Pharyngula

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.

Darwinists have been telling us for years that some of the best evidence for the common ancestry of insects and vertebrates is their Hox genes, which affect the character of body segments during embryo development. For example, a mutation in one Hox gene can cause a fruit fly to sprout a leg from its head in place of an antenna. Remarkably, vertebrates possess Hox genes that are very similar to a fruit fly’s — so similar that a mouse Hox gene can enable normal development in a fly embryo that lacks its corresponding Hox gene. More remarkably, the order in which Hox genes are lined up on the chromosome is the same as the order in which they’re expressed along the embryo’s body axis — a feature known as colinearity. And most remarkably, colinearity is the same in the four Hox gene complexes of vertebrates as it is in the Hox gene complex of the fruit fly Drosophila melanogaster.

This striking similarity in Hox gene colinearity is often cited as evidence for common ancestry. For example, according to a widely used college textbook, “The ordering of the genes within each vertebrate Hox complex is essentially the same as in the insect Hox complex, suggesting that all four vertebrate complexes originated by duplications of a single primordial complex and have preserved its basic organization.” (Bruce Alberts et al., Molecular Biology of the Cell, Fourth Edition, Garland Science 2002, p. 1194)

Last year, however, seven different arrangements of Hox genes were reported in various species of Drosophila — all fruit flies, in only one of the six model systems mentioned by Jenner and Wills. Apparently, the arrangement in Drosophila melanogaster that so strikingly resembles the arrangement in vertebrates has not been inherited from a common ancestor but is a relatively recent acquisition. (B. Negre and A. Ruiz, “HOM-C evolution in Drosophila: Is there need for Hox gene clustering?” Trends in Genetics 2006, doi:10.1016/j.tig.2006.12.001)

So this showcase piece of evidence for the common ancestry of animals – one of “evo-devo’s central themes” — turns out to be false, disproved by analysis of only one of the “big six” model systems.

Why, I’ve read the Negre and Ruiz paper, and know it well. I’ve also written previously on conservation of Hox structure, and am also familiar with that literature. Would you be at all surprised to learn that the major lessons Wells claims are in the paper, that fly Hox organization “has not been inherited from a common ancestor” and that “this showcase piece of evidence for the common ancestry of animals…turns out to be false” are conclusions not only unsupported by the evidence, but are contradicted by the work cited? No? You’re familiar with Mr Wells, then.

If you’re unfamiliar with what the Hox genes are, however, I’ve got a short primer on the subject. Even shorter than that article, I’ll mention that they are a set of genes with a specific DNA binding motif called a homeobox, and they are found in colinear clusters in the genome. That is, they tend to be arranged from 3′ to 5′ on the DNA strand in the same order that they are expressed from front to back in the animal; on one end in the fly, for instance, is a Hox gene called labial that is expressed at the front of the head, and at the other end of the cluster is one called abdominal-B that is expressed at the back of the abdomen. You don’t even need to know what the individual genes do, the interesting thing about them is their special organization on the chromosome.

What the Negre and Ruiz paper does is examine 13 species in the genus Drosophila (and one other dipteran, the mosquito Anopheles gambia), and reconstructs the evolutionary history of the Hox cluster, HOM-C. It is true that there are significant rearrangements in the Hox genes; this is old news, however. We knew even in Drosophila melanogaster that there were significant disruptions from the clean and tidy canonical order. One of the most obvious is that the fly cluster is actually broken in two, one complex called ANT-C and another called BX-C. Wouldn’t it be odd for developmental biologists to insist that strict and invariable colinearity was the sine qua non of homology when we knew from the first organism in which they were identified that their order was not absolute?

Here is the summary illustration of the data from that paper. Each of the genes in the cluster is marked with a thick arrow; dark blue are the Hox genes proper, light blue are Hox-derived genes (they are similar in sequence to the other Hox genes, but have derived and acquired new functions), and red are the non-Hox genes in this region. The similarities between all of the flies are relatively obvious, I think.

i-ea53eccede3a459939404ffb29bf2b60-dros_hox.gif
(click for larger image)

