October 2005 Archives

William Dembski has this odd habit when someone publishes a criticism of his writings. Rather than engage in substantive refutation of those criticisms, he often claims either to be the victim of some cosmic unfairness by the Darwinian Inquisition, or he claims that the person criticizing him is obsessed with him. As an example of the first, I point you to his frantic complaints of copyright violation and ethical mistreatment by Rob Pennock in early 2002, after Pennock had included a couple of essays of his in an anthology he edited called Intelligent Design Creationism and its Critics. He accused Pennock of copyright infringement, but in fact he had the written permission of the actual copyright owners, Metanexus. The owners of Metanexus published a public exoneration of Pennock in the matter.

For an example of the second strategy, I point you to his having called Richard Wein, Wesley Elsberry and Jeffrey Shallit his “internet stalkers” because they - gasp! - read and criticized his work. And in public. The nerve of these people, actually analyzing and critiquing the work of a scholar! He hasn’t done much to actually answer their critiques, mind you, but he’s called them “obsessed” and it appears that he thinks that actually defeats their arguments. Now he’s back making more weird accusations about the Dover trial, involving Shallit yet again. He writes:

Continue reading Dembski’s Obsessive Complaints of Obsession at Dispatches from the Culture Wars

The most recent issues of Natural History and Skeptical Inquirer magazines feature articles on Darwin, evolution, and, as SI puts it, the ID wars.

The Tangled Bank

The next Tangled Bank is coming up on 2 November 2005, at The Examining Room of Dr. Charles. Get your links sent in to Dr Charles, PZ Myers, or host@tangledbank.net by Tuesday.

Also, darn it, I had a few new volunteer hosts to schedule, and I lost some email. Remind me if you were hoping to host in December or January, and heck, if anyone is interested in hosting it anytime, let me know.

Join Alabama Citizens for Science Education to protect Alabama education.

The Associated Press is reporting this morning that Alabama state textbook committee several textbooks because they contained information on evolution.

The state textbook committee Thursday recommended dozens of science textbooks to be approved by the state school board for Alabama students, but rejected three elementary-level books for containing material on evolution which was deemed “controversial” for that age group.

The books were considered supplementary readers, meaning they could not be used as the sole textbook in the science curriculum, said Ron Dodson, a member of the committee, who presented the recommendations to the school board.

Each of the three elementary books rejected contained “controversial material at a grade level that is not developmentally ready for such controversial material,” according to a series of Sept. 28 memos sent to school board members. The books also didn’t meet the state’s science guidelines and were not “appropriate for the maturity level of the age group” they were targeting, the memos said.

The book “Geologic Time” (Perfection Learning Company) was rejected for an illustrated diagram that shows humans evolving from apes. Similarly, “Reptiles” (Heinemann-Raintree Classroom), incorporates two pages on reptiles evolving from amphibians. “Orangutan” (Heinemann-Raintree Classroom) discusses natural selection – a key part of the evolutionary theory.

In addition the committee has recommended that textbooks still contain a disclaimer.

The committee made its recommendations with the stipulation that high school biology textbooks would continue to carry a disclaimer which describes evolution as “a controversial theory” in the first paragraph and says in the second paragraph that any statement about the origin of life is “not fact.”

The purpose of the disclaimer is to give room to teachers who want to discuss alternative theories, namely creationism.

In addition it looks like some board members want textbooks to contain creationism.

However, after the meeting, school board member Betty Peters said she had hoped to see the textbooks discuss alternative theories of life, including creationism and intelligent design, in addition to evolution. She said that despite the disclaimer, many teachers are still afraid to teach about theories that are not included in textbooks. …

“I’m not saying advocate it, just open it for discussion,” Peters said.

Matthew J. Brauer, Barbara Forrest, and Steven G. Gey offer a timely, 149 page, review of intelligent design creationism and the constitution in Is It Science Yet? Intelligent Design, Creationism and the Constitution published in the Washington University Law Quarterly.

Matthew J. Brauer is Research Staff, Lewis-Sigler Institute for Integrative Genomics, Princeton University; B.A. (1988), University of California, Berkeley; M.S. (1988), University of Texas; Ph.D. (2000), University of Texas.

Barbara Forrest is Professor of Philosophy, Department of History and Political Science, Southeastern Louisiana University; B.A. (1974), Southeastern Louisiana University; M.A. (1978), Louisiana State University; Ph.D. (1988), Tulane University.

Steven G. Gey is David and Deborah Fonvielle and Donald and Janet Hinkle Professor of Law, Florida State University; B.A. (1978), Eckerd College; J.D. (1982), Columbia University.

Pharyngula: An evolutionary prediction

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PZ Myers has written a very interesting article on the evolution of insect wings. In the discussion of this article, JH Marden’s work on stonefly larvae came up and Marden now responded with a very nice example of an evolutionary prediction.

The York Daily Record reports on the testimony by Dover Board Member Heather Geesey who wrote a letter to the editor stating:

Dover Board Member Heather Geesey Wrote:

“You can teach creationism without its being Christianity”

But things only got better…

Slate: Monty Python’s flying creationism

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William Saletan has a very funny article on Slate titled The Brontosaurus Monty Python’s flying creationism.

Behe offered a number of interesting criticisms of Darwinism. But it’s impossible to focus on any of these criticisms, because they were so completely overshadowed by the brontosaurus in the room: ID’s sophomoric emptiness.

It seems that more an more media and scientists are realizing the scientific vacuity of Intelligent Design.

Note: I have corrected the many spelling errors. I blame it on an unfamiliar keyboard:-)

William Dembski has a peculiar post up in which he says,

Ask yourself why, after submitting almost 200 pages of materials against me in his expert witness report and after submitting to a deposition with the Thomas More Law Center in July, Jeffrey Shallit did not take the witness stand in Dover for the plaintiffs. Answer: his obsessiveness against me and ID made him a liability to the ACLU. If you don’t believe me, go here and here.

Um, Shallit was called as a “rebuttal expert”. The plaintiffs and defense each announced six expert witnesses on April 1, 2005. One month later, rebuttal experts were announced. The defense announced Steve Fuller and Stephen Meyer (director of the Discovery Institute ID program). Plaintiffs announced Jeff Shallit. However, Dembski dropped out of the case (or was withdrawn, or something – see the October 29 squabble at the American Enterprise Institute between the Discovery Institute and Thomas More Law Center about the withdrawal of Dembski, Meyer, and Campbell, online at NCSE). Without Dembski testifying, Shallit had no one to rebut, since his expert report specifically addresses Dembski’s arguments.

Speaking of withdrawing experts…

UPDATE: 10-28-05: The Kansas BOE issued a news release later yesterday saying that they were immediately addressing the copyright issue, and that they still intended to have the science standards on the November agenda. I have posted the news release in Comment 3 below. End update

From the National Academy of Sciences today:

Kansas Denied Use of National Science Education Standards National Science Education Standards.

October 26 – The National Academy of Sciences and the National Science Teachers Association have refused to grant copyright permission to the Kansas State Board of Education to make use of publications by the two organizations in the state’s science education standards. According to a statement from the two groups, the new Kansas standards are improved, but as currently written, they overemphasize controversy in the theory of evolution and distort the definition of science.

These two organizations issued a joint statement, sent letters to the state BOE officially notifying them of this refusal to grant copyright permission, and released a lengthy response to those parts of the Kansas standards to which they object. All three of these documents can be downloaded from the NAS News Today webpage. These are strong and well-written statements, and, as a member of the writing committee, I appreciate this support from these national organizations very much .

Here are some excerpts, and a few comments.

