April 2006 Archives

IBM researchers have shown how science explores new and innovative approaches to discover DNA patterns which are shared by areas of the human genome that were considered to have little or no influence on its function and areas which do have function.

From the IBM Press Release

As reported today in the Proceedings of the National Academy of Sciences (PNAS), regions of the human genome that were assumed to largely contain evolutionary leftovers (called “junk DNA”) may actually hold significant clues that can add to scientists’ understanding of cellular processes. IBM researchers have discovered that these regions contain numerous, short DNA “motifs,” or repeating sequence fragments, which also are present in the parts of the genome that give rise to proteins.

Professor Steve Jones presented a lecture at the Royal Society on evolution and creationism. The lecture can be watched at this link

Science is about disbelief. It accepts that all knowledge is provisional and that any theory might in principle be disproved. Some theories are better established than others: the earth is probably not flat, babies are almost certainly not brought by storks, and men and dinosaurs are unlikely to have appeared on earth within the past few thousand years. Even so, nothing is sacred in 1905 classical physics collapsed after a seemingly trivial observation about glowing gases and the same is potentially true for all other scientific theories.

Unlike ID, science is indeed tentative and can accept false positives. In addition, science can in fact accept our ignorance in some matters. This ignorance is often seen as evidence for design. Such gap arguments are what make Intelligent Design scientifically vacuous.

Many biologists are worried by a recent and unexpected return of an argument based on belief by the certainty, untestable and unsupported by evidence, that life did not evolve but appeared by supernatural means. Worldwide, more people believe in creationism than in evolution. Why do no biologists agree? Steve Jones will talk about what evolution is, about new evidence that men and chimps are close relatives and about how we are, nevertheless, unique and why creationism does more harm to religion than it does to science.

I will have to listen to Jones’s talk. I certainly agree with him that intelligent design does a lot of harm to religion. As far as science is concerned, it mostly serves to confuse people with what many have come to accept as a scientifically vacuous approach.

Steve Jones won the Aventis Prize for Science Books (then known as the Rhone-Poulenc Prize) in 1994 for ‘The Language of the Genes’. In 1997 he was awarded the Royal Society’s Michael Faraday Prize - the UK’s foremost award for communicating science to the public.

Some good news from our British friends.

A statement opposing the misrepresentation of evolution in schools to promote particular religious beliefs was published today (11 April 2006) by the Royal Society, the UK national academy of science.

The statement points out that evolution is “recognised as the best explanation for the development of life on Earth from its beginnings and for the diversity of species” and that it is “rightly taught as an essential part of biology and science courses in schools, colleges and universities across the world”.

Royal Society Press Release

I just can’t imagine how stressful it is to be an ID advocate. You’ve got all this maze of sound-bites and talking points to navigate, all vetted by professional Public Relations operatives and carefully studied to send the appropriate message, and then you get distracted one moment, open you mouth and - BAM - you mess it all up. Here’s one more example. Do you remember ever hearing ID advocates proclaim that “we should follow the evidence wherever it leads”? If not, you haven’t been paying attention (don’t worry, you can still catch up here or here, for instance). If you believed the ID advocates’ spin, however, you probably should have read the small print, because apparently there’s at least one exception: you are allowed not to follow the evidence after all, if doing so will take you to conclusions that may challenge your religious beliefs. In fact, it’s actually better not to even try to follow it there, just in case.

Everyone has probably heard that the new White House Press Secretary is Tony Snow, formerly a talk show host on Fox News. Those who were paying attention last year may remember that he is also pretty clearly a straight-up creationist, or at least credulously repeats their talking points. See:

Tony Snow (2005). “Why can’t we have a rational debate.” TownHall.com. August 12, 2005

Media Matters (2005). “Tony Snow’s evolutionary falsehoods.” Media Matters for America. August 12, 2005.

Media Matters (2005). “The many falsehoods of Tony Snow.” Media Matters for America. April 19, 2006.

What got Tony Snow writing essays about ID and how hard it was to have a rational debate? I may have had a wee bit to do with that.

No ID here at all. Move along. Nothing to see.

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For months and months, right up to February 2006, we in Ohio were told that the “critical analysis of evolution” benchmark and lesson plan wasn’t ID. ID advocates on the Ohio State Board of Education – Michael Cochran and Deborah Owens-Fink – told us that; the author of the “critical analysis” lesson plan, Bryan Leonard, told us that; the DI repeatedly trumpeted “no ID!” on its web site. No ID at all here, folks, we were assured. Perish the thought!

But in a recent Seattle Times article, Bruce Chapman, President of the Discovery Institute, was reported to have said that Ohio’s State Board of Education eliminated intelligent design when it discarded the creationist benchmark and lesson plan in February. According to the story,

Already, he [Chapman] said, an effort in Ohio to include intelligent design in school curricula failed when some state school-board members said the Dover case settled the issue. (Italics added)

”… an effort in Ohio to include intelligent design”. Well, well. Who woulda thunk it!

The DI’s Media Complaints Division took immediate umbrage. Rob Crowther complained that the reporter got it all wrong. Crowther wrote

It isn’t just the theory of intelligent design that Postman has trouble getting straight, it is the facts of what is going on in the public policy debate. He writes that:

“an effort in Ohio to include intelligent design in school curricula failed when some state school-board members said the Dover case settled the issue.”

Notice what Crowther left out in the sentence that he quoted from the story: “Already, he said,…”. The reporter didn’t say it, he reported what Chapman said – the antecedent of “he” in that sentence is Chapman.

And now, the rest of the story …

Galapagos tortoise webcam!

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Over at the American Museum of Natural History is an online exhibit on Darwin, that features a Galapagos tortoise webcam! It’s rather soothing, the tortoises aren’t very speedy. (Hat tip to Margaret)

Over on the DI’s new Declaring-Victory-in-Superficial-Public-Debates-Where-No-Federal-Judges-are- -Present-to-Enforce-Actual-Rules-of-Evidence-and-Keep-You-Honest blog, Bruce Chapman highlights a news story on a recent debate at North Carolina State University. Describing the four-person panel, Chapman writes,

North Carolina State University has shown, however, that the topic can be debated with the fairness and civility that ought to characterize academic discussions. On Thursday, April 20, before a crowd of some 200 people, a biologist and philosopher defended intelligent design, and a biologist and philosopher defended Darwinism.

The articles says that the two ID defenders were “Gerald Van Dyke, an NCSU botany professor, and Robert Hambourger, an NCSU associate professor of philosophy.” I was pretty sure I had heard of pretty much all publicly speaking ID supporters who had something resembling a biology PhD – it is easy to remember them, because it is a very short list. So who was this Gerald Van Dyke guy? It turns out he is indeed an honest-to-goodness Professor of Mycology at NCSU. He works on pathogenic fungi that attack agricultural crops.

Even though I didn’t remember him specifically, he seemed familiar for some reason.

An argument is ORFaned

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Paul Nelson has a “new” argument against common descent. It revolves around the discovery of ORFans, “orphan Open Reading Frames”, ie stretches of DNA that appear to code for a protein (an Open Reading Frame, ORF), but that we have no current idea of what the protein is or does, or what other proteins it is related to (hence ORFan). A powerpoint presentation from one of Dr. Nelson’s talks that mentions ORFans is here. ORFans also loom large in Dr. Nelsons rather forceful commentary on a post by Sahotra Sarkar describing a debate between them.

Are ORFan’s a significant problem for evolution? No, not in the least. The ORFan story, while still not completely understood, represents a good example of how science works, and why it’s a good idea to actually understand evolutionary biology before you criticise it (and why it’s a good idea to not stop reading in 2003).

Tangled Bank Episode LII

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The Tangled Bank

The latest edition of the Tangled Bank is coming straight to you from Coruscant…and the opening text is almost as long as the latest from Lucas, although fortunately it doesn't say anything about the trade federation and boring treaties.

