December 2006 Archives

“How Old Is It?”

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The promise of the administration of the National Park Service (NPS) to conduct a high-level review of its policy of selling the creationist book, “Grand Canyon: A Different View”, has gone unfulfilled for three years. A press release from the Public Employees for Environmental Responsibility (PEER) takes aim at the near-terminal foot-dragging of the ideology-driven NPS administration in Washington D.C. A three-year promise of this sort is well past its sell date.

Washington, DC — Grand Canyon National Park is not permitted to give an official estimate of the geologic age of its principal feature, due to pressure from Bush administration appointees. Despite promising a prompt review of its approval for a book claiming the Grand Canyon was created by Noah’s flood rather than by geologic forces, more than three years later no review has ever been done and the book remains on sale at the park, according to documents released today by Public Employees for Environmental Responsibility (PEER).

Here’s a thought for a New Year’s Resolution for the NPS administration: do the review and clear up this issue.

The well-known liberal rag the National Review has a column from John Derbyshire on Kitzmiller plus one year. It’s worth a read:

Those of you who have been watching the blogs over the last few days know that a kerfluffle has gone on about Richard Dawkins’s position on religion and religious freedom. Basically, Dawkins signed this scary-sounding petition, it was linked from the Official Richard Dawkins website, an ID blog that likes to think the worst about Dawkins freaked out, Ed Brayton freaked out because the plain reading of the petition (to American ears; see below) seemed anti-civil liberties, then PZ Myers freaked out in reaction to Ed, etc., etc. PZ did helpfully get some clarification from Dawkins, who then retracted his signature of the petition, but the disavowal didn’t cover the issues of whether or not the government should prevent parents from giving their children religious instruction, leading to yet more thinking of the worst on the ID blogs and yet more confusion in the comments on the blogs of PZ and Ed.

Well, I know that it is far more fun to spend endless threads bickering about what Richard Dawkins probably meant and whether or not it is good or evil, but as PZ noted, it really is better to email the guy. We can’t blame Ed for not doing so, because the petition had a clear meaning on its face. But it seemed to me that the problem was that the petition meant very different things in British vs. American contexts. I sent my hypothesis to Dawkins and he has confirmed it; I comment a bit more at the bottom.

Convocation on Intelligent Design Creationism with Robert Pennock

(#12066 ; 58 minutes; 12/11/2006 ) Robert T. Pennock, the scientist, philosopher and author of “Tower of Babel, The Evidence Against the New Creationism” speaks on the controversial movement to include intelligent design creationism in the curricula of public schools.

Contrived dualism and other ID fallacies

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On Nobel Intent, John Timmer discusses recent attempts by Intelligent Design Evangelical Activists (IDEA) to ‘rally its base’. Mostly this involves returning to the good old creationist claims about evolution and mutations but it also involves ad hominem attacks on Judge Jones who ruled in a devastating manner on the topic of Intelligent Design, causing Behe to describe Judge Jones as “the former head of the liquor control board who signed off on a tendentious brief by a product liability trial lawyer.””

Of course, it was Behe’s own testimony which provided much of the ammunition for the lawyers and helped Judge Jones make his ruling. Not surprisingly, Behe claims that his testimony has been misinterpreted or misunderstood. So far, it seems that Behe is unable to accept personal responsibilities for his testimony.

Behe’s confusion about falsification

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On UcD, the following statement by Behe is being discussed. I will show that IC or falsification of IC has nothing to do with Intelligent Design since IC is merely a negative statement about natural selection, and flawed by definition. Nevertheless, this is a good opportunity to expose the fallacies behind ID think and educate people about its flaws and why it has remained scientifically vacuous.

Behe Wrote:

The National Academy of Sciences has objected that intelligent design is not falsifiable, and I think that’s just the opposite of the truth. Intelligent design is very open to falsification. I claim, for example, that the bacterial flagellum could not be produced by natural selection; it needed to be deliberately intelligently designed. Well, all a scientist has to do to prove me wrong is to take a bacterium without a flagellum, or knock out the genes for the flagellum in a bacterium, go into his lab and grow that bug for a long time and see if it produces anything resembling a flagellum. If that happened, intelligent design, as I understand it, would be knocked out of the water. I certainly don’t expect it to happen, but it’s easily falsified by a series of such experiments.

Note that Behe’s claim does not logically follow: Namely that if something cannot be explained by one of the processes of evolution, namely natural selection that we then have to assume that it was intelligently designed. Even though we have no competing explanations as to who, what, how or when. In other words, ‘intelligently designed’ becomes a place holder for our ignorance.

On Nobel Intent, John Timmer discusses amongst others the contrived dualism of many ID relevant claims

He also relied a lot on the “contrived dualism” argument: design was supported by the failure of evolutionary explanations, because no other alternative was possible. This was stated with extraordinary specificity when Behe answered questions, as he more or less claimed that ID was accessible to experimental studies because finding the limits of evolution would reveal design (more on that later).

Answering Krauze and Sternberg

Krauze has written a response to my debunking of the Souder report, and it includes a response from Richard Sternberg to one small portion of my critique. What is most remarkable about the response, I think, is how much is left entirely undisputed. Neither Krauze nor Sternberg even mentions, much less attempts to dispute, the argument that Sternberg acted unethically in regard to the publishing of the Meyer paper, and that truly is the single most important issue. If that much is true, then whatever hostility he met with by his colleagues is entirely justified. And neither of them even tries to dispute my arguments for that conclusion.

