November 27, 2005 - December 3, 2005 Archives

The mainstream media, and a growing number of academics have “discovered” the threat that the new creationism, AKA intelligent design, poses to science education in the United States.

That’s the good news.

The bad news is that some of these newly minted ‘experts’ will be proffering up their solutions, many of which will be shallow, and some even counterproductive. The recent proposal for high school debates on evo/creato by Michael Balter is an example. During the long and contentious discussion of Balter’s editorial and proposals, a research article by Prof. Steve Verhey was introduced by Balter who claimed it was a vindication of his proposal. A short while later Verhey also joined the discussion. That Verhey’s work did not support Balter is clear, as was stated explicitly by Verhey,

I don’t know what to say about high school evolution education. I don’t think my approach would work there. Perhaps it could work, but it would take too much time. Evolution can’t be avoided in HS biology classes, and creationism/ID can’t be presented as even vaguely valid alternatives, so we are where we are.

Since the paper in question had not been seen in print, we deferred further discussion of its contents. Dr. Verhey has now kindly made the PDF of his paper available to Panda’s Thumb readers. Note also that he has also presented key portions of his raw data as well.

I commend Dr. Verhey’s efforts and transparency which are in the best scientific tradition, and I will insist that any comments by PT readers will also. Dr. Verhey and I have exchanged a number of emails over the last two weeks concerning his paper, and the data which informs his conclusions. These emails (with only trivial edits) form the bulk of the following post. Quite obviously any cogent remarks regarding Dr. Verhey’s paper and the material below will require that one has read and understood the paper. Non-cogent remarks will be simply deleted.

Though I’m not an MD myself, much of my research and my reading centers on medical issues, while another passion (as regular readers certainly must have noticed) is the “controversy” over evolution, and educating the public about the issues involved with that. So, in a nice convergence of these two topics, the American Medical Association has published an Op-Ed on the topic of evolution denial (with quotes from PT-ers Burt Humburg and Glenn Branch as an added bonus).

I’m afraid we live in loopy times. How else to account for the latest entries in America’s culture wars: science museum docents donning combat gloves against rival fundamentalist tour groups and evolution on trial in a Pennsylvania federal court. For those keeping score, so far this year it’s Monkeys: 0, Monkey Business: 82. That’s 82 evolution versus creationism debates in school boards or towns nationwide—this year alone.

The most important part of his piece, IMO, addresses the role of the medical community in this “controversy:”

(Continue reading at Aetiology…)

One thing I love about this place is how random interesting tangents will spring up in the comments. I wrote a brief post awhile back about some funny/sad AiG cartoons, which morphed into a discussion of snake evolution in the comments section. Dr. Fry’s comments in that discussion led to 2 follow-up posts on his work on the evolution of snake venom, and in the second thread, here, Steviepinhead has mentioned a new Archaeopteryx finding with better-preserved feet:

Steviepinhead Wrote:

…A new Archaeopteryx fossil with exquisitely-preserved feet has been found. In previous finds, the feet were fairly scrunched up. Because there were enough other bird-like features, the less faithfully-preserved feet were assumed to be bird-like as well, with a rear-pointing toe.

It turns out that that toe actually points forward, and is set off to one side, strongly resembling the arrangement of toes of Velociraptor and similar dinosaurs.

Thus, Archaeopteryx turns out to be even more of a mosaic of bird and dino features than previously thought. You might even call it a transitional fossil.

Early-bird fossil features dinosaur feet

A Letter to the Editor

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Today’s (1 December 2005) edition of USA Today included a column on Intelligent Design written by Cal Thomas and Bob Beckel. The entire column is objectionable, but Thomas’ conclusion was by far the worst part. The rest of this post, which also appears on my personal blog, has been submitted in response as a letter to the editor.

….….….. Dear Sir:

On June 30, 1860 a famous (and perhaps fictional) encounter took place between the scientist Thomas Henry Huxley and the Bishop of Oxford, Samuel Wilberforce. The occasion was a discussion of Darwin’s recently published book Origin of Species, and according to legend Wilberforce concluded his remarks by asking Huxley whether he was descended from an ape on his father’s side or his mother’s. This bit of ancient history popped into my mind when I read Cal Thomas’ remark at the end of the column that he and Bob Beckel wrote on Intelligent Design in yesterday’s paper.

Unlike our understanding of evolution itself, which has advanced tremendously in the last century and a half, Thomas’ idea of a clever response seems to be on a par with the good bishop. Thomas’ remark, “Maybe we can offer [scientists] some bananas as an incentive. As they eat them, they can contemplate their heritage,” does not have any more of a place in a reasonable discussion than did Wilberforce’s.