“One science question”

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Both RPM and Chad beat me to posting this survey [edited to add: and Janet too! Freakin’ quick triggers…], which I’ve had in my drafts box for a week. So, before absolutely everyone else beats me to it, I thought I’d pose the questions to y’all, and see how you would answer the question, “What is one science question every high school graduate should be able to answer?”

(Continued at Aetiology)

Evo-Devo in NYR Books!

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This really is an excellent review of three books in the field of evo-devoFrom DNA to Diversity: Molecular Genetics and the Evolution of Animal Design (amzn/b&n/abe/pwll), Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom (amzn/b&n/abe/pwll), and The Plausibility of Life:Resolving Darwin's Dilemma (amzn/b&n/abe/pwll)—all highly recommended by me and the NY Times. The nice thing about this review, too, is that it gives a short summary of the field and its growing importance.

This post contains my commentary on the Annotated Bibliography on the Evolution of the Immune System, now online in the NCSE Kitzmiller archive. The Annotated Bibliography describes the significance of each publication listed in the Supplementary Material for the recent Nature Immunology article on the “immune system cross” during Behe’s testimony in Kitzmiller v. Dover. For article, click here. For the full Annotated Bibliography, click here. The Annotated Bibliography has reached an approximately final state, but I would still be interested in any additional comments people might have. My overall point with all this, of course, is that unless and until ID proponents (1) acknowledge the existence of this scientific literature, (2) admit that their previous statements about the nonexistence of this literature were wrong, and (3) substantively rebut this literature, providing a better and more detailed explanation for the immune system, then they aren’t even beginning to be scientifically serious.

As you read through this, keep in mind the Discovery Institute’s hiliarious commentary in their recent book attempting to rebut to the Kitzmiller decision, Traipsing Into Evolution:

Consider [Judge Jones’s] skewed summary of the evidence relating to the irreducible complexity of the immune system. He cited Kenneth Miller’s speculative assertions as if they were facts, while refusing even to mention biochemist Michael Behe’s detailed rebuttal during the trial. (Traipsing, p. 45, italics added)

Speculative? I guess in ID-Land, dozens of publications in top journals confirming key expectations is “speculation”, whereas the vague statement that divine intervention occurred sometime, somewhere, for unspecified reasons is considered rock-solid. Even better, Traipsing then quotes from Behe’s “detailed response” to the immune system section of Jones’s opinion. However, the book neglects to point out that Behe tried exactly the same silly arguments in his direct testimony at trial, and they were specifically debunked on cross-examination. For more on Behe’s “detailed rebuttal”, see here.

ID Arguments from Creationist Sources

One of the folks at William Dembski’s blog has issued a challenge. He claims that all of the arguments that we use to establish that ID is substantially the same as creationism are based on false premises (he’s wrong about that) and he says:

Why can’t ID opponents focus on the arguments, themselves, and show how they are equivalent to Creationism? If ID really is just repackaged Creationism, why not just expose the arguments for what they are and be done with it?

I take him up on his challenge and show the creationist roots of all of the major ID arguments in a post at Dispatches from the Culture Wars. Comments may be left there.

A new Dr. Steve

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This should have happened last week, but longtime PT contributor and author of the much-beloved “The Quixotic Message”, or “No Free Hunch”, and also the equally beloved Quixotic References, formerly known as theyeti, and catcher of broadheaded skinks and legless glass lizards, mild critic of hydrogen as an alternative fuel, HAS SUCCESSFULLY DEFENDED HIS PHD!!! (although he somehow lost his original post announcing this). He somehow managed to do this while writing all of these great PT posts, including classics like Phillip Johnson’s Bold Stand and Phillip Johnson’s Bold Stand, Redux.

More importantly, Steve can now finally achieve his true reason for getting a PhD, which was to join the list of Project Steve Steves.

I don’t actually know what Reuland’s PhD was about, something biomedical I think, but for now I think I will assume it had something to do with getting Sunbeams From Cucumbers.

Cold Case Kansas

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The Douglas County Sheriff is closing the case of Mirecki’s beating because they can’t find any leads.

The trail has gone cold in the investigation of a roadside beating reported late last year by a Kansas University professor.

Douglas County Sheriff’s Office spokeswoman Lt. Kari Wempe said Thursday that detectives had finished their paperwork related to religious studies professor Paul Mirecki’s report that he was beaten by two unknown men on Dec. 5, 2005, on a roadside south of Lawrence.

The office has not identified any suspects and, unless any new leads come in, the investigation is finished.

At the time, Mirecki was under fire for comments he had posted online critical of organized religion.

Now back when Mirecki was assaulted some pundits claimed that he had staged the beating. Given that the case has closed without any charges filed, it would appear that those pundits owe Mirecki an apology.

Hopefully, Pianka and the Texas Academy of Science are still watching their backs.

Steve Jones, the award-winning geneticist and author, argued that suggesting that creationism and evolution be given equal weight in education was “rather like starting genetics lectures by discussing the theory that babies are brought by storks”.

Link

The Game PlanHere in the pounding-nails-into-the-ID-coffin department of the Panda’s Thumb, we are still hard at work. Longtime PT posters Andrea Bottaro, Matt Inlay, and I have just published a “Commentary” essay in May 2006 issue of Nature Immunology. (Update: Subscription no longer required. Thanks to NI.) See the NCSE announcement and more background at the NCSE Evolution Education and the Law website.

The article is:

Bottaro, Andrea, Inlay, Matt A., and Matzke, Nicholas J. (2006). “Immunology in the spotlight at the Dover ‘Intelligent Design’ trial.” Nature Immunology. 7(5), 433-435. May 2005. (Subscription no longer required: DOI | Journal | Google Scholar | PubMed | Supplementary Material)

Therein, we review the now-notorious episode in the Kitzmiller case where, during Eric Rothschild’s dissection of Michael Behe, Rothschild challenged Behe’s claims about the scientific literature on the evolutionary origin of the immune system by piling up on Behe’s podium a stack of books and articles on the evolution of the immune system. Behe responded that he had not read most of it, but dismissed it out of hand, and this cavalier attitude seems to have been one (of many) factors that impressed Judge Jones and persuaded him to issue the thorough, detailed ruling that he did.

Barbara Forrest’s role in Kitzmiller

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Many people have played important roles in exposing the scientific vacuity of Intelligent Design and its religious foundations. On Red State Rabble, Pat Hayes describes the role played by Barbara Forrest in bringing down ID. Barbara Forrest and Paul Gross are the authors of the highly insightful book Creationism’s Trojan Horse: The Wedge of Intelligent Design published in 2004 by Oxford University Press

Pat Hayes Wrote:

In the months since the Dover decision, leaders of the intelligent design movement have played and re-played the trial a thousand times. The Discovery Institute and the Thomas More Law Center have had a very public falling out. Intelligent design proponents have come to refer to Judge Jones, a lifelong Republican who was appointed by George W. Bush, as an activist judge.

What they have not done, as a movement whose leaders are nearly all men, is come to grips with the great role played in their embarrassing defeat by Barbara Forrest, a tiny but very determined woman from Louisiana, who simply took their own words and turned them against them.

Evolving spots, again and again

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flyspot_tease.jpg

It's all about style. When you're out and about looking for mates, what tends to draw the eye first are general signals—health and vigor, symmetry, absence of blemishes or injuries, that sort of thing—but then we also look for that special something, that je ne sais quoi, that dash of character and fashionable uniqueness. In humans, we see the pursuit of that elusive element in shifting fashions: hairstyles, clothing, and makeup change season by season in our efforts to stand out and catch the eye in subtle ways that do not distract from the more important signals of beauty and health.

