Is it just me, or is there something particularly ludicrous and pitiful about Ruse (or anyone) discussing with Paul Nelson what evidence would make Paul Nelson change his mind about ID, when Nelson isn’t even man enough to lift his head up out of the sand the tiny bit required to admit that the earth is old, that this is a hard evidentiary fact, that denying it is as perverse as denying that the Earth is round, and that the promotion of the young-earth view in evangelical churches is one of the greatest frauds in American history?

Of course, Ruse is too much of a softy to ask these kinds of questions,* which is exactly why the IDers keep inviting him (and paying him) to do these debates.

(* To be clear: Ruse is useful and a pro-science warrior on many things, but one thing he doesn’t do much of is challenge the creationists scientifically and force them to deal with the hard evidence that challenges their beliefs. Doing this takes a lot more work of course and only a few people are good at it.)

According to the Waco Tribune‘s story on the Baylor controversy:

Intelligent design asserts that certain things in the universe can result only from an intelligent cause or God.

HT: Andrea Bottaro

The NCSE reports on some “shocking” developments in Texas

McLeroy accused of hostility to science education and religious tolerance

In a press release dated August 7, 2007, the Texas Freedom Network accused Don McLeroy, who recently was appointed as the new chair of the Texas state Board of Education, of harboring “a shocking hostility to both sound science education and religious tolerance.” TFN’s charge was based on the transcript of a 2005 talk McLeroy gave at Grace Bible Church in Bryan, Texas, on the debate over teaching evolution and “intelligent design.” “This recording makes clear the very real danger that Texas schoolchildren may soon be learning more about the religious beliefs of politicians than about sound science in their biology classes,” TFN President Kathy Miller said. “Even worse, it appears that Don McLeroy believes anyone who disagrees with him can’t be a true Christian.”

I wonder how the many Christians who disagree with McLeroy feel about this?

And for those who were wondering about the nature of Intelligent Design, they need not worry any further:

Denyse O’Leary notes some of the differences between creationists and Intelligent Design proponents:

Then the creationists in turn help the ID theorists by making clear what creationism is and what it is not. Creationism is about the BIBLE, see? It’s not about intelligent design theories like Behe’s* Edge of Evolution or Dembski’s design inference.

It’s extremely uncommon for me to find myself in agreement with Denyse on anything (and it’s not a comfortable feeling), but in this case I do think she’s got a good point. Creationism is certainly explicitly based on the Bible, and Intelligent Design certainly is not. In fact, that’s probably the Achilles’ Heel of the entire Intelligent Design movement.

Say what you will about the Young-Earth creationists, about Ken Ham and Kent “Prisoner #06452-017” Hovind, they are steadfast in their belief in the literal truth of the Bible, and steadfast in their refusal to lie about that belief. They believe that they are right, and they are not willing to publicly deny their faith. In that, they stand in stark contrast to Intelligent Design.

Over on UD, Paul Nelson claims that he is representing the “Darwinian tree of life” position correctly when he asserts that the tree must trace to a single cell, not just a single species:

It looks like somebody either never heard of Dover, or refused to learn from their lesson. It seems the local ID supporters of Chesterfield County aren’t happy:

So far, the official actions of the CCSB have been limited to issuing a rather vague and confusing statement. ID proponents had hoped to influence the selection of science textbooks, but they started their campaign too late, and the CCSB approved the selection of standard biology texts. But there is still much concern about the situation in Chesterfield. ID supporters, backed by a local conservative group called the Family Foundation, are energetic and well-organized, as evidenced by their ability to deliver a petition with more than 1,100 people who questioned the use of “evolution-only” science texts.

Energetic and well-organized supporters of pseudoscience… sounds like a one-way ticket to another budget-busting, unwinnable multimillion dollar lawsuit. Virginia, you can do better than these guys.

The Alliance for Science has the full story. If you are a Virginia resident and want to get involved, please contact them. Also, visit the link to learn much more about the story, and also about Shawn Smith’s blog that tracks the Intelligent Design Creationism movement in Chesterfield County. Let’s keep sound science in Virginia science classes and get the jump on things before they can stir up trouble.

Crossposted at Neurotopia

Over at Uncommon Descent, the blog of William Dembski and friends, a contributor has a post up discussing Peter Duesberg’s aneuploidy hypothesis for cancer (which Orac discussed here for more background). The post itself is a bit confusing–it’s titled “When Darwinism Hurts,” and according to the author’s clarification, it’s about “Darwinism” leading us down the wrong path as far as cancer research goes. (Though whether cancer would be due to mutations in specific genes or in chromosomes, it’s still an evolutionary process, but I digress…) To me, anyway, the more interesting portion was in the comments section, where both DaveScot and Sal Cordova imply also that HIV might not cause AIDS; more over at Aetiology.

