more knowledgeable about this than I, so I won’t go say more about this specifically until he has a chance to chime in.

      As far as Gould goes, beyond the subject of Haeckel; you know, I really enjoyed his essays and learned a lot about evolutionary theory from him but you’re right, he really could go off the rails sometimes.


    • Woody: I’m really glad to see someone who has actually looked at Haeckel’s books. To answer your reference question (and then some):

      The corresponding statement in the first edition of “Naturliche Schopfungsgeschichte” (1868) [History of Creation] is on page 435. Plate XIV implies the same thing, resembling the plate (and discussion) on the classification of animals in von Baer’s “Uber Entwickelungsgeschichte der Thiere” (1828). Haeckel’s “Generelle Morphologie” (1866) has a corresponding statement in his definition of Amniota (Vol. II:CXXXII), “The anamniotes include the three classes of fish, amphibians, and Dipnoi; the amniotes are the three classes of reptiles, birds and mammals. The amniotes are distinguished from the anamniotes mainly by the possession of the embryonic amnion, and the fact that they breathe through gills at no time of their lives. ” This last reference bring us back to Haeckel’s first relevant publication.

      If you are interested in this because of creationist claims and complaints, remember the motto of Troy’s blog. You [I’m speaking abstractly, not implying “you” directly] can’t say gills+slits = “gill slits” as creationists do. This would be like demanding that I prove dragonflies can breathe fire, or complaining that I can’t use the word “cell” for a membrane-bound structure containing organelles because they know uncle Charlie lives in a cell ever since he was caught stealing cars. Kiemenbogen/Kiemenspalten (gill arches/gill slits [clefts]) are “terms of art” used by German embryologists to refer to the structures originally described by Rathke in vertebrate embryos (as Troy states). Rathke’s first paper considers that the structures in the embryos of air-breathing vertebrates might be for respiration (which was entirely reasonable as an initial reaction); the second paper states he was convinced they don’t. Rathke’s friend, the famous Karl Ernst von Baer, was then motivated to investigate this topic, and produced two papers, declaring the standard number of five arches and four cleft in all vertebrates. Baer’s huge “Uber Entwickelungsgeschichte der Thiere” (1828) uses a chick embryo as a model for vertebrate development, and refers to its Kiemenbogen/Kiemenspalten constantly, also praising Rathke for his discovery that air-breathing vertebrates have embryo structures clearly resembling those of fish. The terms were widely used for the forty years before Haeckel published, and continued thereafter. Haeckel followed the common terms in use at the time. In the late 1830s, Visceralbogen [visceral arches] and Schlundbogen [pharyngeal arches] were suggested by Reichert and Rathke respectively as alternatives after further research showed that the first two arches become the mandible and hyoid [and associated structures] in jawed vertebrates. In my research, I have found no one who claimed that Kiemenbogen *were* gills or functioned as gills, except Agassiz (as Troy states) – and he was a creationist. It is creationists who have to demonstrate that “gill slits” = gills was the actual meaning in nineteenth century embryology, not those they attack.

      On Gould:
      In the past, I’ve done a lot of head banging over Gould’s book. Before having experience with the original literature, I whizzed by Gould’s discussions about Haeckel without problem. Going back after reading Haeckel and others of his time, I couldn’t make sense out of even his basic descriptions. Once I got into American neo-Lamarkians of the late 1800s/early 1900s, Cope, Hyatt, and their followers, I found clear statements resembling Gould’s descriptions, especially on the mechanism of recapitulation. After laying down the ground rules for the Mechanism of Recapitulation, apparently based on the neo-Lamarckians (note the Cope/Hyatt comments in the text), Gould talks about Haeckel and how the earlier mechanism discussion applies to him. The meanings of Haeckel’s basic terms palingenesis and cenogenesis are altered by Gould, the former greatly so (Haeckel defines these and discusses them frequently in Anthropogenie [Evolution of Man], especially starting with the 3rd Ed.). Gould talks about having to find scattered bits and pieces, and Haeckel never describing a mechanism in one place. I see this as “just trust me,” without the evidence – something I’ve looked for. Gould also talks about how Haeckel seemed uninterested in mechanisms. I agree with this part. Haeckel was a morphologist, and was clearly more interested in the pattern of evidence from embryology, comparative anatomy, and paleontology than in the mechanics of change. It is this very thing that Gould and I agree on that contrasts with so many attacks on Haeckel. I see an endless stream of writers saying what Haeckel was wrong about, much handed down as “common knowledge” for a century or more, and that wouldn’t stand up even to casual scrutiny. All you have to do is open his books.