Flies do the same thing, exhibiting genetic traits that draw the attention of the opposite sex, and while nowhere near as flighty as the foibles of human fashion, they do exhibit considerable variability. Changes in body pigmentation, courtship rituals, and pheromones are all affected by sexual selection, but one odd feature in particular is the presence of spots on the wing. Flies flash and vibrate their wings at prospective mates, so the presence or absence of wing spots can be a distinctive species-specific element in their evolution. One curious thing is that wing spots seem to be easy to lose and gain in a fly lineage, and species independently generate very similar pigment spots. What is it about these patterns that makes them simultaneously labile and frequently re-expressed?

Continue reading "Evolving spots, again and again" (on Pharyngula)

The US News and World Report recently released their 2007 rankings for graduate schools. The report covers both professional and graduate programs like medical and law schools and science Ph.D. programs. The science Ph.D. programs are split into disciplines and subdisciplines. Bellow, I’ll share with y’all the rankings of the two subdisciplines most relevant for what we do here: Ph.D. programs in Ecology/Evolutionary Biology and Paleontology. These rankings are not entirely accurate because any program that is part of a medical school (like Stanford’s EEB) is not listed in these ranking but instead is considered as part of the medical school rankings. (Disclaimer: My program is listed in the EEB rankings.)

Rank Ecology & Evolutionary Biology Rank Paleontology
1 University of California–Davis 1 University of Chicago
2 University of California–Berkeley 2 Harvard University
3 Harvard University 3 University of Michigan–Ann Arbor
4 University of Chicago 3 Yale University
5 Duke University 5 University of California–Berkeley
6 Cornell University 6 University of Kansas
6 University of Michigan–Ann Arbor 7 University of Cincinnati
8 Indiana University–Bloomington 8 University of Iowa
8 Princeton University 9 University of Texas–Austin
8 University of Georgia 10 Ohio State University

So, if any of our readers are looking to go to graduate school in evolutionary biology, they should give a good look to these programs. If you want to look at genetics/genomics/bioinformatics, biochemistry, or other fields that also relate to evolution you’re going to need to pick up a copy of the US News and World Report’s rankings.

Though much of the attention to and reports of intelligent design/creationist shenanigans come from the United States, we’re certainly not the only ones inundated with deniers of evolution and other sciences. A self-described UK evolution “sceptic” is journalist Melanie Phillips, who writes for The Daily Mail. She’s annoyed many scientists in the country due to her views not only on evolution, but also on vaccination (such as this article from earlier this year), drawing the ire of many who point out that she doesn’t understand the underlying science.

She’s proven her critics correct again, with a recent article touching on everything from the Da Vinci Code, to religion/lack thereof, and to, of course, evolution.

(Continue reading at Aetiology)

The DI Denies Its Own Nature

Yesterday, the Baylor student newspaper printed an article that referred to the Discovery Institute as a “conservative Christian think tank”. The DI, as you can imagine, didn’t like that description one bit because, frankly, they’ve spent so many years selling the silly notion that they’re not a conservative Christian think tank and it’s just annoying when all that propaganda doesn’t pay dividends. They fired off a letter and the Baylor paper caved in immediately and pulled the article and made a “correction”. A brief look at the evidence will show that the paper got it right the first time.

Continue Reading at Dispatches from the Culture Wars. Comments may be left there.

The God Meter

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A week or so ago, I attended “Darwinian Evolution in the 21st Century,” the 21st Regional Conference on the History and Philosophy of Science (Friday evening and Saturday, April 7 and 8, 2006) at the University of Colorado. The conference kicked off with talks by Rob Pennock and Betty Smocovitis on Friday night and continued Saturday with eight contributed papers. Anyone who is in the Boulder-Denver area at roughly this time next year will doubtless be rewarded by attending the 22nd conference.

Victor Stenger of the University of Colorado presented a talk called “ Can Science Study the Supernatural?” He concluded, correctly in my opinion, that it can. Indeed, Professor Stenger considers that we are studying claims of the supernatural when we study ESP, near-death experiences, the Shroud of Turin, or religious visions or miracles. Some of these turn out to have plausible natural explanations, but we could not have said a priori that they would necessarily. Many people accept studies of the supernatural when “supernatural” is interpreted to mean ESP or near-death experiences but demur when the question is phrased, “Can Science Study Religion?” or “Can Science Study God?” as opposed to the broader “supernatural.” I will argue, with Professor Stenger, that science can indeed study claims of religion when those claims are factual statements about the natural world or purport to be factual statements about the natural world. But I will take issue with his contention that science has disproved the existence of God and show why I think it is a politically dangerous argument.

najash_tease.jpg

It's a busy time for transitional fossil news—first they find a fishapod, and now we've got a Cretaceous snake with legs and a pelvis. One's in the process of gaining legs, the other is in the early stages of losing them.

Najash rionegrina was discovered in a terrestrial fossil deposit in Argentina, which is important in the ongoing debate about whether snakes evolved from marine or terrestrial ancestors. The specimen isn't entirely complete (but enough material is present to unambiguously identify it as a snake), consisting of a partial skull and a section of trunk. It has a sacrum! It has a pelvic girdle! It has hindlimbs, with femora, fibulae, and tibiae! It's a definitive snake with legs, and it's the oldest snake yet found.

Continue reading "Najash rionegrina, a snake with legs" (on Pharyngula)

Show Up.

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How involved in politics should scientists be? What factors are important when it comes to making that decision?

For some of us, the answer to that comes fairly easily. One or two of us managed to evade the stereotype of the scientist-of-the-future, and caught the involvement bug because we were popular enough to win a role in student government early in our lives. A few of us were caught in a different stereotype - the children of the flower children - and have never known what it is like to not be involved in political causes. A bunch of scientists are just plain incapable of keeping their noses out of anything they bump into, whether it directly involves science or not.

The decision is harder for others. There are a few scientists who really do have an ivory tower mindset, and actively try to avoid anything that smacks of politics. Many put so many hours into their science that they don’t have any to spare for politics. More are apathetic to politics, or disillusioned, or simply unaware of the issues.

Both the involved and uninvolved should read a new article in PLoS Biology. The article, “Scientific Illiteracy and the Partisan Takeover of Biology,” provides some reasons to get more involved in the political process and some hints as to where the efforts of scientists might most effectively be focused.

Read More (at The Questionable Authority):

Mark Psiaki, Associate Professor at the Sibley School of Mechanical & Aerospace Engineering which is part of the Cornell University and advisor of Cornell’s IDEA club provides us with some insights into the minds of ID activists. I will leave most of his claims without comments as they speak best for themselves.

Mark Psiaki Wrote:

The principle of irreducible complexity does not give one all of biology, but if true, it serves to divert the biologist from wasting time by trying to answer a question to which there is no scientific answer.

Guest Post: Follow-up to last night’s panel discussion on ID/Evolution

How more upfront can one be about the scientific vacuity of Intelligent Design?

Of course Irreducible Complexity is flawed in many ways such as 1) it limits itself to Darwinian pathways 2) it concludes that IC systems are not just evidence against Darwinian theory but also in favor of Intelligent Design (false duality) 3) Darwinian pathways to IC systems have been identified.

How to make a bat

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fossil_bat.jpg

or•gan•ic | ôr'ganik | adjective. denoting a relation between elements of something such that they fit together harmoniously as necessary parts of a whole; characterized by continuous or natural development.

One of the wonderful things about how development works is that organisms function as wholes, and changes in one property trivially induce concordant changes in other properties. Tug on one element, changing it's orientation or size, and during embryogenesis any adjacent elements make compensatory adjustments, so that the resultant form flows, fits, and looks organic. This isn't that surprising a feature of development, though, unless you have the mistaken idea that the genome encodes a blueprint of morphology. It doesn't; what it contains is a description of interacting agents that work together in a process to produce a complex result. Changes in genes and regulatory elements can essentially produce changes in rules of development, rather than crudely specifying blocks of morphology.