HOM-C structural evolution in the Drosophila genus. The Hox gene complex has suffered a high number of structural changes during the evolution of the
Drosophila genus. Three major rearrangements (shown as squares: A, Antp-Ubx; B, Ubx-abdA; and C lab-pb), seven microinversions (circles) and six gene transpositions
(inverted triangles) have been identified and mapped to the phylogenetic tree by comparative analysis. The structure of the HOM-C in each species has been analysed from
its complete genome sequence, except Drosophila buzzatii. Coloured arrows represent genes and their orientation; Hox genes are in dark blue, Hox-derived genes in
light blue and non-Hox genes in red. The Ccp gene cluster and the tRNAlys (denoted lys) cluster are not depicted in detail. (Subdivisions indicate the presence of several
genes, although not the exact number, which varies between species.) Double diagonal lines in the cluster diagrams represent discontinuities in the sequence, and yellow
shadows indicate equivalent breaks. The different segments are drawn in the order of the ancestral HOM-C and do not represent the actual order, orientation or distance
between chromosome segments. Crosses indicate different gene orientation in adjacent diagrams and have no phylogenetic meaning.

Ah, but look at the differences. The yellow bars indicate breaks in colinearity; the cluster has been broken up at those places and the pieces located in different regions of the genome. The X’s indicate inversions, a place where a stretch of the DNA has been flipped around relative to its neighbors.

The species D. simulans, D. sechellia, D. melanogaster, D. yakuba, and D. erecta are all closely related, and have the same Hox organization, with the genes in the same order and a break between the Antp and Ubx genes. Their more distant cousin, D. ananassae, has the same break, but also an inversion of the Dfd gene. Looking at even more distant relatives, flies that split from the melanogaster line over 60 million years ago, we see that D. grimshawi, D. virilis, D. mojavensis, and D. buzzatii do not have the Antp/Ubx split, but a different one, between Ubx and AbdA.

Actually, if you look closely at that diagram and puzzle out the rearrangements, something interesting pops out at you: the pattern of seemingly arbitrary changes in the arrangement of the genes fits neatly into a nested hierarchy, as if, for instance, the last common ancestor of D. melanogaster and D. willistoni had the Antp/Ubx split, and they just inherited the common pattern.

What? The evidence in the paper shows a pattern of inheritance of structure and variations from structure in the Hox genes? But didn’t Wells claim it showed that the arrangement wasn’t evidence of inheritance? How…odd.

You might have been tipped off that this was a story about evidence for evolution in a clade by the first four words of the title of the paper, “HOM-C evolution in Drosophila“. I suspect that the good Mr Wells may not have read that far.

There’s more. The paper is trying to explain the mechanism behind this slow pattern of changes in the Drosophila lineage, and it makes a good argument. The ancestral Hox pattern has a regulatory function; they are in that order because of a regional regulatory mechanism that switches the genes on in a timed sequence as the animal develops from anterior to posterior, that corresponds to their order on the chromosome. Flies, however, have a greatly accelerated rate of development. They have compressed the time of embryogenesis so much that a timing mechanism no longer works well, and instead they have evolved more complex individual regulatory elements for each gene. The regional control has eroded away, replaced by independent local control; as that has happened, the constraint that keeps them locked in a cluster has faded, and the genes have been free to drift apart.

Note that this is an evolutionary and developmental explanation for the phenomenon. It’s a successful account from an evo-devo research program, not a refutation of an evolutionary history. Mr Wells seems to have been wrong again.

I summarized a paper in 2004 that told this same story. It described the pattern of evolutionary change in Hox clusters in the chordate lineage, and we see exactly the same phenomenon, illustrated here.

i-63aee35fe44ca7b5a16f08af944c6303-hox_cluster_evolution.gif
Discrete changes of Hox gene complements in chordates. The chordate ancestor gained a rich set of posterior genes, which were inherited in the three subphyla but partly lost in ascidians. Central genes were gradually lost in tunicates, with larvaceans keeping anterior and posterior genes only. Whereas the Hox cluster was multiplied in vertebrates (with subsequent losses of a few paralogues in some clusters), the cluster degenerated in tunicates, and ultimately disappeared in larvaceans. The loss of central genes and of the Hox cluster coincides with a partition of Hox expression domains, which largely overlap in cephalochordates and vertebrates (ascidian data are still lacking). The motor of both events might be the decrease in size and transition to determinative development.

Animals that develop very rapidly and/or have very strictly defined (determinative) cell lineages in their embryos tend to evolve more discrete gene-by-gene regulatory control, lose the coarser control of whole blocks of genes, and the Hox clusters tend to disintegrate. One animal described in that work, the tunicate Oikopleura dioica, has completely lost the Hox clustered structure, scattering the individual Hox genes far and wide in the genome. Others have broken it up into several clusters.