      Don Frack

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  11. I just found your blog from Jerry Coyne’s post today at whyevolutionistrue. Your gill arch article was utterly absorbing and satisfying for a lay person like me. It’s wonderful to get to understand just how richly detailed and cohesive the evidence on gill arches is, including the diagrams and links to stuff like the surgeons’ description of removing a gill arch atavism from a young Indian girl. I appreciate how careful you are to define your terms precisely, and to call attention to ambiguities like the difference between a diagram used for illustrative purposes versus a photographic-like reproduction, and to anticipate how you might be misunderstood or misrepresented so as to be completely clear, without getting bogged down. And also how organized and thorough your analysis is, and how clearly and understandably written. Bravo and thanks!

    Liked by 1 person

    • Thank you very much! Yes, I try keep in mind when I’m writing that a lot of people may not be as into this stuff as I am, so while I don’t shy away from scientific terms and concepts, I will usually try to either give a plain English explanation or at the very least link to somewhere that does. And as for anticipating misunderstandings or misrepresentations, that comes from years of experience in dealing with creationists. I often put a lot of time and effort into these posts (hopefully that shows) and I am glad that people are finding them interesting and informative, it makes the work worthwhile. Thanks again.


  12. Also visiting from Coyne’s post, and will read. Did just make a start when I saw this:

    “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.”

    Just the other day this compelled me to believe the Actinopterygii (and I guess the Sarcopterygii) may in the future be considered to branch of from Chondrichthyes. Wouldn’t that make them monophyletic?

    “”The common ancestors of all jawed vertebrates today organized their heads in a way that resembled sharks,” said Finarelli, PhD, Lecturer in Vertebrate Biology at University College Dublin. “Given what we now know about the interrelatedness of early fishes, these results tell us that while sharks retained these features, bony fishes moved away from such conditions.”

    Furthermore, the analysis demonstrated that all of these early members of the modern gnathostomes are clearly separated from what now appear to be the most primitive vertebrates with jaws: a collection of armored fishes called placoderms.”


  13. In case my previous comment comes through, I see my mistake. Monophyletic would mean redefining these groups.

    Still, a nice testament to evolution as well, seeing the common origin by way of the head organization!


  14. “(Kiwi) … small flightless birds found in New Zealand”

    Unless a goose is considered a small bird, I wouldn’t call Kiwis small. There are a variety and the smallest I’d seen is still the size of a small breed of chicken – certainly not small in comparison to numerous other bird species.


    • Well, yeah, depending on how you look at it. They’re not particularly small as birds in general go, but as far as Ratites (ostrich, emu, rhea etc.) go, they’re relatively small.

      I think what I had in mind was some nature film I had seen on them in the past where they seemed to be around the size of a chicken, which is still a decent size for a bird when you average them out with all the finches and sparrows etc.. So, still, point taken.


  15. Pingback: Gills, Stars and Important Issues « blueollie

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  17. I also came from Jerry Coyne’s WhyEvolutionIsTrue and I’m very glad I did.

    Congratulations on an excellent and well written article. I have lurked in a discussion about Haeckel and gill slits between a creationist and the JREF stalwarts but the above sets out all the points in such a clear and logical manner that even a long lapsed biologist as myself could follow it.

    Liked by 1 person

  18. I am also from WEIT where I just left a brief post on “begging the question”. It is not simply another way of saying ‘raising the question’ it is a particular logical fallacy where the proposition to be discussed is first assumed as a premise, ie, “I believe in the Bible because the Bible is true”. http://en.wikipedia.org/wiki/Begging_the_question
    Excellent post though, really enjoyed it.


    • Argh! Death by a thousand minor criticisms!

      Just kidding. Yes, I thought briefly about that when I wrote it and just went with it as it has become a common alternate definition of the phrase (see the “Modern usage” section of the Wikipedia article you linked to). However, I shall bow to philosophical and grammatical tradition and change it to “raises the question”. Thanks.


    • Marella, while I feel your pain, indeed I am one with your pain, you may not be aware that the phrase “begs the question” has over the last decade, we know not how, been decisively “reanalyzed” by a younger generation (a phenomenon that linguistics researchers like Steven Pinker assure us is a normal and inevitable occasional feature of language evolution).