What does this mean for evolution? It means that subtle changes to the rules of development can be caused by small changes to genes (and especially, to regulatory regions of genes), and that the resulting morphological changes may be dramatic, but are still integrated organically into the form of the organism as a whole. Our understanding of how development works is making it clear that large scale macroevolutionary change may be much easier than we had thought.

Here's an example where this insight is clarifying the evolution of an organism: the fossil record of bats shows an abrupt appearance of fairly sophisticated creatures with elongated digits, clearly capable of gliding or powered flight, with no known intermediates. We expect there were less fully flight-ready predecessors, but fossil preservation is not kind to small, delicate boned animals. It's also possible that the transitional period was fairly brief; it looks like turning a paw into a long-fingered membranous wing may be a fairly simple change on a molecular level.

Continue reading "How to make a bat" (on Pharyngula)

Recent research on the origins and evolution of the genetic code have shown how “The standard genetic code enhances adaptive evolution of proteins” in a paper by Wen Zhu, Stephen Freeland, Journal of Theoretical Biology 239 (2006) 63–70

Not only is the genetic code ‘optimal’ in the sense that the effects of point mutations or mistranslations on the phenotype are minimized, a property which seems to argue for stasis, but the genetic code also speeds up the rate of adaptive evolution, a property which seems to argue for rapid change.

Again we see how the concept of robustness and evolvability are intricately linked in the genetic code.

On The Design Paradigm Salvador Cordova ‘responds’ (sic) to various claims about evolution and irreducible complexity. As I will show, the response further establishes the scientific vacuity of Intelligent Design.

Salvador Cordova Wrote:

You said, “You should also read up on existing evolutionary explanations for complexity such as scaffolding and Co-option “. No rather you should try to refute the well reasoned issues posed by the displacement theorem and the improbabilities associated with large scale co-option.

Nice redirection from examples of IC systems arising by natural pathways to yet another poorly developed concept of ID namely the displacement theorem. While the displacement theorem once again shows that ID is all about the supernatural, it also shows that as long as the system is ‘open’ to external information, there are no real issues. In other words, whether the external information is the environment or some supernatural or natural designer, it does not help ID’s cause. See Bad Math for more comments on Dembski’s claims.

As to the probabilities of ‘large scale co-option’ I notice the absence of much of any argument, calculations etc to support this claim.

While the scientific vacuity of Intelligent Design has been well documented, it does not hurt to show how Intelligent Design compares to evolutionary science.

NEW LONDON, Conn. - Phillip Barnes, associate professor of biology at Connecticut College, will explore the nature of science by contrasting evolutionary biology with intelligent design in a free and public lecture on Thursday, April 20, at 4:30 p.m. in Room 014 of the F.W. Olin Science Center.

His talk, “Evolution and Intelligent Design,” will include a discussion of the predictive power of the science of evolution “and its relevance for setting public policy in the potential avian flu epidemic, while intelligent design provides no relevant predictions or information for public policy,” Barnes said. Time for questions and discussion will follow.

Link

No, your other left!

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Bergstrom_2006_flatfish_polymorphs.jpgI have just come across the world’s coolest flatfish picture, and I just thought I would share. Apparently seven of the world’s 550 species of flounder are actually polymorphic for which side of the juvenile becomes the new “top” side in the adult flatfish. Apparently either eye can pop out and rotate to the new top. This says some rather interesting things about the developmental processes involved.

For more, go check out the webpage describing the research of famed flatfish researcher Dr. Carolyn Bergstrom of Bamfield Marine Science Centre in Bamfield, British Columbia.

See also this random talk.origins discussion, on “Why did the flatfish’s eye move from one side to the other?,” and this funny reply, and this other random talk.origins post.

Seems ID activists do not shy away from inflation after all… In this case inflation of claims about a course taught by Allen MacNeill at Cornell.

The Cornell IDEA Club then posted a notice on their blog about the course, pointing out that it would be a seminar in which intelligent design theory would be discussed in the larger framework of its relationship to evolutionary theory. However (perhaps because of the source), this was immediately picked up by several websites supporting ID (most notably World Net Daily) and spun as “Cornell to Offer Course in Intelligent Design.”

Link

Of course our friends at Uncommon Descent decided to join the fray with Cordova’s posting ID Course at Cornell.

Seems ID is desperate for attention but why not spend all this effort and energy on making ID scientifically relevant? Or is that too hard? Let’s read on:

Thermodynamics, Again

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A while back Mark Perakh wrote this essay dissecting the attempt by mathematician Granville Sewell to revive the thermodynamics argument against evolution.

Actually, Sewell's argument was so bad that I felt there was even more to say beyond Mark's fine analysis. The fruits of my labors are now available at CSICOP's Creation and ID Watch website.

We’ve already documented the profoundly silly response of the Discovery Institute and ID advocates to the recent announcement of the finding of Tiktaalik roseae; now let’s look at the response of more traditional creationists. Two creationist groups, the young earth Answers in Genesis and the old earth Reasons to Believe, have put out press releases (what is it with creationists and press releases?) claiming to have debunked the finding and shown that it poses no problem for creationism. As we will see, this is wishful thinking to the point of delusion on the part of both organizations.

Continue Reading at Dispatches from the Culture Wars. Comments may be left there.

neutrality, evolution and ID

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Note: Much of the introduction has been rewritten to correct some errors about the nature of the blog and the name of the blog (PvM)

Allen MacNeill, who has announced the Cornell Course “ Evolution and Design: Is There Purpose in Nature?” has a personal web blog called “The Evolution List”. In a posting titled Where The REAL Action Is In Evolutionary Biology MacNeill addresses the role of neutrality in evolution.

Since ID activists seem to have some problems understanding the importance of neutrality, such as the fact that neutraility is a selectable trait, I responded as follows: Various people have pointed out that the language used in my response is overly technical. I will attempt in a future posting to address the various concepts in more detail and hopefully make them more accessible to all interested parties

Sobering thoughts on ID

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Intelligent Design activists have become more and more insistent, given the recent court rulings, that Intelligent Design is not religious (wink wink) as it merely identifies ‘designed’ objects and does not say anything about the ‘designer(s)’. While others have already shown how vacuous such claims are, a recent paper takes a different take on this issue. Elliott Sober in a paper titled INTELLIGENT DESIGN THEORY AND THE SUPERNATURAL – THE “GOD OR EXTRA-TERRESTRIALS” REPLY describes how ID points to a supernatural intelligent designer.

The study was reported in the journal Nature

Asa Issie, Aramis and the origin of Australopithecus Nature 440, 883-889 (13 April 2006)

Tim D. White, Giday WoldeGabriel, Berhane Asfaw, Stan Ambrose, Yonas Beyene, Raymond L. Bernor, Jean-Renaud Boisserie, Brian Currie, Henry Gilbert, Yohannes Haile-Selassie, William K. Hart, Leslea J. Hlusko, F. Clark Howell, Reiko T. Kono, Thomas Lehmann, Antoine Louchart, C. Owen Lovejoy, Paul R. Renne, Haruo Saegusa, Elisabeth S. Vrba, Hank Wesselman and Gen Suwa

The latest fossil unearthed from a human ancestral hot spot in Africa allows scientists to link together the most complete chain of human evolution so far.

The 4.2 million-year-old fossil discovered in northeastern Ethiopia helps scientists fill in the gaps of how human ancestors made the giant leap from one species to another.

That’s because the newest fossil, the species Australopithecus anamensis, was found in the region of the Middle Awash - where seven other human-like species spanning nearly 6 million years and three major phases of human development were previously discovered.

Source

A new study in the journal Pediatrics suggests that a tonsillectomy may improve the condition of kids diagnosed with attention defecit/hyperactivity disorder (ADHD). I think it’s an excellent case of some true “alternative explanations” for the data that the creationist/ID types often crow about.

