November 2007 Archives

This Austin American Statesman article, State science curriculum director resigns, has the scoop.

Chris Comer is out of a job. She was a nine-year veteran in the position of director of science curriculum for the Texas Education Agency (Texas-speak for the state’s “department of education”). The TEA administration essentially forced her resignation.

So, why would TEA do that? Comer forwarded an email from the National Center for Science Education announcing a talk by Dr. Barbara Forrest to several people with the following addition: “FYI”.

The call to fire Comer came from Lizzette Reynolds, who previously worked in the U.S. Department of Education. She also served as deputy legislative director for Gov. George W. Bush. She joined the Texas Education Agency as the senior adviser on statewide initiatives in January.

Reynolds, who was out sick the day Comer forwarded the e-mail, received a copy from an unnamed source and forwarded it to Comer’s bosses less than two hours after Comer sent it.

“This is highly inappropriate,” Reynolds said in an e-mail to Comer’s supervisors. “I believe this is an offense that calls for termination or, at the very least, reassignment of responsibilities.

How did that play out?

In documents obtained Wednesday through the Texas Public Information Act, agency officials said they recommended firing Comer for repeated acts of misconduct and insubordination. But Comer said she thinks political concerns about the teaching of creationism in schools were behind what she describes as a forced resignation.

Apparently, not being a team player in the The Republican War on Science is a firing offense at the TEA. Why forwarding an announcement concerning a talk whose topic is highly relevant to the conduct of science education by an internationally recognized speaker should cause TEA administrators a problem escapes me. One is forced to wonder whether Ms. Comer would be looking for a new job if instead she were forwarding emails announcing talks by DI fellows about “intelligent design” creationism.

(Read more (including the text of the offending email) at the Austringer and PZ Myer’s “Fear of Barbara Forrest” at Pharyngula)

Update: If it wasn’t before, this radio show is online as RealAudio at the BBC Website.

I don’t think this has been blogged yet. Earlier this month BBC Radio 4 broadcast a double interview with Michael Majerus, oft-mentioned on PT for his peppered moth research, and Jerry Coyne, a well known evolutionary biologist and regular critic of ID/creationism, and an oft-cited critic of aspects of the peppered moth research.

Quentin Cooper, the reporter, does an excellent job reviewing the whole history of the situation, the influence of Coyne’s critique, and Majerus’s new results. The piece tells the key points of the whole complex story in just a few minutes. And at the end, Coyne basically says that it’s time for the peppered moths to go back into the textbooks, which is a significant thing to say given Coyne’s past criticisms.

Links:

Majerus, M. E. N. (1998). Melanism: evolution in action. Oxford ; New York, Oxford University Press.

Coyne, J. (1998). “Not black and white.” Nature, 396: 35-36. (Free online here (HTML), here (pdf))

Quentin Cooper, Michael Majerus, Jerry Coyne (2007). “The Peppered Moth.” Interview on The Material World, BBC Radio 4, October 11, 2007. http://www.bbc.co.uk/radio4/science[…]071011.shtml

In Rocks of Ages Stephen Jay Gould famously argued for Non-Overlapping Magisteria (NOMA), the notion that science and religion appropriately address different domains of knowledge (magisteria), and that therefore there is no necessary conflict between them so long as each sticks to its own domain. While that argument has its detractors, it was alive and well a few weeks ago in Ohio.

On November 14, with four high school science teachers I attended a panel presentation at the Center for Science and Industry in Columbus, the presentation being co-sponsored by COSI, the Ohio State University, and WOSU, the Columbus PBS station. The presentation was titled “The Intersection of Faith & Evolution: A Civil Dialogue.” The panelists were Jeff McKee, a paleontologist from Ohio State University, Patricia Princehouse, who lectures on evolutionary biology and philosophy at Case Western Reserve, David Ruppe, a pastor and scholar of religion, and Francis Collins, the Director of the Human Genome Project and an evangelical Christian. (I mention Collins’ religious affiliation because he was the only presenter for whom it was explicitly mentioned in the introductions.)

The event was heavily over-subscribed, with the organizers having to open several satellite venues with video feeds of the live event at COSI. Having got my reservation in early, I was in the second row in front of the panel along with one of the teachers, where we had easy access to the microphone for audience questions.