Wells has a naive and incorrect view of Hox structure (it’s very peculiar; he was purportedly trained as a developmental biologist, and this ought to be common knowledge among the people I consider my peers and betters in this business. How he missed the basics, explained in multiple papers and books, I don’t know.) He seems to think the evidence for common descent of animals is a rigid core of unchanging DNA sequence, held in common in all animals. This is not true. What we have is roughly outlined common core, all right, but the evidence for evolution and common descent is a pattern of variation in that core Hox structure that fits a branching, lineal relationship.

In fact, I’d suggest that if we did see a fixed, invariant gene structure, free of variation between flies and frogs, it would be better evidence for design than evolution. Evolution is characterized by chance variation and interesting noise, except where it is constrained by selection, and the inheritance of contingencies in a lineage — and that’s exactly what we see in the paper Wells misleadingly claimed showed that common descent was false.

I really think that Jonathan Wells is … oh, wait. Al is delivering some choice words about Cy Tolliver. Just picture that, and you’ll have captured the essence of my opinion of Mr Wells, and I won’t have cluttered the old blog with such a ripe collection of pungent expletives.


Negre B, Ruiz A (2007) HOM-C evolution in Drosophila: is there a need for Hox gene clustering? Trends in Genetics 23(2):55-59.

Comments

  1. #1 llewelly
    April 4, 2007

    Thank you for another beautiful article on hox genes. But aren’t you going to talk about this gorgeous crawling crinoid that Afarensis mentioned? Abstract .

  2. #2 Maureen Lycaon
    April 4, 2007

    Looking at even more distant relatives, flies that split from the melanogaster line over 60 million years ago . . .

    Wow, the Drosophila genus is THAT old? I had no idea.

  3. #3 Doc Bill
    April 4, 2007

    By Jove, I think he’s talking about Wells:

  4. #4 Doc Bill
    April 4, 2007

    Try again for the link

  5. #5 djlactin
    April 4, 2007

    he was purportedly trained as a developmental biologist,

    Actually, according to this DI release, his Ph.D. from Berkeley is in ‘molecular and cell biology’.

    Small quibble, but it’s probably the explanation for his incompetence in your field.

    http://www.discovery.org/scripts/viewDB/filesDB-download.php?id=444

  6. #6 Paguroidea
    April 4, 2007

    Thanks for the excellent post PZ! And thanks Doc Bill for the link. I think we have a good idea of the “choice words” now.

  7. #7 Ick of the East
    April 4, 2007

    Deadwood is great.
    And just like the DI, it even has Wu merchants.

  8. #8 Rodrigo Veras
    April 4, 2007

    Simply beautifull explanation!!! Thanks PZ!!!!

    But what really annoys me in the ID movement is that the mess they can do in just two or three paragraphs needs much more space to be repared. Fourtunaly, as a biologist I simply love to read a good and well written scientic text like yours.

  9. #9 Scott Hatfield, OM
    April 4, 2007

    Unfortunately, PZ, the only thing I watched today was ‘Happy Feet’ at the urging of one of the offspring. I’m afraid that G-rated fare does not allow me to sublimate any particularly colorful phrases that come to mind.

    Thus: “The Rev. Wells is a lying sack of crap.”

    Ah, that feels much better. I do apologize to any of the hard-working, tax-paying and otherwise entirely decent sacks of crap that may now feel besmirched by association.

    Self-medicating…SH

  10. #10 John C. Randolph
    April 4, 2007

    But, if drosophila have been around for 60 million years, then what were they all doing before the earth was created six thousand years ago? Were they all hanging out in God’s Big Terrarium in the Sky or what? Wouldn’t they have been bored to death in the meantime?

    -jcr

  11. #11 amph
    April 4, 2007

    The highly organized Hox configuration seen in the vertebrate clusters is actually unique for that subphylum: It appears that the vertebrates later (probably during the chordate to vertebrate transition) acquired the global control regions that are essential for their strict temporal control. So, whereas in some animal lineages Hox organization declined, in vertebrates the global control regions emerged, taking profit of the already clustered nature of the Hox genes, and taking their functions one step (or actually many steps) further. A prime example of evolution understood at the molecular level.
    As for Wells, who cares? He obviously is a liar and not interested in facts. It is impossible to convince someone like him of anything reasonable at all, and the people misled by him are not likely to read Pharyngula.
    @Rodrigo Veras: being destructive is obviously always easier than being constructive

  12. #12 Dave T
    April 4, 2007

    Whether it’s Dr. Wells bearing false witness or Judge Moore worshipping a graven image, the Pharisaic Christians are never more likely to be breaking one of their God’s commandments than when they are trying to advance the cause of that God.