A Citizens for Science organization has been finally organized for Pennsylvania. Pennsylvania Citizens For Science (http://www.pacfs.org/) is “A non-profit group dedicated to strong science education in Pennsylvania public schools.” The mission of PACFS is

To make sure that the Pennsylvania Citizens for Pseudoscience, Bad Science, and Fake Science (they go by different names, of course) have no influence on science instruction in Commonwealth public schools. Our efforts are currently focused on protecting the ability of teachers to teach exclusively non-supernatural explanations for the origin of the universe, the origin of life, and descent with modification (“evolution”) in science classes. Currently, teachers are often too scared to teach these topics, and thus evolution is given a mere 50 minutes or avoided altogether. The group does not oppose the discussion of supernatural phenomena in mythology, religion, or philosophy courses, or in private schools, homes, or churches.

We also try especially hard to promote the teaching of evolution in elementary schools, when children are most curious about dinosaurs, our similarity to other primates, and the origin of species and life itself. The group mascot is Phacops rana, a really cute trilobite from the Devonian, and the state’s official fossil.

If you care about science education in Pennsylvania, go join.

Yesterday, I was in Athens, GA meeting Dr. Steve “Number 22” Henikoff, who was visiting the Department of Genetics at the University of Georgia. Steve Henikoff is a Howard Hughes Medical Institute Investigator and works at the Fred Hutchinson Cancer Research Center in Seattle, WA.

On Wednesday morning we talked science over breakfast before I dropped him off at the department to talk to various professors and students through out the day. At the end of his day in Athens, he gave a packed talk to the department about his research on histone variants, nucleosome inheritance, and epigenetic inheritance.

On an interesting note, Steve Henikoff and PT author Reed Cartwright (with Luca Comai) have back to back papers coming out in November’s Plant Cell on HOTHEAD reversion, which Reed will expand on in a week or so.

Last week I wrote about the fact that Michael Behe claimed under oath in the Dover case that his book, Darwin’s Black Box, received even more thorough peer review than a scholarly article in a refereed journal. Now more and more facts are coming to light. We only know the names of 3 of the 5 reviewers - Michael Atchison, Robert Shapiro and K. John Morrow. Atchison, I’ve already documented, did not review the book at all. He had a 10 minute conversation about the book over the phone, without ever seeing the text, with an editor who was concerned about whether it would sell, not whether the science was solid. Skip Evans contacted Robert Shapiro and was told that he did review the book, and while he agreed with some of his analysis of origin-of-life research, he thinks his conclusions are false. He did, however, say that he thought that Behe’s book was the best explanation of the argument from design that was available.

Now, what of Morrow? As it turns out, this is the best of all. Over on the Panda’s Thumb, a commenter has left the text of an email from K. John Morrow in response to an inquiry about his review of Behe’s book. I contacted Dr. Morrow and we’ve spent some time on the phone over the last couple days discussing the situation. He has given me permission to post his response in full, with one disclaimer:

He dashed this response off pretty quickly in response to an inquiry and in retrospect he isn’t certain whether he reviewed the book for Free Press, who ultimately published the book, or for an earlier publisher who was considering publishing it. His recollection from a decade ago is that after he had given his review of the book and the review written by Russell Doolittle of part of the book, the editor told him that they didn’t think they were going to go ahead with publishing the book. But he can’t be certain at this point whether that was an editor for Free Press or an editor from a different publisher who was considering the book for publication. Ultimately this doesn’t matter. Behe himself named Morrow as a reviewer of the book in his testimony, so his views on the book are obviously germane to the question of the rigor of the peer review and whether it determined whether the book should be published. With that disclaimer, the post of his full response after the fold:

Continue reading Two More of Behe’s Reviewers Speak Out at Dispatches from the Culture Wars.

Shapiro on DBB Review

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by Dr. Robert Shapiro

As the author of over 100 peer-reviewed scientific papers and 4 science books for the public, I can add the following comments. I was sent an examination copy of Darwin’s Black Box when it was in near-final form. At that point in most cases, a contract has been signed, advance payments against anticipated revenue have been sent to the author, and the publisher is committed to publication, except under unusual circumstances. I was acting as an editorial consultant, rather than a peer reviewer. In my experience, the principal concern of the editor of a Trade (mass-market) book at that point is that the book be marketable, rather than factually correct (libel is undesirable, but is the responsibility of the author). Peer review, for a scientific journal, is a very different process.

(And not in a supportive way). PZ and Orac discussed a recent New England Journal of Medicine editorial critical of intelligent design. Though the article had several shortcomings, it’s always a bonus to see other scientists treating ID as a valid threat (not in the scientific sphere, of course, but in the “hearts and minds” of the populace). Now the Journal of Clinical Investigation, another fairly heavy-hitter as far as medical journals go, recommends to its readers, Don’t be stupid about intelligent design. Kudos to them…now come the nitpicks. :)

(Continue reading at Aetiology)

Larry Caldwell (Litigious ignoramus) has issued a press release trumpeting a victory in his federal lawsuit against the Roseville, California school district.

Over at EvolutionBlog, I have posted this follow-up to Andrea’s post below. At issue is the ludicrous charge, posted at Denyse O’Leary’s pro-ID blog, that Stephen Jay Gould had such a low opinion of natural selection that he would not have signed the NCSE’s Steves statement. It wasn’t hard to find quotes from Gould’s writing that should really put this question to rest. For example, from Essay 12 of his book Ever Since Darwin, we find this:

Modern evolutionists cite the same plays and players; only the rules have changed. We are now told, with equal wonder and admiration, that natural selection is the agent of exquisite design. As an intellectual descendant of Darwin, I do not doubt this attribution.

Stephen Jay Gould was one of the most prolific writers in the history of science. If you want to know what Gould thought about evolution, the solution is to go to the library, retrieve one of his books, and read it. But in the shameless, value-free, twilit world of ID hucksters, such initiative is frowned upon.

It doesn’t take much to get some attention from the upper echelons of the Intelligent Design movement. All you need is two things:

1. an argument against mainstream evolutionary theory, no matter how old and stale (e.g.: “mutations are not really random”, “we can tell design when we see it”, “natural selection is a tautology”, “common descent is an illusion” etc)

and

2. some sort of claim of authority to prop up that argument (“I have a PhD in a science-related field”; “I design/engineer things for a living, so I know how design works”; “I have written a pioneering/forthcoming/acclaimed book on the topic”; etc).

Of all the latter kind of claims, the most bizarre I have heard is probably the one underlying the latest post at Denyse O’Leary’s blog: she believes a guy’s take on evolution and on Stephen J. Gould’s ideas, because Gould used to spend time at his beach house. Seriously.

(Please note - an update now follows the main entry)

‘New recruits’ said needed for intelligent design

In the Dover circus (updates continue here), a sociologist named Steve Fuller testified yesterday on behalf of the defense. What was a theme of his testimony? Recruit the younger generation to give ID theory a boost–since apparently, the senior level ID “theorists” haven’t been able to come up with jack squat.

Introducing “intelligent design” to high school students could help the idea gain wider acceptance among mainstream scientists, a sociology professor testified Monday in a landmark federal trial over whether the concept can be mentioned in public school biology classes.

Fuller said minority views can sometimes have a difficult time getting a toehold in the scientific community, but students might be inspired to develop intelligent design as future scientists if they hear about the concept in school.

“You have to provide openings where you have new recruits to the theory,” Fuller said. “Unless you put it into the school system, it’s not going to happen spontaneously.”

And later in the article:

“It seems to me in many respects the cards are stacked against radical, innovative views getting a fair hearing in science these days,” he said.

Once again, it makes you wonder how such “minority views” as a bacterial cause for ulcers and symbiogenesis ever made it without a political lobby.

Edited to add: once again, Mike Argento nails it.

Fuller said intelligent design is, essentially, a half-baked idea, pretty much something the intelligent design guys have whipped up without doing much in the way of producing evidence.