My reply to Thomas is more or less the same as Huxley’s reply to Wilberforce: if I had a choice between having a monkey as a grandfather or having as a grandfather someone who has great intellectual gifts and influence, but uses those gifts and that influence merely to inject ridicule into a serious debate, I would, without hesitation, choose the monkey.

Michael Dunford Graduate Student, Department of Zoology, University of Hawaii at Manoa.

Hi everyone. I have a few free minutes from my extensive itinerary (currently in Australia again) to let people know that I will be heading to the UK shortly. Chris Nedin, with whom I am currently staying, will be heading over there next week and I am taking the opportunity to travel with him (although I’ll be travelling much closer to the front of the plane than Nedin, as befits my role as roving ambassador and famous panda). I plan to take Nedin around the British Natural History Museum in South Kensington, London on Saturday Dec 10th to educate him in matters evolution in general and palaeontology in particular. Should be fun (for me anyway). Any locally-based readers of the Panda’s Thumb are welcome to join us, and I will be happy to pose for photos and sign autographs, and maybe later accept generous quantities of fine alcoholic beverages at a local public house. I plan to be under the big dinosaur in the entrance hall at 11.00 am, and, as I’m pretty confident of being the only panda present, I should be easy to spot. However, on the off chance that other panda’s may be present, I’ll be the one wearing the mortarboard. I you plan to attend, I’d be grateful if you could contact me either through this forum, or directly via [Enable javascript to see this email address.], just so that I know how long to hang around.

Look forward to seeing you in London

Professor Steve Steve

Dembski’s Designed Duplicity


On his blog, William Dembski is trying once again to argue that the intelligent designer need not be God: Everyone knows he doesn’t mean it, of course, but this is the pretense that they must maintain for purposes of their legal strategy. Unfortunately, their own words keep tripping them up in the attempt. He writes:

In those programs, Stewart & Co. had some lines that were not only funny but also memorable. The one that sticks out poked fun at ID: “We’re not saying that the designer is God, just someone with the same skill-set.” That line is now being reused on the debate circuit, with Eugenie Scott, for instance, deploying it this November at a debate at Boston University (go here).

Although the line is funny, it is not accurate. God’s skill-set includes not just ordering matter to display certain patterns but also creating matter in the first place. God, as understood by the world’s great monotheistic faiths, is an infinite personal transcendent creator. The designer responsible for biological complexity, by contrast, need only be a being capable of arranging finite material objects to display certain patterns. Accordingly, this designer need not even be infinite. Likewise, that designer need not be personal or transcendent (cf. the “designer” in Stoic philosophy).

Now let’s look, for the umpteenth time, at how the Discovery Institute - where Dembski is a senior fellow - defines intelligent design:

Continue Reading at Dispatches From the Culture Wars. All comments should be left there.

Tangled Bank #42

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The Tangled Bank

Are you ready to read over 40 science articles today? Tangled Bank #42 is up.

For readers in Virginia, let me mention that NCSE Executive Director Eugenie Scott will be giving two talks this week in our neck of the woods.

On Wednesday, November 30 she will be at Oakton High School, 2900 Sutton Road, Vienna, VA, from 7:00-9:00 PM. More information can be obtained by writing to

On Thursday, December 1 she will be speaking at the Fairfax campus of George Mason University, again at 7:00 PM, in the Johnson Center- Dewberry Hall South. Driving directions and parking information is available here.

Scott's full speaking schedule is available here.

I will be attending Wednesday's event. Sadly, a prior engagement will keep me away on Thursday.

That's the title of the cover story of the October 2005 issue of the Jewish magazine Moment. Nosson Slifkin is an orthodox rabbi living in Israel. His heresy - surprise! - was defending the theory of evolution.

Here's a brief excerpt:

[The voice on the phone] informed Slifkin that four prestigious rabbis had opened his “Torah Universe” series and found three of its four books to contain heresy. Two of the volumes centered on animal-related issues: The Camel, the Hare and the Hyrax discussed the kosher traits of animals that do not appear in the Torah, while Mysterious Creatures debunked the existence of mythical beasts---including mermaids, phoenixes and unicorns---that are discussed in the Talmud. The rabbis were especially troubled by The Science of Torah, a book that focused on Darwinism and the age of the universe. The man on the phone informed Slifkin that he had until the end of the day to retract his books. If he didn't, the charge would be made public and other prominent rabbis would join the campaign against him.