      It has come to be so widely used to mean merely, “raise the question” [shudder], and smart journalists like Rachel Maddow on MSNBC, and Jonah Lehrer in The New Yorker, use it this way so insouciantly, and with such evident editorial impunity, that Troy cannot fairly be said to have used it, as you imply, “incorrectly.”

      Some meanings become endangered as their habitat shrinks, and marvels of deftness and precision tragically go extinct, but we can find consolation in reflecting that, whilst this planet has gone cycling on according to the fixed law of gravity, endless new locutions most beautiful and most wonderful have been, and are being, evolved.


  19. Just arrived from “PandasThumb”. Sure glad I clicked on the link. Non-scientist but most interested in evolution and de-bunking creationist claims and attempts to teach it in our schools. This is such a nicely done piece of work…so thorough yet well organized and understandable even for the less evolved like me! Thanks so much…and keep up the good work!

    Liked by 1 person

  20. Pingback: Science tidbits June 18, 2012 « Teaching Sapiens

  21. Great entry Troy. Terrific job. As a developmental biologist, I must say that I insist that my students never call the pharyngeal arches, clefts and pouches “gill slits.” These structures are the anlagen of adult structures, and even in fish, they are the primordia of the adult gill slits. Therefore, I do not like calling them gill slits, since it infers that they are mature gill slits, which they are not. Also, to call them gill slits obscures (in my view) the powerful homology of the pharyngeal pouches, arches and clefts among all the vertebrate groups. All vertebrate embryos form these structures and the contribute to essentially the same adult derivatives (which have different final morphotypes in the adults of the different species), express essentially the same groups of genes, and have the same anatomical relationships to various neural, circulatory and muscular derivatives. This is powerful evidence for common descent and if students call them gill slits, they throw up their hands and say that mammals do not have gills and miss the connections. That’s my two and a half cents. Cheers!

    Liked by 1 person

  22. Pingback: Carnival of Evolution #48: The Icelandic Saga! « Random Information

  23. Pingback: Gill Slits « Eye on the ICR

  24. To deny that humans have nothing to do with other life on earth is like trying to deny that pollution is harmful. Who in their right mind would want to posit that we are not connected to the other life on earth? I have read, with great interest, the books of Zecharia Sitchin and he has some very interesting ideas about how humans were given genes from human-like creatures from Niburu. We certainly have a lot of exploring to do before we can “know” exactly the whole story of life on earth.


  25. What is so very exciting is comparing the behaviors and habits of humans and how closely we mimic other forms of life. Not only are we like other life, we are also very different. Viva la difference!!!!


  26. Pingback: EMBRYOLOGY en Ontwikkelingsbiologie « Tsjok's blog

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  28. What is your personal accreditation? Do you have a degree in anything, or do you just travel the world, talking to other people who do?



    • Hi Brittany,
      I am without a degree or formal scientific training (a couple classes in biology and geology at community college not withstanding). I am a largely self taught amateur naturalist who has spent many years studying the scientific (and creationist) literature and a smattering of the history and philosophy of science. [The contents of my personal library can be viewed at this link, note: this does not include periodicals.]

      I have also attended a few scientific conferences (DinoFest International Symposium II & III, Cal-Paleo 99, AAAS Annual Meeting 2001). And, yes, I have talked to many others who do have formal background in science. For example my best friend, who I also consider a mentor, has a Masters degree in zoology.

      Basically I know a little (more than most lay people) about a lot when it comes to biology and paleontology (and their histories). If I could claim expertise, it would be in the study of creationists and their arguments against mainstream science. Something you cannot get a degree in.


  29. Very nice work, My credentials: BS in Comparative Zoology, MD (PM&R and wound care) religion: Unitarian
    Although it makes the discussion more complicated yet you might do a little more to point out evolution from a common ancestor as opposed to evolution from “Monkeys”… OK fish


    • Thanks! RE: common descent. I understand what you mean, though I tried to make that point implicitly by usually referring to the “gill slits” of amniote embryos (which covers a fair amount of zoological ground) and not just those of humans. If I did tend to focus somewhat on our species it is because people are all creationists really care about.

      They will happily dismiss whole Families (Felidae, Canidae, Equidae) and Classes (trilobites) as mere variations within created “kinds”, but to them the human species, despite all our telltale primate characteristics, must be a “kind” unto itself. Their theology demands it.

      This makes establishing that humans do in fact have gill-like structures as embryos is especially significant when arguing with creationists.


