July 2008 Archives

Evolving snake fangs

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Ontogenetic allometry in the fang in the front-fanged Causus rhombeatus (Viperidae) displaces the fang along the upper jaw. Scale bars, 1 mm. We note the change in relative size of the upper jaw subregions: i, anterior; ii, fang; iii, posterior. d.a.o., days after oviposition.

I keep saying this to everyone: if you want to understand the origin of novel morphological features in multicellular organisms, you have to look at their development. "Everything is the way it is because of how it got that way," as D'Arcy Thompson said, so comprehending the ontogeny of form is absolutely critical to understanding what processes were sculpted by evolution. Now here's a lovely piece of work that uses snake embryology to come to some interesting conclusions about how venomous fangs evolved.

Basal snakes, animals like boas, lack venom and specialized fangs altogether; they have relatively simple rows of small sharp teeth. Elapid snakes, like cobras and mambas and coral snakes, are at the other extreme, with prominent fangs at the front of their jaws that act like injection needles to deliver poisons. Then there are the Viperidae, rattlesnakes and pit vipers and copperheads, that also have front fangs, but phylogenetically belong to a distinct lineage from the elapids. And finally there are other snakes like the grass snake that have enlarged fangs at the back of their jaws. It's a bit confusing: did all of these lineages independently evolve fangs and venom glands, or are there common underpinnings to all of these arrangements?

An interesting new paper is just out today in PLoS ONE. You recall the announcement a few years back that soft tissue that resembled organic tissue had been isolated from a Tyrannosaurus femur. This started off a huge controversy in the field (and beyond)–researchers disagreeing with each other whether the structures seen were indeed blood cells and vessels; creationists crowing about how this finding represented “proof” that the earth was indeed young and dinosaurs had existed just a few thousand years ago; and of course, talk of cloning and DNA analysis. On the side of “soft tissue = dino blood” were findings that reported identification of the iron-containing protein heme (potentially from the red blood cells) and morphology of cells and vessels similar to that seen in modern-day ostriches and emu. However, the new paper by Kaye et al. provides an alternative explanation: that the structures aren’t actual vessels and cells, but are instead iron-rich bacterial biofilms. Read the rest over at Aetiology

Rumbles on The Right

There’s an amusing dispute going on between the Discovery Institute and Little Green Footballs, the latter of which recently unveiled some very interesting details about links between Islamic and Christian creationists. Needless to say, the DI folks are demonstrating their usual haphazard acquaintance with the truth.

Following up PZ’s previous post about blind fish, I want to quote a section of R. A. Fisher’s “The Genetical Theory of Natural Selection”. Fisher is credited as being one of the founders of modern evolutionary biology, which drove him to create modern statistics.

This quote begins on page 128 of the 1999 complete variorum edition. I think it was originally written in 1930.

The power of the means of dispersal alone, without the necessity for selective discrimination in either region, is excellently illustrated by the theory, due to Ray Lankester, which satisfactorily accounts for the diminution or loss of functional eyes by the inhabitants of dark caverns. Ray Lankester pointed out that the possession of the visual apparatus is not merely useless to such animals but, by favoring their migration towards sources of light, will constantly eliminate them from the body of cave inhabitants, equally effectively whether they survive or perish in their new environment. Those which remain therefore to breed in the cavern are liable to selection in each generation for their insensibility to visual stimuli. It should be noted that with such very restricted habitats migrational selection of this sort might attain to very high intensity in consequence produce correspondingly rapid evolutionary effects.

Very interesting perspective isn’t it?

Christopher Hitchens was impressed by the existence of blind cave organisms, and wrote that they argue against a linear progression in evolution. He's quite right; creationism doesn't explain why their god tossed in to salamanders and fish a collection of complex developmental mechanisms that the animals simply throw away and do not use. Evolution does — descent from a sighted ancestor explains how blind cave animals can still possess the machinery for a lost organ.

