Regular readers on this group may remember Steve Fuller whose contributions as an “expert witness” for the defense in the Kitzmiller law suit were quoted by the plaintiffs as well as the judge to show that ID was not science?

Last year, Steve Fuller released a book titled “Science v. Religion? Intelligent Design and the Problem of Evolution” which was recently reviewed by Sahotra Sarkar in “Notre Dame Philosophical Reviews”. Sarkar’s scathing review exposes the vacuity of Fuller’s arguments, a vacuity we have come to expect from ‘Intelligent Design’.

Not wanting to be left out, Denyse O’leary, validates the quality of the work by Sarkar by referring to him as a “third-rate Darwin hack”. Furthermore, Denyse, in her continued display of ignorance, responds to Sarkar’s observation that Fuller predicts that Darwinism (by which he means the entire framework of evolutionary theory) will be dead by the end of the twenty-first century and will be replaced by something more akin to ID creationism with “What about the Altenberg 16? “.

This video from the “American Association for the Advancement of Science, “ (AAAS), a non-profit science society, explains why religion and science need not be in opposition. It is a response to the intelligent design propaganda movie, “Expelled: No Intelligence Allowed,” with Ben Stein. AAAS also released a written statement. See AAAS Statement Decries “Profound Dishonesty” of Intelligent Design Movie For more on how AAAS works to promote constructive dialogue between religious and scientific leaders, see this link

Enjoy the video below the fold

A powerful video addressing how science and faith can work together without damage to either.

Well the school is starting up again, and this blog will be slower than usual for a while until the authors get into the swing of things.

On my side of things, I have an upgrade planned for site now that Movable Type 4.21 has been released. I’m currently running it on my blog and will implement it when I’m satisfied with it and have enough time on a weekend.

I’ve also revealed a secret project that I’ve been toying with off and on for a few months: pre-submission comment validation. I hope to enable this technology on PT, to help out those of you who find writing valid markup difficult. However, I need y’all to go give it a hard time to find the bugs.

Commenting on the testimony of the plaintiffs’ expert witnesses in the Kitzmiller trial, someone said (paraphrased) “It was the biology course you never took but wish you had.” Reading the raw transcripts of the testimony one can easily believe that.

But it gets better. I just discovered that Nick Matzke took Kevin Padian’s testimony and integrated Padian’s slides, so one can see what Padian was talking about as he described the paleontological evidence for evolution and the misrepresentations in Of Pandas and People. I don’t recall it having been flagged here before.

That had to have been a heckuva job for Nick, but it was sure worth it. Reading it with the slides right there, the flow of the testimony is beautiful. The integrated presentation is a significant resource for teachers and others in this arena. I commend it to folks’ attention.

by Douglas L. Theobald, Assistant Professor of Biochemistry, Brandeis University

Jeffrey Shallit pointed me to a youtube video, in which David Berlinski makes the following remarkable claim: “… von Neumann, one of the great mathematicians of the 20^th century, just laughed at Darwinian theory. He hooted at it.”

For those even tangentially familiar with the Hungarian mathematician John von Neumann, this will come as a shock. One may ask, however, with some justification: who cares what a non-biological mathematician thinks about evolutionary theory? After all, anyone speculating outside of their field of expertise is simply doing that, and their opinion should carry no more weight than anyone else who talks about something they know little about. John von Neumann, however, is not just any mathematician, and his seminal work on self-replicating automata and game theory has had important, fundamental implications for evolutionary biology (as have, more indirectly, his contributions to ergodic theory, numerical analysis, and statistics).

Former Discovery Institute’s Senior Fellow Jeffrey P. Schloss has become the target of several ID Creationists’ ire, such as Dembski, Denyse O’Leary and Richard Weikart.