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

Doushantuo embryos dethroned?

Almost ten years ago, there was a spectacular fossil discovery in China: microfossils, tiny organisms preserved by phosphatization, that revealed amazing levels of fine detail. These specimens were identified as early animal embryos on the basis of a number of properties.

  • The cells were dimpled and shaped by adjoining cells, suggesting a flexible membrane—not a cell wall. This rules out algae, fungi, and plants.
  • The number of cells within each specimen was usually a power of 2. This is something we typically see in cleaving embryos, the sequence from 1 to 2 to 4 to 8 to 16 cells.
  • They were big. Typical somatic cells in animals are 5-10 µm in diameter, but ova can be a millimeter or more in diameter, and individual blastomeres (the cells in the cleavage stage embryo) can be several hundred µm across. These cells and the whole assemblage were in that size range.
  • The individual cells were uniform in size, as seen in many cleavage stage embryos, and contained organelles arranged in a consistent pattern.
  • They were often found encapsulated in a thin membrane, similar to the protective membrane around embryos.

There are some concerns about the interpretation, though. One troubling aspect of their distribution is that they are all only in the cleavage stage: we don't see any gastrulas, the stage at which embryonic cells undergo shape changes and begin to move in a specific, directed manner. Studies of taphonomy (analyses of the processes that lead to fossilization) have shown that these later stages are particularly difficult to preserve, which potentially explains why we're seeing a biased sample. Another unusual bias in the sample is that all of the embryos exhibit that regularity of division that produces equal-sized blastomeres—yet many invertebrate embryos have early asymmetric cleavages that produce recognizable, stereotyped distributions of cells. That asymmetry could be a feature that evolved late, but at the same time, some of the fossils were described as resembling molluscan trefoil embryos. Why aren't the examples of early asymmetry translated into a later asymmetry?

Now there's another reason to question the identity of the Doushantuo microfossils: they may be bacterial.

Continue reading "Doushantuo embryos dethroned?" (on Pharyngula)

Ode to the Flagellum

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The evolution of the flagellum Youtube video based on Nick Matzke's hypothesis by CDK007

History and Cobb County

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Many were taken by surprise by the Cobb County School Board’s decision to settle the Selman case, give up their practice of putting evolution “warning labels” in textbooks, and pay $167,000 in fees to the plaintiffs. They had fought this case for four years, and succeeded in getting the Court of Appeals to vacate the district court decision for a retrial. Perhaps the third time Cobb’s sticker got in front of a court would be the charm.

Well, the reality was that this was not likely at all.

In the spirit of the season, Tom Lehrer, Weird Al Yankovic and overwhelming evidence, and as we can’t do flash animations with flatulence noises, once more the Panda’s Thumb Offensive Morris Dancing Troop and Precision Yodelling Team bring you …

The Twelve days of DISCO redux:

On the first day of DISCO the DI gave to me … No original peer-reviewed work.

On the second day of DISCO the DI gave to me … A Dover Pro-Science Victory, and no original peer-reviewed work.

On the third day of DISCO the DI gave to me … Judge Jones Bashing, A Dover Pro-Science Victory, and no original peer-reviewed work.

On the forth day of DISCO the DI gave to me … More Science-Free Books, Judge Jones Bashing, A Dover Pro-Science Victory, and no original peer-reviewed work.

On the fifth day of DISCO the DI gave to me … More Sternberg Spin! More Science-Free Books, Judge Jones Bashing, A Dover Pro-Science Victory, and no original peer-reviewed work

On the sixth day of DISCO the DI gave to me … Clogging Student Blog sites. More Sternberg Spin! More Science-Free Books, Judge Jones Bashing, A Dover Pro-Science Victory, and no original peer-reviewed work

On the seventh day of DISCO the DI gave to me … Clueless Dover Denial, Clogging Student Blog sites. More Sternberg Spin! More Science-Free Books, Judge Jones Bashing, A Dover Pro-Science Victory, and no original peer-reviewed work

On the eight day of DISCO the DI gave to me … No Biologic Institute Research, Clueless Dover Denial, Clogging Student Blog sites. More Sternberg Spin! More Science-Free Books, Judge Jones Bashing, A Dover Pro-Science Victory, and no original peer-reviewed work

On the ninth day of DISCO the DI gave to me … More Judge Jones Bashing, No Biologic Institute Research, Clueless Dover Denial, Clogging Student Blog sites. More Sternberg Spin! More Science-Free Books, Judge Jones Bashing, A Dover Pro-Science Victory, and no original peer-reviewed work

On the tenth day of DISCO the DI gave to me … Conspiracy Paranoia, More Judge Jones Bashing, No Biologic Institute Research, Clueless Dover Denial, Clogging Student Blog sites. More Sternberg Spin! More Science-Free Books, Judge Jones Bashing, A Dover Pro-Science Victory, and no original peer-reviewed work

On the eleventh day of DISCO the DI gave to me … A Cheesy Flash Animation, Conspiracy Paranoia, More Judge Jones Bashing, No Biologic Institute Research, Clueless Dover Denial, Clogging Student Blog sites. More Sternberg Spin! More Science-Free Books, Judge Jones Bashing, A Dover Pro-Science Victory, and no original peer-reviewed work

On the twelfth day of DISCO the DI gave to me … A Cobb county pro-science Victory, A Cheesy Flash Animation, Conspiracy Paranoia, More Judge Jones Bashing, No Biologic Institute Research, Clueless Dover Denial, Clogging Student Blog sites. More Sternberg Spin! More Science-Free Books, Judge Jones Bashing, A Dover Pro-Science Victory, and no original peer-reviewed work

S.multipunctatus.jpg

Regular readers of my own blog may remember that I have a softspot for tropical catfish. The genus Synodontis (Cuvier 1816) is interesting for a number of reasons. For example, S. multipunctatus (the gorgeous fish pictured above) is the only fish known to practice brood parasitism: it manages to mix it eggs with those of mouthbrooding cichlids in Lake Tanganyika, its larvae grow faster than those of the host and feed on them.