Given all of the recent ignorant yammering about “junk DNA” on the Discovery Institute’s blog and other ID blogs – unfortunately partially derived from a fair bit of ignorant yammering in the science media on the same topic – I think it is worth it to post a very simple and insightful post from April 2007 by T. Ryan Gregory entitled “The Onion Test.” Gregory is a professor at the University of Guelph and runs genomesize.org, an online database of animal genome sizes. He has recently become one heck of science blogger (at Genomicron) and has been doing a yeoman’s job of attempting to explain patiently and calmly to the world what the real scientific issues are with genome size, the “junk DNA” concept, and the problems with the ubiquitous-but-bogus storyline about junk DNA. Said ubiquitous-but-bogus storyline goes something like this: “Scientists have found that junk DNA is functional! Weren’t scientists (er, other scientists) stupid to think it was junk! What morons! Three cheers for our pet idea, which is that junk DNA does X.” ID advocates, who don’t even have an “X”, repeat the story but instead just riff off the vague idea that someone somewhere has explained what the function of “junk DNA” is, have played this storyline for all it’s worth, adding a completely vapid “We told you so!” on top of it.

For a dose of reality, I recommend that everyone read Gregory’s Onion Test. I quote it below for your convenience.

Well, my own personal copy of Michael Behe’s new book The Edge of Evolution arrived via amazon.com today, so I suppose it is fair game. I have linked to a few early blog comments (see more from ERV), and Michael Ruse has a short newspaper comment out today. And several other reviews are coming out in the near future in Science, Discover, etc. None of them positive at all, but it’s amazing how much attention someone can get by sacrificing scientific rigour and inserting divine intervention instead.

I don’t have a full review of the book and I won’t for a bit since I am working on other things. But I want to get dibs on one peripheral but particularly shocking and egregious error that Behe makes in The Edge of Evolution. The error is simple but it points to what I have become convinced is the true core of the mishmash known as “intelligent design”: sloppiness and wishful thinking.

So I guess DaveScot and Dembski didn’t like Mark Chu-Carroll’s critique (which I linked to) of Behe’s usage of fitness landscape concepts in The Edge of Evolution.

Well, if anyone is still having trouble getting it, check out Good Virus, Bad Creationist at the blog ERV. The reason I say it’s the best Behe critique ever is the style. L.O.L.

PS: And watch out for ERV. She’s clearly going to run the planet someday, or at least the NIH.

Review copies of Michael Behe’s new book The Edge of Evolution are now out – the book is officially coming out on June 5 – and now the reviews are starting. Mark C. Chu-Carroll at Good Math, Bad Math, has beat us all to the punch. I perceived many of these problems while giving The Edge of Evolution my own read-through, but it takes a mathematician to comment on Behe’s abuse of fitness landscapes and probability arguments with the appropriate sense of outrage.

I am sure we will have much more on Behe’s latest starting in June. My first take is that The Edge of Evolution is basically an incompetent attempt to provide a biological foundation for the silly assumptions that were made in Behe and Snoke’s (2004) mathematical modeling paper in Protein Science. (You will recall that it received its most thorough critique here at PT and also in a rebuttal written in Protein Science by Michael Lynch; and a biological rebuttal in this 2006 paper in Science – see also summary by Adami.)

After you have been in the habit of creationism-watching for a few years you become extremely familiar with all of the usual creationist arguments, half-baked talking points, unchecked assertions taken as obviously true, etc. If you really get into it you learn the creationist movement’s long and specific history, and you learn that whatever form of creationism you are studying at the moment inevitably traces back basically to American protestant fundamentalism, and before that to something sometimes called “naive Biblicism.”*

But there comes a point when you don’t think you can learn anything much new about the creationists. You might stumble on a new mutation of a creationist urban legend or quote mine, or a new bit of creationist history like Dean Kenyon actually being a young-earther despite this fact being carefully hidden by the ID movement for 15+ years. But basically, you don’t expect to find out much that is new.

Well, if you thought you were at this point, you would be wrong. A review article in this week’s Science magazine (with a special focus on behavioral science) shows that scholars can ring out yet another twist in creationism studies.

This just in from Randy Olson. Free to forward:

FLOCK OF DODOS airing on Showtime Thursday May 17 at 8:30 EST/PST

Facts regarding status of tenure case at Iowa State

Partial quote:

Why was tenure not granted to Guillermo Gonzalez?