While I can appreciate that the history and evolution of former Senior Fellow Schloss is of concern to some ID Creationists, they, perhaps inadvertently, present us with evidence that serious scholars find it necessary to abandon Intelligent Design as preached by the Discovery Institute. In addition, the replacements seem to lack much of a scientific background (Medved comes to mind)

And in case of Schloss, the reasons are quite compelling as laid out in a recent ASA article. The article itself causes Dembski to make some strong comments about ASA, and cause Denyse to lose her temper as I will discuss. However, before addressing some of the creationists’ responses, I will first attempt to discuss the evolution of Jeff Schloss and his excellent review of “Expelled” which seems to have caused so much concern amongst ID Creationists, and for good reasons as Schloss presents an extremely well argued and still balanced critical rebuttal of “Expelled”.

This news comes via PTer and historian of science John Lynch. I don’t know what to think about this, it contradicts everything I used to think about Darwin, but honesty demands that the public and the scholarly world be informed of the uncomfortable facts.

A precious historical find

Category: History and Philosophy (often of Science) Posted on: August 11, 2008 2:35 PM, by John Lynch

Amazing letter from Charles Darwin to Klara Pölzl, one that likely to change Darwin scholarship for the future. Written in 1881, a year before his death, Darwin could clearly see the vast implications of his life’s work for Twentieth century thought. I’m going to have to take some time to digest this before I comment.

The initial phase of the California Creationist Lawsuit is over, and quality education is the decisive winner. Kevin Vicklund has Judge Otero’s decision, as well as a very nice analysis of the ruling up over at his blog. If you’ve been following the case closely, you can probably jump right over there for the details. If you haven’t been tracking the events closely, or want a quick review of the case, keep reading. I’m going to go over the history first, then I’ll talk a bit about what Friday’s decision means, and what is likely to happen with the case in the future.

The lawsuit (ACSI v. Stearns) was filed in federal court in August of 2005 by the Association of Christian Schools International, Calvary Chapel Christian School, and parents acting on behalf of their children, who were students at Calvary Chapel. They were challenging the University of California’s decision to refuse to accept several of their courses as fulfilling UC’s admissions requirements. The rejected courses covered the academic spectrum, with English, history, and science classes all failing to meet UC’s scrutiny. The common element in the rejected courses was that they did not actually teach the material that UC requires from incoming students. Instead, the rejected courses taught a radically wrong “Christian perspective”.

For most of us, the rejection of the courses was nothing more than the natural consequence of the Christian schools’ decision to reject reality and teach fantasy. From their perspective, it represented an unconstitutional attack on their freedom of religion. The court, obviously, did not agree. To see why, we really need look no farther than the introduction to the biology textbook used in one of the rejected courses:

Read more at The Questionable Authority, where comments may be left.

The important thing about Intelligent Design is that it is not a theory - which is something I think they need to make more clear. Nor is Intelligent Design an explanation. Intelligent Design is a challenge. It’s a challenge to evolution. It does not replace evolution with something else.

Jerusalem Post: One on One: Broadcast views

We don’t have enough geology around this joint, so here’s some elsewhere.

Folks have undoubtedly seen the claim by “Dr.” Carl Baugh that a human footprint has been found with a dino print partly overlapping it. Gary Hurd has done a nice analysis of a decent photo of the specimen and (surprise!} concludes that it’s a fake. Gary even identifies signs that suggest how the specimen’s patina was faked. Go and read Gary’s writeup.

Joe Meert also has a nice post up on a guy who appears to be Kent Hovind’s clone, “Dr.” Ron Carlson. Carlson makes absolute hash of geological dating and the history of science, and Joe does a nice job on him. I doubt, though, that Carlson will answer Joe’s email.

The UK based Channel 4 is airing a three series program titled The Genius of Charles Darwin

He has presented television documentaries for Channel 4 including The Root of All Evil? and The Enemies of Reason. He is well known for his atheism and his forthright criticism of religious doctrine. In the forthcoming Channel 4 series Dawkins on Darwin he argues that Darwinism provides a more thrilling view of creation than any religion.

The first episode can be viewed at Google Video

The next few months the BBC and other channels will be producing some interesting programs for the celebration of the 200 year anniversary.

Make sure you check out the Channel 4 Site as it provides some useful materials.