  30. Dude,

    You’re SUCH an idiot. You’ve bought into the textbook lies hook, line, and sinker. Why don’t you get off your lazy good-for-nothing ass and go do your homework. Do the leg work and do your OWN research. Human babies DO NOT have “gill slits” or whatever else you want to call them. I suggest you get your dumb ass to an abortion clinic and you start looking at the aborted human babies VERY closely. At 8 weeks it’s as big as a quarter with all 5 fingers, all 5 toes, and looks EXACTLY like a human being. NO tail. NO “gill slits.” NO stupid evolutionary bullshit fairy tale nonsense. Look at one earlier than that. Still NO evolutionary idiocy. You’re buying into lies published in textbooks that modern micro-biology and other sciences can and have proven wrong. You’re brainwashed so deeply into believing this bullshit, it’s unbelievable. It’s people like you who are dangerous fanatics because you cling to the lies with your dying breath, even while the evidence screams contrarily in your face. Your blog should be re-named to “Brain-Dead Pigeon Playing Chess with Actual Intellectuals.” The brain-dead pigeon, of course, would be you. You wouldn’t last 5 minutes in a debate with me. I’d slowly and systematically shred you to pieces. You evolutionists are a funny bunch. Evolutionists with minds greater than yours have attempted to debate Creationists and have lost EVERY time. Yet you, in your pathetically feeble attempt with this blog, try to accomplish what they cannot, have not, and never will. You’re fighting a losing battle, bub. Truth always wins out in the end. I’ve debated University professors before because some of their students, unable to defend against me, suggested I debate them. They were more intelligent than you will ever hope to be. Quoting bullshit from books and avoiding all the factual evidence does not make or prove your case. It makes you desperate. What’s more interesting is that the majority of idiots who argue for, defend, and promote evolution are nothing but uneducated, spood-fed suckers; the people who have NEVER spent ANY time in ANY scientific field their entire life. They merely learn the bullshit from bullshit textbooks and then spout the bullshit as if it were factual. The number of scientists who are actually evolutionists is a minority. Most scientists, who follow where their work leads, believe in some kind of intelligent design, though they don’t believe in God and would never call it God. Most scientists in ANY scientific field KNOW there is NO evidence to support evolution whatsoever. In fact, many of the more intelligent adherents to evolution ALSO know there is NO evidence and have said as much. But brainwashed fools, like the writer of this blog, have bought hook, line, and sinker into the religious fairy tale philosophical lie that is evolution. Try doing your research HONESTLY instead of being a spoon-fed half-wit that believes everything he reads in bogus textbooks that aren’t worth the paper they’re printed on.

    Your comment on another of your blogs just goes to show the problem with sites like Wikipedia, Wiki Answers, Yahoo Answers, etc. You suggested that you “edit the Wikipedia article,” which shows how dishonest you are. These sites are NOT answer sites; they are OPINION sites. Quite often, the person asking the question picks the answer he/she WANTS to hear rather than the answer that is the most correct or truest. When you see answer reference Wikipedia information, and even the Wikipedia information is WRONG, there’s something wrong. Everyone is welcome to their own opinion, but when fact enters the scenario, opinions become irrelevant. Opinions only matter where likes and dislikes are concerned. It is my opinion that blue is the best colour. It may be someone else’s opinion that red is the best colour. Since there is NO right answer to what is the best colour, and no way of actually determining if there IS a best colour, it is nothing but opinion. But when facts and evidence enter the scenario, your opinion goes out the window with it and you had BEST have the intelligent mind to disregard your opinion and get in line with the facts and evidence. Otherwise, you are rightly labeled a fool and an idiot. So do not say to someone, “Well, that’s your opinion” if you THINK they are wrong or they ARE wrong. There is NO opinion where facts are concerned!

    For example: If I told the writer of this blog that it was okay for him to have his opinion about the “gill slits,” that’d just be STUPID. If neither of us really knows, THEN we can have opinions. But as soon as the EVIDENCE comes into play, our opinions are meaningless and we need to conform to the truth revealed. The evidence is AGAINST him and therefore he CANNOT have an opinion any more. He either gets in line with the truth, or he continues to reject that truth out of stubborn idiocy and we all call him a moron. It’s that simple.


