“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 of the comparative embryology in 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 that 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.

Read on»

leetle devil frog!

[Hat tip to Mom (she clips anything evolution related out of the paper for me).]

Does intelligent design “theory” lack a mechanism?

No, says the Discovery Institute’s Center for the Renewal of Science and Culture’s resident attack Chihuahua Casey Luskin (and, yes, I’m stealing that John), who reports that he was recently confronted with this question at a talk he had given:

Last month I spoke at the University of Arkansas, and during the Q&A, a skeptic complained that ID theory lacks a “mechanism.” I explained that intelligent agency itself functions in that role, serving as a known cause / mechanism which produces high levels of complex and specified information (CSI).

[Snip a bunch of slides with various quotes from Luskin’s fellow Discoveroid (stealing that too) Stephen Meyer that don’t add anything to this discussion.]

[…] Intelligent agency, therefore, is a mechanism which we can observe and understand in the world around us, and from those observations we know it alone is capable of producing high CSI. But the skeptic wasn’t satisfied with this argument. He insisted what ID lacks is a mechanism that, at the direction of an intelligent agent, could be capable of instantiating information, or design, in the real world.

And this unnamed skeptic was correct. Intelligent design creationists prattle on endlessly about “complex specified information” in nature and how they think that “an intelligence” is required to explain it but they never explain how this “CSI” gets from the mind of their “designer” (wink, wink) to the features of the natural world it is supposedly intended to explain. In other words, even if we were to grant their source of “CSI” they’ve got nothing to offer on where the rubber actually hits the road.

As we spoke after the talk, I asked him, “Why should it be so hard to believe that intelligent agents can implement their designs in the real world? After all, we see intelligent agents manipulating the information in DNA all the time.”

Yes we do Casey. Intelligent agents who are physical beings with physical brains, physically manipulating physical DNA with physical tools.

As the skeptic was a philosopher, he was apparently unaware of the burgeoning field of genetic engineering, where biologists manipulate the information in DNA to produce new biological functions. Unfortunately, this hardened ID critic was probably still not convinced after I explained that it’s easy to believe intelligent agents might have ways of implementing their designs in the natural world — since we see it happening, reported in the scientific literature on a regular basis. This new research discussed in Nature News shows exactly how intelligent agents can manipulate information in DNA to create new structures and functions. There is no reason, in principle, why an intelligent agency must lack a mechanism for implementing designs in the natural world.

And if we ask these physical genetic engineers what mechanisms they use to manipulate physical DNA they won’t respond by merely pointing out that they are intelligent agents and that that fact should tell you all you need to know about the process.

This is the same fallacy that ID creationists engage in when they liken their ideas to the SETI (Search of Extra Terrestrial Intelligence) program. “SETI is looking for signs of intelligence” they say, “we’re doing the same thing.”. But just as with the genetic engineers we are talking about physical ET’s, ostensibly with physical transmitters, sending out signals propagated via some part of physical electromagnetic spectrum.

The reason for all this obtuse deflection about genetic engineers (and aliens) and tedious repetition about “CSI” is that the actual answer to the question of what the mechanism for intelligent design is that it is magic.

Their “intelligent designer” is God (everyone knows this); and God implemented his designs through unknowable miraculous means, end of story.

However, if they were to divulge this they know would lose their pretense of doing science and would be admitting to the fact that what they are actually engaging in is apologetics.


Luskin, Casey (1012) “Responding to the Challenge that Intelligent Design Lacks a “Mechanism”“, evolutionnews.org (blog) downloaded on 5-27-2012

[Hat tip to The Sensuous Curmudgeon.]

Penn Jillette on the President and our stupid drug laws

Preach it brother Penn!

He’s absolutely right on this. What is the point of imprisoning people for using marijuana? Is it supposed to be for their own good? To protect them from themselves? The most chronic (no pun intended) user of marijuana might not be very productive but that is about the worst you can say about them. The majority of marijuana smokers are productive members of society, that is unless they get busted and imprisoned. Once that happens they’re convicted felons who will be a lot less likely to get a decent job.

“Sorry, we had to ruin your life to keep you from ruining your life.”


As far as health effects, sure if you are a very regular user you might risk long term diseases like those tobacco smokers face but I’ve yet to hear of a marijuana smoker who smoked a fraction of what tobacco smokers do (not counting those who smoke both). How many two pack a day weed smokers are there out there? That would be around 40 joints a day! And it is essentially impossible to overdose on marijuana. If you aren’t operating a motor vehicle or heavy machinery, the only way you could kill yourself with weed is to get enough to build a bonfire and jump into the middle of it.

On the other hand with alcohol, which is legal, one need not get into a car to die. Just hop on down down to the local liqueur store, buy yourself, say a 1.5 liter bottle of your favorite hard stuff (I prefer tequila), guzzle it within an hour or so and say hello to alcohol poisoning!