The Institute for Creation Research has a project called RATE, whose intent was to overturn radiometric absolute dating methods as evidence for an old age of the earth. One of the arguments that they made was that diamonds contain significant levels of the radioactive carbon 14 (14C) isotope, indicating that they cannot be older than about 50,000 years old, and thus point to a young age of the earth. This sort of technical wrangle is something beloved of young-earth creationists (YECs), and indeed one such person going by the handle “tripa” has commented here (n.b., on Austringer, where the original essay was posted) on another thread about the RATE diamond study.

Physicist Kirk Bertsche has responded to the RATE diamond and coal studies with an essay hosted on the American Scientific Affiliation website. Dr. Bertsche notes a number of inconvenient facts that undercut the arguments made by ICR’s advocates, including standard procedures within radiocarbon AMS work that were ignored or not followed properly, and indications from the RATE measurement results themselves whose obvious interpretation points to sample contamination. It is an elegant take-down of yet another antievolution argument whose pseudo-technical gloss is intended to impress rather than to inform.

The ASA also hosts several other essays concerning the RATE project.

(Original article at the Austringer)

During a well attended meeting on Monday August 4, 2008, Mount Vernon science teacher John Freshwater denied having burned or branded a person

“I have never branded or burned a person,” Freshwater told the board

And yet, during the investigation, he told

He said that he uses the device about twice a year and has done so for 21 years. At the end of the experiment the kids are excited and ask if they can touch it. He said that he demonstrates it on his own arm by making an “X” and then lets them touch it voluntarily. He said that the incident in question occurred in December 2007. He remembers getting from 3 to 8 volunteers, but couldn’t remember the order or all of the names.

He said that the device is owned by the school, he received verbal instructions on using it 21 years ago, and has never seen any written instructions. He said that he has not had a complaint in 21 years regarding his use of the device. The device leaves a red mark after one or two seconds of touching, but no blisters. He denied any religious discussions during this or any previous occurrences. He said that he would never hurt a student.

The investigators also talked to several former students of Freshwater, contrary to Freshwater’s claims.

The current or former students that were interviewed that had participated in the December 2007 incident or other similar incidents in earlier years described the demonstration in the same manner as had Mr. Freshwater with one exception. The all described the mark Mr. Freshwater put on his arm as a “cross”. One student stated Mr. Freshwater would mark the student with a cross unless the student requested a different type of marking. It was the default mark. The pictures below were provided by the parents.

While Freshwater may argue that marking the arm with a cross is not branding or burning, this seems to be largely an issue of semantics. The report describes how at least in one instance, the mark remained painful and visible for an extended period of time (the report mentions three to four weeks).

The report thus concludes

Mr. Freshwater did improperly use an electrostatic device on the student who filed the complaint and other students in his science class in a manner that was not in compliance with the manufacturer’s instructions. While there did not appear to be any intent by Mr. Freshwater to cause injury to any student, he was not using the device for its intended purpose. Contrary to Mr. Freshwater’s statement he simply made an “X” not a “cross,” all of the students described the marking as a “cross” and the pictures provided depict a “cross”.

Over the next few weeks, the History Channel is showing a fascinating series called “Evolve.” Here is the synopsis of the first episode, titled “Eyes”:

They are one of evolution’s most useful and prevalent inventions. Ninety five percent of living species are equipped with eyes and they exist in many different forms. Learn how the ancestors of jellyfish may have been the first to evolve light-sensitive cells. Discover how dinosaur’s evolved eyes that helped them become successful hunters. Finally, learn how primates evolved unique adaptations to their eyes that allowed them to better exploit their new habitat, and how the ability to see colors helped them find food. …

While there were a few minor bio-gaffes, for the most part the show was excellent. There was no hand-wringing over offending creationists; instead, the show stayed right on the science. It pointed out that eyes have evolved from scratch numerous times in the animal kingdom, but also that just a few ancient genes were involved in these separate processes. The explanation of why predators need eyes with overlapping coverage toward the front - to better locate hapless prey - was done well. Conversely, the eyes of rabbits, which are almost on opposite sides of the head, serve to give that creature 360-degree vision, a sure benefit for avoiding predators. And finally, humans look forward also, but probably not for predation, but rather navigating in the tree limbs. A good explanation for why primates needed color vision was given, also: the primates’ ability to see shades of red helped them find the red-orange nutritious young leaves in the tree canopy, thus avoiding wasting time on mature, green, and hard-to-digest leaves in the trees.