The show started with a short skit that had three teen-aged kids in sleeping bags talking about the age of the stars (billions vs. thousands of years), why they’re different (physics vs. begats), and whether one of the girls could be both a pastor and a scientist. The resolution, of course, was the claim that the two aren’t antithetical. (That it was a girl who felt that quandary was a tip-off to the general theological stance of the evening.)

In “sex, lies and a math mistake” I described how the Discovery Institute’s rapid response to the NOVA program on ID (a booklet called “The Theory of Intelligent Design: A briefing packet for educators, to help teachers understand the debate between Darwinian evolution and intelligent design”) was filled with egregious math errors and lies.

Perhaps it’s getting cold down under (and I don’t mean Australia), but the Discovery Institute has actually corrected the math mistake in their booklet.

Of course, they did not acknowledge making a mistake, nor did they acknowledge making a correction.

They simply re-announced the release of the revised booklet, without mentioning that it was a revision.

Anyway, there has been a little progress. Now all they need to do is to get rid of the aforementioned lies.

The recent NOVA special about the Dover trial has given me a sense of deja vu, as the Discovery Institute predictably rehashes all of the bad arguments they made against the decision after it came out. As I’ve said in speeches about the trial, it took Judge Jones about 10 seconds to go from a conservative good old boy who wouldn’t dare sell out his benefactors (Bush and Santorum) to a self-aggrandizing liberal judicial activist out to destroy America.

In his latest screed on the DI blog, Casey Luskin puts his usual intellectual dishonesty on display, falsely declaring that Judge Jones “admits” that his ruling was “activist” on the flimsy basis that he made a statement that Luskin is able to twist to fit his own anachronistic definition of judicial activism. Here is the rather absurd definition of judicial activism that he offers:

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

One of the joys of procrastination is that sometimes if you wait long enough, someone else really will take care of things. I mention that because Ed Brayton just did a good job dismantling Casey Luskin’s latest whine about how big bad Judge Jones was such a nasty judicial activist for daring to issue a ruling in the Dover, PA Intelligent Design case that addressed the question of whether or not ID is good science. I was planning a long and detailed post on the same thing, but now all that I have to do is highlight one point that Ed didn’t make in his post.

As Ed points out, there were a number of reasons for Jones to rule on that point. For starters, he had to look at that if he wanted to handle the case in front of him the same way that the Supreme Court handled its last creationism case. (That’s called following precedent.) He also needed to look at that point in order to apply the test commonly used by the Federal Courts when they look at Establishment Clause cases. (That’s also called following precedent.) As Ed also notes, both the plaintiffs and the defendants specifically asked the judge to rule on that point.

What Ed doesn’t mention is that the plaintiffs and the defendants were not the only ones who asked Judge Jones to rule on whether or not Intelligent Design is good science:

Read more (at The Questionable Authority, where comments may be left):

On the one hand, we’ve got Casey Luskin over at Evolution “News” and Views opting to take the High Road, castigating those mean-spirited “Darwinists” for their naughty behavior in this holiday season.

Luskin’s November 24, 2007 piece, PBS Special Brings Out Darwinists Lacking the Thanksgiving Spirit, concludes with this:

I enjoyed celebrating Thanksgiving by being thankful for the people in my life. I just hope that such e-mailers were able to let go of their intense anger and hatred and find some reason for giving thanks over this holiday season.

On the other hand, we’ve got the official website for the upcoming Ben Stein movie “Expelled - No Intelligence Allowed” plugging a little video they’ve made called Darwin Daze Sock Hop.

So how does displaying Genie Scott’s panties advance the Intelligent Design Movement? Read on…

Unholy row over university lecture event

Second-year dental student Emily Mackie said the university’s decision to call its inaugural Dundee Christmas Lecture “Why Evolution is Right … and Creationism is Wrong” is badly timed and insensitive to Christians.

The lecture is being given by Steve Jones, professor of genetics at University College, London, who claims that all biologists support the theory of evolution and that “intelligent design”—the belief that life was created as part of a divine plan—is wrong.

Steve Jones presented a similarly titled lecture “Why creationism is wrong and evolution is right” at the Royal Society in 2006

From the Leiter Reports

Leiter Wrote:

A blog devoted to shilling for Intelligent Design has posted a link to the paper by myself and Michael Weisberg critiquing attempts to apply evolutionary psychology to law. It appears the author of the post, one Denyse O’Leary, a Canadian journalist who is a notorious apologist for ID creationism, thought our article was of a piece with the skepticism about natural selection that is her raison d’etre. The second commenter appears to have noticed what Ms. O’Leary missed.