Slifkin subsequently found himself losing speaking engagements. Jewish libraries were pulling his books off the shelves, and his publisher halted publication of his books.

I may be an atheist, but I am also Jewish. As such, I am deeply ashamed that some of my fellow Jews are capable of such insanity. I have provided further excerpts and commentary in this post at EvolutionBlog.

We are as worms

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Genes in us multicellular eukaryotes are characterized by a peculiar feature: the DNA sequence is interrupted by stretches called introns that are transcribed into mRNA, but then cut out so that their sequence is not represented in the final protein product. The gene is spliced together out of portions called exons, excluding the introns, a bit of post-transcriptional editing that permits splice variants to be made, and that can increase the diversity of gene products. It's still a very strange and inefficient way to go about making proteins, though, and one that isn't necessary—bacteria, for instance, get along just fine without this intron nonsense.

Continue reading "We are as worms" (on Pharyngula)


The AP is reporting that the National Zoo’s Panda club had a photo shoot today: Panda cub gets its close-up.

More than 100 reporters and camera crews from around the world got their first look at the fuzzy creature as they filed past his indoor enclosure in five different shifts. And the 4 1/2-month-old cub did not disappoint.

He chased his zookeeper around, trying to nibble at the hems of her jeans. He pulled himself over the ledge of the habitat’s rocky centerpiece. He tumbled onto his back, and he gummed at the bamboo stalks that will someday form his diet.

CNN even has a video of the tyke.

Cornell’s New IDEA Club


The Chicago Tribune has an article up about a new IDEA (Intelligent Design and Evolution Awareness) club at Cornell University, where the president recently delivered a scathing critique of intelligent design in his annual address to the school. The article includes many misconceptions and falsehoods, beginning with the first premise uttered by the new chapter’s founder:

The national spotlight recently has focused on school boards in Kansas, Pennsylvania and elsewhere that are grappling with calls for including intelligent design, a concept critical of Charles Darwin’s theory of evolution, in science curricula. But a significant new front in this cultural conflict is opening in the halls of American higher education, spearheaded by science students skeptical of evolution and intrigued by intelligent design.

One of them is Hannah Maxson. A math and chemistry major at Cornell University, she founded an Intelligent Design and Evolution Awareness (IDEA) Club here this fall.

”In my opinion, both intelligent design and Darwinian evolution are science. Both have philosophical implications. Intelligent design implies the universe is somewhat directed. Darwinian evolution implies a naturalistic worldview,” Maxson, 21, said.

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

The latest issue of Science (volume 310, number 5752) says some nice things about The Panda's Thumb in their Netwatch section:

Darwin's contemporaries Thomas Huxley and Joseph Hooker championed his theory in print and in lectures. If they were alive today and had a little attitude, they might craft something like The Panda's Thumb, a Web log in which a cadre of Darwin's modern-day defenders pummels antievolution pseudoscience such as "intelligent design" (ID). The site gets its name from a Stephen Jay Gould essay about the giant panda's adaptation for stripping bamboo leaves--it's a jury-rigged feature a clever designer wouldn't engineer. Panda's Thumb regulars--who range from Ph.D.s and grad students to a businessman and a lawyer--comb the news media for follies to expose and errors to correct. The site provided blanket coverage of the recent trial on the Dover, Pennsylvania, school board's decision to require teaching of ID (Science, 18 November, p. 1105). Panda's Thumb also highlights evolution-related research, such as a study showing that the antibiotics produced by our immune systems may not be a panacea for drug-resistant bacteria.

Coopting cooption

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Since I don’t think I posted this before, all of the PDFs of the Kitzmiller v. Dover trial are now available on NCSE’s website – in searchable, error-free form, which was not previously the case. See also the TalkOrigins HTML version of the transcripts, complete with graphics, links, and HTML anchors for each question (just click on the “Q”).

In case you were wondering, variations on the word “flagellum” appeared 385 times during the trial. I was about to suggest that this count beats the total of all previous usages of the word “flagellum” in all trials, anywhere in history, but then I remembered the original meaning of “flagellum”, which is the latin term for “whip.”

(Rumor has it that immune system fans were disappointed that their favorite “irreducible complex” system only got 145 mentions. Then again, only the plaintiffs seemed to enjoy talking about the immune system…)

Also, the United States District Court, Middle District of Pennsylvania has just posted all of the Proposed Findings of Fact from the Defense and Plaintiffs on their website.