“Eyes” will be repeated, and other episodes are on their way, including “Guts” and “Jaws.” (check local schedules for air times):

Friday, August 01: Eyes

Saturday, August 02: Eyes

Tuesday, August 05: Guts, Eyes

Wednesday, August 06: Guts, Eyes

Sunday, August 10: Eyes, Guts

Monday, August 11: Guts

Tuesday, August 12: Jaws

Wednesday, August 13:Jaws

After being depressed by the History Channel’s apparent obsession with woo-woo topics like UFOs and Bigfoot, the new ‘Evolve’ series is an encouraging sign. Kudos, History Channel!

Blogosphere Reaction: Daily Kos PZ Myers

An interesting new paper is just out today in PLoS ONE. You recall the announcement a few years back that soft tissue that resembled organic tissue had been isolated from a Tyrannosaurus femur. This started off a huge controversy in the field (and beyond)–researchers disagreeing with each other whether the structures seen were indeed blood cells and vessels; creationists crowing about how this finding represented “proof” that the earth was indeed young and dinosaurs had existed just a few thousand years ago; and of course, talk of cloning and DNA analysis. On the side of “soft tissue = dino blood” were findings that reported identification of the iron-containing protein heme (potentially from the red blood cells) and morphology of cells and vessels similar to that seen in modern-day ostriches and emu. However, the new paper by Kaye et al. provides an alternative explanation: that the structures aren’t actual vessels and cells, but are instead iron-rich bacterial biofilms. Read the rest over at Aetiology…

There’s an amusing dispute going on between the Discovery Institute and Little Green Footballs, the latter of which recently unveiled some very interesting details about links between Islamic and Christian creationists. Needless to say, the DI folks are demonstrating their usual haphazard acquaintance with the truth.

Following up PZ’s previous post about blind fish, I want to quote a section of R. A. Fisher’s “The Genetical Theory of Natural Selection”. Fisher is credited as being one of the founders of modern evolutionary biology, which drove him to create modern statistics.

This quote begins on page 128 of the 1999 complete variorum edition. I think it was originally written in 1930.

The power of the means of dispersal alone, without the necessity for selective discrimination in either region, is excellently illustrated by the theory, due to Ray Lankester, which satisfactorily accounts for the diminution or loss of functional eyes by the inhabitants of dark caverns. Ray Lankester pointed out that the possession of the visual apparatus is not merely useless to such animals but, by favoring their migration towards sources of light, will constantly eliminate them from the body of cave inhabitants, equally effectively whether they survive or perish in their new environment. Those which remain therefore to breed in the cavern are liable to selection in each generation for their insensibility to visual stimuli. It should be noted that with such very restricted habitats migrational selection of this sort might attain to very high intensity in consequence produce correspondingly rapid evolutionary effects.

Very interesting perspective isn’t it?

Christopher Hitchens looks at what blind salamanders have to say about creationism.

In previous essays (here and here), we learned that genes encoding new proteins can and do, often, arise de novo in the course of evolution, contradicting one of the central tenets of ID proponents. The means by which these genes arise are many. One of these, suggested by Cai at al. (the subject of one of the earlier essays), involved the adaptation of a gene encoding an evolutionarily-conserved non-coding RNA via the appearance, by mutation, of appropriate translation initiation and termination (“start” and “stop”) codons. This mechanism represents an intersection of sorts between the subject of protein evolution and another matter of discussion on these blogs, namely the existence, evolution, and “function” of junk DNA. In this essay, I review a 2007 study by Debrah Thompson and Roy Parker (“Cytoplasmic decay of intergenic transcripts in Saccharomyces cerevisiae”, Mol. Cell. Biol. 27, 92-101) that adds a great deal of clarity to this mode of gene and protein evolution.