Creationists often try to validate their position by saying that both they and mainstream scientists start from the same data, but that creationists use their “Bible glasses” to interpret it, while scientists view it through their “evolution glasses.” In other words, they’re not wrong–it’s just a different interpretation of the same data, and where you end up depends on your initial biases and worldview. Though this is bogus when it comes to creationism, there are indeed real debates in the literature, where two hypotheses may be similarly compelling.

(Read more at Aetiology)

With the recent discovery of Tiktaalik, and the paper in Science showing that yet another complex biological system has now yielded to an evolutionary explanation, evoution has been in the news quite a bit lately. That inevitably leads to thoughts about how best to present evolution to the public. I offer some thoughts on that subject in two entries over at EvolutionBlog: Part One here and Part Two here. Part One discusses Bill Nye's appearance on the MSNBC show Countdown, and some of the press releases related to the Science paper. Part two discusses this article, from today's New York Times, about the recent film Flock of Dodos. Enjoy!

Advice for Schools

Here is an excellent, short, readable article for teachers and school administrators on what they can teach about Intelligent Design. See also this article briefly explaining the Kitzmiller case.

Tangled Bank #51

The Tangled Bank

We have a new Tangled Bank up, and it's enough to make this old Seattle boy homesick—the premise is to bring up all these nice science links during a walking tour of the city. If only they did sell Tiktaalik at the Pike Place Market…

Yet more desperation at the DI

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In the latest misaimed blast from the Whine and Cheese Division of the Discovery Institute, Michael Francisco expresses shock and dismay at the idea that people would actually claim that Intelligent Design and creationism are the same thing:

Finally, during the debate over [Kentucky Governor] Fletcher’s school board nominees, one House member argued they should “send a message that we are not a state that will fall prey to intelligent design, which is nothing more than creationism.” This argument merely repeats the common misconception that intelligent design and creationism are the same.

With all the effort that those dedicated Discovery Institute folks have put into trying to convince people that ID really isn’t creationism, what could possibly make people think that it is?

Read more (at The Questionable Authority):

Rio Rancho Policy Amended

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Last night (April 10th), the Rio Rancho School Board held a hearing on it’s controversial “Science Policy 401.” rrboardroom.jpg

After hearing from about 30 of the more than 100 people packed into the board room, the board deleted the phrase from the original policy

When appropriate and consistent with the New Mexico Science Standards, Benchmarks, and Performance Standards, discussions about issues that are of interest to both science and individual religious and philosophical beliefs will acknowledge that reasonable people may disagree about the meaning and interpretation of data.

and replaced it with this one, taken directly from the New Mexico Science Standards, Benchmarks, and Performance Standards

“Students shall understand that reasonable people may disagree about some issues that are of interest to both science and religion (e.g., the origin of life on earth, the cause of the big bang, the future of the earth).”

New Scopes documentary

I don’t watch a lot of TV, but I’m always up for a good documentary. The History Channel this week is running a series, 10 days that changed America. According to the website,

The History Channel selected 10 teams of award-winning documentary filmmakers to spotlight “10 historic events that triggered seismic shifts in America’s political, cultural or social landscape.” The programs, including the one filmed in Dayton, include archival footage, reenactments, historic artifacts and interviews.

On Wednesday, April 12th, they’ll air “Scopes: The Battle over America’s Soul” (9PM EST). Should be interesting; I see that Answers in Genesis is already complaining about it.

Here’s the latest update in the continuing saga of UT Professor Eric Pianka, and the articles from the Seguin Gazette-Enterprise.

I got up early this morning, and made several phone calls to try and get to the bottom of why all mention of Pianka had been expunged from the paper. Bottom line: big misunderstanding, and the articles are now back online. It had absolutely nothing to do with the paper trying to dodge responsibility for its actions, or the paper not standing behind the articles, or any of the other possibilities that I had thought were likely. It appears that I didn’t have the full story, and jumped to some conclusions in the earlier articles that were not entirely justified.

Read More (at The Questionable Authority):

Update: I’ve added some substantial comments 81029 and 81054 that might be lost in the comment roll, but add some important perspective to Behe’s arguments.

Michael Behe is known as the author of the concept of Irreducible Complexity (IC, but see [note 1]). However, he has given several different, not entirely consistent, definitions of IC. Everyone is familiar with the “multiple parts” definition, fewer will be familiar with the “neutral mutational steps” definition (1) and fewer still with the idea that amino acids interactions themselves are IC (2, see my critique of this). Indeed, Behe’s recent paper with David Snoke (3) relied on a combination of the last two definitions (see our critique), and Behe also used the latter definition in the Dover trial (3).

A paper just out in the journal Science has effectively refuted the claims of the Behe and Snoke paper (4)

It looks like Jerry Adler of Newsweek has seen the same problem I did with the reaction of the “leading researchers” of ID to Tiktaalik. See “Evolution: If It Walks Like a Fish…

PS: See also this cartoon from Kansas, and also this cartoon.

Fish can hold breath for months

If you thought you were the champion of holding your breath under water as a kid, think again. Crucian carp, a fish closely related to the goldfish, can live months without oxygen, scientists have discovered.

“Anoxia related diseases are the major causes of death in the industrialized world,” said Goran Nilsson, a professor at University of Oslo. “Evolution has solved the problem of anoxic survival millions of years ago, something that medical science has struggled with for decades with limited success.”

While ‘Intelligent Design” failed to resolve onf of the major causes of death, evolution has been far ‘smarter’.

Probably no area of law is more misunderstood and more abused for baseless threat value than libel. Forrest Mims' threat is just the latest example. I'm going to briefly explain how defamation law works and why it's silly and irresponsible for people who disagree with each other to threaten such lawsuits. I'll use Mims' accusation of libel as an illustration.

A number of people commenting on my last article noticed and highlighted the disappearance of stories related to the Pianka affair from the website of the Seguin Gazette-Enterprise. Dave Thomas picked up the story, and posted it here. I’m going to provide a bit more detail on the scope of the paper’s dishonest and despicable conduct, along with the text of an email that I’ve sent them.

Read More (at The Questionable Authority):

Boy, this is not turning out to be a good week for the creationists. Now the famous museum of Kent Hovind, aka Dr. Dino, has been closed. Read “Park could face extinction” in the Pensacola News:

In Mike Dunford’s PT blog The Seguin Gazette-Enterprise and Misrepresentation of Pianka., some commenters noticed that the Seguin Gazette-Enterprise was pulling all articles mentioning the Pianka affair. I was trying to get to that article on the Gazette as well, but was also unable to find it. That is, until I started hunting around the internet caches. I have retrieved parts of the article; see below the fold for before and after (scrubbing) comparisons. The Seguin Gazette-Enterprise must be more than a little nervous. It’s quite a story.

My opening bid: the April 2nd, 2006 Cover Page is still accessible on-line. I’m making a virtual wager (this is a virtual pub, after all), and that is that the Cover Page will be gone by Monday.

Will Chloe get the download before Mims’ minions destroy the hard disk? Will Harry Potter be able to defeat the spell of invisibility the Gazette is putting on all articles Pianka? Read on…

IMPORTANT UPDATE

Mike Dunford has a post called The Seguin Gazette-Enterprise, My Foot, and My Mouth that explains why the Seguin Gazette mistakenly yanked the Pianka articles, and notes that they are now all back on-line.

And back they are: you can now get to the articles for April 2nd, 4th and 5th at the Seguin Gazette.

A new mystery: in the last two stories, reporter Jamie Mobley’s name has been changed to Jamie Maxfield.