Dr. Gonzalez was evaluated for tenure and promotion to associate professor by the tenured faculty in the Department of Physics and Astronomy. That evaluation was based on an assessment of the excellence of his teaching, service, scholarly research publications and research funding in astronomy, using standards and expectations set by the department faculty. The consensus of the tenured department faculty, the department chair, the College of Liberal Arts and Sciences, the dean of Liberal Arts and Sciences, and the executive vice president and provost was that tenure should not be granted. Based on recommendations against granting tenure and promotion at every prior level of review, and his own review of the record, President Gregory Geoffroy notified Gonzalez in April that he would not be granted tenure and promotion to associate professor.

The PNAS Early Edition webpage has just posted a series of papers from the December 2006 National Academy of Sciences Sackler Colloquium, “In the Light of Evolution: Adaptation and Complex Design,” organized by Francisco Ayala and John Avise. The series of papers, on topics ranging from color vision to beetle horns, is now available (I will post the list below the fold). Eugenie C. Scott (aka Genie) was invited to speak at this meeting about evolution education and the history of opposition to it, and the speakers wrote papers to be published in PNAS and a forthcoming NAS volume.

Genie brought me on as a coauthor on the paper she was asked to write. This became:

The Discovery Institute’s Casey Luskin is all atwitter about a new web article from German creationist Wolf-Ekkehard Lönnig [1] about how the giraffe is some kind of massive problem for evolution. Major planks [2] include the alleged lack of transitional fossils between the different fossil giraffe genera (never mind that creationists elsewhere typically accept that the differences between mammalian genera are small, and put the “created kind” or “basic type” at a higher taxonomic level), some confusion about whether one of the giraffe vertebrae is cervical or thoracic or something in between (note to creationists: read about homeotic shifts), and the allegation that there is no evidence for a feeding advantage for tall giraffes, relying on the fact that male giraffes are taller than female giraffes and a 1996 paper in American Naturalist (Simmons & Scheepers 1996, “Winning by a Neck: Sexual Selection in the Evolution of Giraffe”) that attempted to buck conventional wisdom and suggest that sexual selection was the cause of long necks in giraffes.

Sadly, the last plank is particularly bogus, since it completely ignores and displays no knowledge of a massively relevant and quite brilliant paper, published just back in January 2007 in American Naturalist, that constitutes an experimental demonstration of the relative feeding advantage of giraffe height:

The American Enterprise Institute has an interesting discussion title Darwinism and conservatism: Friends and Foes? with Larry Arnhart, from the Northern Illinois University and John Derbyshire, from the National Review, and George Gilder, and John West, from the Discovery Institute.

Gilder ended with a particularly ironic comment about emergent properties

George Gilder wrote:

When people talk about emergence, it’s a new popular way of saying “I have no clue”.

Does Gilder realize how this describes ID far better?

As a side note: West repeated the specious claim that Doug Axe’s probabilities were relevant to a working protein.

John Derbyshire’s contribution is excellent.

Although many have read the transcripts of the Kitzmiller v. Dover trial (HTML version | PDF version) and found them interesting, reading the transcripts does not give the full sense of what it was like to be in the Kitzmiller courtroom. In real life, in addition to the witness answering questions, the lawyers and witnesses were constantly referring to exhibits that were digitally projected onto a large screen on the right wall of the courtroom. Usually the exhibits were just documents, but when the science witnesses testified, their powerpoint presentations contain fossils, flagella, and everything else in between. I think it is safe to say that the testimony is much easier to understand when read with the demonstrative exhibits available (the exhibit lists and a few exhibits are available online).

However, it takes a lot of work to convert the slides to web format, add captions, embed them in HTML, etc. But as a first step, I and others at NCSE have done this for Kevin Padian’s testimony (testimony+slides | just slides).

I’d like to direct you all over to Red State Rabble to read Pat Hayes’ post this morning entitled “Discovery’s Disturbing Legacy.”

The ID movement has failed scientifically (never having got off the ground), in the courts, and at the ballot box in school Board elections at the state and local level. This has not fazed the Discovery Institute, which is now concentrating on the culture war tactic of associating science (“Darwinism”) with Nazism, eugenics and other cultural evils.

I have just read the latest post of young-earth creationist/Discovery Institute fellow/Biola professor/blogger John Mark Reynolds. I think I am just going to have to occasionally serve the role of his guilty conscience in matters scientific. He has apparently thrown his own scientific conscience down a well somewhere, or he wouldn’t be able to say the wildly hypocritical things he does.

Well, not exactly… But the following press release allows us to explore a common confusion amongst ID proponents, in addition to providing more compelling evidence supporting common descent.