You wanna talk societal effects? How many violent crimes do you think get committed under the influence of  alcohol vs. marijuana? I bet they aren’t even in the same galaxy. Yes there is violent crime associated with marijuana on the trafficking end but that is due to the fact that it is illegal (the same was true of alcohol during prohibition).

There is no rational reason why marijuana is illegal while alcohol is legal and the fact that it is, is part of our national insanity.


[Hat tip to Ed Brayton]

Is the human knee joint “irreducibly complex”?

This is a re-post, in slightly modified from, of one of my Talk Origins Archive feedback responses (from back when the Archive had a feedback section, specifically March of 2002)

Luke asked:

Please email me your response if possible. I don’t want to categorize myself as a evolutionist or creationist. I was visiting the other website I think it was creationist or similar, your guys arch enemies; anyways I was trying to find proof to support modern man evolving from ape, and they had an extensive article written about the human knee and how it has sixteen parts and minus just one and its useless. Apes have non locking knees and because of their makeup you aparently can’t evolve it into a locking one you have to start from scratch. Evolution and mutations from what I’ve read only allow for small changes no mutation can allow for the formation of a complex organism with sixteen moving parts? The knee would have to be built all at once it couldn’t evolve or it would have no use. How do you suggest that apes dumped their knees and immediately mutated new ones with sixteen brand new parts? I would like to believe it could happen just seems far fetched?

This argument originates from an article (Critical Characteristics and the Irreducible Knee Joint) published in the Creation Ex Nihilo Technical Journal (Vol. 13, No. 2, 1999) by a British engineer named Stuart Burgess.

From my reading of the article it seems to be highly flawed, especially in its almost total lack of discussion on the comparative anatomies of living non-human apes (gorillas & chimps etc.), extinct hominins (australopithecines, early Homo) and modern humans. This lack of attention to comparative anatomy (and physiology) is typical of anti-evolutionists and it leads them to continually talk about the anatomy/physiology of various organisms as if they exist in a vacuum (examples: The woodpecker or The bombardier beetle). They focus on some extreme example of organ or system in a particular species as if it is totally unique to that species. The fact is that when one looks at other closely related species one usually finds that there are variations on the extreme example that the anti-evolutionists have focused upon.

For instance the bombardier beetle that anti-evolutionists often cite is just one species of a whole group of beetles (“Ground beetles”, Family Carabidae) many of which have some variation on a chemical defense mechanism, using the same basic chemicals (which exist in many beetles in varying amounts), but used in differing ways. The specific example that anti-evolutionists cite sprays an explosive mixture out of its abdomen in a fairly well aimed stream at its attackers, however there are other Carabid beetles that spray with less accurate aim, and others that merely excrete bad tasting chemicals out of their abdomens when attacked. There is a whole spectrum from fairly simple to fairly complex defense mechanisms. Anti-evolutionists only talk about the more complex variant.

This discussion of the human knee is another example of this sort of argument in a vacuum.

While I am not an expert in the comparative anatomies of the living non-human apes and humans, as far as I am aware there is no material difference between them. That is, every bone, muscle, ligament, tendon, and cartilage in the human knee has its corresponding representative in the knee of chimpanzees and the other great apes (and presumably in the knee of their concestor). Yes they are shaped somewhat differently. Yes they are proportioned differently. But as far as I know all the same parts are there (if there are any primatologists or physical anthropologists out there, please correct me if I am wrong). [Note: see the 2nd Lovejoy quote provided by Adam Benton in the comments section below.]

As for fossil hominins, the knees of more derived types like Homo erectus (which are either “fully human” or “just apes” depending on what anti-evolutionist you talk to) seem to be virtually identical to those of H. sapiens. As for the knees of the more basal species of Homo (H. habilis) and the australopithecines these become increasingly like those of living non-human apes the farther back in time one goes. Exactly the sort of thing one would predict if humans evolved from an “ape-like” ancestor. The knee of Australopithecus afarensis (which most anti-evolutionists say is “just an ape”) retains a number of “ape-like” features but also has characteristics like those of later hominins including H. sapiens. In other words it is an intermediate form in this regard.

The knee bones of a modern human, an australopithecine and a chimpanzee.

See The ICR and Lucy: Bearing False Witness Against Thy Neighbor for more comparative photos, or refer to any good text on human evolution for comparative illustrations.

Burgess does mention living apes briefly but only to dismiss them as being poor bipedal walkers. However this is a problem for his argument for irreducible complexity (IC), at least as I understand Michael Behe‘s (the person responsible for the recent popularity of this term) definition of the term, in that while the knees of living non-human apes are slightly different in form, and are not as efficient for use in bipedal walking as those of humans, they do work, and they can walk bipedally.