Lake Tanganyika is, of course, famous for the cichlids which have been studied as an example of a rapid, recent radiation which was caused by environmental change (in this case, fluctuations in water level). It is also home to to other endemic fauna, including ten species of Synodontis. A recent study has used mitochondrial DNA to study the history of the genus in the region.

Read more over at Stranger Fruit

The Vise Strategy Undone

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Barbara Forrest has written an article that will supposedly appear in January’s print edition of Skeptical Inquirer but is available online now. Titled, The “Vise Strategy” Undone, it’s a recount of the events leading up to and including the Dover trial. And it contrasts William Dembski’s pre-trial fantasies about forcing “Darwinists” to testify under oath (his self-described “vise strategy”) against what actually happened, which is that pro-science testimony carried the day while Dembski and most of his crew chickened out.

Although we’ve all been inundated with tales of Dover for the last year, this article contains a lot stuff that was new to me. This part was my fave:

Dover’s problems actually started in 2002. Bertha Spahr, chair of Dover High School’s science department, began to encounter animosity from Dover residents toward the teaching of evolution. In January 2002, board member Alan Bonsell began pressing for the teaching of creationism. In August, a mural depicting human evolution, painted by a 1998 graduating senior and donated to the science department, disappeared from a science classroom. The four-by-sixteen-foot painting had been propped on a chalkboard tray because custodians refused to mount it on the wall. Spahr learned that the building and grounds supervisor had ordered it burned. In June 2004, board member William Buckingham, Bonsell’s co-instigator of the ID policy, told Spahr that he “gleefully watched it burn” because he disliked its portrayal of evolution.

That’s so wrong on so many levels that I don’t even know where to begin.

(Cross-posted to Sunbeams from Cucumbers.)

The University of Kansas Hall Center for the Humanities has put online the videos from this fall’s “Difficult Dialogs” series. Included are talks by Ken Miller, Judge Jones, Richard Dawkins, Eugenie Scott, and Michael Behe. We had some previous discussion of the Behe talk here. (Apparently Behe was the ID guy who “discovered” that lawyers file a lot of paper with the court before, during, and after a trial, including Proposed Findings of Fact, which of course would be obvious if one had looked at the Kitzmiller documents archive that NCSE has maintained since the trial began.)

DMPC Announces the 2006 Winners of the Disease Management Intelligent Design Awards™

Hat tip to Glenn Branch on this. Here is an organization that knows how to best put the shoddy reputation of the term “intelligent design” to good use:

The Disease Management Purchasing Consortium (DMPC), the most comprehensive source of information about the disease management industry, announced today the winners of the “2006 Disease Management (DM) Intelligent Design Awards,” given annually to those contributions which most set back the evolution of the disease management and wellness fields. Just as engineers say that more is learned from a single bridge which collapses than from 100 which stay up, there are serious lessons to be learned from these often-humorous failures.

Intelligent Design™ as a phrase synonymous with failure… seems apt to me.

Spongeworthy genes

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Oscarella lobularis

What are the key ingredients for making a multicellular animal, or metazoan? A couple of the fundamental elements are:

  • A mechanism to allow informative interactions between cells. You don't want all the cells to be the same, you want them to communicate with one another and set up different fates. This is a process called cell signaling and the underlying process of turning a signal into a different pattern of gene or metabolic activity is called signal transduction.

  • Patterns of differing cell adhesion. But of course! The cells of your multicellular animal better stick together, or the whole creature will fall apart. This can also be an important component of morphogenesis: switching on a particular adhesion molecule (by way of cell signaling, naturally) can cause one subset of cells to stick to one another more strongly than to their neighbors, and mechanical forces will then sort them out into different tissues.

These are extremely basic functions, sort of a minimal set of cellular activities that we need to have in place in order to even begin to consider evolving a metazoan. Fortunately for our evolutionary history, these are also useful functions for a single celled organism, and while the metazoa may have elaborated upon them to a high degree, there's nothing novel about the general processes in our make-up. The principles of signaling and transduction were first worked out in bacteria, and anyone who has a passing acquaintance with immunology will know about the adhesive properties of bacteria, and their propensity for modulating that adhesion to build complexes called biofilms.

So let's take a look at the distribution of signaling and adhesion molecules in single-celled organisms, multicellular animals, and most interestingly, a group that is close to the division between the two (although more on the side of multicellularity), the sponges.

Continue reading "Spongeworthy genes" (on Pharyngula)

December Animalcules is up

The latest edition of Animalcules, a monthly carnival of microbiology blogging, is up over at Aetiology.

The email exchange between Dembski and Richard Dawkins continues. Dawkins just posted an email that Dembski sent to him in 2004 (2003 actually, referring to “early next year”, which would be 2004).