Do you think the Discovery Institute would let this challenge pass by? Of course not. They put their top man on the job, so Casey Luskin wrote a rebuttal. After a long weekend and before a busy day of work, it always makes me happy to find a new Luskin screed — they're so dang easy to shred. Here's his devastating critique:

Snake segmentation

Blogging on Peer-Reviewed Research

Life has two contradictory properties that any theory explaining its origin must encompass: similarities everywhere, and differences separating species. So far, the only theory that covers both beautifully and explains how one is the consequence of the other is evolution. Common descent unites all life on earth, while evolution itself is about constant change; similarities are rooted in our shared ancestry, while differences arise as lineages diverge.

Now here's a new example of both phenomena: the development of segmentation in snakes. We humans have 33 vertebrae, zebrafish have 30-33, chickens have 55, mice have 65, and snakes have up to 300 — there's about a ten-fold range right there. There are big obvious morphological and functional differences, too: snakes are sinuous slitherers notable for their flexibility, fish use their spines as springs for side-to-side motion, chickens fuse the skeleton into a bony box, and humans are upright bipeds with backaches. Yet underlying all that diversity is a common thread, that segmented vertebral column.

(Click for larger image)

Vertebral formula and somitogenesis in the corn snake. a, Alizarin staining of a corn snake showing 296 vertebrae, including 3 cervical, 219 thoracic, 4 cloacal (distinguishable by their forked lymphapophyses) and 70 caudal. b, Time course of corn snake development after egg laying (118-somite embryo on the far left) until the end of somitogenesis (~315 somites).

The similarities are a result of common descent. The differences, it turns out, arise from subtle changes in developmental timing.

Blind Salamanders

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In previous essays (here and here), we learned that genes encoding new proteins can and do, often, arise de novo in the course of evolution, contradicting one of the central tenets of ID proponents. The means by which these genes arise are many. One of these, suggested by Cai at al. (the subject of one of the earlier essays), involved the adaptation of a gene encoding an evolutionarily-conserved non-coding RNA via the appearance, by mutation, of appropriate translation initiation and termination (“start” and “stop”) codons. This mechanism represents an intersection of sorts between the subject of protein evolution and another matter of discussion on these blogs, namely the existence, evolution, and “function” of junk DNA. In this essay, I review a 2007 study by Debrah Thompson and Roy Parker (“Cytoplasmic decay of intergenic transcripts in Saccharomyces cerevisiae”, Mol. Cell. Biol. 27, 92-101) that adds a great deal of clarity to this mode of gene and protein evolution.

Bless their hearts. The Creationists over at Answers in Genesis are working their perfectly designed fingers to the bone. Blowing the Discovery Institute out of the water by not only publishing a for-realsies science journal (well, at least once), but also performing ‘semi-technical’ research!

Darwin at the Drugstore? Testing the Biological Fitness of Antibiotic Resistant Bacteria

While its just adorable to see them working so hard, their crippled understanding of basic science leaves this semi-technical article completely worthless.

Our good ol’ buddy Casey Luskin at the Discovery Institute Media Complaints Division has just put up an impressively mistake-strewn story about the “Altenberg 16” meeting in Vienna. In real life, the meeting discussed the possibilities for an “Extended Synthesis” in evolutionary biology which incorporates development, evolvability, complexity theory, etc. into the old “Modern Synthesis” of population genetics. But in the land of cranks & ID/creationists, the Altenberg 16 meeting has become the latest bit of evidence that evolution is a theory in crisis. The primary person who got the crazy-train going was “journalist” Suzan Mazur, who has written a series of stories that mis-portray almost everyone and everything involved and, no matter what her interviewees tell her, end up with the inevitable conclusion that evolution is on its last legs. No one seriously informed would pay attention to this kind of schlock, but ID/creationists will jump on anything with a vestige of credibility (in this case an allegedly serious journalist – is she a freelancer or what?). When meeting organizer Massimo Pigluicci got wind of the misinformation being passed around about the meeting, he wrote a great explanation of what it was actually about and why Mazur et al. were wrong.

