A reader who has been stymied by TypeKey (I wish I could fix that bug) informs me that mturner, one of the creationists at the ARN message board, thinks he has rebutted my post on whale limb evolution, claiming that Thewissen et al. have actually found evidence for Intelligent Design creationism. It’s fairly typical nonsense from the ARNies, but it’s so amusing I had to rebut his rebuttal.
ARN is a weird place. There are several patient, intelligent people working it to correct the babble that the flaming idiots who dominate the board put up. I am not that patient, so I can’t stomach the fools who frequent it, and mturner is one of the nastiest and dumbest of the lot. You can read his comments at ARN, or just go below the fold here—I’ve put the full text in this post.
As per your link, PZ says, ” The main players in limb formation, the genes Sonic hedgehog (Shh), the Fgfs, and the transcription factor Hand2, are all still present and fully functional in these animals. What has happened, though, is that there have been novel changes to their regulation. Even loss of structures is a consequence of changes and additions to regulatory pathways.” So, would you explain how changes in “regulatory pathways”, that is, changes in developmental direction without mutation of the regulatory gene, [cutely named “Sonic Hedgehog”–you irrepressible scamps, you!], is accomplished via RMNS and not ID, that is, by EAM?
mturner has his own pet name for Intelligent Design: Endogenous Adaptive Mutagenesis. As near as I can tell, the only difference is that he gets to string 3 big words together, which makes him sound clever. Or pompous. EAM is not documented anywhere, nor is there any evidence for it; if you read that ARN thread, you’ll notice people asking mturner to explain this EAM thingie, and his reply is that it’s all documented in the ARN archives. Never trust a theory whose sole provenance is the archived rantings of a web site full of kooks.
Oh, and RMNS is their weird jargon for “Random Mutation and Natural Selection”.
The way regulatory pathways are changed without modifying genes is by changes in cis regulatory regions—pieces of DNA associated with a particular gene that control the transcriptional machinery. Random changes to these regions can change their affinity for transcription factors and change the timing and position and degree of activation of the gene. See? That wasn’t hard.
PZ then says, “This retention of major genetic pathways should be obvious just looking at a whale. They evolved from four-limbed tetrapods, and lost their hindlimbs as more and more locomotor function was committed to the tail and flukes, yet they still retain forelimbs.” Buit golly, PZ, “use it or lose it is just plainLamarxckism, not RMNS!!
That is, it’s EAM! Have you come top join us on the Bright Side?
No, it isn’t Lamarckism (or even “plainLamarxckism,” whatever that is. In my few glances at ARN, it’s never quite clear what are typos and what are yet more peculiar neologisms bred in the hothouse atmosphere of the asylum.)
The swimming power stroke for cetaceans is given by the tail. The hindlimbs were not particularly useful for propulsion, but they were lumpy, protruding objects that interfered with hydrodynamics. Variations that reduced the drag of the hindlimbs would have a selective advantage in a swimming animal.
Next PZ says, “It is the same set of genes that operate in the hind- and fore-limbs, so of course you can’t just get rid of them–this is a case of selective limb loss.” Golly, who or what did the “selecting”?!? Your passing gamma ray, your genomic screw-up, or, as EAM maintains, the organism itself?!?
While the hindlimbs were useless in swimming, the forelimbs still retained significant utility as a steering mechanism. Mutations that knocked out both pairs of limbs would be disadvantageous, because having a nice torpedo shaped body but no way to steer it doesn’t lend itself well to survival. Mutations that reduced hind limb size while sparing the forelimb were most advantageous.
PZ then digs himself down a little deeper–“In addition, the genes have multiple functions making simple gene loss untenable. Shh, for instance, is a critical signaling molecule involved in the specification of midline structures in early development, and loss of the gene as a whole is lethal.” But hey, this time RMNS pulled it off, eh? One more little miracle to we can attribute to blind chance rather than smart management, hmmm? Oh. PZ, you’re such a mook!
I don’t think mturner quite got the point of the article. Shh is not a gene that we vertebrates can spare; there was no loss of the gene, but only a change in its pattern of regulation. This was made quite clear, I thought, in the title of the article.
Our mook continues–“What evolution did was to modify the domains of expression, selectively inactivating limb genes in the hindlimb region.” “What evolution did”!!!!? Here ol’ PZ pulls the standard Genomic Darwinist ploy of attributing causation to the effect caused. How dumb [not to mention illogical to the point of irrational] is that? How many times must we point out to you daydreamers that evolution, an effect, cannot cause itself. Nothing can! Something “modified the domains of expression”, alright, but it wasn’t “random genetic mutation”, it wasn’t “natural selection”, and it sure as hell wasn’t “evolution”, because the modification is the evolution. So, then, what did all this very selective modifying/redesigning? The organism, via Endogenous Adaptive Mutagenesis.