It sparked a memory that I had seen it before. So I asked around. It turns out that in late 2003 Dembski sent the following email to most of the people he is spamming right now. In response to this letter in the UK Guardian by Dawkins, Dembski emailed the following. It really…well, any comment would be superfluous.

I’ve been back from the Australian Health and Medical Research Congress, a 6 day research fest, for a couple of weeks now. However, my brain is still full with the heady delights of the work I experienced there. My students gave reasonably well received talks, and I have a whole grab bag of experiments to do now (or get my students to do). While there were many things that were of deep societal interest at the conference, one of the things that struck me most was a throwaway line in a lecture about cell adhesion. Nectin, a “molecular Velcro” that helps cells stick together is a member if the Ig superfamily.

To explain why it set a light bulb off in my head, and how the knowledge that molecular Velcro shares a structure with immunoglobulins throws deep insight into the evolution of the adaptive immune system, I will beg you patience and do a very brief review of the immune system first.

The funny thing about the Discovery Institute’s Media/Judge Jones Complaint Division is how it deals with defeat. Oftentimes we will see weeks and weeks of vigorous posting about this or that political fight – but then, if they lose, they often just completely ignore it, like nothing happened.

The Office of Sternberg Coddling

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There is another issue about L’Affaire Sternberg that I think needs to be expounded upon, one that doesn’t seem to have been addressed much at length up to this point. And that is the role of the Office of Special Council (OSC) in releasing their preliminary findings that tried to make a martyr out of Sternberg.

Below the fold I will go into a fair amount of detail about how this came to be.

Tangled Bank declares War on Christmas

The Tangled Bank

A Tangled Bank is a good spot from which to launch an ambush—so Salto Sobrius is on the attack!

P.S. Scienceblogs had a server upgrade last night that has gone awry. Everything still looks fine, but the backend is a mess, and you won't be able to make any comments, and we won't be able to make any new entries, until it is all repaired…which will be shortly, we hope.

P.P.S. "Shortly" means it seems to have already been fixed. Hooray!

Evolution of vascular systems

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Once upon a time, in Paris in 1830, Etienne Geoffroy St. Hilaire debated Georges Léopole Chrétien Frédéric Dagobert, Baron Cuvier on the subject of the unity of organismal form. Geoffroy favored the idea of a deep homology, that all animals shared a common archetype: invertebrates with their ventral nerve cord and dorsal hearts were inverted vertebrates, which have a dorsal nerve cord and ventral hearts, and that both were built around or within an idealized vertebra. While a thought-provoking idea, Geoffroy lacked the substantial evidence to make a persuasive case—he had to rely on fairly superficial similarities to argue for something that, to those familiar with the details, appeared contrary to reason and was therefore unconvincing. Evolutionary biology has changed that — the identification of relationships and the theory of common descent has made it unreasonable to argue against origins in a common ancestor — but that difficult problem of homology remains. How does one argue that particular structures in organisms divided by 600 million years of change are, in some way, based on the same ancient organ?

One way is sheer brute force. Characterize every single element of the structures, right down to the molecules of which they are made, and make a quantitative argument that the weight of the evidence makes the conclusion that they are not related highly improbable. I'll summarize here a recent paper that strongly supports the idea of homology of the vertebrate and arthropod heart and vascular systems.

Continue reading "Evolution of vascular systems" (on Pharyngula)

The Year in ID

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What a year it has been for the Discovery Institute and the Intelligent Design movement! Over at Stranger Fruit, I detail the advances that ID has made in the short time since Judge Jones delivered his ruling in Kitzmiller v. Dover.

Update: John West has offered his version of the year for ID. Compare and contrast at your leisure

Talkorigins

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Some of you may have noticed that the Talk.Origins Archive was not accessible today. Its hosting company changed the IP address for the server that the Archive is on. The new IP address is currently propagating through the DNS network and you will be able to access the site again as soon as your ISP updates its records.

Also we’ve ordered a new server for PT and will have access to more bandwidth soon.

Update:

Current plans have us switching to the new connection tonight. This means that PT may go offline for you until your ISP picks up the new IP.

News Flash: Cobb County Case Settled

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A little birdie just called to tell me that the Cobb County evolution disclaimer case has been settled, and on very favorable terms for our side. Americans United is sending out a press release which says, in part:

In an agreement announced today, Cobb County school officials state that they will not order the placement of “any stickers, labels, stamps, inscriptions, or other warnings or disclaimers bearing language substantially similar to that used on the sticker that is the subject of this action.” School officials also agreed not to take other actions that would undermine the teaching of evolution in biology classes.

It should be noted that this happens one day before the one year anniversary of the ruling in Kitzmiller, and I don’t think that is coincidental here. When the appeals court remanded this case back to the district court, not only was the case reopened for a new trial but the judge also reopened discovery and decided to allow expert witnesses to testify. I strongly suspect that this was a big influence on making the defense settle the case. After watching how effectively we used expert testimony in the Dover case, they couldn’t like that prospect. It is perhaps also worth noting that this is what real lawyers do in lieu of putting out silly “studies” based on word counts.

The AU press release is here. NCSE story is here.

The Discovery Institute is promoting a new report from a conservative Indiana Congressman about the Sternberg affair. For those who don’t recall, Richard Sternberg was the editor of the Proceedings of the Biological Society of Washington, a journal loosely associated with the Smithsonian Institution, when they published the now-infamous paper by DI Program Director Stephen C. Meyer. This is very important for their PR campaign to position themselves as victims of persecution, but the facts of the case simply do not support the conclusions of the report.