Ms O’Leary is also still in denial about processes of regularity and chance being able to generate information. While she has been insisting that her background does not allow her to evaluate the claims of ID when they involve science or mathematics, she surely seems to be accepting them as the Gospel.

Hint: Processes of variation and selection can trivially increase information in the genome. Even Dembski seems to have come to accept this and now he claims that such processes smuggle in information. Of course they do, they transfer information from the environment to the genome.

Duh…

From Mike Elzinga whose comments deserve their own posting

It doesn’t require a federal judge to figure out if ID/Creationism is a science or not.

Anyone can go through the list of activities of the ID/Creationists and pseudo-scientists and compare them to the activities of working scientists.

Do typical working scientists engage in the following activities when advancing new ideas?

Do they pitch them to naive audiences while complaining they can’t get a fair hearing in the science community? Do they form institutes that spend millions of dollars to crank out propaganda pushing their idea and criticizing the scientific community? Do they issue talking points to grass-roots organizations and political groups to be argued in churches and local newspapers around the country? Do they publish books on their ideas in the popular press and claim they are peer-reviewed?

Casey Luskin, continues his “assaults” on Judge Jones’ devastating ruling for Intelligent Design while conveniently forgetting the Discovery Institute’s Amicus Curiae to the case.

Luskin argues that, based on an statements made by Judge Jones on the “Lehrer Newshour”, the ruling by Jones should be considered flawed:

Luskin Wrote:

First, Judge Jones admitted that a key question his ruling answered was whether intelligent design was “good science,” and he states that “after six weeks of largely expert testimony, I came to the conclusion that it simply was not good science” (emphasis added). This proves his judicial activism because it shows that, in his mind, a key question was not the constitutionality of Dover’s policy in particular, but rather a broad sweeping question about whether ID is “good science,” something that is totally inappropriate and unnecessary for the federal judiciary to answer in such a case over the constitutionality of a science curriculum.

Why is this claim so ironic? Well, if you read the submissions of the Discovery Institute to the judge, they argue that since ID is science, it cannot be ruled to be unconstitutional. In other words, they insist that the judge resolves the issue of ID being science. When he actually does this and he rules contrary to their expectations, the judge suddenly becomes an activist judge.

The Discovery Institute’s own website demonstrates that their amicus brief was submitted to argue “… about secular purposes for teaching about the scientific theory of intelligent design”” (October 31, 2005)

So what was the argument of the Discovery Institute which forced the judge to rule on the issue of ID being science?

There is a wonderful article in todays issue of Nature on bioluminescent organisms in the deep seas. We like to think of the deep seas as dark, since virtually no light filters into the abyssal depths from above. However, the deep sea abounds with bioluminescence, bacteria and sea life of all sorts glow gently in the depths, enough to seriously hamper the Antares deep sea neutrino telescope that is searching for the flashes of light the represent the rare interactions of neutrinos with other matter (subscription required).

As fascinating as bioluminescence is in its own right, the article links to an amazing paper. One that puts yet another dent (if that is possible) in Dr. Behe’s key thesis; that multi-amino acid binding sites are difficult to evolve. But how does the ability of a fish to see red refute a central argument of Dr. Behe’s “Edge of Evolution”

The newest latest bestest spiffiest edition of the Tangled Bank is now online at From Archaea to Zeaxanthol.

A recent discovery in stem cell research is no minor event: researchers have figured out how to reprogram adult cells into a state that is nearly indistinguishable from that of embryonic, pluripotent stem cells. This is huge news that promises to accelerate the pace of research in the field.

The problem has always been that cells exist in distinct states. A skin cell, for instance, has one set of genes essential for its specific function activated, and other sets of genes turned off; an egg cell has different patterns of gene activation and inactivation. Just taking the DNA from a skin cell and inserting it into the egg cell isn’t necessarily going to create a functional egg cell, because genes essential for egg cells may be switched off in the skin cell DNA, and we don’t know how to specifically switch them on. The process of somatic cell nuclear transfer has been hit or miss for that reason, with very high failure rates—scientists are basically trying to make the right configuration of genes switch on by giving the nucleus a good hard kick, and hoping that something in the cells will reconfigure the pattern of gene activation into something appropriate.