And that’s why it should be taught to ninth-graders in Dover.

You know, I can come up with a lot of half-baked ideas that no one in their right mind would want to teach to kids in Dover. Let’s see. How about this? Cows think in Spanish. Discuss.

A major development in the Dover trial yesterday. The Discovery Institute had submitted a brief in the case last week and Judge Jones issued an order denying that brief’s use in the case. Our attorneys had filed a motion to strike that brief from the proceedings on the grounds that it was an attempt to get the expert testimony of Stephen Meyer and William Dembski on the record in the case after they had pulled out as expert witnesses, thus avoiding being cross examined on their claims. The judge agreed, ruling:

As all parties and amici filers are well aware, both Mr. Dembski and Mr. Meyer are no longer expert witnesses for the Defendants. Over the course of this trial we have provided both parties with every opportunity to present their expert witnesses, and accordingly the parties have engaged in thorough cross-examination of the opposing experts. We thus find it to be fundamentally unfair to receive a brief that frequently references an expert report, that was originally prepared for use in this case when Mr. Meyer was to be offered as a defense expert witness, and which contains the full revised report of Mr. Meyer as an attachment to the brief. The inclusion of such information in an ad hoc unsolicited fashion, when Plaintiffs have not had the opportunity to cross-examine such expert witness is clearly inappropriate under the circumstances. In fact, “Appendix A” of the amicus brief is entitled “Revised Report of Stephen C. Meyer, Ph.D., May 19, 2005” and it is clearly an expert report prepared in anticipation of Mr. Meyer’s testimony at trial. We will not countenance what is clearly a “back door” attempt to insert expert testimony into the record free of the crucible of trial and cross-examination.

In addition, after a careful review of the Discovery Institute’s submission, we find that the amicus brief is not only reliant upon several portions of Mr. Meyer’s attached expert report, but also improperly addresses Mr. Dembski’s assertions in detail, once again without affording Plaintiffs any opportunity to challenge such views by cross-examination. Accordingly, the “Brief of Amicus Curiae, the Discovery Institute” shall be stricken in its entirety.

Huge development in the case. Stay tuned for more.

The Onion Does it Again.

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Oh, the Irony!

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No sooner do I finish Jack Krebs blog entry about John Calvert’s dishonest remarks at a recent public presentation than I find this amusing essay (PDF format) linked to over at William Dembski’s blog.

The title of the essay: “Are We Liars?” The author: John Calvert.

I offer some thoughts on the subject in this post over at EvolutionBlog. Enjoy!

In the following exchange, Behe seems to be uncertain as to what intelligent design really does. When asked about exaptation, he answers that exaptation is consistent with intelligent design (but what isn’t…). He then claims that intelligent design ‘only focuses on the mechanism of how such a thing would happen’.

Q. But it is certainly, exaptation – for example, a bird wing developing from some kind of feathered structure on a dinosaur that didn’t necessarily allow flight, that’s what evolutionary biologists propose, and they call it exaptation?

A. That’s entirely possible, and that’s consistent with intelligent design, because intelligent design only focuses on the mechanism of how such a thing would happen. So the critical point for my argument is, how such things could develop by random mutation and natural selection.

Q. And again, intelligent design doesn’t describe how it happened?

A. That’s correct, only to say that intelligence was involved somewhere in the process.

Desperate times ask for desperate arguments

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The Discovery Institute has submitted an incredibly poorly argued Amicus Brief in the Kitzmiller case. But let’s first try an interesting experiment.

Let’s try the ‘reverse Pandas experiment’, replace intelligent design with creationism and see where the evidence leads us (to use a common creationist ‘argument’)…

ID report from Down Under

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During my visit to Sydney (Australia), a coalition of 70,000 Australian scientists and educators has published an open letter condemning the teaching of intelligent design in school science classes.

Professor Mike Archer, the Dean of Sciences at the University of New South Wales, seems to have been one of the leading forces behind this initiative.

ABC AUstralia: Scientists, teachers protest intelligent design

Australian scientists have been outspoken about Intelligent Design.

Australia’s world-renowned physicist Paul Davies say ID is codswallop, not science but creationism in disguise.

The Australian September 03, 2005

I don’t use the word “lie” loosely. I know it means deliberately saying something that one knows not to be true.

But in this case, I am willing to claim that John Calvert lied to the audience at his presentation at a conference hosted by the conservative American Enterprise Institute in Washington D.C. this past week. I hope to write more about Calvert’s presentation there, which was in conjunction with a speech by Barbara Forrest, but here I want to concentrate on one comment made by Calvert concerning Kansas Citizens for Science.

Ask Prof. Steve Steve #1

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Welcome to the first edition of Ask Prof. Steve Steve. Our first question comes from Jeremy Porath of Purdue.

Professor Steve Steve,

I read an article a while back about a group of Australian scientists who were attempting to bring back an extinct animal, the Tasmanian Tiger (or Thylacine) with cloning.

However, about two years ago, I read a book (What Do Martians Look Like?) that contained a rant against Jurassic Park that lead me to believe this sort of endeavor would be impossible. The relevant portions of the book and article are quoted on my LiveJournal.

I was hoping that you, or one of your colleagues, could perhaps shed some light on this and tell me which group is “correct”–or both, or neither, as the case may be.

Many thanks, Jeremy Porath, Junior, Purdue University

Jeremy, the Tasmanian Tiger cloning experiment is possible because the species only went extinct in the last 100 years. Unlike, dinosaurs Tasmanian Tiger DNA is still young enough to be potentially usable.

What else could I have done?

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I had a deadline for a “real” science article that was receding into the past at an alarming rate (to my co-author if not the journal editors).

So, what did I do? Of course! I wrote a totally unrelated item about creationist lies from Answers in Genesis. The motivation was when a young creationist was floating big chunks, err, posting large sections from an Answers in Genesis article about the origin of the Moon written (sort of) by Michael Oard.

John Stear was kind enough to post it on NAiG entitled “Oard’s Moonbeam”.

Robert Shapiro on Behe and ID

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Michael Behe took quite a flogging in Dover. Particularly embarrassing was the revelation that the “peer review” by one scientist of Darwin’s Black Box that Behe himself has described as more rigorous than the process journal submissions go through turned out to be a ten minute phone conversation. PZ Myers closed his blog entry on the matter by saying he’d “love to hear what Shapiro had to say about that book.”

Dr. Robert Shapiro is another scientist who reviewed DBB. Reading PZ’s closing line, I started wondering myself. So I emailed Dr. Shapiro and asked him what he thought of DBB, and Behe’s ideas, and he has been kind enough to give me permission to reprint his response, unedited and in full, here. Thank you, Dr. Shapiro.

Dear Mr. Evans,

I felt that Professor Behe’s book has done a better job of explaining existing science than others of its kind. I agree with him that conventional scientific origin-of-life theory is deeply flawed. I disagreed with him about the idea that one needed to invoke intelligent designer or a supernatural cause to find an answer. I do not support intelligent design theories. I believe that better science will provide the needed answers.

Sincerely yours, Robert Shapiro

In an email to me concerning this post, Matt Inlay points out that had Behe’s submission been to a scientific journal Dr. Shapiro’s review would have forced Behe to either change his conclusion of ID, or remove it entirely.

Teaching the Controversy

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My colleague, Taner Edis, Associate Professor of Physics at Truman State University, sent the following e-mail to a mailing list in which we both participate. The e-mail is reproduced here with permission. Read it carefully before you gloat about the shellacking we think our side is delivering in the Kitzmiller trial.