I have a detailed and comprehensive response to this report at Dispatches from the Culture Wars. Comments may be left there.

The Discovery Institute’s attempt to call Judge Jones a plagiarist for his decision in Kitzmiller was a publicity stunt, and it flopped. Nobody fell for it because it was easy to confirm the fact that judges follow proposed findings of fact all the time—that this is a routine and even a praiseworthy practice—and that the DI’s “statistics” were essentially invented, by using such weasel words as “virtually verbatim.” Moreover, we showed that their attempt to prove that courts disapprove of the practice was silliness. The cases they cited to not only did not show that Jones did anything wrong, but in some instances, were examples of routine creationist quote mining. For example, Mr. Luskin cited to Bright, but we showed that Bright said pretty much the opposite of what he claimed it said.

The DI’s position weakened further when they tried over and over again to claim that they weren’t calling Jones a plagiarist—a clumsy attempt at a paralepsis, indeed. “Oh, no,” they said, “in legal circles Jones wouldn’t be called a plagiarist”—and so forth—things that were all attempts to call him a plagiarist without actually coming out and saying it. Then they did call him a plagiarist, for a speech which had been transcribed—even though Jones had indicated that he was quoting from a published source, and even though the transcription probably didn’t reflect quote marks because spoken presentations often don’t use the word “quote.…”

Anyway, now rather than admitting that this was all just an idiotic publicity stunt, Casey Luskin has a post at the DI’s blog trying to defend the idea that Jones was doing something wrong.

Tripoli 6 sentenced to death

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The 5 Bulgarian and 1 Palestinian health workers accused of having infected Lybian patients with the HIV virus were found guilty and sentenced to death today in Tripoli, despite international outcry and molecular phylogenetic evidence demonstrating their innocence. As much as it is tempting to snarkily frame this as a court victory for anti-evolution forces, the situation is too serious.

Follow the story and do what you can to add your voice to the outrage. Visit the Amnesty International web site for updates. Donate if you can.

Kenneth Miller, professor at Brown University and expert witness for the plaintiffs in the Kitzmiller v. Dover Area School District, replied to William A. ‘Divine Wind’ Dembski this morning with some suggestions for good video. I know I’d like to see it. Fortunately, he used “reply all” in responding to Dembski, so I got it in my inbox. I thought that the PT community would like to see it, too, so I asked Prof. Miller if I could get his permission to post his email, and he kindly agreed. It is appended below the fold.

DI Plagiarizes Law Review Article?

It seems that the Discovery Institute, while disingenuously libeling a Federal judge for his routine use of findings of fact from a plaintiffs’ brief, has been engaged in plagiarism of its own work in a context where such copying is strictly forbidden. Virtually every law review has strict rules against publishing articles that substantially copy one’s own previously published works, yet the DI’s David DeWolf and Casey Luskin submitted an article to the Montana Law Review that was 95% identical to what they had written in the book Traipsing Into Evolution. Prof. Peter Irons has issued a press release concerning this, which is available at Dispatches from the Culture Wars. Comments may be left there.

Dembski’s motive

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On UncommonDescent, Dembski ‘explains’ his motivation behind the Judge Jones School of law:

Dembksi Wrote:

Just to be clear, my aim in this flash animation was not to shake up the convictions of convinced Darwinists. Rather, my aim was to render Judge Jones and his decision ridiculous in the eyes of many young people, who from here on will never take Darwinian evolution or him seriously. If the cost of accomplishing this is yet another lowering of my estimation in the eyes of PT or Richard Dawkins, that’s a price I’m only too glad to pay — heck, I regard that as a benefit of the deal.

David Opderdeck correctly observes that

The problem here is three-fold, IMHO: (1) it inculcates a disrespect for the legal system; (2) it rests on a false premise of “plagiarism”; and (3) it discredits your substantive work, particularly among those of us who really know how the legal process works.

Davescot tried to object and David responded

Molecular Clocks

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Over at Dembski & Co., there are some recent posts (here, here, and here) complaining about molecular clocks and arguing that well known and long established limitations of molecular clocks invalidate evolutionary biology.

I find it sad that a week after scientists used molecular clocks to show that the Tripoli Six did not cause an HIV outbreak, the anti-evolutionists at UD throw up some posts ignorantly questioning the well established and understood procedure. I feel like arguing that anti-evolutionists want these six innocent health workers to be executed, but I’m sure that is not the case. They just don’t get the science or even care to. But the science is important, and the ignorance engendered by anti-evolution can have life-and-death consequences.

Mathematician, theologian, and philosopher William A. Dembski branches out, now lending his vocal talents to a Flash animation taking a low-humor poke at federal district court judge John E. Jones III. Jones is represented as a pull-to-speak doll spouting snippets of his decision in a high-pitched voice with added farting noises, and various pro-science advocates (myself included) are represented as pulling the string. Dembski read aloud various portions of the 2005 decision of the court in the Kitzmiller v. Dover Area School District case, and then pitch-shifted up the result. Pitch-shifting in pop culture is most famously associated with David Seville, the stage name of Ross Bagdasarian, whose single, “Witch Doctor”, went to the top of the charts in 1958. Seville’s other pop culture contribution with pitch-shifting was The Chipmunks, the musical phenomenon that later became a cartoon franchise, with characters Alvin, Simon, and Theodore as the chipmunks and Seville as songwriter/manager/father figure.