Anne Minard of National Geographic News writes on July 9th

The discovery of a missing link in the evolution of bizarre flatfishes—each of which has both eyes on the same side of its head—could give intelligent design advocates a sinking feeling.

CT scans of 50-million-year-old fossils have revealed an intermediate species between primitive flatfishes (with eyes on both sides of their heads) and the modern, lopsided versions, which include sole, flounder, and halibut.

So the change happened gradually, in a way consistent with evolution via natural selection—not suddenly, as researchers once had little choice but to believe, the authors of the new study say. … Though known for their odd eye arrangement, no flatfish start life that way. Each is born symmetrical, with one eye on each side of its skull.

As a flatfish develops from a larva to a juvenile, one eye migrates up and over the top of the head, coming to rest in its adult position on the opposite side of the skull. … Palmer added that the new work is “a fantastic paper” that helps resolve a mystery “that’s bedeviled evolutionary biologists for more than a century.

“It’s really been a major, major puzzle to evolutionary biologists.”

As expected, the Magisterium of Intelligent Design was quick to condemn the finding as simply floundering around, while the Institute of Creation Research has a turbot-charged attack on the finding, pointing out that flatfish are sole-ly members of the flatfish ‘kind,’ and putting National Geographic in it’s plaice.

Nick Matzke, one of the world's leading experts in detecting absurdities in creationist texts, has discovered a real howler from Casey Luskin. Luskin is complaining that he, Junior Woodchuck lawyer for an intellectually bankrupt propaganda mill, can't find the wrist bones in Tiktaalik when Neil Shubin, world-class paleontologist, is directly describing them. This is, admittedly, a fairly high-level discussion by Shubin, but it's amusing that Luskin isn't tripped up by the science — it's his command of the English language that lets him down.

When discussing Tiktaalik's "wrist," Shubin says he "invites direct comparisons" between Tiktaalik's fin and a true tetrapod limb. Surely this paper must have a diagram comparing the "wrist"-bones of Tiktaalik to a true tetrapod wrist, showing which bones correspond. So again I searched the paper. And again he provides no such diagram comparing the two. So we are left to decipher his jargon-filled written comparison in the following sentence by sentence analysis:

1. Shubin et al.: "The intermedium and ulnare of Tiktaalik have homologues to eponymous wrist bones of tetrapods with which they share similar positions and articular relations." (Note: I have labeled the intermedium and ulnare of Tiktaalik in the diagram below.)

Translation: OK, then exactly which "wrist bones of tetrapods" are Tiktaalik's bones homologous to? Shubin doesn't say. This is a technical scientific paper, so a few corresponding "wrist bone"-names from tetrapods would seem appropriate. But Shubin never gives any.

"Waaaaah," whines Luskin, "Shubin didn't tell us the names of the corresponding tetrapod wrist bones!"

Only he did. I guess "eponymous" is too difficult a word for a Junior Woodchuck.

Shubin is saying that there are bones with the same positions and articulations with neighboring bones in tetrapods and Tiktaalik, and that they have the same names. They have a small wrist bone that articulates with the ulna called the ulnare, and they have another bone called the intermedium. They have the same names.

Here's a nice diagram, color-coded and everything, just for Casey. Here are some fish:

And some tetrapods:

These clowns at the DI would be much funnier if more people would realize that they are performance artists with little talent and no expertise, except in lying and tripping over their own shoes.

Carl Zimmer has also noted Luskin's absurd error.

Tom McIver’s Library of Creationist Materials Available


Tom McIver, a member of Ohio Citizens for Science who works in the library at John Carroll University in Cleveland, is a long-time professional student of the creationism movement. His dissertation was Creationism: Intellectual Origins, Cultural Context, and Theoretical Diversity, which I am told will be put online by NCSE one of these days (Glenn? Josh?). Tom has written widely on various associated topics. For example, he had a 1988 article on Gap Theory in Creation/Evolution, published by the American Humanist Association, and an exhaustive(-ing?) bibliography he compiled, Anti-Evolution: An Annotated Bibliography, is scheduled for reissue as a paperback in 2008.