  13. #13 Jud
    April 4, 2007

    First, and more important: Thank you for the excellent brief and simplified explanation of the history of Hox cluster changes and the reasons for same.

    Second and less important: It’s only too evident that the same college-dorm-bullshit-session level of misunderstanding of evolution and biology that Wells, et al. bring to creating their pro-ID explanations also infects their attempts to point out ‘flaws’ in evolutionary theory. Ironically, the real flaws or gaps in the theory (though not in its fundamental explanatory power) that do exist are wonderful opportunities for new research and learning.

    If evolutionary theory was really the ‘Darwinist’ orthodoxy imagined by those for whom an unchanging orthodoxy is the necessary core of their world-view (untrammeled by any conceivable contrary facts, see Egnor’s latest), labs across the world would be shut down in favor of reading rooms where the words of Darwin’s “Origin…” and “Descent…” could be parsed sentence by sentence.

  14. #14 Mike Haubrich
    April 4, 2007

    As for Wells, who cares? He obviously is a liar and not interested in facts. It is impossible to convince someone like him of anything reasonable at all, and the people misled by him are not likely to read Pharyngula.

    And this is precisely the value of Pharyngula. PZ’s explanations help me understand what is going on with Wells, as I would be completely unable to sift through Wells to find the BS without Dr. Myers being here to clarify.

  15. #15 A. Shickelgruber
    April 4, 2007

    S thrfr thr s n Gd nd w shld rs txs whnvr th stt wnts t, xcpt fr dfns.

    Dsn’t tht bt sm t p, PZ?

  16. #16 Stanton
    April 4, 2007

    Did you ever get the idea that the actual reason why Dr Wells got his doctorate was because someone secretly bribed the university an obscene amount of money so that they could pretend that he passed his coursework?

  17. #17 amph
    April 4, 2007

    And this is precisely the value of Pharyngula. PZ’s explanations help me understand what is going on with Wells, as I would be completely unable to sift through Wells to find the BS without Dr. Myers being here to clarify.

    By no means did I mean to criticize PZ for posting about Wells, I was just expressing my feeling that Hox genes are so much more interesting than loonies like Wells.
    To me the value of Pharyngula is primarily in the writings on (developmental) biology. Of course I also appreciate seeing how he (PZ) takes care of those nuts, but sometimes I think he is doing them too much honor. But I am in Europe and perhaps I underestimate the importance of Wells et al.(we have our own fools, though).

  18. #18 Ric
    April 4, 2007

    Great comparison… Wells is like E.B Farnum. Then again, so is Dembski.

  19. #19 CalGeorge
    April 4, 2007

    What a maroon! Whant an ignoranimus! Hahahahahaha!

    http://frogstar.soylentgeek.com/wav/ltbb_052.wav

    How to write a Jonathan Wells “paper”:

    1) Read legitimate evo-devo peer-reviewed scientific paper.
    2) Stew.
    3) Pray.
    4) Write pseudo-critique.
    5) Add boilerplate last paragraph:

    “So this showcase piece of evidence for [critiqued feature of evolutionary theory] turns out to be false [yadda yadda yadda].

    6) Post drivel on Internet.
    7) You’re done!

  20. #20 Faithful Reader
    April 4, 2007

    Slightly OT

    You watched Deadwood instead of the Nova about the cuttlefish? The toxic little flamboyant one was very neat and seemed to show a new evolutionary development. It’s little, it walks and can’t swim well, but its toxicity protects it.

  21. #21 tristero
    April 4, 2007

    After reading your post, I read the entire Wells post and was totally confused, I thought maybe my confusion came from my failure to understand some of the science. It seemed clear enough but I am a layman, after all.

    So…I re-read Wells and your post. Then I carefully studied the graphic you reprinted from the Negre and Ruiz article. I still couldn’t believe it, so I read it all a third time.

    Layman, schmayman. As Dylan sez, y’don’t need a weatherman to know which way the wind blows. And Wells is, as the physicists say, not even wrong. That’s how trivially obvious it is that the diagram of the various arrangements of the Hox genes in D. Menagaster and related flies powerfully suggest evidence of inheritance. That’s how trivially obvious it is that the article completely contradicts Wells.