What the discovery by Takahashi et al. accomplishes is to reveal how to specifically switch on the right pattern of genes for a pluripotent stem cell. They have discovered the reset button for mammalian cells: a simple trigger that puts the cells in the right state to become anything else.

Continue reading “Stem cell breakthrough” (on Pharyngula)

Over on the DIscovery Institute’s weblog, Casey Luskin writes:

In 2005, a federal judge banned Pandas outright from science classrooms in Dover, Pennsylvania — but only after denying FTE [Foundation for Thought and Ethics] the right to appear before the court to defend the book.

Hmmm. Why does that sound odd?

Maybe because Jon Buell, President of FTE, did actually appear in the courtroom of Judge John E. Jones III, and there attempted to defend the book. Of course, Buell made a laughingstock of himself, of FTE, and of the sham called “intelligent design” – pretty serious work for just one day in court, I’d say. NOVA’s focus on the bad boys of the Kitzmiller v. DASD case could have been filled out to three “B”s, Bonsell, Buckingham, and Buell, if only Jones had ruled favorably on FTE’s motion to intervene.

Who is to blame for FTE’s inability to take part in the trial portion of KvD? It isn’t Judge Jones. This is a matter of public record, something that Luskin should have been aware of before spinning stuff. One can make a case for either FTE President Jon Buell or IDC advocate and FTE Academic Editor William A. Dembski having tripped up on this one, as becomes clear with just a small excursion to the transcript of the court’s consideration of FTE’s motion to intervene. At the time that FTE finally decided to file its motion to intervene, it was already late in May, 2005. Notably, this only happened about the time that the Thomas More Law Center and the Discovery Institute were apparently having some serious behind-the-scenes disagreements over the conduct of the case. FTE seemed to be far more willing to act on DI orders than the TMLC had proved to be, so having FTE obtain a co-defendant role in the case was likely a high priority for the DI. This may explain the DI’s continuing angst over the exceedingly poor showing that Buell had in court, so much so that they won’t even draw attention to it, but instead place blame – erroneously, of course – on Judge Jones.

Did FTE receive due process? It is hard to argue that they did not, given the copious public record demonstrating that they did. That seems to be why Luskin just tosses off a slur, apparently hoping that no one will take a closer look. There are several elements of interest in Buell’s testimony, including the howler that FTE is not a religious organization, the curious silence of Dembski, and Buell’s ignorance of the one issue that might have given FTE entry to the case.

(Continue reading at the Austringer)

Hot off the press: Metagenomic data contains genetic evidence of the smallest primate ever discovered, by far. The bigfoot people should apply this technique. (Mark my words, it’s just a matter of time.)

By SA Smith

It is one thing to correct Michael Behe, some structure guy with zero research experience on HIV-1 evolution. But considering the sheer number of DI “fellows” who are lawyers, and the fact I’m just a biology student with zero experience in law, I found it rather strange that I caught something the DI lawyers evidently had no problem with:

First, the sex. I’ll admit right up front that this post has nothing to do with sex, except for the general nature of what the ID movement is trying to do to public science education in this country.

Before moving on to lies, let’s take care of the math mistake first.

Last week, in response to the splendid PBS/NOVA production on the Dover trial (Judgment Day: ID on Trial”), the Discovery Institute hacked out a booklet for teachers, called “The Theory of Intelligent Design: A briefing packet for educators, to help teachers understand the debate between Darwinian evolution and intelligent design”. The packet was prepared by the Institute’s John West and Casey Luskin, both of whom apparently slept through all of their math and ethics classes.

On Page 12 of 24, the PDF document declares

“Five states (Kansas, New Mexico, Pennsylvania, South Carolina, and Minnesota) have already adopted science standards that require learning about some of the scientific controversies relating to evolution.”

But on page 13, they declare that

“Four states (Minnesota, New Mexico, Pennsylvania, and South Carolina) have science standards that require learning about some of the scientific controversies relating to evolution.”

These people clearly have trouble with numbers bigger than three, as PZ pointed out last week: : four is not five.

And that brings us back to lies. Five states, five lies, courtesy of the Discovery Institute.