Several bloggers have dissected the Discovery Institute Media/Judge/Transitional Fossil Complaints Division’s pitiful response to the Nature report on the new fish-tetrapod transitional fossil, Tiktaalik roseae. The author, Rob Crowther, is just coming off his failed conspiracy theory on Dover and the ACLU, so I guess he might still be a little shaky. Compare these two statements, from the beginning and ending of the same paragraph of Crowther’s original post:

These fish are not intermediates, explain Discovery Institute scientists I queried about the find.

What is clear is that forms like Tiktaalik are a melange of primitive and more developed features.

They’re not intermediates – they’re just…intermediate!

UPDATE: As I was writing this, Crowther updated the piece. He must have seen the same problem I did. Look at the same two sentences now:

Jon Buell and the Dover Ruling

Jon Buell, the head of the Foundation for Thought and Ethics and publisher of the book Of Pandas and People (Pandas), has written a long essay criticizing Judge Jones’ ruling in the Dover case. That’s hardly a surprise, of course. The judge ruled against his position, how could he do anything but criticize it? Unfortunately for him, his criticisms don’t hold up under scrutiny because they are based on false claims, legal ignorance and, in at least one case, an outright lie. This may be a long one, so let’s get started.

Continue Reading at Dispatches from the Culture Wars. Comments may be left there.

Mims – yes, Mims, the instigator of the whole fiasco about how noted ecology Eric Piana wants to kill everybody and the Texas Academy of Science agrees – is now sending around vague threats to those in the Texas Academy of Sciences that dare speak up for the non-insanity of their own organization and their recent Scientist of the Year awardee. Pharyngula has put up the email.

If anyone needed any more evidence that creationists are morbidly irony deficient, this is it.

—– **Update- 7 April 06, 18:00 HST ** All of the Sequin Gazette-Enterprise articles linked to in this article are no longer available through those links, and I am currently unable to find them as live links elsewhere on their site. I will be emailing the paper for comment shortly, and will attempt to contact them by phone for an explanation if that does not work. —–

It’s been several days since the attacks on University of Texas ecologist Eric Pianka first began, and there’s no end in sight. Yesterday, Texas governor Rick Perry’s office compared Pianka to the Nazis, and today he is being required to talk to the FBI so that they can make sure that he’s not a terrorist. Meanwhile, various portions of the right-wing community are continuing to rave against Pianka - the Uncommon Descent folks alone have no less than four posts up on the topic today.

Also today, the Seguin Gazette-Enterprise (the local paper that got the ball rolling on this whole affair) posted the transcript of another, more recent, speech by Pianka. This is interesting because the transcript is for the same speech discussed in the April 2nd Gazette-Enterprise article that was picked up by the Drudge report, sparking the national outcry. Having the transcript available makes it much easier to critically examine the news article about the speech, and to see how well the material in the article reflects what was actually said.

Read more (at The Questionable Authority):

Forrest M. Mims III is in the news with claims of sinister and monstrous evil revealed in Eric R. Pianka’s talk at the Texas Academy of Sciences (TAS) last month. Mims followed up with two petitions to the TAS against Pianka. As Mims himself reports, though, he was not alone in listening to Pianka’s talk. Kathryn Perez was also in attendance and, shortly after the story broke, related on several weblogs that she did not hear the things Mims claims to have heard. She is putting together a petition of her own for the TAS to discipline Mims, and has been collecting signatures from others who attended the talk.

Perez now is getting email from Mims telling her to cease and desist, claiming defamation of his character.

Well, what a difference a day makes. After several days of the wingnuts advertising, promising, and slavering over the prospect of the transcripts of Pianka’s lectures being put online, they have finally got around to doing it. Discovery Institute fellow/young-earth creationist/Of Pandas and People coauthor Nancy Pearcey has put up a (mysteriously partial) transcript of Pianka’s first lecture, the one that Forrest Mims saw at the Texas Academy of Science in early March. And the Seguin Gazette-Express, which has been credulously spouting Mims’s unsupported allegations from the very beginning, and which spread them to the world via the Drudge Report, has finally put up the promised transcript of Pianka’s second lecture, at St. Edward’s University (Austin, TX) last week, which is evidently has the same topic, title, and content. Pianka has given this lecture, entitled “Kill all humans with ebola!!”The Vanishing Book of Life,” seven times now, clearly in a clever attempt to hide his views from the public.

Well, we can now see why the wingnuts were dragging their feet: they haven’t got squat on Pianka. Read the first lecture. Read the second lecture. Even I was shocked: from the hysteria stemming from Mims’s and the Seguin Gazette-Express‘s reports, I was at least expecting a frothing-at-the-mouth, eco-wacko speech from Pianka. But it’s actually milder stuff than I was expecting. Sure, there are several statements and assertions that Pianka makes that I dislike or dispute, and he definitely gets emotionally worked up about what humans are doing to biodiversity – but there is nothing, nothing, indicating that Pianka advocates killing 90% of the world population, and nothing indicating that Pianka hates humanity.

Here is the shocking conclusion of Pianka’s lecture, where he exhorts his audience to go bioengineer airborn ebola and kill off as much of humanity as possible:

Trollart on Tiktaalik

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People have been talking about the discovery of two more new gaps in the fossil record of the fish-tetrapod transition, which occurred when scientists found a predicted intermediate fossil, which they named Tiktaalik. Well, Alaskan artist Ray Troll, at his website TrollArt.com, has gone one better and illustrated the T-shirt version already:

Someone in Texas forwarded this to me, from the Texas Academy of Science:

Subject: Texas Academy of Science and Dr. Eric Pianka Date: Tue, 4 Apr 2006 15:17:19 -0600

Pizza with the Guys

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I dined yesterday with folks in San Francisco. The FASEB coference is going on now there. Larry Moran and John Harshman are attending, so I decided to visit with them. Both Larry and John should be familiar to readers of the talk.origins newsgroup. Harshman and I met before, at the Evolution 2005 conference in Alaska. Nick Matzke and Wesley Elsberry from NCSE came along, too.

John picked the place, Zante’s Pizza on Mission. Why there? “You can get pizza anywhere, and you can get Indian food anywhere, but if you want Indian pizza, you have to come here,” he explained. We got a large non-veggie version, and the rest of the fellows said it was delicious. I’m somewhat upset at how few restaurants there are that provide for my particular dietary needs.

Over dinner, the conversation started with how to make the point that evolutionary biology is not incompatible with faith while not encouraging a double standard on who gets to express their support of evolutionary biology. Larry is concerned that atheists are being told to keep quiet, and even being the targets of criticism, while people of faith loudly proclaim their religiosity when talking on the topic. Then, we discussed the recent breaking news – Pianka under attack by Mims, lies being made about Brian Rehm in the Dover, PA case, and so forth. Oh, and Wesley insisted that we get a picture of the group. He’s funny that way. From left to right, there’s Nick Matzke, Wesley Elsberry, John Harshman, yours truly, and Larry Moran. That John Harshman, he’s such a card. Next time, I’ll give him rabbit ears in the picture and see how he likes it.

Paleontologists have uncovered yet another specimen in the lineage leading to modern tetrapods, creating more gaps that will need to be filled. It's a Sisyphean job, working as an evolutionist.

tiktaalik_sm.jpg

This creature is called Tiktaalik roseae, and it was discovered in a project that was specifically launched to find a predicted intermediate form between a distinctly fish-like organism, Panderichthys, and the distinctly tetrapod-like organisms, Acanthostega and Ichthyostega. From the review article by Ahlberg and Clack, we get this summary of Tiktaalik's importance:

First, it demonstrates the predictive capacity of palaeontology. The Nunavut field project had the express aim of finding an intermediate between Panderichthys and tetrapods, by searching in sediments from the most probable environment (rivers) and time (early Late Devonian). Second, Tiktaalik adds enormously to our understanding of the fish--tetrapod transition because of its position on the tree and the combination of characters it displays.