    My confusion wasn’t because I didn’t understand everything the first time I read it. No, what was so hard to understand was how Wells could dare to lie like that – and he has to be lying because no one with a doctorate in biology can be that stupid; I can easily explain his error to my 10 year old – knowing full well that 24 hours won’t pass before the lie is exposed and all over the Internet.

    I can only assume Wells lied to influence ignorant legislators who have neither the background nor the inclination to evaluate what surely appears to them as an abstruse scientific dispute that is impossible for a layman to judge. But there’s no science in dispute at all!

    That’s the dirty truth of “intelligent design” creationism. There is absolutely no there there.

  22. #22 Alann
    April 4, 2007

    I am confused by something:

    Well’s quotes a textbook as “The ordering of the genes within each vertebrate Hox complex is essentially the same as in the insect Hox complex…” (emphasis added)

    The subcaption for the diagram read “… The different segments are drawn in the order of the ancestral HOM-C and do not represent the actual order, orientation or distance between chromosome segments.,” (emphasis added)

    Doesn’t this indicate that the textbook (or Well’s quote) is mis-stating the matter?

    I can see how the similarities in the genes indicate common ancestry, but it seems like the genes ended up scattered all over the place (compared to vertebrates).

    I know this is kind of like not seeing the forest for the trees, but doesn’t this provide a grain of truth to Well’s argument in that colinearity is presented as an example but is not actually present? (and before you yell at me, I know that his jump from an issue with colinearity to a complete dismissal of Hox genes is logically ridiculous)

  23. #23 cleek
    April 4, 2007

    I can only assume Wells lied to influence ignorant legislators who have neither the background nor the inclination to evaluate what surely appears to them as an abstruse scientific dispute that is impossible for a layman to judge.

    indeed. when i read the Wells excerpt above, he seemed to make sense, but only because the specifics of Hox genes and developmental biology are well out of my area of expertise (i’m a programmer, not a biologist). if i had encountered Wells’ article on its own, there’s little chance i’d have known he was lying. in fact, i probably would’ve assumed his facts and analysis were correct, though maybe a little superficial because his intended audience isn’t scientists. and because i find this stuff interesting, but not interesting enough to try reading the source papers to verify, he would’ve fooled me.

    so, keep up the good work, PZ.

  24. #24 PZ Myers
    April 4, 2007

    Ah, no, the diagrams do accurately represent the order within a segment. That caveat about “The different segments are drawn in the order of the ancestral HOM-C and do not represent the actual order” refers only to the broken clusters — ANT-C and BX-C are drawn with that break (the yellow bar) between them, but in the order they were in in the ancestral Hox cluster. Clearly, since they could be anywhere in the genome, on a different chromosome for instance, there isn’t an order retained across the break, and the authors are just being absolutely clear about a convention of the diagram. You can’t even talk about a distance if they’re on different chromosomes!

  25. #25 PZ Myers
    April 4, 2007

    I missed the cuttlefish. My Tuesdays are horrible messes, with pretty much non-stop lab teaching all afternoon, and yesterday I had appointments with students all morning and a Campus Assembly meeting in the evening. Then once I got home I had to fix dinner and shovel six inches of wet, sloppy snow off of my driveway. Once I got to sit down, it was too late, and seeing this ghastly collection of lies from Wells compelled me to write a rebuttal, instead. With Al Swearingen giving the bastards hell in one window in the corner of the screen, a bottle of pale ale by my side, and a copy of the TIGS paper in hand. Then I passed out.

  26. #26 Vreejack
    April 4, 2007

    Excellent explanation, thank you. By the way, what is this “common text book” that Wells mentions? Maybe I should get a copy. Unfortunately I spent all my time in college studying engineering, so my knowledge of science is not as thorough and rigorous as I would like.

  27. #27 rrt
    April 4, 2007

    “…he was purportedly trained as a developmental biologist…How he missed the basics, explained in multiple papers and books, I don’t know.) He seems to think the evidence for common descent of animals is a rigid core of unchanging DNA sequence, held in common in all animals.”

    I think this is an observation of a recurring creationist theme. Creationists tend to think in absolutes, in simple inviolable laws. Wells may or may not believe the concrete, oversimplified version of Hox colinearity that he fabricates, but he surely knows that his audience is prone to thinking in that way. So he presents it as fact, and cries foul when reality doesn’t match his illusion.