One of the interesting segments of the Michael Behe cross examination begins on page 42 of the Day12AM transcript, and it concerns a paper that Behe wrote with David Snoke. That paper, called Simulating Evolution by Gene Duplication of Protein Feature that Requires Multiple Amino Acid Residues, was based upon a computer simulation that attempted to answer the question of how long it would take cumulative point mutations in a single gene to produce a new trait - the interaction of two proteins - requiring a change in multiple amino acid residues if there was no selective advantage to preserve any of the individual mutations until they were all present and the final result was fully functional. For Behe, this is a simple example of irreducible complexity:

Thus in order for a protein that did not have a disulfide bond to evolve one, several changes in the same gene have to occur. Thus in a sense, the disulfide bond is irreducibly complex, although not really to the same degree of complexity as systems made of multiple proteins.

This paper has been lauded by ID advocates as an excellent example of ID-stimulated research. The DI has listed it as an example of genuine peer reviewed research that supports ID. William Dembski has declared that Behe and Snoke’s research “may well be the nail in the coffin [and] the crumbling of the Berlin wall of Darwinian evolution.” Unfortunately for them, this paper didn’t hold up well under questioning during the Dover trial.

Continue reading Behe Disproves Irreducible Complexity at Dispatches from the Culture Wars.

Scientists in Australia have taken a stand against ID. The Weekend Australian reports:

Ban design theory in class: scientists Leigh Dayton, Science writer October 21, 2005

A COALITION of more than 70,000 Australian scientists and science educators has condemned the teaching in science classes of “intelligent design” - a creationist-like theory of the origin of life.

In an open letter published today in major newspapers, including The Australian, the group says it is “gravely concerned” that intelligent design is being taught in schools as an alternative to evolution.

“It’s important scientists take a stand on this because intelligent design is nothing more than creationism dressed up in a tuxedo,” says Mike Archer, dean of science at the University of NSW and the driving force behind the letter. “It’s the same mishmash of theology and science.”

The letter urges governments and educators to oppose the teaching of intelligent design in the nation’s science classes.

This morning both Casey Luskin, at the DI’s “news” blog and Dembski at his Uncommon Dissent blog posted extensive quotes from Austalian newspapers concerning this.

pycnogonid

I'm going to introduce you to either a fascinating question or a throbbing headache in evolution, depending on how interested you are in peculiar details of arthropod anatomy (Mrs Tilton may have just perked up, but the rest of you may resume napping). The issue is tagmosis.

The evolutionary foundation for the organization of many animal body plans is segmental—we are made of rings of similar stuff, repeated over and over again along our body length. That's sufficient to make a creature like a tapeworm or a leech (well, almost—leeches have sophisticated specializations), but there are further steps involved in making a fly or a spider or a human. There is an arrangement of positional information along the length of an animal, so one segment can recognize whether it is near the head or the tail, and the acquisition of new patterns of gene expression based on that positional information that cause the development of specialized structures in different segments. That process of specializing segments is called tagmosis. It's how a fly forms mouthparts in head segments, legs and wings in thoracic segments, and no limbs at all in abdominal segments.

The relationships between segments and how they are specialized are key features in identifying patterns of descent in the arthropod clade. An analysis of those elements in an obscure group, the pycnogonids, has uncovered a surprising relationship—they seem to be related to well known Cambrian organism. You'll have to read through to the end to discover what it is.

Continue reading Pycnogonid tagmosis and echoes of the Cambrian (on Pharyngula)

Behe Blasted on Peer Review

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During the cross examination of Michael Behe in the Dover trial, he was questioned about whether the peer review process for his book, Darwin’s Black Box, was as rigorous as for a scholarly article in a refereed journal. He replied that it was even more rigorous. That led to an exchange that seriously impeached the credibility of Behe’s testimony. I have one report on it here and John Lynch has another report on it here.

Ask Prof. Steve Steve

Prof. Steve Steve always seems to have time to spare during his travels. (Traveling by parcel seems to give him some down time.) Now he and some colleagues have decided to answer questions submitted by students, teachers, and parents.

If you’ve got a question about science or cultural issues around it, drop the furry professor a line at [Enable javascript to see this email address.] or [Enable javascript to see this email address.].

Please include your name, school, town, and science course, as appropriate.

by Joe Meert

There were two days of talks given at the recent GSA meeting. Abstracts can be found at: http://gsa.confex.com/gsa/2005AM/fi[…]on_16049.htm and http://gsa.confex.com/gsa/2005AM/fi[…]on_16171.htm.

I’ll report as best I can on these two days beginning with day 2. I’ll try not to interject comments although it is hard to avoid.

dread_pirate_steve_steve2.jpg Do you worship Prof. Steve Steve?

How about showing it this Halloween?

Dress up as the fuzzy professor for Halloween and send us a photo to enter the costume contest. Worthy entries will receive prizes like t-shirts or maybe a visit from the Professor himself.

To submit your photo, upload it to the Internet and place a link to its location in a comment to this post. You must give us a way to contact you in your comment either an email or a link to a site with an email address.

(Note that the actual prize has not been decided yet.)

I think I'm liking the Kitzmiller case.

Not only is it looking like the creationist side is going to go down hard, but it's also accomplishing something very useful: it's exposing the incompetence, hypocrisy, and pariah status of one of the current Icons of Intelligent Design, Michael Behe. He's a guy the Discovery Institute loves to trot out as a star of their show. He has a Ph.D. in biochemistry! He's a professor at a respectable university! He published articles in real scientific journals! He has published a bestselling book!

It's no wonder the DI peddled away from this trial as quickly as their tricycle would take them…Behe is getting eviscerated. And all the lawyers had to do was expose his own words.

Continue reading "Contributing to Behe's sense of martyrdom" (on Pharyngula)

Tangled Bank #39

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Tangled Bank #39 is now available at The Questionable Authority. Enjoy.

Plesiosaur poop!

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plesiosaur

As Chris Clarke told me, "They were big ducks!" Two newly discovered elasmosaurid plesiosaur specimens from the Cretaceous contained a surprise that told us a little more about their diet.

Continue reading "Plesiosaur poop!" (on Pharyngula)

The Rio Rancho (NM) School District adopted a slickly-worded “Science” policy in August, which many fear will open up the classrooms of this Intel bedroom community to “Intelligent Design.” (See earlier reports on the Thumb here, here, here, here, and here.)

Now, the school employees union has sued to stop the policy, and the Saga has made the National News.

Intelligently designed avian flu?

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Ah, how rare is it that my interest in stomping creationists and my interest in infectious disease collide. But I guess that when there’s a topic as hot as avian influenza, it’s inevitable that even the folks at the DI will sit up and take notice, as Casey Luskin has in this post: Avian Flu: An Example of Evolution?

First, as Luskin admits in the article, the answer to his titular questions is, “well, duh; of course it is.” And alas, it doesn’t get any better from there.

Continue reading (at Aetiology)

In a post Monday, October 17, 2005 on the Discovery’s Institute’s Evolution News and Views blog, (a misnomer if I’ve ever heard one), Casey Luskin makes the following comment in regards to the Caldwell’s recent suit against the evolution website:

Caldwell thus does not allege that teaching evolution endorses religion. Rather Caldwell is alleging that when the government specifically suggests to students that “religion need not conflict with evolution,” that the government is telling students what their religious beliefs should be. According to Caldwell, this form of telling students how their religious beliefs should deal with evolution constitutes impermissible religious endorsement on the part of the government.

There is an important misconception here that also came up at the Kansas hearings. Informing people about different religions’ views on the nature of God’s relationship to the natural world, and thus those religions’views on the relationship between science and religion, is not the same as endorsing those views. More specifically, it is educationally appropriate to highlight the beliefs of Christians and other theists who accept evolution in order to combat the mistaken notion that Christians can’t accept evolution: doing so is not the same as saying that such theists are correct. Scientifically, we can’t pass judgment on any theological position, but we can offer accurate observations about the scope of religious belief.