  31. Case in point about what I said in the above post. The author of this blog said in response to Brittany, “I am without a degree or formal scientific training.” As I said, this is the case with the majority of those who call themselves evolutionists. They attempt to argue bullshit they know NOTHING about and then IGNORANTLY try to call it “science.” If the author of this blog would study DNA, he’d learn that what evolution suggest is IMPOSSIBLE. 99.999999999% of ALL mutations are FATAL!!!!! DNA reads forwards and backwards, like the word “RACECAR.” It also overlaps, like the two sentences “I LIKE CHOCOLATER THAT EVENING.” However, it overlaps by ENTIRE chapters. If you make ONE change for the positive, the results in MULTIPLE changes for the negative. The reverse is affected negatively, as is every overlap. Furthermore, new information CANNOT be added to existing information naturally. You can LOSE information, but you will NEVER gain new information. A human being can be born with 4 arms (a MUTATION of already existing information), or a human being can be born WITHOUT arms (a LOSS of information), but a human being will NEVER be born with wings (the ADDITION of NEW information). Also, our DNA has a built in correction maker. If two midgets get together and have a child, what is the result 99.9999999% of the time? A full-grown average human being, taller than his/her parents. The author has NO degree or formal training and yet tries to argue PSEUDO-SCIENCE against REAL science. He needs to get his head out of his ass and wake up and smell the coffee.


  32. Dude,

    Go read a REAL medical textbook without the evolution bullshit AND go visit an abortion clinic. In fact, make a trip to your local micro-biology lab while you’re at it and take a look for yourself under the microscope. The evidence is stacked against you. Quit buying into the evolutionary bullshit like an idiot.


    • Find me a medical textbook that does not discuss pharyngeal pouches in human embryos. And the homologies (innervation, blood supply, derived structures) hold across vertebrates, including fish. It’s clear from your posts that your only information comes from creationist sites. Also that you did not read Troy’s article, as he quite clearly explains how the term “gill slits” is a misnomer. You just saw “gill slits” and went ballistic. Well done.

      By the way, each human being has around 100 new mutations (as do all organisms).

      “The number of scientists who are actually evolutionists is a minority. Most scientists, who follow where their work leads, believe in some kind of intelligent design, ”

      I can vouch for that being entirely wrong. However, I’m signing off now, as I actually have some work to do (i.e., real science) and have no need to engage further with a rampaging ignoramus.

      Liked by 2 people

      • Christine “Dude” Janis: By the way, each human being has around 100 new mutations (as do all organisms).

        You beat me to it. If 99.99 etc. etc. etc. percent of mutations were lethal then we’d all be dead.


  33. Pingback: Round 2 of: What “hope” do you have being an evolutionist? | Playing Chess with Pigeons

  34. Pingback: Journey #14: “There is no evidence for evolution” | My Journey - Questions & Observations of a Skeptic

  35. You seem to have touched some (vagus) nerves Troy. Well done! You know you’re getting to them when the spittle starts to fly from their keyboards.

    Liked by 1 person

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  37. Thanks for the only fact based and annotated explanation I could find. One ludicrous website told an imaginary story about an abortion doctor convincing a women that her embryo was still in the fish stage, therefore okay to abort. The clinics don’t need to drum up business, and no MD would waste his time talking to a client that’s what his staff is for. Why do old men worry so much about abortions? The writer of that silly nonsense referred to the woman’s theoretical 10th grade science class for details explaining embryonic development that could only have been taught pre-1950 and not in the Bible Belt, Over and over creationist sights verify facts by referring to unnamed professors and anecdote.

    I vented too, but you’re just singing to pigs. Oh you know that. Thanks
    PS Abortion is a terrible thing for women but not as terrible as the alternative. Don’t old farts remember coat hanger deaths, and infertility? And pregnancy suicides.


    • A recent comment asked why old men worried about…..
      People staring at mortality cling to their religion for immortality anyone with a view that alters their immage of religion also shake their link with immortality thus must force their religious views on those who believe differently.
      While a agree with the premmis of the comment, as a doctor I disagree with the comment that doctors don’t have time to explain. Those of us who care take the time! The comment by the doctor about the stage of development sounds like a doctor talking down to his patient to be quick instead but definitely not a political statement!


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  42. I came here from Steve Pinker’s Twitter page. Great article from 2012.
    This is my first take on embryology and I am glad I’ll die less stupid.
    Such a piece of work helps dissolve creationism in the long run.
    Congratulations, Troy!