    In other words, I think part of this is about reality not following the kinds of rules creationists think it should.

  28. #28 Monado
    April 4, 2007

    They sound like Monty Python’s Inquisition: Their problem is ignorance–No, their problem is ignorance and arrogance…. Their problem is ignorance, arrogance, and a refusal to face facts…. No, their problem is ignorance, arrogance, a refusal to face facts, and trotting out the same old debunked claims. No, wait! Their problem is ignorance, arrogance, refusal to face facts, trotting out the same old debunked claims, and a habit of calling other people liars without being able to prove a single lie… Among their problems are…

  29. #29 Apikoros
    April 4, 2007

    Then I passed out.

    Well, no wonder!

    I’ve often asked myself, PZ, how you manage the time to write such lengthy and eloquent posts on your blog and hold a demanding job while constantly keeping a squinty eye on the creationists. Now I know that you do it through extreme multitasking.

    My hat is off to you.

  30. #30 Greg Peterson
    April 4, 2007

    The problem with people prone to lying all the time is that they probably assume other people lie all the time, too. That would help explain how someone like Wells can miss the plain meaning of something and claim that it must actually mean its opposite.

    The Nova on cuttlefish was fantastic, visually, but I was getting really annoyed at the pervasive misrepresentation of evolution. I fully understand the appeal of and occasaional need for metaphorical language, but someone getting their information on evolution from that show would have the distinct impression that evolution is controlled by what an organism needs or wants, that evolution has teleology and direction. Creationist wankers exploit that sort of misinformation. It wouldn’t take that much to find better ways of explain this material more accurately, and with a neon freakshow like a cuttlefish to draw in the crowds, what a great opportunity to slip in a little real science. I hate being even a little critical of Nova, which does a world of good, generally, but they majored on video trickery (having electronica play in time with the cuttlefish’s flash display to give it a “Close Encounters of the Third Kind” vibe, goofy fast-motion camera trickery) and minored on scientific accuracy.

  31. #31 no1uno
    April 4, 2007

    Dang, sorry you missed the cuttlefish show PZ. I was looking forward to hearing your take on it. Some of the claims on cuttlefish intelligence seemed a little loose. I don’t recall exactly, but one researcher seemed to be making pretty strong claims, suggesting they are more intelligent than vertebrates, even mammals. That seemed vague and possibly misleading at best. Which vertebrates? Which mammals? I am not a biologist and I am not suggesting I know enough to dispute an expert in the field, but it seemed like he was being deliberately misleading for the impact value. Smarter than mammals! Wow! Other than that the show was the best I’ve seen in some time, beautiful camera work of the color changing cuttlefish illustrating some pretty intriguing research (to a layman anyway).

  32. #32 TheBrummell
    April 4, 2007

    With Al Swearingen giving the bastards hell in one window in the corner of the screen, a bottle of pale ale by my side, and a copy of the TIGS paper in hand. Then I passed out.

    Sounds like a pretty good working definition of the process of doing science, to me.

    I often rely on the aphorism: never assume malice (as an explanation) where incompetence will suffice.

    In the case of Wells, incompetence will no longer suffice as an explanation – even a fool is correct by accident on occassion. Wells is lying, plain and simple, every time he writes two words in a row. My hat is off to anyone who can read through a full sentence of his without screaming and crying.

  33. #33 Jokermage
    April 4, 2007

    Evolution is characterized by chance variation and interesting noise, except where it is constrained by selection, and the inheritance of contingencies in a lineage

    I don’t know why, but I really like how you said this.

  34. #34 Jud
    April 4, 2007

    PZ said: “I missed the cuttlefish.” Slightly OT, but –

    How do you get your TV, over-the-air (antenna), cable, satellite? There are DVRs (generically, “Tivos”) that record stuff so conveniently and with such fidelity to the original that they’re a whole ‘nother level from the old VCR. Many of them will record in hi-def, which is a lovely way to watch Nova *or* Deadwood.

  35. #35 Scott Hatfield
    April 4, 2007

    (cheerfully) I knew alcohol was somehow involved.

    It’s nice to see how many others on this thread have concluded that this particular creationist is not just a religious ideologue, but a lying sack of crap.