Let me tell a story from Kansas concerning this issues, and then draw some conclusions.

Of Prions and People

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Spurred by a host of new findings in molecular and cellular biology, in recent years an increasing number of determined biologists have come to envision processes that contradict century-old biological assumptions and seem to defy the expectations of Darwinian evolutionary theory…

Naaah, I am not talking about ID. I am talking about prions, the specter of Jean Baptiste de Lamarck, and “heretical” views about biology. And what must be truly baffling for conspiracy-minded ID advocates, the inflexible “Darwinist orthodoxy” seems to positively dig this “heresy”. Now, that must hurt…

Since there appears to be an ongoing confusion about the work by Haeckel, the relevance of his work to Darwinian theory and the work by von Baer, I have researched these issues and despite the somewhat unorganized nature of my thoughts and findings, I have decided to present the results now rather than wait another 1 or 2 months before I have time to revisit this issue in more depth.

In Iconoclasts of Evolution: Haeckel, Behe, Wells & the Ontogeny of a Fraud The American Biology Teacher Volume: 67 Issue: 5 Pages: 275-282, authors, Pickett, Kurt M., Wenzel, John W., and Rissing, Steven W. examine the arguments by Behe and Wells about Haeckel and von Baer.

They conclude that, contrary to the claims (by Wells and Behe):

Darwin did not rely on Haeckel, but rather on von Baer. von Baer’s stance against ‘evolution’ is irrelevant. Behe (1998) and Wells (1999, 2000) are deeply confused or intentionally confusing regarding the history and significance of this well-known field, an area they claim has special meaning in their political movement.

A particular ironic statement is made by Wells:

But Darwin persisted in citing him [von Baer] anyway, making him look like a supporter of the very doctrine of evolutionary parallelism he explicitly rejected

Jonathan Wells, Icons of Evolution 2000, page 86.

I wonder how Wells feels about the DI bibliography, given the above objections.…

Careless reading?

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Wishful (or careless) reading seems to be an ongoing ‘problem’ at the people at the Center for the renewal of science and Culture of the Discovery Institute.

When the University of Idaho reiterated its commitment to teaching scientifically relevant theories in science classes, the Discovery Institute (DI) was quick to accuse the university of attacking academic freedom. What caught my eye however was the following statement.

Rob Crowther Wrote:

The University of Idaho maintains that the edict censoring science wasn’t focused at [Scott] Minnich, but it seems that even [Eugenie] Scott found that hard to believe.

So what is it that Eugenie Scott said that led Crowther to make this statement?

Education Law and Evolution

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Wildernesse (Tiffany) is a beautiful law student who just happens to be married to a handsome evolutionary biologist. Today in her class on education law they discussed evolution and creationism. She has written about it on her blog, go check it out.

Oh well. I wish people were more educated. I’m not even well-educated on this subject, but I know that a lot of what is spouted off out there is nonsense. (My definition of well-educated for laypersons is whether you can explain a frequency-dependent selection model, a phylogenetic tree, and why humans are taxonomically classified as an ape. If you can’t do those things, what makes you think you know enough? I am arbitrary and I love it.) I wish people didn’t feel they had to cram their religious beliefs into a stunted mold and become blind to the utterly awe-inspiring natural mechanisms of our world. Let God out of the box.

Larry Caldwell's wife Jeanne Caldwell has reportedly filed a lawsuit against the National Science Foundation and UC Berkeley for violating the Establishment Clause. In substance it's the same complaint that was publicized some time ago on National Review Online, and which, as I explained back then, is absolutely without basis in the law.

Of Pandas and People, coverIt seems like a lifetime ago now, but it was only December 7, 2004 when I posted the original “Panda-monium” post on PT, linking to NCSE’s new webpage of resources on Of Pandas and People. At the time, I was relatively new to Pandas. However, even back then it struck me that Pandas was a particularly important work, because it was published in 1989 and thus substantially predated the rest of the “intelligent design” corpus. At the time, I remarked that:

The Tangled Bank

You've got less than a week to get your submissions in for the Tangled Bank, due to arrive at The Questionable Authority next Wednesday. Write and send those links to me or host@tangledbank.net by Tuesday evening!

Pandas and Man at Harvard

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During a break in the Dover Trial, I traveled to historic Cambridge, MA to attend the Fifteenth 1st annual Ig Nobel Prize ceremony. Visiting Cambridge allowed me to visit several friends at Harvard University, where the Ig Nobels were held. Over the years, Harvard has attracted many famous evolutionary biologists, but also many creationists. Not counting its pilgrim founders, who had no knowledge of the modern scientific method (“methodological naturalism,” as my creationist friends call it nowadays) developed in the 17th century after the puritans fled England, Harvard has been home to a few influential creationists, from Louis Agassiz in the 19th century to modern day Intelligent Design creationists. I had a chance to visit them both on this trip, and you’re welcome to join me on my travels.

Verbal Sparring in Florida

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Dearest Cheri: whether you inundated the committee with every other standard used in the civilized world does not address the point at issue, which is whether you handed the committee the completely useless “Santorum language” with the implication that it had any legal force with respect to drawing up science standards.

(Continue reading… on The Austringer)

The Cambrian Revisited

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Although I hate to give credibility to statements which are so anti-science, I also believe that educating those who are willing to hear the “rest of the story” is important.

Point in case:

In a recent blog posting, Denyse O’Leary stated the following on the Cambrian explosion. Since her comments may be of direct interest to this group, I would like to repeat them here and discuss why they are flawed.

On October 6th, the Discovery Institute issued a press release titled Dover Trial Witness Plays Misleading Word Games In Effort to Redefine Intelligent Design.

The release declares

“Forrest is playing word games, without looking at the meaning of the words,” said Casey Luskin, program officer for public policy and legal affairs at Discovery Institute’s Center for Science & Culture, in response to an intelligent design opponent’s testimony.

Plaintiff’s witness, Dr. Barbara Forrest, pointed to the word “creation” in early drafts of the supplemental textbook Of Pandas and People which in her opinion is evidence that intelligent design was the same thing as creationism.

“At the time the authors began work on Pandas, there was no widely accepted way to describe the scientific position being advocated there,” said Luskin, “namely that there are indicators of design in nature, that scientists should remain open to the possibility of intelligent causes, and that such evidence does not tell us the identity of the designer.” …

Luskin’s comment is funny, because Discovery’s Jonathan Witt said the exact opposite recently!

This post describes a discovery by Dr. Thomas D. Schneider which is a much stronger proof of intelligent design than all those incessantly disseminated books, essays and interviews by the fellows of the Discovery Institute. We expect that the ID advocates will promptly acknowledge our contribution to their case. (Thanks to Dr. Schneider for this guest contribution.) The full text of Dr. Schneider’s epochal breakthrough paper can be seen here

It’s always nice when there’s a groundbreaking article in the literature, and the subject just happens to be your baby. My current research focuses on Streptococcus agalactiae (group B streptococcus, GBS), a bacterium that is the leading cause of neonatal meningitis in the United States. It also is a leading cause of invasive infection in the elderly, and can cause sepsis and toxic shock-like syndrome in healthy adults. No vaccine is currently available.

But what’s garnered attention recently hasn’t been any clinical presentations or new case reports of GBS disease; it’s the bacterium’s DNA. Specifically, the whole genomic sequences of 8 different strains of GBS, and the conclusions the authors have come to regarding bacterial genetic diversity–that it may be “endless.”

Continue reading (at Aetiology).

The Nitty Gritty Bit

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This essay is authored by Dr. Thomas D. Schneider. We thank Dr. Schneider for this guest contribution.