Tom has been on creationist tours, taken courses at the Institute for Creation Research, and has generally immersed himself in the topic for more than 20 years. He has even written poetry on ID:

Added July 15:

Please note the addition of links to NCSE’s library listing as well as Tom’s library listing. I note with interest that there is minimal overlap – less than 20% shared holdings – between Tom’s library and NCSE’s.)

John Freshwater was interviewed by Bob Burney on the April 28th, 2008 on 880 WRFD. I listened to the interview and was amazed by how Freshwater’s friends help undermine his own case

Bob mentions that one of his son’s is in Freshwater’s class

Bob: And from day 1, John, he has been telling me what a wonderful teacher you are and the fact that you present both sides to issues and which is just wonderful and unfortunately kind of rare in the schools today.

So what do you guess, did Freshwater tell about the two sides of homosexuality? Or was this a topic in which John decided to tell only one side of the story?

From CNN we learn that

The report also cites evidence that Mr. Freshwater told his students that “science is wrong because the Bible states that homosexuality is a sin and so anyone who is gay chooses to be gay and is therefore a sinner.”

Listen to the rest for more foolishness.

The Rise of Muslim Creationism

Couple of interesting stories about the efforts of Turkish Muslim creationist Harun Yahya (nee Adnan Oktar). From the New Humanist:

Oktar is a figure fairly well known to Darwinists and despite his claims to scientific competence is clearly little more than a crank. However what had changed, according to the report, was the scale and ambition of Oktar’s pseudo-scientific message. Since 2006 copies of a substantial, glossy and smartly packaged book called Atlas of Creation, credited to Harun Yahya, had been arriving at schools and universities across Europe. In Spain, France, Switzerland and Denmark clear evidence of the growing resources and confidence of European Muslim creationism was thudding on to the mat. The book is the first of a projected seven-part series, and parts two and three have already begun arriving at educational institutes Europe-wide.

(via NF)

And from Reuters:

Well-illustrated and free of theological jargon, they preach that Islam is the one true faith and Darwinism, by undermining religious belief, has led to the discord, atheism, terrorism and extreme political ideologies plaguing the world.

Reader-friendly, the books appeal to Muslims trying to square modern science with their faith in an inerrant Koran, much like Christian evangelicals who read the Bible literally and support creationism or intelligent design theories.

(via LGF)

Freshwater the story continues


After the attempts by Coach Daubenmire to defend Freshwater have failed miserably, most recently on Geraldo, an “official site” named “ Bible on the Desk” has been created which claims to be the official site for Freshwater. Its most visible attribute is a Donate button and a FoxNews interview.

Discovery [sic] Institute fellow John West has a long article at National Review praising the recently enacted Louisiana creationism law, which is of course disguised as a “protection” for “dissenting” teachers who are being persecuted by The Man. John Derbyshire, also at National Review, has an excellent response to it here, indicating that at least some prominent conservatives are fed up with the pseudoscience. (LGF, too.) According to West, the law simply gives teachers “a modest measure of protection” when they try to “question[]…the ‘consensus’ view on…scientific issues.” Of course, the law is more than that: it is an attempt to cleverly phrase an invitation to religious propagandists to use government-run, taxpayer-supported schools as a forum to teach religion to other people’s children.

To Derbyshire’s excellent analysis, I would add only the following.

Read the rest at Freespace…

Tangled Bank #109

The Tangled Bank

Greg Laden has created a festival of LOLcats for the latest edition of the Tangled Bank. Should I be appalled or amused? Science is serious business! We never laugh, we're all supposed to be like Mr Spock!