Continue reading "Tiktaalik makes another gap" (on Pharyngula)

My colleague, Steven Mahone, with Colorado Citizens for Science, was taken by the latest episode of the popular series, “The Sopranos.” Evidently, producers, artists, and writers in the entertainment industry are very much aware of the whole evolution-creation-ID debate that affects our culture. Here is Mr. Mahone’s recap of the relevant scenes:

Seed magazine writing contest

Details can be found here. I thought this may be of interest to some folks here, as the essay topic is on that we’ve discussed here previously:

Amidst emerging competitive threats from abroad (China and India in particular) and heated debates over intelligent design, stem cells and climate change: What is the future of science in America? What should the US do to preserve and build upon its role as a leader in scientific innovation?

Top prize is $1000 and publication in Seed magazine. Entry deadline is June 30, 2006.

Over at the DI blog, Michael Francisco picked up on the Manzari and Cooper article and ran with it, coming dangerously close to crossing the line that separates legitimate criticism from outright defamation. He bluntly accused the school board of knowingly and intentionally making sure that they had to pay $1 million in attorney’s fees. Why would a school board willfully insure that a million dollars was taken out of the budget of the schools their children attend? Well, they wouldn’t, except in the fevered imaginations of demagogues like Francisco, who conveniently ignores the facts, the law and common sense in his attacks. But somewhere along the line, he must have gotten a warning from someone at the DI that he’d better edit his post or they were risking a lawsuit from the board because last night it suddenly contained all these weasel words and phrases missing from the original post. Knowing the tendency of the IDers to try and disappear things down the rabbit hole, I archived the original post and have placed the key accusations side by side.

Continue Reading at Dispatches from the Culture Wars. Comments may be left there.

The “intelligent design” activists are promoting some new spin about the Dover case. (See previous posts: here, here, and here.) Basically the creationists have decided to blame the current Dover Area School Board for the million dollar legal fees that the district has to pay. The basis for the claim is that the current board rejected a proposal to recend the “intelligent design” creationism policy after the trial was over and before Judge Jones issued his ruling. As law student Michael Francisco of the Discovery Institute says:

In essence, the new Dover school board was fully aware that keeping the policy in place increased the risk of expensive attorneys fees. Manzari & Cooper explain why it now appears that there was collusion between the ACLU, AUSCS, and Dover school board members. If what Manzari and Cooper say is true, this alleged collusion allowed the school board to effectively guarantee the Kitzmiller decision at a purchase price of $1 million dollars. This appropriation of public funds should be cause for outrage. Check out the Manzari & Cooper article for more shocking details.

The ID movement has issued a great deal of rhetoric about “academic freedom” and “censorship” and how they allegedly can’t get research grants, even though they never seem to actually come up with specific research proposals.

Well, the shoe is now on the other foot. Nature today reports on a grant review received by Brian Alters, an education professor at McGill who specializes on evolution education, and who was an expert witness in the Kitzmiller case, much-cited by Judge Jones:

Doubts over evolution block funding by Canadian agency Study to measure ‘popularization of Intelligent Design’ refused funds. Hannah Hoag

A Canadian federal agency has denied funding to a science-education researcher partly because of its doubts about the theory of evolution.

Brian Alters, director of the Evolution Education Research Centre at McGill University in Montreal, had proposed a study of the effects of the popularization of intelligent design — the idea that an intelligent creator shaped life — on Canadian students, teachers, parents, administrators and policy-makers.

At a public lecture on 29 March, Alters revealed excerpts from the rejection letter he received from the Social Sciences and Humanities Research Council (SSHRC). The letter stated that, among its reasons for rejection, the committee felt there was inadequate “justification for the assumption in the proposal that the theory of evolution, and not intelligent-design theory, was correct.”

Another point about the American Enterprise article: had the new Dover school board eliminated the Intelligent Design policy while the case was under consideration, would that act have (in Manzari and Cooper’s phrase) “stave[d] off a courtroom defeat”? The answer is no.

The American Enterprise article that Wesley Elsberry blogged about complains about the ACLU seeking recovery of a million dollars worth of fees from the Dover School Board after its victory in the Kitzmiller case. Joe Manzari and Seth Cooper react scornfully to this: “If the ACLU happens to sue your small hometown and then demands $1 million dollars for their lawyers, would you call them generous and charitable? Strangely enough, that’s exactly what they’ve done to the small town of Dover, Pennsylvania.…”

But there’s nothing strange about this at all. In fact, the entire purpose of attorneys fees in public interest litigation—the field in which I make my living—is to ensure that when people go to court to vindicate public rights against wrongful acts by the government, they are not forced to shoulder the cost of doing so. In Owen v. City of Independence, 445 U.S. 622 (1980), the Supreme Court explained why people who sue cities for violating their civil rights should be able to recover money damages from the wrongdoing cities:

The knowledge that a municipality will be liable for all of its injurious conduct, whether committed in good faith or not, should create an incentive for officials who may harbor doubts about the lawfulness of their intended actions to err on the side of protecting citizens’ constitutional rights.… [Since] it is the public at large which enjoys the benefits of the government’s activities, and it is the public at large which is ultimately responsible for its administration…it is fairer to allocate any resulting financial loss to the inevitable costs of government borne by all the taxpayers, than to allow its impact to be felt solely by those whose rights…have been violated.

Id. at 651-55.

If government officials don’t want their cities to be forced to pay attorneys fees awards, they should take the wise step of not violating the Constitution, and then they won’t have to worry about it. In fact, the ACLU, like other public interest firms, go through a great deal of trouble and risk when they seek to defend the Constitution against wrongful official conduct, and much of the time their efforts are rewarded only by small donations from people who agree with their cause. It is actually pretty unusual that such firms get attorneys fees awards for their work, but when they do, not only do they deserve it for performing an important public function, but such awards also serve an important purpose in creating incentives for officials to act rightly, and for citizens to keep an eye on their elected officials.

Pim van Meurs alerted me to another just plain false broadside from the Discovery Institute*. Joe Manzari (American Enterprise Institute) and Seth Cooper (formerly of the Discovery Institute) say that Brian Rehm, one of the plaintiffs in the Kitzmiller v. Dover case, had a “clear” conflict of interest in being part of the new school board that specifically turned down a proposal to rescind the “intelligent design” policy.

One might assume the new board’s first item of business would be to rescind the old board’s evolution policy. Not so. During their first meeting on December 5th, former Dover Board member David Napierski proposed a resolution to rescind the old board’s evolution policy (prior to any court ruling). Acting as a private citizen, Napierski procured the opinion of an attorney, who said that a vote to rescind the evolution policy could stave off a courtroom defeat and significantly reduce or eliminate legal costs and fees. Yet the new board rejected Napierski’s proposal to rescind the old policy.

What’s more, one of the new board members who rejected any attempt to rescind the old evolution policy was also a plaintiff in the lawsuit whose outcome was pending. Dover C.A.R.E.S candidate turned new Dover Board member Bryan Rehm was represented by the ACLU and AUSCS. Yet, in a clear conflict of interest, he participated in the new Dover Board’s consideration of the resolution to rescind the evolution policy.

Wow. That’s pretty bad, isn’t it? So what’s the evidence that bears upon this serious allegation of misconduct on the part of an elected government official? It turns out that the major claim is contradicted by information easily obtained online. I guess easily for people other than AEI “research assistants” and former DI “policy analysts”.

(* Correction added: Cooper is noted at the bottom of the article as a former policy analyst for the DI. We had to wait a few hours for the Discovery Institute’s official false broadside to appear. Now Ed Brayton has a great takedown of the official DI post.)