Bwa ha ha!

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Just when you think the ID guys can’t get any sillier and more immature, you see stuff like this. Dembski admits on his blog:

Over at www.overwhelmingevidence.com there is a flash animation featuring Judge Jones spouting inanities (inanities that he actually did write or say). There’s been a design inference made that it’s my voice in the Jones animation. A disgruntled former UD commenter KeithS slowed it down and lowered the pitch. Well, it’s true, it actually is me.

Now I’m wondering if the reason we’ve seen Dembski’s writing output decline is because he is spending all his time designing anti-Judge Jones flash animations. And I’m wondering who did the grunts.

Update: see below the fold.

Lame Ducks Weigh In

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It looks like the lame ducks in Washington have decided to issue an opinion and an appendix accusing the Smithsonian of discriminating against Sternberg and politicizing science. That’s right; anti-evolution politicians are accusing the Smithsonian of being the one responsible for politicizing science. It comes as no surprise that the media complaints division is on the story. Expect WorldNet Daily and other reputable news organizations to run with the story.

The opinion was prepared by congressional staff and was commissioned by Congressman Mark Souder, the chairman of the subcommittee on criminal justice, drug policy, and human resources, and who in 2000 co-hosted a Discovery Institute briefing on intelligent design aimed at persuading congress that ID needed political support. Soon after the briefing, he even read a defense of ID, given to him by the Discovery Institute, into the congressional record. On his website you can find the typical pedestrian arguments against evolution.

So it comes as no surprise that the staff of this friend of the DI has decided that the Smithsonian violated Sternberg’s rights and that new laws need to be passed to establish affirmative action for anti-evolutionists. Because, according to them, judging anti-evolutionists on the merit of their views of science is discrimination. Next they’ll be telling us that Los Alamos should hire people who have doubts about gravity.

Yawn. Can’t they come up with anything original after their devastating loss in Dover?

Darwin, Marx and Bad Scholarship

Edward T. Oakes may be a good teacher of theology at St. Mary of the Lake, but he is a lousy historian of Darwinism. Witness the following statement from his review of Richard Weikart's work, From Darwin to Hitler: Evolutionary Ethics, Eugenics, and Racism in Germany:

Spencer might well have been the first to coin the phrase "survival of the fittest." But Darwin enthusiastically adopted it in the 6th edition of his Origin of Species as a substitute term for "natural selection." Nor did he ever demur when other advocates of evolution's social application came pleading their case. Karl Marx asked if he might dedicate Das Kapital to Darwin, which request Darwin declined only because he did not want to offend the religious sensibilities of his deeply Christian wife.

There are a host of problems with this short extract. Find out more at Stranger Fruit, where you can leave comments.

Larry Moran has a long post here reflecting on the DI’s portrayal of Judge Jones as a plagiarist. At first, Moran felt that Jones had really done something wrong, but he appears to have taken to heart the explanations here and elsewhere that judges are expected to follow the proposed findings of fact of the party whom they find most convincing. It seems like a simple, innocent misunderstanding. But Moran goes on to make comments that seem like criticisms of the legal culture’s standards of ethics and “standards of brilliance,” that I think deserve some discussion.

Read the rest at Positive Liberty

In its latest issue, New Scientist has published a story—Intelligent design: The God Lab—and an editorial—It’s still about religion—about that double-secret, DI funded research center: the Biologic Institute.

The reticence cloaks an unorthodox agenda. “We are the first ones doing what we might call lab science in intelligent design,” says George Weber, the only one of Biologic’s four directors who would speak openly with me. “The objective is to challenge the scientific community on naturalism.” Weber is not a scientist but a retired professor of business and administration at the Presbyterian Whitworth College in Spokane, Washington. He heads the Spokane chapter of Reasonstobelieve.org, a Christian organisation that seeks to challenge Darwinism. …

Last week I learned that following his communication with New Scientist, Weber has left the board of the Biologic Institute. Douglas Axe, the lab’s senior researcher and spokesman, told me in an email that Weber “was found to have seriously misunderstood the purpose of Biologic and to have misrepresented it”. Axe’s portrayal of the Biologic Institute’s purpose excludes religious connotation. He says that the lab’s main objective “is to show that the design perspective can lead to better science”, although he allows that the Biologic Institute will “contribute substantially to the scientific case for intelligent design”.

Clearly, the Discovery Institute has established the Biologic Institute a few decades too late. The Institute for Creation Research and the Creation Research Society have been doing research to challenge naturalism for a long time. They are so prestigious in the field that they have even created their own research journals for publishing their papers. This does not bode well for the Discovery and Biologic Institutes because they will have a hard time breaking the stranglehold that those two research centers have on the industry. For decades now, the ICR and CRS have been telling us that their research is going to revolutionize science in five years time. How can the Biologic and Discovery Institutes compete with such success?

We here at the Thumb wish the Biologic and Discovery Institutes all the luck in turning the ID public relations campaign into a working scientific program. They’ll need it.

Get Out the Vote

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If you haven’t voted for us today, now is the time to do it.

Casey Luskin has a response to some of the criticisms that we and others have made against the DI's silly publicity stunt about the Kitzmiller decision. We've pointed out that courts use proposed findings of fact in this way all the time and that appellate courts are fine with it in almost all cases. But Luskin claims that, no, "[t]he Third Circuit, which governs all federal courts in Pennsylvania, has strong law discouraging judges from simply adopting 'verbatim or near verbatim' the findings of fact of parties in a case." This, as we would expect, is not really accurate.