    And, Stanton, someone needs to do the detective work where UC Berkeley and Wells’ doctorate are concerned. If we connect the dots it seems likely that Philip Johnson and the DI had a lot to do with shepherding Wells’ doctoral program.

  36. #36 Torbjörn Larsson
    April 4, 2007

    Then I passed out.

    Obviously drinking too deep from the Wells of lies isn’t good for us.

    But thanks for the splendid rebuttal on a complex subject!

  37. #37 Torbjörn Larsson
    April 4, 2007

    Then I passed out.

    Obviously drinking too deep from the Wells of lies isn’t good for us.

    But thanks for the splendid rebuttal on a complex subject!

  38. #38 vhutchison
    April 4, 2007

    Is Wells knowingly practicing ‘pious lies’ or is he just that stupid? Given his religiosity and Mooney background, I vote for the former.

  39. #39 thwaite
    April 4, 2007

    What Jud said.

    And if you have decent reception of over-the-air (OTA) digital broadcasts, your Mac can serve as both an HDTV and a DVR (Tivo-like gadget) with the addition of El Gato Systems’ “EyeTV Hybrid” for a relatively modest price. I have one; it works as advertised; the cuttlefish broadcast is spectacularly gorgeous in static-free color (which goes only a little ways to ameliorate the light-weight science).

    Morris is zip code 56267 per a google search. Plugging that into the tool at antennaweb.org to determine what television is received there shows just the one PBS station, with analog and digital broadcast channels:

    KWCM 10 PBS APPLETON 182° 30.2 10
    KWCM-DT 10.1 PBS APPLETO 182° 30.2 31

    I highly recommend publicizing the existence of such free digital video broadcasts. It’s the only source which lacks Digital Rights Management, and is thus the leverage for limiting DRM application to other video media (in a way analogous to the current situation with audio, per iTunes and EMI).

  40. #40 PZ Myers
    April 4, 2007

    Well, actually, we have cable mainly for the network access, and the family TV is banished to the dank basement where my son has a lot of his clutter stored. When I want to watch TV I ask my daughter if I can watch it on the little set she has in her bedroom.

    Someday, though, when the kids stop sucking my wallet dry with tuition payments, maybe I’ll get a nice big flat-screen HDTV for the living room, and play cephalopod videos all day. That’s going to be some years down the road, I’m afraid.

  41. #41 thwaite
    April 4, 2007

    Hope on two fronts:

    * Nature airs another cephalopod program this week:
    Encountering Sea Monsters (who writes these titles?) of uncertain production date.

    * ElGato makes a separate product, their ‘eyeTV 250’ which turns VHS video from antenna, cable or VCR directly into MPEG-2 data via its hardware encoding. Plug it into your Mac’s USB port and stream to disk with minimal CPU load. Doesn’t do time-base correction or anything sophisticated but works well. Can be scheduled like a Tivo.

  42. #42 Scienceavenger
    April 4, 2007

    An excellent discussion of a technical topic PZ. It is amazing how much biology there is to know, and how ridiculous it is that creationoists think they can levy meaningful criticisms without that knowledge.

    rrt said: Creationists tend to think in absolutes, in simple inviolable laws.

    Exactly. That is why they see no problem with horribly outdated information, and why they interpret every change in scientific theory as some sort of refutation. To them truth is handed down from on high, never to be changed, so a change is a refutation, QED.

  43. #43 stefan
    April 4, 2007

    My well-researched theory is that life evolved in pretty exactly in the way everybody here thinks it does, EXCEPT on a different planet. Then, about 6 thousand years ago, some unnamed Deity (wink wink) SWITCHED that planet for a brand spanking brand new one, right off the land-separated-from-waters assembly line. Everybody moved en mass right into the new planet, not noticing any change. A dinosaur nibbling on a choice fern didn’t notice because it and the fern were transported simultaneously. The only strangeness was that the new stars didn’t appear for another day or two, but of course ferns and dinosaurs were too focused on each other at the time to care much about that.

    My research used to explain, exactly, how people (generally white, middle-class with 2.1 children representing all the genders – just like in the pictures) co-existed with the dinosaurs, but my dog ate that part so you’ll all just have to wait for it to emerge from the other end.

    Therefore those HOX thingies must mean that, uh, well, they mean something or other.

  44. #44 Chris Nedin
    April 5, 2007

    no1uno wrote:

    “Some of the claims on cuttlefish intelligence seemed a little loose. I don’t recall exactly, but one researcher seemed to be making pretty strong claims, suggesting they are more intelligent than vertebrates, even mammals. That seemed vague and possibly misleading at best. Which vertebrates? Which mammals?”