Tastes great, less filling

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A few months back, Nature published a series of papers on the completion of the chimpanzee genome, including a massive comparison of the human and chimp genomes (free online). One of the major utilities of having two closely-related genomes to compare (in addition to showing that humans and chimps have close common ancestors, as in Ken Miller’s testimony on Day 1 of the Kitzmiller v. Dover trial) is that genes that are evolving rapidly under natural selection can be detected.

At the time, an odd observation stuck in my head: not only were things like immune system genes evolving rapidly (as they do in apparently all mammals studied thus far – it’s a war zone out there with the microbes), but according to Table 4 of the Nature article, so were some olfactory and taste receptor genes. This seemed rather odd, given that humans are not exactly first among the beasts when it comes to sniffing capabilities, or, I presume, tasting (although according to this PNAS article, our “gustatory receptors” are doing rather better than our olfactory receptors, many of which have become pseudogenes).

Even with our modest capabilities in this area, however, there are evidently some pretty important things that at least our taste receptors can do. Protect humans from malaria, for example. Read Carl Zimmer’s latest to find out how.

Have you ever wondered how Kevin Bacon and the lights of fireflies related to malaria and power grids? I know it’s something that’s kept me up many a sleepless night. One word: interconnections.

Many of you have probably heard of the “Six degrees of Kevin Bacon” game. This is based on the work of Stanley Milgram beginning in the 1960s, and brought up again more recently in a 1998 Nature paper, “Collective Dynamics of ‘Small-World’ Networks,” by mathematicians Watts and Strogatz. Milgram conducted a number of studies using his “lost letter technique,” in which letters were sent out and then needed to be forwarded onto reach their destination. In one instance, Milgram sent out 160 letters to individuals in the midwest, with instructions to pass them along to acquaintances who would be most likely to reach his stockbroker friend back east. Almost all of the letters that reached the stockbroker did so via one of 3 friends—and most did it within 6 steps–hence the “six degrees of separation” idea. Similarly, Duncan Watts first became interested in the “small world problem”—the idea that all of us are more closely connected than we realize—after watching fireflies flash in synchrony, and wondering how they accomplished that. What Watts, Strogatz, Milgram, and others were investigating boiled down to a series of links in a network—hubs and connectors. As Watts and Strogatz showed in their 1998 paper, all it took to make a “small world” from a regular network was the addition of a few “short cuts” (see figure from their paper, right). This elegant and seemingly simple structure of networks explains not only connections between movie stars and scientists but also cellular metabolism, ecology webs and the World Wide Web itself.

Continued at Aetiology

It starts with a very good line:

Natural selection is not natural perfection.

Read on to learn about another tradeoff in our makeup that is a consequence of our evolutionary history. (Although I want to be the first to predict that someone will use this information to reinforce their belief in the curse of Ham).

Mysterious Trichoplax

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BioEssays regularly runs a feature called "My Favorite Animal"; this month's choice is barely an animal at all, the placophoran Trichoplax adhaerens. I've written about Trichoplax before. It's a strange creature, a small flat blob that creeps amoeba-like over the substrate, that replicates by simply splitting in two, and that seems to have no distinguishing features at all—no head, no sense organs, no nervous system, no gut, just a collection of cells that hang together and slurp up algal slime. They are, however, multicellular, and their bodies contain at least four functionally distinct cell types, and the molecular evidence suggests affinities to other animal groups (they have a ProtoHox/ParaHox gene, for instance)…so they are definitely metazoans. They are just the simplest, barest kind of metazoan we can find now.

Continue reading Mysterious Trichoplax (on Pharyngula)

2001 winner of the Nobel Prize for Physics, Eric Cornell, gave a speech at his induction into the American Academy of Arts and Sciences. The Time article is an adaptation of this speech.

Cornell claims that science isn’t about knowing the mind of God, but about understanding nature and the reasons for things. For science, Cornell claims, Intelligent Design is a dead-end idea because it claims that the scientific reason for things is that God wanted it that way. Cornell calls on scientists to keep Intelligent Design out of science classes, and to keep moral and religious judgments out of science.

Time; 11/14/2005, Vol. 166 Issue 20, p98-98, 1p, 1c

Remember Behe’s testimony?

After being denied the much sought after status as ‘scientific’, Intelligent Design has run into another roadblock, upsetting the time line laid out in the Wedge Strategy

Intelligent design — already the planned subject of a controversial Kansas University seminar this spring — will make its way into a second KU classroom in the fall, this time labeled as a “pseudoscience.”

In addition to intelligent design, the class Archaeological Myths and Realities will cover such topics as UFOs, crop circles, extrasensory perception and the ancient pyramids.

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