The lawsuit filed by Texas science educator Chris Comer (see Chris Comer Sues Texas Agency: ‘Neutrality’ is Endorsement of Religion) has been posted by the National Center for Science Education.

A juicy tidbit from the lawsuit:

… the Agency’s firing of its Director of Science for not remaining “neutral” on the subject violates the Establishment Clause, because it employs the symbolic and financial support of the State of Texas to achieve a religious purpose, and so has the purpose or effect of endorsing religion. By professing “neutrality,” the Agency credits creationism as a valid scientific theory. Finally, the Agency fired Director Comer without according her due process as required by the 14th Amendment — a protection especially important here because Director Comer was fired for contravening and unconstitutional policy.

Oh yeah - Watch NCSE’s video about Chris Comer.

NOTE TO COMMENTERS: The topic of this thread is Chris Comer’s lawsuit against the Texas Education Agency. Do not clutter this thread with unrelated topics like evidence of Christ’s resurrection, evidence for the Origin Of Life (OOL), etc. I won’t be as lenient as I was in the last thread on this topic.

Last fall, Texas science educator Christina Comer was fired for simply advising colleagues of an upcoming talk on Intelligent Design Creationism by professor Barbara Forrest. (See Expelled: Texas Education Agency Fires Staffer for Announcing Talk by Barbara Forrest for some of the details.)

Now, Comer is fighting back. USA Today reports on July 3rd that

A former science curriculum director for the Texas Education Agency has filed a federal lawsuit alleging she was illegally fired for forwarding an e-mail about a speaker who was critical of teaching a controversial alternative to evolution.

Christina Comer, who lost her job at the TEA last year, said in the suit filed Wednesday against the TEA and Education Commissioner Robert Scott that she was terminated for defying an unconstitutional policy that required employees to be neutral on the subject of creationism — the biblical interpretation of the origin of human life.

The e-mail, which was intercepted by a state education leader, was about a speaker coming to Austin who had critical views of creationism and the teaching of intelligent design.

The federal courts have ruled that teaching creationism as science in public schools is illegal under the U.S. Constitution’s provision preventing government establishment or endorsement of religious beliefs. “The agency’s ‘neutrality’ policy has the purpose or effect of endorsing religion, and thus violates the Establishment Clause,” the lawsuit said. … The lawsuit seeks a court order overturning the TEA’s neutrality policy on teaching of creationism and declaring that her dismissal was unconstitutional and her reinstatement to her old job.

Discuss. And, have a safe and happy 4th of July!

Charles Johnson has some thoughts on the sesquicentennial of evolutionary science.

Note: this turned into kind of a rough draft of an essay, and I think the part about the origin of life and complexity of the cell would be publishable in perhaps an education journal. So I welcome any comments on the argument, supporting or undermining points, etc. I don’t have my references folders handy at the moment but I have references in mind for all of the factual assertions, although more are always welcome. I’m very happy to acknowledge commentators if this does get published, or even have a coauthor if someone else is interested in working on this. Thanks!

I have not been able to blog much lately, due to minor distractions like grad school and actually having a social life for once (don’t everyone gasp at once an suck all of the air out of the room). But now it is summer and I am in a coffee shop, and I am feeling frisky. I just came across blogs by Jeff Shallit and PZ Myers responding to an essay in The Scientist entitled “What neo-creationists get right” by Gordy Slack, journalist and author of an excellent book on the Dover trial, The Battle Over the Meaning of Everything: Evolution, Intelligent Design, and a School Board in Dover, PA. (And Slack’s reply to PZ and PZ’s surreply.) Slack argued that part of the reason for the persistence of creationism is that evolutionists often react with “ridicule and self-righteous rage” on some issues where creationists might have a point, or are at least not so clearly wrong.

I consider both Slack and his critics friends and colleagues, and both sides make some valid points. But I think many of the arguments that both Slack and his critics make in this particular instance don’t work.