Note: please remember that evolutionary theory does not postulate that humans are descended from other living apes, like chimps or bonobos, rather we share a common (ape) ancestor with those species.

So, assuming that knee joints of the ancestor of later hominins was essentially the same as those of the living non-human apes and could, like them, walk in a bipedal manner at all, then it would be possible for there to be a selective advantage for any slight modifications in their descendants which lead towards an increase in efficiency of bipedalism.

The human knee seems to me to be a poor example of an IC structure.

Some of Burgess’ other arguments just seem nonsensical to me. For example he states:

The knee joint presents a major challenge to the evolutionist because it is unique, and because there are no intermediate forms of joint between a condylar joint and the other two limb joints found in animals and humans – the ball and socket joint and the pivot joint. (Burgess, 1999)

I fail to understand Mr. Burgess’ challenge here. Knee joints did not evolve from elbow, shoulder, or hip joints. Rather knee joints have been knee joints since their origin in the first tetrapods. The same applies to the other types of joints. So why would we expect to find “intermediate forms” between them? That Burgess even posses this as a supposed problem for evolution demonstrates a significant lack of understanding about evolutionary theory and the fossil record.

Ichthyostega; an early tetrapod and its hind leg bones. Its “knee” was the joint between the femur and the tibia and fibula.

It is a curious thing that Behe’s principle of IC as an argument for design turns the traditional argument from design on its head. It used to be argued that those features of organisms that seem perfectly sculpted to suit their needs, or seem well designed from an engineering point was evidence for design. Now, under Behe’s IC principle of design, it doesn’t matter how clunky, ungainly, and poorly designed from an engineering point of view something is, it only matters that it is supposedly irreducibly complex.

Apparently the “Designer” under this new design “theory” is a (supernatural) cosmic Rube Goldberg.

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My Weekend at the O.C. Freethought Alliance Conference

The Orange County Freethought Alliance Conference (3rd Annual) is “in the can” and I had a blast. I went as part of a contingent from my local Atheist, Agnostic & Skeptics Meetup group, which had purchased a table at the event. The table was right up front next to the speakers table, all the people in our group were great and there were lots of interesting talks presented! I got to meet lots of new people and say hi to familiar friends and colleagues.

Here are a few of the new people:

Dave Silverman, president of the American Atheists who was famously challenged by Bill O’Reilly to explain how every day the tides go in and go out with “never a miscommunication”.

Aron Ra, a very popular YouTube anti-creationist and veteran of the talk.origins newsgroup. I had three people think I was him, before he arrived, though I’m not sure why. Considering how many things we share in common, it is somewhat surprising it took this long for us to run into each other.

And last but actually First the Lord Himself…

Mr. Deity, AKA “El“, AKA the very funny Brian Keith Dalton. If you don’t know who Mr. Deity is, go right now to his YouTube channel and start with episode one. See also the official Mr. Deity website.

The end of the conference came late Sunday afternoon just as a partial solar eclipse started and the organizers had two telescopes set up with special filters to allow us to safely view it. One of the scopes just showed the sun as a white disk with the moon cutting into it but the other actually allowed you to just make out the filaments of the many loops, flares and prominences in the corona of the sun. I have seen many pictures and films of these phenomena before but this was the first time I actually saw them with my own eyes. Incredible.

A NASA photograph showing solar prominences etc.

Once again I have a really great time and all the people I talked to, especially those at our table were a lot of fun. Thanks to Aaron for organizing our contingent and to the other members of our group for being such good company! My only regret is I got a bit distracted and got out of there kind of quickly at the end and didn’t get a chance to say a proper goodbye to them or to my friend and colleague Barbara Forrest (who was one of the speakers). Hopefully I’ll get to see them all again soon.

If you’re interested you can watch a streaming video or buy a DVD of the event from the O. C. Freethought Alliance (look for the guy in a black t-shirt with the long hair near the front) and if you live in the area consider attending the 4th Annual O. C. Freethought Alliance Conference in 2013. You just might see me there in person.

Pay no attention to the creationists behind the ID curtain!

Dr. Barbara Forrest of Southeastern Louisiana University (AKA “Evil, evil woman“), who testified to devastating effect during the 2005 intelligent design trial, Kitzmiller v. Dover (Pennsylvania), has written a scathing expose of the recent shenanigans that intelligent design proponents have been up to in Louisiana (and Tennessee) which I highly recommend you read.  It seems that once again the ID proponents are having difficulty keeping their creationist petticoats from showing.

I’m shocked! Shocked, I tell you!

See: Discovery Institute to LA Family Forum: “Repeat after me: ‘The LA Science Education Act is *NOT* a creationism law.’”