Intelligent Design advocates frequently state that living things are too complex to have evolved. This article shows how Claude Shannon’s information measure has been used as a well-regarded proxy for ‘complexity’ to predict the information that is required for a genetic control system to operate. This measure is called Rfrequency because it is computed from the frequency of binding sites in the genome for proteins that do the genetic control. Using information theory, we can also precisely measure the information in DNA sequences at the binding sites, a measure that is called Rsequence. In nature we observe that Rsequence is close to Rfrequency, which implies that Rsequence must have evolved towards Rfrequency. A model that you can run on your computer demonstrates this evolution, starting from no pattern in the binding sites and ending with the two measures being equal within the noise of the measurement. The amount of information evolved in the model is far more than the Intelligent Design claim can withstand. Given 2 billion years for evolution on this planet there was plenty of time to evolve the observed complexity.

The article is based on this paper . A web site accompanies the paper, giving many more details about the computer model and how to run it.

Continue reading The Nitty Gritty Bit here

Dog Bites Man

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I was going to title this post something like, “Casey Luskin totally misunderstands and misrepresents something related to biology,” but the title I settled on seems to sum up the news level involved much more concisely. In this instance, Casey attempts to explain away some of the evidence for human-chimp common descent that was presented by Ken Miller during his testimony last week in the Dover case.

Read more (at The Questionable Authority):

Calling all Iowans…I’m working on getting a Citizens for Science group up and running in the state. At this point in the game, I have a group of about 20 people from around the state (mostly Iowa City/Cedar Rapids, Des Moines/Ames, and Cedar Falls) who are interested, and we’re still very early in the planning stages. We’re looking for people who are interested in participation at any level. Drop me an email if you’re interested!

Florida flip-flop

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Carl Zimmer examines the situation in Florida, bringing up Yecke and Jeb Bush and the interesting conundrum that while they are trying to pander to the Intelligent Design creationists, they have also enticed the Scripps Institute to open a Florida branch campus.

I don't know how long Florida will be able to go on this way, trying to attract the biotech industry while its leading state officials try to teach its students that creationism is an equally valid way of understanding life. Sooner or later, something's got to give.

You can't encourage ignorance while trying to reap the benefits of knowledge for long. That's the balancing act the creationist-friendly politicians are trying to play, though; I think they're just hoping they can keep wrecking the foundation now, and that everything will collapse after they're safely out of office.

Matthew and Me

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I am at Kitzmiller v. Dover Area School Board supporting the plaintiffs with my unique expertise. As the holder of the B. Amboo Chair in Creatoinformatics at the University of Ediacara, I was invited to attend an “evolution is stupid” seminar at Dover Fire Station 6. The seminar was mainly an infomercial for Mr. Kent Hovind’s DVDs.

The lone bright spot was that I was able to meet Matthew Chapman, the great-great-great-great-grandson of my idol, Josiah Wedgewood. (Oh, yeah–I almost forgot–he is also related to Charles Darwin.)

I ended up chatting with Chapman, my good buddy Burt Humburg, and some reporters, but they didn’t allow me to say much.

Matthew Chapman and Prof. Steve Steve

Update: USA Today managed to identify my colleague, Dr. Patricia Princehouse, but they seem to have forgotten my name, referring to me only as “a panda puppet.” What is journalism coming to these days?

I just read, for the second time, an article by Doug Kern that’s available at Tech Central Station. After my blood pressure came back down a bit, the article got me to thinking. The tone of the piece is annoying and condescending, and there is far more in it that is wrong than is right, but it illustrates a number of the political problems that we face all too well.

The title of the article is, “Why Intelligent Design is Going to Win.” The thesis statement is short and simple: “Intelligent Design theory is destined to supplant Darwinism as the primary scientific explanation for the origin of human life. ID will be taught in public schools as a matter of course.”

Read more (at The Questionable Authority)

Another Dover news carnival

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After spending most of the week stranded deep in the mire of proposal writing, I’ve rewarded myself with a day off. Actually, it’s not so much a matter of rewarding myself as it is a matter of attempting to resusitate the last remaining shreds of my sanity. So instead of continuing to pickle my brains in the volumnous literature surrounding the history of genetic divergence in various species of Drosophila, I decided to take some time to skim through a number of the news articles that the Dover trial has spawned in the last week. (Why I thought this would help maintain my sanity should serve to indicate just how brain-corroding the scientific proposal process actually is.)

Rather than taking as inclusive a look as I did last time, I think I’m mostly going to focus on the more annoying articles this time. It might just have been my mood this week, but it certainly felt like there was a heck of a lot more stupidity being aired this time.

Read More (At The Questionable Authority)

Drawing a Line in the Academic Sand

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Two recent articles in Inside Higher Ed News are presenting a good overview as to how academics view Intelligent Design.

Drawing a Line in the Academic Sand and Common Ground on Intelligent Design

The first article discusses the statement by the President of the University of Idaho.

President White Wrote:

“Because of the recent national media attention on the issue,” reads President Timothy P. White’s letter, “I write to articulate the University of Idaho’s position with respect to evolution: this is the only curriculum that is appropriate to be taught in our bio-physical sciences.” The short letter goes on to allow for the teaching of “views that differ from evolution” in other courses, like religion and philosophy, but not as a scientific principle, which is “testable and anchored in evidence.”

They quote Harold Gibson, a University of Idaho spokesperson

Gibson said that if he were a faculty member interested in “intelligent design,” he would actually feel better because of the letter. “It clearly states there is a place for teaching of views that differ from evolution, as long as they’re in faculty approved curricula,” he said

Thus far this week, I’ve discussed the history of pandemic influenza in general, and avian flu in particular. I’ve discussed some issues that must be addressed to prepare us for a pandemic, and the groundbreaking resurrection of the Spanish influenza virus. Today I want to end the series with a look at how prepared we currently are as a nation, and highlight some personal preparedness steps you can take.

If you recall from Tuesday, the first outbreak of H5N1 was back in 1997. The anthrax attacks were in 2001. Surely by now we’re prepared for some kind of serious, large-scale, biological event, right? Well…

The Feds: “um, er, the dog ate my homework?”

The U.S. is still working on finalizing its Pandemic Influenza plan, which it keeps promising will be done “soon.” But scientists are a bit skeptical…

“We need more than just a plan; we need the resources to actually activate it,” said Jeffrey Levi, a pandemic specialist at the Trust. “The real test of the plan will be whether it comes with dollars attached.”

The current draft of the administration’s plan fills several hundred pages. It describes the role of the federal government in coordinating the response to a flu pandemic and outlines steps to be taken at all levels of government before and during an outbreak.

In addition to production and stockpiling of vaccines and antivirals, the plan seeks to conduct research, prepare public education campaigns and develop ways for hospitals to handle large numbers of patients.

Continue reading (at Aetiology)

As we’ve pointed out before on the Panda’s Thumb, the proposed intelligent design textbook Of Pandas and People indicates that intelligent design was simply a rebadging of creationism. In view of that, let’s look at the short chapter of the 1993 edition of Pandas which discusses human evolution. Here are some quotes from that chapter:

Does the fossil record provide any evidence for either the Darwinian or the intelligent design view of man? (p.107)

Homo erectus had a larger brain (950cc) than Homo habilis, and walked with an upright posture, like man. … It had significant anatomical differences from modern man that have prevented its classification as Homo sapiens. (p.110)

Design adherents, however, regard Homo erectus, as well as the other hominids discussed in this section, as little more than apes, and point instead to the abrupt appearance of the culture and patterns of behavior which distinguish man from apes. (pp.112-3)

Who are these “design adherents” who regard Homo erectus as “little more than apes”?

From the York Daily Record we receive the following article how desperate the defense was to discredit Forrest.