In 2004, Richard von Sternberg was editor of a journal that published a paper by “intelligent design” advocate Stephen C. Meyer. The society that published the journal issued a statement saying that the paper’s inclusion had been a mistake, and that they would tighten up the review and acceptance process. Afterward, Sternberg would complain that he was a victim of religious discrimination. Since then, ID advocates have made much of the alleged poor treatment of Sternberg, turning his name into a verb: to be “sternberged”, in their view, is to be stripped of “academic freedom”, the ability to take unpopular stances and express edgy and even antisocial opinions without fear for one’s job and other elements of normal day-to-day living.

That makes it sound like ID advocates are taking a stand for a principle.

But that would be the wrong impression.

“Academic freedom” is just a piece of convenient rhetoric so far as ID advocates are concerned: useful when they feel an ID advocate needs some cover, and trampled on whenever someone in academia says something that they don’t like.

Or is claimed by another ID advocate to have said something that they don’t like.

(Continue reading at … The Austringer)

The wingnut echo chamber has recently gone insane over the idea that Eric Pianka, an distinguished and much-loved ecologist at UT, advocates mass genocide by ebola in order to bring down world population. The allegation was leveled by disgruntled creationist Forrest Mims, and rapidly spread to the blogosphere via places like Dembski’s blog (three posts!) and Telic Thoughts, and then went to the Drudge Report and caused a national media firestorm appearing in my local paper by Monday morning. I smelled a rat from the beginning, and now I have been proved right. KXAN News36 in Austin, TX, has just debunked the whole thing, and for good measure has posted a 20-minute unedited interview with Pianka which everyone must watch to realize the full depravity of what the wingnuts have done here. Pianka says several times that Mims is a “crazy kook” that “distorted and changed everything I said.” The death threats that have flooded Pianka and the Texas Academy of Sciences are also a nice touch.

Taphonomy of fossilized embryos

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There are these fossilized embryos from the Ediacaran, approximately 570 million years ago, that have been uncovered in the Doushantuo formation in China. I've mentioned them before, and as you can see below, they are genuinely spectacular.

parapandorina.jpg
Parapandorina raphospissa

But, you know, I work with comparable fresh embryos all the time, and I can tell you that they are incredibly fragile—it's easy to damage them and watch them pop (that's a 2.3MB Quicktime movie), and dead embryos die and decay with amazing speed, minutes to hours. Dead cells release enzymes that trigger a process called autolysis that digests the embryo from within, and any bacteria in the neighborhood—and there are always bacteria around—descend on the tasty corpse and can turn it into a puddle of goo in almost no time at all. It makes a fellow wonder how these fossils could have formed, and what kind of conditions protect the cells from complete destruction before they were mineralized. Another concern is what kinds of embryos are favored by whatever the process is—is there a bias in the preservation?

Now Raff et al. have done a study in experimental taphonomy, the study of the conditions and processes by which organisms are fossilized, and have come up with a couple of answers for me. Short version: the conditions for rapid preservation are fairly easy to generate, but there is a bias in which stages can be reliably preserved.

Continue reading "Taphonomy of fossilized embryos" (on Pharyngula)

Editor’s note: Now that Judge Jones has issued his opinion in the landmark case Kitzmiller v. Dover, Professor Steve Steve feels that he is finally free to publicly discuss his role in the case. Prof. Steve Steve is the official mascot of the Panda’s Thumb blog. For the previous adventures of Prof. Steve Steve, see the this link. For the full story of Prof. Steve Steve’s expert witness experience, please click the link below.

Editor’s note #2: Alert reader David Fickett-Wilbar has noted that the name of Matthew Chapman’s great-great-great-great grandfather and Prof. Steve Steve’s true hero, pottery magnate and Lunar Society Member Josiah Wedgwood, was misspelled as “Josiah Wedgewood.” Prof. Steve Steve attributes this to some really good bamboo beer and the prominence of the Discovery Institute’s revealing Wedge Strategy during the court case. Prof. Steve Steve notes that at least he didn’t put Alfred Russel (one “L” please) Wallace’s photo on the cover of Darwin’s Autobiography. Prof. Steve Steve also notes that his copyeditor, Nick Matzke, has been sacked.

Courtroom sketch of Prof. Steve Steve by Mary Kay Fager, Courtroom artist, 645 St. John's Drive, Camp Hill, PA, 17011, or (717) 737-8088

Courtroom sketch of Prof. Steve Steve by Mary Kay Fager, courtroom artist. She is available for:

  • Conventions, Fairs, Shows, Board Meetings, Shopping Malls, and Parties
  • Commission work in oils, pastels, water color and ink
  • Personalized work in cards, stationary, pamphlets and program covers
  • Courtroom sketching

Write to: Mary Kay Fager 645 St. John’s Drive Camp Hill, PA 17011 Or phone (717)737-8088

Lauri Lebo >At trial, Dover’s sacrificial lamb’ Buckingham reflects on becoming defense targetYork Daily Record Mar 26, 2006. pg. 1/07

Salient quote:

While the Discovery Institute’s opposition to Dover’s curriculum policy has been widely reported, Buckingham said at first Cooper was enthusiastic and supportive. Cooper offered to send him materials about intelligent design.

“He’d call me to see if we were going to go forward,” Buckingham said.

But gradually, as the publicity continued, the attorney began to suggest that the board should not move forward on the curriculum change because it could lead to a lawsuit.

“He was afraid we were going to lose the case,” Buckingham said. “And he thought, if we did lose the case, it was going to set intelligent design back for years.

“He just didn’t think we were the proper people to be pushing this at this time,” Buckingham said.

The day after the school board voted in October 2004 to include intelligent design in its biology curriculum, Discovery Institute posted a news release saying it didn’t support the school board.

“I think they thought we jumped their gun, so to speak,” Buckingham said.

Good Math, Bad Math, and David Berlinkski

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David Berlinski is the Disco Institute’s ex-pat math jester (vying with Dembski for the lead in that role). He apparently regards himself as a polymath, taking on evolutionary biology from his vantage point in Paris. He’s been taken down on the Thumb a number of times – see, for example, here and here – and Jason Rosenhouse has also nailed Berlinski for his misrepresentations of evolutionary biology, concluding

So, once again, we have caught Berlinski making stuff up. There is almost no intersection at all between Berlinski’s points and those made by Dawkins and Coyne, and where there is overlap the latter had a far different points in mind than the former. But then, if they didn’t resort to total fiction the anti-evolutionists would have nothing to say at all.

Recently the Disco Institute put up Berlinski’s analysis of the probability of the naturalistic origin of life. Math is allegedly Berlinski’s field of expertise, so it seems reasonable to imagine that he’d do a better job in it. But Mark Chu-Carroll at Good Math, Bad Math gives it a look, concluding

This is what mathematicians call “slop”, also known as “crap”. Bad reasoning, fake numbers pulled out of thin air, assertions based on big numbers, deliberately using wrong numbers, invalid combinatorics, and misapplication of models. It’s hard to imagine what else he could have gotten wrong.

That’s pretty much the same conclusion that Rosenhouse reached regarding Berlinski’s work. Give Chu-Carroll’s full post a read.

RBH

Figure 3 of Jansen & van Baalen (2006): An example of a snapshot of spatial beard chromodynamics.Here’s another peer-reviewed scientific article, published in Nature, that was probably published in the vicinity of April 1 due to its title:

Vincent A. A. Jansen and Minus van Baalen (2006). “Altruism through beard chromodynamics.” Nature 440, 663-666 (30 March 2006).

I will demonstrate in this paper that all the Indo-European languages and probably all languages on earth evolved from ancient Hebrew.

The conventional wisdom is that Hebrew and the languages of Europe share only three words: amen, hallelu-Yah, and Kokah-Kolah. The 3000-year-old manuscripts known as the Dead Ashkenaz Scrolls, however, contain ancient Hebrew roots so old that they are not found in the Hebrew Bible: they survive only in Yiddish. This discovery dispels the usual belief that Yiddish is a Germanic language; rather, the manuscripts show that German is a Yiddic language.

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