To summarize the recent Open Letters series, some time ago a student of HIV, Ms Smith posted a list of binding sites found in the HIV-1 protein Vpu that contradicted Dr. Behe’s assertion that HIV has evolved no new protein-protein binding sites. Central to this was the demonstration that HIV-1 Vpu had evolved into an ion channel, a viroporin. Over two months later, Dr. Behe wrote a response, which did a disservice to Ms Smith on many levels, most especially by ignoring the key argument about Vpu viroporin. I remonstrated with Dr. Behe about this in an Open Letter. Dr. Behe publishing a series of responses to this open letter, which I responded to post by post as they were published.

As you may realize, Dr. Behe has finally conceded that he was wrong, and Vpu viroporin represents a real example of protein-protein binding. I have suggested that he issue an erratum to this effect, thanking Ms Smith for bringing this example to his attention (and the HIV Vpx duplication, which he also claimed didn’t exist). This is the very stuff of science, we all at some stage support ideas that were wrong, but when we realize they are wrong, we give them up. I thank Dr. Behe for acknowledging his mistake.

Along the way we have also learned that Dr. Behe’s citations don’t actually support his statements in “edge of Evolution”, his estimation of HIV mutation rates and effective population numbers is off by orders of magnitude, and his rationale for excluding viral protein-cellular protein binding has no biological basis (and is inconsistent).

For ease of perusal, I have put the links for all the Open Letters into this one post.

The Original Open Letter, where I protest at Dr. Behe’s treatment of Ms Smith.
An Open Letter Part 2, where I detail Vpu viroporin and point out that Dr. Behe’s references do not support his assertions.
An Open Letter Part 3, where I chide Dr. Behe for his continuing poor treatment of Ms Smith.
An Open Letter Part 4, where I go into more detail about why Dr. Behe’s attempt to exclude certain binding sites is not valid.
An Open Letter Part 5, where I dig even deeper into binding sites, and show why Dr. Behe’s attempt to exclude certain binding sites is not valid in even more detail.
An Open Letter Part 6, where I point out that Dr. Behe’s population and mutation rate estimates for HIV are wrong by orders of magnitude.
An Open Letter Part 7, where I thank Dr. Behe for admitting he was wrong, point out that “impresessedness” is not a biologically valid standpoint, and show that yet another reason for excluding viral protein-cell protein interactions is invalid.

Steven Novella made a point on the recent episode of The Skeptic’s Guide to The Universe (best podcast ever, by the way), and on his blog Neurologica that I thought deserved underlining. Discussing the transitional fossil Tiktaalik, which lies between modern fishes and modern amphibians, Novella points out:

What is especially cool about Tiktaalik is that the researchers, Edward B. Daeschler, Neil H. Shubin and Farish A. Jenkins, predicted that they would discover something like Tiktaalik. These paleontologists made the prediction that such a transitional form must exist in order to bridge the gap between fish and amphibians. Even more, they predicted that such a species should exist in the late Devonian period, about 375 million years ago.

So they spent several years digging through the earth on Ellesmere Island in Northern Canada, because geological and paleontological evidence suggested that exposed strata there was from the late Devonian. They predicted that, according to evolutionary theory, at this time in history a creature should have existed that was morphologically transitional between fish and amphibians. They found Tiktaalik - a “fishopod,” beautifully transitional between fish and amphibians.

But wait, I thought the creationists had told us that evolution wasn’t subject to experiment…?

It seems the Discovery Institute’s newest Senior Fellow is radio talk show host Michael Medved.

Here is the Nov. 15^th U.D. announcement:

William Dembski Wrote:

Michael Medved, nationally syndicated talk radio host and bestselling author, has joined the Discovery Institute in the role of senior fellow. The position cements a longstanding friendship and recognizes a commonality of values and projects across a spectrum of issues.

Why is this FANTASTIC news for the cryptozoological community?

It’s because Medved is Big on Big Foot.

Skeptical? Good! There are data to listen to on this page; look for show# 232, Monday February 19, 2007, “Big Foot With Michael Medved,” “Medved talks about recent news reports that there is a Big Foot.”

Don’t have highspeed? Read this:

Dan Sytman, Michael’s producer and partner on the radio show, once saw Bigfoot at the edge of a summer camp in the woods. Even before meeting Dan, Michael was a passionate believer in Sasquatch.