Various ID organizations have been active trying ‘muddle the water’, underlining how afraid they must be of the scholarly evaluation of the Wedge Strategy and of Pandas and People.

HARRISBURG — Along about the 658th hour of Dr. Barbara Forrest’s stay on the witness stand, during Day Six of the Dover Panda Trial, I started looking for her horns.

Never did see them.

It was right about the time that defense lawyer Richard Thompson was repeatedly asking about her various memberships in such seditious, treasonous and just plain evil organizations as the New Orleans Secular Humanist Association and the ACLU that it occurred to me to look for her horns.

They weren’t there.

Now, it could be that she was hiding her tail under her trim black pantsuit, but frankly, I didn’t really look.

Supreme Court nominee Harriet Miers has

given 10 percent to 12 percent of her earnings – “if not more” – to the evangelical Valley View Christian Church in Dallas, where she has been a congregant for about 25 years

according to Judge Nathan Hecht of the Texas Supreme Court, who has dated Miers. This Newsday article has the details.

What has this to do with Panda’s Thumb? A lot!

I know I said I was going to discuss a bit more about pandemic preparedness today, but I think I’ll hold off on that to discuss this story:

It sounds like a sci-fi thriller. For the first time, scientists have made from scratch the Spanish flu virus that killed millions of people in 1918.

Why? To help them understand how to better fend off a future global epidemic from the bird flu spreading in Southeast Asia.

Researchers believe their work offers proof the 1918 flu originated in birds, and provides insights into how it attacked and multiplied in humans. On top of that, this marks the first time an infectious agent behind a historic pandemic has ever been reconstructed.

Continue reading (at Aetiology)

With the recent Amicus Brief, it has become even more relevant to address claims that there is a scientific controversy or discussion about intelligent design. I argue that from a scientific perspective the discussion is already over. ID has shown itself to be scientifically vacuous, based on flawed premises.

I am not alone.

It would ‘become the death of science’. Ker Than reports on the ‘controversy’ surrounding intelligent design, pointing out that a new scientific theory must offer something compelling.

But in order to attract converts and win over critics, a new scientific theory must be enticing. It must offer something that its competitors lack. That something may be simplicity, which was one of the main reasons the Sun-centered model of the solar system was adopted over the Earth-centered one centuries. Or it could be sheer explanatory power, which was what allowed evolution to become a widely accepted theory with no serious detractors among reputable scientists.

So what does ID offer? What can it explain that evolution can’t?

To answer this, it is necessary to examine the two main arguments — irreducible complexity and specified complexity — that ID proponents use to support their claim that a Supreme Being is responsible for many or all aspects of life.

Based on an evaluation of the two main arguments, the author comes to a conclusion similar to that of various others who have asked very similar questions.

nodal in zebrafish

Do vertebrate embryos exhibit significant variation in their early development? Yes, they do—in particular, the earliest stages show distinct differences that mainly reflect differences in maternal investment and that cause significant distortions of early morphology during gastrulation. However, these earliest patterns represent workarounds, strategies to accommodate one variable (the amount of yolk in the egg), and the animals subsequently reorganize to put tissues into a canonical arrangement. Observations of gene expression during gastrulation are revealing deeper similarities that are common in all deuterostomes—not just vertebrates, but also the invertebrate chordates (tunicates and cephalochordates) and echinoderms.

What does all that mean? If you think of development as a formal dance, the earliest stages are like the prelude; everyone is getting out of their chairs around the ballroom, looking for partners and working their way towards the floor. The dispositions of the dancers are variable and somewhat chaotic, and vary from dance to dance. Once they get to their positions, however, we're finding that not only is there a general similarity in their arrangements, but they're all dancing to the very same tune. In this case, one of the repeated motifs in that tune is a gene, Nodal, which is active in gastrulation and shows a similar pattern in animal after animal.

Continue reading "The evolution of deuterostome gastrulation" (on Pharyngula)

Tangled Bank #38

The Tangled Bank

It's here! Yet another feast of science blogging is available for your delectation at Living the Scientific Life.

The scientific community is all too familiar with the dangers an influenza pandemic could bring. The politicians and general public are starting to become aware of the issue as well; indeed, one can hardly open a newspaper or turn on the television without hearing about “bird flu.” So, what’s actually being done to prevent an influenza catastrophe? What are the issues? What can be done?

These are the questions that keep public health officials awake at night, because the answer is always that we’re not doing enough. While we may be resigned to the fact that a future pandemic can’t be completely prevented, the damage can be minimized. Today, I’ll discuss the problems we face, and the proposed solutions to counter them, when it comes to pandemic influenza preparedness.

Continue reading (at Aetiology)

Allies of ID creationism have filed a friend-of-the-court brief in the Kitzmiller case which you can read here. It essentially argues that the court should not address the scientific validity or invalidity of ID; "[T]he scientific theory of intelligent design [sic] should not be stigmatized by the courts as less scientific than competing theories," the brief argues. (p. 5) Of course, determining that a set of assertions is not scientific is not necessarily to "stigmatize" those assertions, but simply to understand their nature; it's not stigmatizing a duck to say that if it quacks and waddles and has feathers, it's a duck. ID is not science because it is not a testable explanation of natural phenomena in terms of other natural phenomena. Instead, it's an assertion that phenomena can only be explained by invoking non-rational, non-testable, non-repeatable magical phenomena.

More Zany Young Earth Creationism

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Many readers and posters to PT are well versed in the sheer zaniness of Young Earth Creationism. But even after reading YEC literature for over 10 years, every now and then I’ll come across something that makes me burst out laughing and saying to myself, “No, these guys cannot be serious.”

You really have to exercise some pretzel logic (just to work in a reference to a pretty cool Steely Dan album) to buy into a 6,000 year old earth, and a boat floating around for about a year with 16,000 animals taken care of by 8 people.

A perfect example of this double-jointed mind game came to me in an email from AiG a few days ago containing a link to a PDF pamphlet penned by Ken Ham, AiG’s President. (http://www.answersingenesis.org/Hom[…]ahsflood.pdf)

Aside from offering a series of sheerly absurd explanations of how they fit that many animals on board (they took babies), fed them all (a lot of them hibernated, so they didn’t eat), ventilated the ark (without smelling like their heads were shoved into a gorilla’s armpit), and shoveled up all the poop (probably done by undocumented workers, hence not mentioned in Genesis for tax purposes), Ham also wrote a short section regarding the building of the Ark.

Cardinal backs evolution and “intelligent design”

A senior Roman Catholic cardinal seen as a champion of ”intelligent design” against Darwin’s explanation of life has described the theory of evolution as ”one of the very great works of intellectual history”.

Vienna Cardinal Christoph Schoenborn said he could believe both in divine creation and in evolution because one was a question of religion and the other of science, two realms that complemented rather than contradicted each other.

Schoenborn’s view, presented in a lecture published by his office today, tempered earlier statements that seemed to ally the Church with United States conservatives campaigning against the teaching of evolution in public schools.

Anyone working in the area of influenza virus epidemiology is familiar with the name Robert Webster. A virologist at St. Jude’s Children’s Hospital in Memphis, the native New Zealander has been leading the charge against influenza for well over 40 years. Barely out of graduate school, Webster hypothesized that something like genetic reassortment (which had not yet been discovered) occurred to cause the big changes that appeared among human influenza viruses, driving pandemics. He performed a simple experiment that cemented the course of his career: he found that serum from patients who had survived the 1957 influenza pandemic reacted with avian influenza viruses. Later genetic analyses showed that the “Asian flu” virus had indeed received 3 of its 8 gene segments from birds. It happened again in 1968: the pandemic virus was the result of a reassortment between human and avian influenza viruses. These observations led to more than 30 years of surveillance of waterfowl in many different countries, and the revelation that these waterfowl constitute a reservoir of all known subtypes of influenza virus.