  43. Hi Troy,
    I read your post, and it is very well argued. At the moment, I am a biology student at a local university, and one of my personal headaches is the promotion of either creation-ism or evolution-ism. To be honest with you and with all due respect, I really don’t care for either explanation. As a student, the only thing that I am concerned about is true scientific facts that have been tested at a laboratory to the molecular level. My teacher presented this same example about the gill slits during a microbial genetics lecture. I was just exhausted of listening, so, I raised my hand and said that the information was outdated and more up-to-date data has been collected explaining that they are no longer gill slits, and they are pharyngeal pouches. He asked what was my source, and my reply was, with all due respect, professor, but your source is 150 years old and newer information was out that did not concentrate on a belief based teaching. He stopped and said he will do some more research and get back to us. He continued with the lecture as it was intended. I agree; they look like gills until you dissect it, and then they look like pouches. I know in biology we name a lot of things base on morphological characteristics, and that is a great easy way to remember things.

    The only thing that really gets to me is that either creationist or evolutionist keeps trying to push the subject in school. Honestly, I paid for one of my books close to $300. I feel that my book should be filled with up-to-date information that has been tested, and that is going to help me in the future and not filled with propaganda of any kind. I guess it is easier to print the old stuff than to update the books to what they are intended to do, and that is to provide useful information that can help us treat diseases and give our patients a fighting chance. To this day, I haven’t seen a mermaid or an angel either in nature or in a lab, so, I will have to dismiss both claims as pending research and proper laboratory testing.

    Please don’t take this the wrong way. I am a paying student who is discordant with the never-ending stories.


  44. Pingback: Responding to a comment on my article: “Gill slits” by any other name… | Playing Chess with Pigeons

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  46. Thank you so much for this article!! I remember learning all of this in university in 1993!! What a remarkable example of evolution in vertebrates. I now teach anatomy & physiology in high school for college credit and would to use your article for my class with permission. Dry well presented and explained!! On another note, I’m a practicing Anglican and former Roman Catholic and I cannot express enough
    Y dismay at the lack of acceptance of evolution in Christian circles…seems to me a unique fundamentalist problem and one should never seek to use their faith to justify scientific evidence…so I feel your pain and frustration!!

    Liked by 1 person

  47. Great article.

    “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).” – two links out of three are not valid anymore unfortunately.

    Liked by 1 person

  48. The best explanation for hind limb buds in cetaceans is flippers, not legs. Your skate embryo doesn’t look like the human embryo and the only reason to say human embryos have gill slits is because you believe, without evidence, that humans have fish somewhere in our ancestry.


    • 1. Flippers *are* legs. (They’re not fins, they contain the homologous bones of tetrapod legs, including digits)

      2. The only reason to say that human embryos have “gill slits” (which was, originally, the creationist term for pharyngeal clefts) is because they *do* have pharyngeal clefts, which in fish perforate to form gill slits. You (assuming that you are human, not alien) have a fully perforated pharyngeal cleft that links your middle ear cavity with your pharynx via the Eustachian tube. Thus you have a gill slit (actually the homolog to a fish spiracle) on either side of your head, and if you perforated your ear drum you could blow cigarette smoke out of it.

      So, blow it out your ear, Joe.

      Liked by 1 person

  49. Hi, late to the party. There isn’t any known mechanism that can take populations of fish and have them evolve into tetrapods and then eventually humans. A Common Design is the best explanation for the similarities. Heck, you don’t even have a mechanism capable of producing the genetic toolkits required for developmental biology.

    So stop calling Creationists misleading. Yours is nothing but a lie.


  50. Creationists look at the animal kingdom as poof things appeared as they are at the hand of a creator then try to use the same “logic” to disprove evolution expecting a change in the entire population to appear at once “poof” when the reality is a slight change first in one individual creature (be it a random mutation, a genetic drift or what the heck at the hand of a creator!) giving it a slight survival advantage. It then over many generations becomes the dominant trait in the population. This mutation may be good or not.
    An example of a questionable mutation is sickle cell anemia caused by s single mutation in the hemoglobin molecule taken alone is very harmful if you have two copies of it. However if you have one copy (known as sick cell trait) you are significantly more resistant to malaria. So where do you see more sickle cell trait? In malaria prone areas. Malaria is so deadly that this deadly mutation actually becomes helpful to the population as a wholllle but obviously there is still work to be done!


  51. Pingback: Tổng hợp về phôi thai của Haeckel P5 – Khe mang và các đặc điểm khác – THƯ VIỆN TIẾN HÓA EVOLIT

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