The “Darwin Year”


Following on from Wesley Elsberry's post, readers may be somewhat surprised that Evolving Thoughts hasn't made much of the Darwin bicentennial and the Origin sesquicentennial so far. Well, I haven't needed to, given the number of other folk making hay from this. In particular I recommend Carl Zimmer's piece, over at his new digs with Discover magazine. Carl points out John van Whye's paper that showed that Darwin didn't "sit on the theory for 20 years" but rather followed a preplanned sequence for backing up his ideas. However, when Charles planned this research, he greatly underestimated the time it would take him (the Cirripedia volumes, where he dissected and described all known and extinct barnacles, took him much longer than he anticipated), and so it blew out from 8 to 20 years.

But there's another point I want to make about this anniversary, and it is this: Darwin, as important as he was, is not the crucial man in the history of biology. And to make this claim out, I have to discuss some theories of history, and how they affect the history of science.

Read more at Evolving Thoughts

You’ll be hearing that a lot on science blogs over the next year-and-a-half in the run-up to November 24, 2009, the 150th anniversary of the publication of Charles Darwin’s “Origin of Species”. But we should start with another 150th anniversary that is marked today, July 1, 2008…

One hundred fifty years ago, this date fell on a Thursday. On that Thursday, the meeting of the Linnean Society in London had a reading of an essay by Alfred Russel Wallace and a manuscript chapter extract and a letter from Charles R. Darwin on the topic of tranformism, or the evolution of new species from existing species. This collage of material was presented under a single title, On the tendency of species to form varieties; and on the perpetuation of varieties and species by natural means of selection.

The reading itself produced hardly a ripple in the currents of scientific discourse; the Linnean Society president Thomas Bell noted in his journal that nothing of importance took place in that year. The real story lay in how it came to be that there was a joint presentation of material from Wallace and Darwin, rather than Wallace alone, and in the course of history that followed on.

(Original posting at the Austringer.)

Good ‘ol Creationists. Whether they are farting, or rapping, or challenging respected scientists to a dual, you can always count on Creationist antics for a good laugh.

I get an especially fine kick out of ID Creationisms attempts at courting youngsters. ‘Wacky, zany’ Overwhelming Evidence is just another link farm for Denyse O’Leary, and William ‘Im a REBEL!’ Dembskis companion book to EXPELLED is just a chunky regurgitation of his disastrous presentation at the University of Oklahoma last fall.

But as funny as their clumsy attempts are, parents still have trouble making sure their kids are getting the best science education possible. PT regularly gets emails from concerned parents/aunts/uncles/grandparents who are looking for quality science books for their little ones. I wont be an aunt for another few weeks (twin nieces, WHOO!!), but I jumped up with my favorite suggestions the last time Reed asked for book recommendations. See, I was raised by a librarian and a science/math teacher (how I grew up to be such a nerd, we may never know), and one day my mom brought home the coolest science books ever: Dorling Kindersley’s ‘Eyewitness’ books.

They have a book on Evolution. They have a book on the origin of life (which includes discussion of viruses!). They have a book on prehistoric man. They have a book on ‘great scientists’ (which includes Darwin) as well as one on Darwin.

They have a book for basically any pro-science topic you can think of, and they are written in an unapologetically pro-science manner… So Creationists hate them.

Here is the best part (for me)—Even though most of them are targeted to 7-12 year olds, I still thought they rocked when I got a chance to read them in high school. Beautiful pictures, cram-packed with data and fun facts, they were like a ‘smart’ magazine. The Eyewitness books provide ample opportunities for children and parents to learn something new. Despite their age target, these arent baby books.

And here is a bonus for you pro-science parents out there—if my hometown second grade library stocks these books, there is a good chance you can find (or request them) at your local library!

But the Eyewitness books are by no means the only pro-science kids books out there! Here are a couple others that PT writers suggested:

And Im sure many parents would be happy to have mare reader suggestions in the comments!

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