Over at DI’s blog, John West—who, as I noted before, isn’t a lawyer—is still trying to pretend that defenders of evolution are taking his criticisms hard. Apparently we’re “in a tizzy” over the DI’s complaint that Judge Jones followed the standard procedure of adopting in large part the proposed findings of fact prepared by the side that wins the case. As we’ve noted, this is exactly what proposed findings of fact are for, and West’s claim that Jones did something improper in following a common procedure—a procedure blessed by the Supreme Court, by circuit courts, and so forth—is either profoundly ignorant or even more profoundly dishonest.

Rather than respond to these points, or to me, or to Ed Brayton, or to any of the others who have written about this subject, West cites a commenter to The Thumb—not a blogger at The Thumb, but a commenter—who makes the (correct) argument that the reason courts ask parties to write proposed findings of fact is because this procedure is more likely to avoid mistakes in the details. West responds sarcastically: “That’s right, it’s not the judge’s job to write his or her own opinion, or to do his or her own analysis. It’s better to have the experts do it. Why not just dispense with the job of judge altogether?”

Excuse me, Dr. West, but Judge Jones did write his own opinion. Even your own “study” does not substantiate a claim that the Judge did not write the opinion or do his own analysis: it only makes the (irrelevant) claim that Jones adopted large portions of the factual portion of the opinion—a portion of about 4,000 words out of an opinion about 30,000 words long—from the plaintiffs’ proposed findings of fact. Judge Jones wrote every single word of the opinion, relying heavily on the proposed findings prepared by the side that he found most convincing—which is the standard procedure in courts of law.

West even goes so far as to say that Jones made no “attribution” in the opinion (although, of course, West isn’t calling Jones a plagiarist, you know.…) But Jones attributed every word of it. The opinion begins,

This Memorandum Opinion constitutes the Court’s findings of fact and conclusions of law which are based upon the Court’s review of the evidence presented at trial, the testimony of the witnesses at trial, the parties’ proposed findings of fact and conclusions of law with supporting briefs, other documents and evidence in the record, and applicable law.

In addition, every factual claim in the opinion is supported by a citation to the record.

If West were a lawyer, we could be certain that he would know better—and his conduct would be unprofessional. (It would, in my opinion, violate Rule 8.2(a) of the A.B.A. Model Rules of Professional Conduct.) As Joe McFaul has pointed out, we haven’t heard the actual lawyers in the Kizmiller case echoing the DI’s shameful publicity stunt. I think we all know why. Since he’s not, we might have given him the benefit of the doubt that he simply doesn’t know how trial courts work. But with the rules and the cases presented to him on The Thumb, he is clearly willful in his ignorance.

I have written a comprehensive fisking of the Discovery Institute’s absolutely laughable “study” (yes, these people really do believe that using the word count function in a word processor is a “study”; no wonder they can’t put any actual scientific research) at Dispatches from the Culture Wars. Comments may be left there.

Weekend At Behe’s

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The Discovery Institute has put out a press release that is flabbergasting even by their standards.

In it, they breathlessly announce that

“Judge John Jones copied verbatim or virtually verbatim 90.9% of his 6,004-word section on whether intelligent design is science from the ACLU’s proposed ‘Findings of Fact and Conclusions of Law’ submitted to him nearly a month before his ruling,” said Dr. John West, Vice President for Public Policy and Legal Affairs at Discovery Institute’s Center for Science and Culture.”

Now, Vice President for Legal Affairs John West is not a lawyer, so he may not be familiar with the fact that this is exactly what proposed findings of fact are for. They are proposed findings which a judge, if he or she agrees, then incorporates as his or her own findings. Both the school district and the plaintiffs filed proposed findings, and the judge went with the findings he found most convincing. Incidentally, the school district doesn’t seem to have ever objected to the plaintiffs’ filing their proposed findings.

More on Evolution And Conservatism

My recent post on evolution and political conservatism started an interesting conversation over the relationship between science, conservatism, and libertarianism, between myself and Larry Arnhart. Here is Arnhart’s first post, my reply, his surreply, and my most recent comment.

Science Blogging Conference

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The Science Blogging Conference has been growing quickly. It is now looking for its 100th registrant. Will you be him or her?

Remember, if you come to the conference, Prof. Steve Steve will be on hand to drink you under the table like he drank down Chris Mooney.

While you’re at it, go vote of us again for the Best Science Blog of 2006. You can vote once every twenty-four hours. Right now we are in a race with In the Pipeline for third place. Please don’t let us lose to a the blog of a big-oil executive who wants to open-pit mine the Arctic Wildlife Refuge (or whatever In the Pipeline is really about).

Go Forth and Vote Again

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Have you voted today for the Panda’s Thumb as the best science blog of 2006? Remember that you can vote every 24 hours.

Right now we are in a race for third place with In the Pipeline.

I hate to give my English brother-in-law something to crow about, but a December 7 article in the Guardian, “Ministers to ban creationist teaching aids in science lessons,” by James Randerson, gives him ample opportunity. According to the article,

The government is to write to schools telling them that controversial teaching materials promoting creationism should not be used in science lessons.