    IDiots?

  45. #45 Heleen
    April 5, 2007

    Maureen Lycaon (#2)
    The genus /i/Drosophila existed in the Cretaceous already. A Drosophila antiqua has been found in amber (Wikipedia does not list it).

  46. #46 thwaite
    April 5, 2007

    More intelligent than vertebrates… – well, a more helpful understanding of this has to refer to broad categories of intelligence – of which the null hypothesis is that there are only very few, according to “comparative psychologist” E. M. McPhail as cited here :

    …it has been proposed by McPhail (1987) that there are only three intelligence levels: one represented by animals that can link stimulus and response (“S-R animals”), one represented by animals that can link stimulus with stimulus (“S-S animals”) and one represented solely by humans. Such a position by no means commits one to Skinnerian behaviorism; the reason why operant conditioning fails to inculcate in any animal any behavior that exceeds that animal’s biological capacity is that all species differ in the range and type of phenomena over which S-R and S-S operations can function. According to McPhail, it is these differences of type and range that account for the apparent scala natura of intelligence, for the fact that most of us would regard, say, frogs as less intelligent than dogs. But frogs and dogs, both S-S animals, may differ not in their relative intelligence so much as the kinds of thing, and the sheer number of things, with which they can interact in an intelligent manner.
    If McPhail’s analysis is correct (and no compelling counterevidence seems to have appeared in the decade since it was made) then only humans have an advantage in intelligence over other animals. …

    The author who cites this is a linguist who studies the evolution of language, central to the distinctive human intelligence.

  47. #47 Niket
    April 5, 2007

    Thanks for the clear explanation. The only thing I disagree with is the statement:
    “In fact, I’d suggest that if we did see a fixed, invariant gene structure, free of variation between flies and frogs, it would be better evidence for design than evolution.”

    Wouldn’t that be an evidence that selection pressures and development timescales preclude any deviation from the regional control that necessiates a (relatively) invariant structure?

  48. #48 Keith Douglas
    April 5, 2007

    What an appalling liar Wells is. But what else is news?

  49. #49 Peter
    April 5, 2007

    Thanks PZ. It’s great to get such a well-explained refutation with *DING* good citations that are clearly illuminated. We laypeople need it. Thanks again.

  50. #50 hrm
    April 5, 2007

    Hm.

    http://www.uncommondescent.com/evolution/jonathan-wells-responds-to-p-z-myers-tantrum/

    More spinning from the Wells master (and a pot shot at the NYT for good measure)

  51. #51 JoeG
    April 6, 2007

    Is there any data which would demonstrate that culled genetic accidents can lead to the suite of observed HOX genes (clusters)? That we know about HOX genes does not mean “the blind watchmaker did it”.

    If a PAX6 gene (HOX) from a mouse can be substituted for a PAX6 in Dm and produce a fly-eye, what is it that controls the type of eye?

    Did the alleged common ancestor of mouse and fly also have that PAX6? Did that ancestor even have eyes?

    Or do you guys just want to line up and fight it out?

  52. #52 John
    April 6, 2007

    JoeG asked:
    “Is there any data which would demonstrate that culled genetic accidents can lead to the suite of observed HOX genes (clusters)?”

    Yes, there are such data. PZ explained some of it, but it went right over your head.

    “That we know about HOX genes does not mean “the blind watchmaker did it”.”

    So in your mind, everything that PZ wrote above can be accurately summarized as “we know about HOX genes”?

    “If a PAX6 gene (HOX)”

    Joe, all Pax genes are Hox genes, but not all Hox genes are Pax genes.

    “… from a mouse can be substituted for a PAX6 in Dm and produce a fly-eye, what is it that controls the type of eye?”

    All the other genes, of course. The Hox genes are switches. If I move a light switch from my house to your house, wouldn’t it turn on the lights in your house?

    “Did the alleged common ancestor of mouse and fly also have that PAX6?”

    That’s the prediction.

    “Did that ancestor even have eyes?”

    Don’t know. It wouldn’t have to. Do you realize that the fly’s mouth is homologous to your anus, and vice versa?

  53. #53 RavenT
    April 6, 2007

    Do you realize that the fly’s mouth is homologous to your anus, and vice versa?

    must…resist…low…hanging…fruit…

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