The origin of the brain lies in a worm: Researchers discover that the centralised nervous system of vertebrates is much older than expected

First of all, an “ancient” evolutionary prediction

The findings provide strong evidence for a theory that was first put forward by zoologist Anton Dohrn in 1875. It states that vertebrate and annelid CNS are of common descent and vertebrates have turned themselves upside down throughout the course of evolution.

So how come UcD ‘contributor’ DaveScot considers the findings an argument from incredulity? And what are ID’s explanations and or predictions?

A detailed eyewitness report on the Discovery Institute’s conference revival at Southern Methodist University last weekend has been published. This bit (p. 3) is particularly good:

At this point, we were fed up with the sheer lack of science being discussed. (Remember, ID theorists claim to support a science, not a religion.) So we held up our signs. They bore questions such as, “Why do we have wisdom teeth if they do not fit our jaws?” and “Why did it take 20 species of elephant to go extinct to get two species that survived?” and “Why do the ribosomes (protein synthesizing machinery) in our mitochondria match those of bacteria?” to name a few.

by Douglas L. Theobald

As many of you undoubtedly know, neurosurgeon Michael Egnor is the Discovery Institute’s latest garrulous creationist mouthpiece. In a recent blog entry responding to Michael Lemonick of Time Magazine, Egnor claims that the 19^th century scientists Michael Faraday and James Clerk Maxwell used “the inference to design” to study electricity:

“Let’s ask: what role did the inference to design play for scientists who gave us electricity? … The two scientific pioneers of classical electromagnetism, Faraday and Maxwell, were particularly devout Christians who inferred design everywhere in nature. They believed that God designed everything — including electricity. Their approach to science was pure design inference, undiluted by atheism or materialism…. They worked entirely from the design inference.”

Faraday and Maxwell were Christians who did indeed see design in nature. However, Egnor has it backwards.

The SMU Campus newspaper carried an opinion piece written by Ben Wells who is a junior anthropology major.

The article starts out by describing the political and religious foundation behind the Discovery Institute’s actions

This weekend Dedman Law School’s Christian Legal Society will be hosting a controversial and well-known institute that preaches a religious message masked in a capsule of pseudoscience.

Indeed, the Wedge document outlines clearly how Intelligent Design is meant to be a religious and not necessarily a scientific issue.

A controversial document (reported as the Wedge Document, a 1998 internal memo) stated the Institute’s goal was to “drive a wedge” into “scientific materialism” in order to divorce it from its purely observational and naturalistic methodology and stop the deleterious effects of evolution on Western culture.

Two weeks ago, I demonstrated to Dr. Michael Egnor that his knowledge of early molecular genetics was severely flawed. He responded yesterday, calling me a “pseudo-Darwinist” because those experiments involved, according to him, “designed” variation and “artificial” selection, not random “undesigned” variation and “natural” selection.

He is of course wrong about the experiments, but his rantings about pseudo-Darwinism bring up an interesting point: Egnor himself is a “pseudo-Darwinist”, drawing an absolute dichotomy between natural and artificial selection when it suits him and blurring the two when it doesn’t. Eugenics, according to Egnor, is both the “single incontrovertible Darwinian contribution to the field of medical genetics” (3/28) and the “antithesis of Darwin’s theory” (4/9). But such rhetorical contradictions are what we have come to expect from creationists and ID activists.

For a more detailed trip to the woodshed you can read the following two posts.

My “Backed into a Corner, Egnor Cannot Keep His Arguments Straight”

Orac’s “Irony meter about to explode. Must. Escape”

Bill Dembski and company are having a self-congratulatory session about a new “pro-ID” paper published by Finnish researchers Matti Leisola and Ossi Turunen in Applied Microbiology and Biotechnology. Looking at the paper, you wouldn’t know that it’s a “pro-ID” paper at all because it contains not one shred of evidence in favor of ID, nor does it even try directly arguing for ID (compare this to the Meyer paper, which while riddled with errors, at least put forth pro-ID arguments). On what basis could it possibly be a pro-ID paper? If it weren’t for the fact that Matti Leisola is a creationist, there would be no reason to believe it was intended as such at all.

Nevertheless, Dembski apparently thinks that it’s a pro-ID paper on the basis of its content, presumably because he conflates rational design methodology as used in protein engineering with ID. Of course this is nonsense, and in reality the paper is merely a redundant review of the current state of protein engineering techniques, with most of the space dedicated to the very long list of successes enjoyed by evolutionary methods. There are much better reviews out there, but nevertheless Leisola and Turunen give a decent (if too limited) overview of directed evolution experiments. Then they proceed to argue that rational design methods will start working better once we have more detailed knowledge of the mechanism by which the primary sequence of a protein determines its structure and function. This is an obvious and noncontroversial conclusion, so one is still left wondering how this could possibly be spun as “pro-ID”. I’ll say more about that in a minute, but first let me give a quick overview of the state of protein engineering as it exists today.

