Wells on Hox structure: making the same mistakes over and over again

Jonathan Wells apparently felt the sting of my rebuttal of his assertions about Hox gene structure, because he has now repeated his erroneous interpretations at Dembski’s creationist site. His strategy is to once again erect a straw man version of biologist’s claims about genetic structure, show that biologists have refuted his dummy, and claim victory. The only real question here is whether he actually believes his historical revisions of what we’ve known about Hox genes, in which case he is merely ignorant, or whether he is knowingly painting a false picture, in which case he is a malicious fraud.

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Wells’ flagrantly false commentary on Hox complex structure

This evening, I am watching an episode of that marvelous and profane Western, Deadwood, as I type this; it is a most excellently compensatory distraction, allowing me to sublimate my urge to express myself in uncompromisingly vulgar terms on Pharyngula. This is an essential coping mechanism.

I have been reading Jonathan Wells again.

If you’re familiar with Wells and with Deadwood, you know what I mean. You’ll just have to imagine that I am Al Swearingen, the brutal bar-owner who uses obscenities as if they were lyric poetry, while Wells is E.B. Farnum, the unctuous rodent who earns the contempt of every man who meets him. That imagination will have to hold you, because I’m going to restrain myself a bit; I’m afraid Wells would earn every earthy sobriquet I could imagine, but I’ll confine myself to the facts. They’re enough. The man completely misrepresents the results of a paper and a whole discipline, and does it baldly on the web, as if he doesn’t care that his dishonesty and ignorance leave a greasy, reeking trail behind him.

Let’s start with Wells’ own words.

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Don’t blame the dinosaurs

The mammalian tree is rooted deeply and branched early!

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(click for larger image)
All orders are labelled and major lineages are coloured as follows: black, Monotremata; orange, Marsupialia; blue, Afrotheria; yellow, Xenarthra; green, Laurasiatheria; and red, Euarchontoglires. Families that were reconstructed as non-monophyletic are represented multiple times and numbered accordingly. Branch lengths are proportional to time, with the K/T boundary indicated by a black, dashed circle. The scale indicates Myr.

That’s the message of a new paper in Nature that compiled sequence data from 4,510 mammalian species (out of 4,554) to assembly that lovely diagram above. Challenging the ‘conventional wisdom’ that mammalian diversity is the product of an opportunistic radiation of species after the dinosaurs were wiped out at the end of the Cretaceous 65 million years ago, the authors instead identified two broad periods of evolutionary expansion among the mammals: an early event 100-85 million years ago when the extant orders first appeared, and a radiation of modern families in the late Eocene/Miocene. A key point is that there is no change in rates of taxon formation across the Cretaceous/Tertiary (K/T) boundary—mammalian diversity was rich before the dinosaurs disappeared.

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Evolution of the jaw

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What do you know…just last week, I posted an article dismissing a creationist’s misconceptions about pharyngeal organization and development, in which he asks about the evidence for similarities between agnathan and gnathostome jaws, and what comes along but a new paper on the molecular evidence for the origin of the jaw, which describes gene expression in the lamprey pharynx. How timely! And as a plus, it contains several very clear summary diagrams to show how all the bits and pieces and molecules relate to one another.

The short summary is that there is a suite of genes (the Hox and Dlx genes, which define a cartesian coordinate system for the branchial arch elements, Fgf8/Dlx1 genes that establish proximal jaw elements, and Bmp4/Msx1 genes that demarcate more distal elements) that are found in both lampreys and vertebrates in similar patterns and roles, and that vertebrate upper and lower jaws are homologous to the upper and lower “lips” of the lamprey oral supporting apparatus.

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Jonathan Wells knows nothing about development, part II

Yesterday, I pointed out that Jonathan Wells was grossly ignorant of basic ideas in evo-devo. This isn’t too surprising; he’s a creationist, he has an agenda to destroy evolutionary biology, and he’s going to rail against evolution…same ol’, same ol’. That’s nothing, though. Wells and his fellows at the Discovery Institute have an even more radical goal of fighting natural, material explanations of many other phenomena, and his latest screed at the DI house organ is against natural explanations of development. Not evolution, not evo-devo, just plain basic developmental biology—apparently, he wants to imply that the development of the embryo requires the intervention of a Designer, or as he refers to that busy being in this essay, a postmaster.

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Basics: What is a gene?

I mulled over some of the suggestions in my request for basic topics to cover, and I realized that there is no such thing as a simple concept in biology. Some of the ideas required a lot of background in molecular biology, others demand understanding of the philosophy of science, and what I am interested in is teetering way out at the edge of what we know, where definitions often start to break down. Sorry, I have to give up.

Seriously, though, I think that what does exist are simple treatments of complex subjects, so that is what I’m aiming for here: I talk a lot about genes, so let’s just step way back and give a useful definition of a gene. I admit right up front, though, that there are two limitations: I’m going to give a very simplified explanation that fits with a molecular genetics focus (pure geneticists define genes very differently), and I’m going to talk only about eukaryotic/metazoan genes. I tell you right now that if I asked a half dozen different biologists to help me out with this, they’d rip into it and add a thousand qualifiers, and it would never get done. So let’s plunge in and see what a simple version of a gene is.

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