If you listen to the whole radio segment, be advised that the “severed foot of a Sasquatch found in Spotsylvania County, VA” that was discussed at length turned out to be simply the skinned Hind Paw of a Bear the next day.

Sir Nick of the Matzke Clan actually had to endure listening to Medved trot out the usual creationist canards on his show, back in December 2004, but assures us that

…it was great fun, although during the show I felt a bit like a hobbit in the Mines of Moria scenes from the movie the Fellowship of the Ring: Look out, Medved’s first move is flagrant baiting! [octopus monster] Uh-oh, here comes the bacterial flagellum [big goblin], and on its heels the Second Law of Thermodynamics! [little goblin]. Then, the Discovery Institute list of 300 [“They have a Cave Troll.”]

The Amused Muse has more.

Is this just an attempt to distract the public from the whuppin’ the DI got on NOVA?

Perhaps, but I don’t really think so. They are devious enough, but not that clever.

Dear. Dr. Behe

I am pleased that you have acknowledged Vpu viroporin represents a real, de novo binding site.

Now if you had engaged with this in your response to Ms Smith, my respect for you would have risen immeasurably. To those of you not familiar with graduate and post graduate education, we actually want graduate students to disagree with us, robustly. After all, they are the ones carrying the torch of critical enquiry when we are gone. We don’t want them to accept our say so, “just because”. As scientists and educators our brief goes beyond just those PhD students we supervise, but to all engaged in critical enquiry, regardless of how we feel about their actual mode of delivery [1].

By “playing the man”[2] Dr. Behe, rather than engaging with Ms Smith’s arguments, you abrogated our responsibility as mentors and educators. Imagine the difference if you had dealt with Vpu Viroporin straight up. How about apologizing to Ms Smith now?

I do hope that you will now publish an erratum for your book, where you acknowledge Vpu viroporin. But again you engage in the “unimpressed” rhetoric. It matters not whether we are impressed or not by the outcome of the binding, the fact is that you have claimed that binding of two (or more) proteins to each other is statistically unlikely. It doesn’t matter what they do when bound (after all, as I have repeatedly pointed out, your own example is the haemoglobin S point mutation, which just glugs things up).

ArsTechnica has an interesting article on the next tactic that ID proponents will be taking: first, sow doubt about evolution in high schools, and then push for the teaching of ID in colleges. Hat tip: NoodleFood, which concludes, “the target of Intelligent Design is not just evolution, but the very metaphysics that makes science and technology possible.” Indeed, as I argue in my forthcoming Chapman Law Review article, we seem to be seeing an increasing tendency among ID proponents to embrace postmodernist theories to argue that science and creationism are just equally valid “myths” which deserve equal time under the Establishment Clause. (I will post that article as soon as I am able.)

Dear Dr. Behe

Reflecting on your previous post, and the current one, I would like to note that both your mutation rates (10^-4) and effective population size (10⁹-10¹⁰) are too high. By a factor of around a hundred thousand.

The commonest estimates for HIV mutation rates are between 1x10^-5 and 4x10^-5, with 2.5x10^-5 the most common. Well, what’s a half log unit between friends? More serious is your population size estimate. Here I’d like to introduce you to the concept of effective population size.

Kudos to PBS, it looks like they’ve put up the transcript and the video of “Judgment Day” a day early. Since there are various reports of PBS stations skipping or editing the show to avoid offending their viewers (or something – I guess reality offends some people, but you would think they wouldn’t watch Nova at all in that case), this is all for the good.

By Dr. Donald R. Prothero

It was very interesting to see the Nova broadcast recounting the Dover “intelligent design” trial of two years ago. The furor over the Dover trial may have died down, but by no means is creationism dead in this country. Each time they are beaten in court, they find another way to disguise their religious motives and try to get around the separation of church and state. Legally, they can’t win, but they are still very powerful in the local communities, where school boards are easily swayed by their phony arguments and ability to mobilize lots of church-going folks to attend school board meetings and vote for their candidates.