In 1999-2000, the Kansas State Board of Education was running their PR machine full-bore, trying to convince the public that the central organizing theory of modern biology and biotechnology was a dead idea. Creationist speaker after creationist speaker was flown into town to put on a dog and pony show. If you were a Young-Earth Creationist, you might have seen Duane Gish/Fred Whitehead nondebate. If you liked ID creationism, you might have seen Johnson or Wells. Back then, it was a very big tent.

Well, KCFS wasn’t going to take things lying down, so we thought we’d prepare a few flyers to inform the audience to help them be ready for the creationists when they arrived. One of those flyers, “Jonathan Wells: Who is He, What is He Doing, and Why?” turned out to be pretty important.

Fast forward to Spring 2005, after the creationists had taken over the state board of education again and ran roughshod over the accepted processes of curricular review. They rejected the recommendations of the experts who developed very good standards and held a show trial, in which evolution would be dragged before them to answer the tough ID creationists’ questions.

The details of the story are described elsewhere, but one of the “witnesses” was Jonathan Wells, who during his testimony claimed that he was not influenced by religion. Within the span of an hour, KCFS was able to print several copies of our Wells flyer to distribute to interested members of the press. The result was that in the following day’s newspapers, Jonathan Wells testimony and his quotations were seen in juxtaposition to each other, making of his credibility to journalists what those in the know had deemed of it for years.

Find the flyer on the flipside. It’s also available in RTF format. Please note that the DI has since changed their name from the Center for the Renewal of Science and Culture to simply the Center for Science and Culture. So clearly it’s no longer religious.

I’m sure you’ve seen the posts here at Panda’s Thumb or over at Scienceblogs about the Discovery Institute’s newest protégé, Dr. Michael Egnor. A professor of neurosurgery at SUNY-Stony Brook, Dr. Egnor has been pontificating on how “Darwinism” has nothing to offer to medicine; and indeed, that evolutionary biology has “hijacked” other fields of study. Mike has already aptly pointed out many of Egnor’s strawmen and intellectual dishonesties, so I won’t review them all. I’ve stayed out of the fray until now because I’ve had limited time and others have been handling it quite ably, but he keeps treading into (and butchering) my territory, so I just wanted to point out a few other things Egnor is waving away when he makes statements like this:

Preventing the emergence of resistant strains of bacteria is important work, but the insight that Darwinism brings to the problem – the unkilled ones eventually outnumber the killed ones – is of no help. We can figure that out ourselves. The tough work on preventing the emergence of resistant bacteria is done by microbiologists, epidemiologists, molecular geneticists, pharmacologists, and physicians who are infectious disease specialists. Darwinism, understood as the view that “chance and necessity” explains all biological complexity, plays no role.

Sigh.

Others have already addressed the blatant ignorance of this statement (spouted following a paragraph wherein he claims that the evolution of antibiotic resistance is just a tautology), so I’m actually going to leave the antibiotic resistance stuff alone for the time being. What I want to address instead are other areas where evolution is critical for insights into many of those fields Egnor mentions, especially since my own research is at the convergence of the first three he lists: microbiology, epidemiology, and molecular genetics.

(Continued over at Aetiology).

This is interesting:

Creationists welcomed their new leaders to Knoxville last weekend for a convention held by the Discovery Institute, a Seattle non-profit that acts as a publishing house and endowment for proponents of intelligent design (ID). The institute supports a dozen senior fellows and more than two dozen other scientists. Staff scientists are working to develop an intelligent design curriculum, and advance copies of Explore Evolution, a biology textbook soon to be released by the organization, were available at the convention. Program Director Stephen Meyer told the crowd it is “premature” to teach intelligent design in public schools. Meyer said, “We encourage people not to push this in schools right now.”

The science of ID isn’t fully developed, and it shouldn’t be pushed in schools, but the revolutionary research movement founded with a textbook is producing another textbook! (and another!)

What has the ID movement been up to, following Kitzmiller and subsequent defeats? Apparently, they are going back to their base. In 2006 and 2007, the ID movement has hosted a number of “conferences” around the country. They call them “conferences” because it sounds scientific, but they are more like weekend revivals, actually, where the ID guys are flown in, give their standard talks to the public, and with a full-time professional