I dare not look too deeply into the logic of this paragraph, because clearly that is the way madness lies. Apparently, mturner believes that change occurred by the organism willing its hindlimbs to disappear.
My phrasing was intentional. We don’t know the precise details of the mechanism, but we can describe a change that occured over the course of evolutionary history: a gradual diminution of the hind limbs in early cetacean evolution, followed by a nearly complete shutoff of the hind limb 34 million years ago. We know how that shutoff is accomplished in the modern embryo: by a change in the domain of the Hand2 regulatory gene’s expression. We hypothesize that this is a consequence of changes in the cis regulatory regions of Hand2, or possibly a change further upstream in Hox gene regulation. These kinds of changes can be easily accomplished mechanistically by small changes in the genome. These are ideas that can be tested; the authors describe experiments in mice in which changes in Hand2 expression can lead to limb loss exactly like that seen in whales.
Later, after much detail that explains nothing, PZ says–“Looking at the evolutionary history of whales, the authors think they can pin down when this downregulation of Hand2 occurred. Shutting off that gene causes a complete loss of the limb, so older fossils that show a gradual diminution of the hind limbs must have retained an active Hand2/Shh combination; the complete loss occurred about 34 million years ago, so that would have been the ‘moment’ when this restriction would have caused the final disappearance of the whale’s posterior limbs.” Except that simply stating that “then this happened” is no explanation at all for how, why, when, and where it happened. Description of an event, although PZ and crew have never grasped that fact, is no explanation for that event.
We ask, what is different at the molecular/developmental genetics level between a whale and a mouse? We see that a key difference is the location of Hand2 expression. We therefore postulate that a key step in the generating a morphological difference between mouse and whale is actually a very tiny difference in how one gene is turned on, a difference that is easily caused by common genetic errors. We know when it happened. With a little more digging into the molecular biology, we’ll know exactly how it happened, right down to the single nucleotide changes. We know the chemistry of DNA quite well, and can say exactly what kinds of trivial, every day molecular events would have caused those changes. That’s a convincing case to me.
EAM, whatever it is, is a mechanism without evidence, without a supporting rationale, and which is so murky and undefined that its principal proponent can’t even explain it.
I think I know which side is making stuff up.
hen the Boy Wonder says–“A promising correlation in the fossil morphology is that there was a concurrent reorganization of the vertebral skeleton at the same time that the hind limbs were lost. The distinct identity of the sacral vertebrae was lost, and the caudal vertebrae became more homogeneous. This implies a change in the expression pattern of the Hox genes, which are responsible for anterior-posterior positional information. That suggests that we ought to look upstream of Hand2, and ask what’s going on with Hox gene expression in cetaceans–the changes that streamlined the vertebral column may have simultaneously induced the changes in Hand2.”
“A promising correlation” for whom or what? “that there was a concurrent reorganization of the vertebral skeleton at the same time that the hind limbs were lost” simply makes it even more impossible that this highly selective process was a mere ‘genetic accident’. But the PZ fans out there will just gloss over that Grand Canyon of a hole in their hypothetical explanation.
It is a promising correlation that can lead to a more precise explanation of the mechanism. We know that the Hox genes, in particular the hoxd series, regulates Hand2. We know there was a shift in Hox gene expression in cetaceans—we know that from vertebral identity. A known change in one regulator of Hand2 makes it easier to see how Hand2 expression could have undergone a concordant change.
Uhm, here’s a clue for you, PZ and pals. Your, “looking upstream of Hand2”, to “Hox gene expression in cetaceans” simply isn’t looking far enough “upstream”. You then have to look “upstream” of the Hox genes, and guess what you’ll find when you do that! Oh, come on now, stop crying! You’re big boys now, so act it.
Why, yes. We already know what processes induce changes in genes. We’ll have to look to known, documented mechanisms in genetics and molecular biology. This doesn’t make me cry—it means we’re on familiar ground and can be confident of our understanding.
Then yer man says something sensible–“How do you make a whale? Clearly, you don’t just “lose” the genes required to make hind limbs. You have to revise and add to the control information for existing banks of regulatory genes involved in limb formation.” But the last time I looked, “to revise and add to the control information ” was something ‘mind’ does; intelligence, not happenstance.
No, happenstance does modify the regulatory information in the genome. I’m not sure how anyone can argue otherwise; there is no known physical mechanism to protect regulatory DNA from the forces of “RM”, random mutation, and we can compare the same genes in different organisms or different individuals and see the variations. We see spontaneous mutations crop up all the time. Unfortunately for mturner’s thesis, however, we don’t see ‘mind’ modifying organisms in nature, have no evidence for any kind of directed intervention in the course of evolutionary history, and do see a lot of clumsiness and waste and randomness in development. It’s clear that modifying control information isn’t an exclusive property of mind.
And yet there are people who believe that P.Z. Myers talks sense. Sad, but true.
Cheer up! The good news is that very, very few people believe mturner talks sense.