Both the old-fashioned “young-earth” creationists, i.e. people who believe the earth is only 10,000 years old, and the newer ID creationists push their cases largely by making demonstrably false claims about evolution and the fossil record. Their lies about the fossil record are particularly irritating to geologists and paleontologists because creationists make these claims without any formal training in paleontology, and without any first-hand experience with fossils, or publications in the peer-reviewed scientific literature. They wave their PhDs on the covers of their books, but almost none of them have any relevant training in fossils. Some of the claims you might still find in their books and blogs:

• The “Cambrian explosion” was an instantaneous creation event. Not true—in the past 40 years, paleontologists have documented a 3.5-billion-year history of life from single-celled organisms to multicellular soft-bodied fossils to animals with small shells and culminating with the trilobites and other fossils that mark the early Cambrian Period. Modern dating techniques show this transition took at least 20 million years, and probably longer—hardly an “explosion” in anyone’s sense of the word! Yet creationists of all stripes wave this red herring and ignore the past 40 years’ worth of research.
• There are no transitional fossils. Not true—in my new book, Evolution: What the Fossils Say and Why It Matters, I document dozens of transitional sequences of fossils, showing the evolution not only of individual lineages, but also of transitional forms that span the gaps between major groups—the “macroevolution” that creationists deny.
• Humans did not evolve from ape-like ancestors. Not true—the past 50 years have yielded an amazing array of hominid fossils that provide more than enough “missing links.” Even if there were no fossils, your own genome is 98% identical with that of a chimpanzee. Every one of your cells is testimony to the fact that humans are a product of evolution!

As poll after poll shows, most Americans do not know much about evolution (or science in general), and at least 40% of Americans still believe in the creation myths of the Bible. This is in striking contrast to nearly every other country in the industrialized world, which long ago came to terms with evolution, and have much higher rate of science literacy than Americans do. Our poor science literacy is a national shame, especially in a country where science and technology are so essential and still world-class (at the moment). If these trends continue, however, will we soon be outsourcing many of our science and technology to other countries, as we do our white-collar and blue-collar jobs?

Dr. Donald R. Prothero is a Lecturer in Geobiology at Cal Tech and a Professor of Geology at Occidental College. His new book, published by Columbia University Press is Evolution: What the Fossils Say and Why It Matters.

Dear Dr. Behe

It is good to see that you agree that the Golgi targeting sequence is an example of a binding site. However, you don’t get to ignore it because “viral proteins are special”. As I showed in the post you are supposed to be replying to, this is nonsense. In your book you categorically state HIV has developed no new binding sites, the diagram on page 145 of “Edge of Evolution” has a big zero on it. Yet your own example of a binding site is the haemoglobin S mutation, a single amino acid mutation that just clumps up proteins. You don’t write in your book “HIV has evolved several binding sites, but they don’t count because they are viral-protein-host protein interactions” or “HIV has evolved several binding sites, but they don’t count because they are equivalent to the HbS mutation”, you just write zero

Which is wrong.

An again, you are inconsistent, you are perfectly happy to consider viral-protein binding to cellular protein interactions when you think there is no evidence of them evolving (the gp120-cell surface receptor binding, CXCR4 binding anyone). Still, let us accept that you will ignore any viral-protein-cell protein interaction.

Why did you ignore the viroporin section? An example of viral-protein –viral protein interaction that generates a new structure with important functional consequences. This is a direct challenge to the very heart of your argument.

Just a few notes on post-Nova show stuff. If you missed the show (or evidently some PBS stations didn’t show it), it will be free online on the Nova website starting on Friday, November 16. In the meantime, check out Judge Jones on the NBC Today Show (you may have to search videos on “PBS” if the link doesn’t completely work) and on The Newshour with Jim Lehrer.

Also, Matthew Chapman, great-great grandson of Charles Darwin, put out a call yesterday for, “a Presidential Debate on Science.” I am cynical enough to think that is unlikely, given that there are usually only 3 major debates, but it is worth thinking about pushing the idea – heck, maybe at least a few science-related questions will get raised in the campaign. Unfortunately, the comments section was evidently flooded by creationists, so PT people might want to chip in their 2 cents over there.

Lastly – what did you think? Quite something seeing stuff on TV that first came to the public via PT back in 2005, no? I have now heard several requests for a “cdesign proponentsists” T-shirt…here is one try, although I think it would be most compelling with a “Evolution of Creationism” or “The Missing Link” title (or maybe the front has the evolution of creationism and the back has the missing link…anyone who is inspired may use the graph, by the way).