Webster’s worst fears seemed to be coming true in 1997. Hong Kong was experiencing an influenza outbreak in chickens so severe it had been nicknamed “chicken Ebola.” Humans were also affected. The first case was in a 3-year-old boy from Hong Kong. Though doctors knew he had died of the flu, they were uncertain of the strain, and sent samples off to several high-level laboratories for further testing. When it came back H5N1, the Centers for Disease Control and Prevention sent Keiji Fukuda to Hong Kong to investigate. After a month of searching, he and his team found no further evidence of infection with this avian virus in the human population—so they left, writing off the boy’s illness as a “freak occurrence.” They were premature. By the end of the year, 18 cases had been confirmed; 6 died. Clinical features often included a primary viral pneumonia and death quickly after onset of symptoms. The route of transmission in all cases appeared to be direct bird-to-human contact. Fearing a public health crisis, officials ordered the culling of Hong Kong’s entire poultry population. Analysis of the virus showed it to be a serotype H5N1 virus.

Continue reading (at Aetiology)

Last call for the next Tangled Bank

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The Tangled Bank

Today is the day to get your links in for the Tangled Bank appearing tomorrow at Living the Scientific Life. Send them in to GrrlScientist, me, or host@tangledbank.net.

The Holy Grail of biochemistry is what’s known as the “protein folding problem”. We’ve long known that most proteins’ function is based on their 3-dimentional structures (i.e. their folds), and that these structures are dependent on their linear amino acid sequences. What we haven’t known is how exactly their amino acid sequences determine their structures. This would be an extremely useful thing to know, because currently the only way to determine a protein’s 3D structure is through X-ray crystallography or NMR, both of which are expensive, time-consuming, and aren’t even guaranteed to work. If the protein folding problem were solved, the thousands and thousands of proteins that we’ve sequenced could have their structures deciphered almost overnight, revolutionizing our understanding of how proteins function. Of course it probably won’t happen that way; the protein folding problem will probably be slowly chipped away at rather than solved in one fell swoop, and crystallographers and NMR spectroscopists will remain gainfully employed for the foreseeable future.

But two papers published in a recent issue of Nature from the lab of Rama Ranganathan knocked a chip out of the protein folding problem. Their results show us that protein folding might be simpler than we think.

PT Lauded by Scientific American

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Since no one else has done it, on behalf of my colleagues here I’ll immodestly draw attention to Scientific American’s selection of Panda’s Thumb for one of its 25 “Science & Technology Web Awards 2005”.

If it’s in the media and related to evolution, you’ll find it posted, dissected and debated on this lively and informative watchdog blog. Devoted to debunking all existing and nascent theories related to the anti-evolution movement, the site’s contributors comprise a passel of the world’s most vigilant and passionate biologists, geneticists, students and concerned citizens, for whom stemming the tide of creationism and its offshoots is a fulltime job. The general public can join the fray in the “After the Bar Closes” forum, where political, religious and personal evolutionary arguments are given a full dressing-down by the site’s rowdy, articulate devotees.

The Loom, where Carl Zimmer holds forth on the biological sciences with clarity and erudition, was also selected along with 23 other excellent science and technology sites in whose company we’re honored to find ourselves. Go read ‘em all!

RBH

Eureka Alert

The largest-ever experimental analysis of duplicated genes provides insight into mechanisms of evolution

Zürich, Switzerland – When Mother Nature creates an identical copy of a gene in an organism’s genome, the duplicated copy is usually deleted, inactivated, or otherwise rendered nonfunctional in order to prevent genetic redundancy and to preserve biological homeostasis. In some cases, however, gene duplicates are maintained in a functional state. Until now, the biological and evolutionary forces behind the maintenance of these duplicates as functional components of the genome have remained unclear.

But I thought biologists were too “close-minded?”

Australians Barry J. Marshall and Robin Warren won the 2005 Nobel Prize in medicine Monday for showing that bacterial infection, not stress, was to blame for painful ulcers in the stomach and intestine.

The 1982 discovery transformed peptic ulcer disease from a chronic, frequently disabling condition to one that can be cured by a short regimen of antibiotics and other medicines, the Nobel Prize committee said.

Thanks to their work, it has now been established that the bacterium Helicobacter pylori, which the new Nobel winners discovered, is the most common cause of peptic ulcers.

Woodward and Pitts on ID

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In an article published October 1 in the New York Times, “Evolution as Zero-Sum Game”, Kenneth Woodward makes an interesting observation:

The danger in intelligent design is not just that it is bad science but that it seeks to enlist evidence from science in the service of religious truth. … But the designer God of intelligent design is no more necessary to Christianity (or other monotheisms) than was the deistic God of Newtonian physics. In both cases, God ends up being made in the image of an intellectual system.

And in a column in the Lawrence Journal World today, Leonard Pitts writes,

I would argue that faith and science are in some ways more complementary than contradictory. But it’s telling that where they do conflict, as in the question of human origin, it’s always people of faith who beg for validation. … There is an unbecoming neediness about these constant schemes to dress religion up as science. Why are some people of faith so desperate for approval from a discipline they reject? …

We inhabit a universe vaster than human comprehension, older than human wanderings, more wondrous than human conception. And in the face of that, we do the natural thing. We ask questions and seek answers.

That’s not a denial of God. It is evidence of Him.

It’s hard to avoid hearing about influenza virus these days. In all the noise, it’s tough to sort out the facts from the rumors and conspiracy theories. I’ve already discussed a bit about the basic biology in this post, so I’m not going to review that here (though a good overview can be found here for those of you who need to bone up on your influenza virus virology). So, this week, as a part of Pandemic influenza awareness week, I’ll be writing a 5-part series about various issues regarding influenza. Today, I’ll discuss the history of influenza, focusing on past pandemics. The rest of the week will address the following topics, with the goal of presenting a review of the facts without the scare-mongering:

  • “Avian flu” and H5N1, 1997-present
  • Where we are now—are we ready for a pandemic?
  • How do we prevent/control a pandemic? What models and surveillance can tell us
  • Other issues in influenza

So, without further ado, let’s dive into today’s topic:

A quick trip through the history of pandemic influenza (on Aetiology)

Link Sunday, October 02, 2005 BY MARY WARNER Of The Patriot-News

Darwin and God seem irreconcilable to many Americans. That’s why evolution remains a flashpoint in public schools.

Many others see no conflict, though. And that reconciliation has been a subtext of a closely watched federal trial in Harrisburg about teaching evolution.

“Faith and reason are not only compatible. They are complementary,” testified Ken Miller, a biologist who took the stand to affirm Charles Darwin’s theory as established science.

Behe at the MacLaurin Institute

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Michael Behe was in my neck of the woods last night, and gave a talk titled "Toward an Intelligent Understanding of the Intelligent Design Hypothesis". There was absolutely nothing new in it, no evidence, no hypotheses, no nothin'…so don't trouble yourself to read my account of the event unless you are obsessive about seeing what the anti-evolutionists of the Discovery Institute are up to.

The words of the world

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A study in Science has returned biological methods to linguistic evolution in a reversal of history, and concluded that one can, within limits, reconstruct the history of language. Charles Darwin was not the first person to suppose that historical evolution could be recognised by homologies and represented by tree diagrams. That honour goes to Sir William Jones in 1797, although the tree idea was later. Jones argued that one could compare cognate terms and infer a historical relationship between languages and this has become the foundation of modern philology. For example, words that are based on the idea of "knowing" (including, as it happens, "idea") generate a tree of Indo-European languages. [And like biological evolution, there are "creationists" who think that all language was created in Sanskrit.] Now, a study in Science has returned biological methods to linguistic evolution in a reversal of history, and come up with some interesting conclusions.

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