The packs include DVDs and written materials promoting intelligent design, a creationist alternative to Darwinism, that were sent to every school in the country by the privately-funded group Truth in Science. Advocates of the theory argue that some features of the universe and nature are so complex that they must have been designed by a higher intelligence. Last week, the Guardian revealed that 59 schools had told Truth in Science the materials were a “useful classroom resource”.

For more details, check here http://education.guardian.co.uk/sch[…]s&feed=8

and for a sardonic comment, check here http://redstaterabble.blogspot.com/[…]ck-mole.html

Reasonable Kansans has a positive writeup of a lecture Behe gave yesterday in Kansas. It seems that the “intelligent design” activists are still smarting from their loss in Dover a year ago. It looks like Behe and his DI breathern are trying out some new talking points about the trial.

It’s worth a read to keep up with the continuously morphing public relations campaign of the “intelligent design” activists: Reasonable Kansans: Behe Lecture.

Oliveiria_etal_2006_HIV_phylo_Tripoli6_Fig2.jpgBecause I’ve apparently been living in a cave, I only just heard the full story of the “Tripoli Six”: five foreign nurses and a doctor that the Libyan government has imprisoned for seven years, tortured, and sentenced to death by firing squad for allegedly causing an outbreak of 400 cases of AIDS in a Libyan children’s hospital in 1998. Apart from the problems with torture and firing squads, the major problem here is that these poor people didn’t do it. The infections were caused by poor hygiene practices, like reusing needles, that existed at the hospital long before these nurses arrived in 1998. But the Libyan government is scapegoating some foreigners to distract the populace from the fact that the government is the real criminal here.

What does this have to do with evolution, you ask? Well, out here in the real world (outside of Libya and creationist circles), the way you tell where an HIV strain actually came from, and when, is by doing a standard molecular phylogeny. If you are a creationist who doesn’t believe in this sort of thing then you should really just stuff it, because the criminal courts, relying on their “beyond reasonable doubt” standard, have been using phylogenetic methods as forensic evidence for years (so much so that an HIV phylogeny was used on the TV show CSI).

Pile it on!

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Remember last month when Nature published that crank creationist letter from Polish politician and scientist Maciej Giertych? Well this week Nature has published responses to that letter. PZ has posted the list on his blog: ‘Pigpile on Maciej Giertych!’.

Go check them out and come back here and tell me which one is the best.

Tangled Bank #68

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The Tangled Bank

Take a voyage with Captain Collins on the 68th Tangled Bank expedition. No squid or pirates were spotted this time, but it's still fascinating stuff.

The 2006 Weblog Awards

The Panda's Thumb and several other worthy blogs have been nominated for the Weblog Awards, in the category of Best Science Blog. Here are the nominees:

Pharyngula
John Hawks Anthropology Weblog
RealClimate
Deltoid
Good Math, Bad Math
Mixing Memory
The Panda's Thumb
In the Pipeline
Bad Astronomy Blog
SciGuy

Voting begins on Thursday, December 7. Vote early and often, and may the best html-formatted display of text information from an online database win.

According to a short blurb, “Dawkins Versus the Gods,” by Eliot Marshall, in the December 1 issue of Science, Richard Dawkins has started a new foundation dedicated to promoting science and reason. Here is Mr. Marshall’s blurb in its entirety:

After scanning the titles in a local bookshop, Oxford University geneticist Richard Dawkins discovered that “real science” was “outnumbered three to one by pseudoscience.” Concerned that “the enlightenment is under threat,” the author of The God Delusion has created and will help fund the Richard Dawkins Foundation for Science and Reason. The new charity, with U.S. and U.K. branches, will support research on “the psychological basis of unreason,” produce videos and books, and run a Web site (richarddawkins.net/foundation). Another goal, “to oppose … well-financed efforts to teach creationism in science classes,” will put it up against the U.K.–based Truth in Science, which recently sent “intelligent design” promotional packs to 5700 British secondary schools. Truth in Science claims it received 59 positive responses.

The foundation’s Website is very preliminary right now, but the trustees plan to incorporate in both the US and the UK, partly for tax reasons. The Website includes a video by Professor Dawkins, which I will not discuss because the transcript is posted as well; links to books by Steven Pinker, Daniel Dennett, Matt Ridley, and Sam Harris (but not, alas, Why Intelligent Design Fails); and a short list of lecturers, not least P.Z. Myers. We can additionally look forward to a calendar and a newsletter.

I wish Professor Dawkins luck, but I fear it is 300 years after the Enlightenment, and unreason seems to be increasing, not decreasing. He (and we) have a long, hard row to hoe.

Our Scientific Output

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Several weeks ago I got curious about what the collective scientific output was by members of the Panda’s Thumb, both authors and advisers. So I took a poll.

Because not every Pandit is an evolutionary biologist or even a scientist, I could not just do a poll based on EB scientific paper. The engineers who’ve worked on classified government projects wanted to be able to include their technical reports in the survey. The philosophers and historians of the group wanted to count their work in the humanities as well. So I ended up with three major categories: Science Papers, Humanities Papers, and Technical Reports. In addition, the Total Publication category covers all three of these as well as other academic/professional publications not covered by them. And finally, the Evolution Related category is a subset of the Total Publication category.

Here are the results, from a total of 31 responses.

Science Papers Humanities Papers Technical Reports Total Publications Evolution Related Publications
Total 978 103 305 1467 124
Average 31.5 3.3 9.8 47.3 4.0
Std Dev 67.7 7.6 18.2 80.2 8.0

Raw data is below the fold.

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