Bless their hearts. The Creationists over at Answers in Genesis are working their perfectly designed fingers to the bone. Blowing the Discovery Institute out of the water by not only publishing a for-realsies science journal (well, at least once), but also performing ‘semi-technical’ research!

Darwin at the Drugstore? Testing the Biological Fitness of Antibiotic Resistant Bacteria

While its just adorable to see them working so hard, their crippled understanding of basic science leaves this semi-technical article completely worthless.

Our good ol’ buddy Casey Luskin at the Discovery Institute Media Complaints Division has just put up an impressively mistake-strewn story about the “Altenberg 16” meeting in Vienna. In real life, the meeting discussed the possibilities for an “Extended Synthesis” in evolutionary biology which incorporates development, evolvability, complexity theory, etc. into the old “Modern Synthesis” of population genetics. But in the land of cranks & ID/creationists, the Altenberg 16 meeting has become the latest bit of evidence that evolution is a theory in crisis. The primary person who got the crazy-train going was “journalist” Suzan Mazur, who has written a series of stories that mis-portray almost everyone and everything involved and, no matter what her interviewees tell her, end up with the inevitable conclusion that evolution is on its last legs. No one seriously informed would pay attention to this kind of schlock, but ID/creationists will jump on anything with a vestige of credibility (in this case an allegedly serious journalist – is she a freelancer or what?). When meeting organizer Massimo Pigluicci got wind of the misinformation being passed around about the meeting, he wrote a great explanation of what it was actually about and why Mazur et al. were wrong.

Anne Minard of National Geographic News writes on July 9^th

The discovery of a missing link in the evolution of bizarre flatfishes—each of which has both eyes on the same side of its head—could give intelligent design advocates a sinking feeling.

CT scans of 50-million-year-old fossils have revealed an intermediate species between primitive flatfishes (with eyes on both sides of their heads) and the modern, lopsided versions, which include sole, flounder, and halibut.

So the change happened gradually, in a way consistent with evolution via natural selection—not suddenly, as researchers once had little choice but to believe, the authors of the new study say. … Though known for their odd eye arrangement, no flatfish start life that way. Each is born symmetrical, with one eye on each side of its skull.

As a flatfish develops from a larva to a juvenile, one eye migrates up and over the top of the head, coming to rest in its adult position on the opposite side of the skull. … Palmer added that the new work is “a fantastic paper” that helps resolve a mystery “that’s bedeviled evolutionary biologists for more than a century.

“It’s really been a major, major puzzle to evolutionary biologists.”

As expected, the Magisterium of Intelligent Design was quick to condemn the finding as simply floundering around, while the Institute of Creation Research has a turbot-charged attack on the finding, pointing out that flatfish are sole-ly members of the flatfish ‘kind,’ and putting National Geographic in it’s plaice.

Tom McIver, a member of Ohio Citizens for Science who works in the library at John Carroll University in Cleveland, is a long-time professional student of the creationism movement. His dissertation was Creationism: Intellectual Origins, Cultural Context, and Theoretical Diversity, which I am told will be put online by NCSE one of these days (Glenn? Josh?). Tom has written widely on various associated topics. For example, he had a 1988 article on Gap Theory in Creation/Evolution, published by the American Humanist Association, and an exhaustive(-ing?) bibliography he compiled, Anti-Evolution: An Annotated Bibliography, is scheduled for reissue as a paperback in 2008.

Tom has been on creationist tours, taken courses at the Institute for Creation Research, and has generally immersed himself in the topic for more than 20 years. He has even written poetry on ID:

Added July 15:

Please note the addition of links to NCSE’s library listing as well as Tom’s library listing. I note with interest that there is minimal overlap – less than 20% shared holdings – between Tom’s library and NCSE’s.)

John Freshwater was interviewed by Bob Burney on the April 28^th, 2008 on 880 WRFD. I listened to the interview and was amazed by how Freshwater’s friends help undermine his own case

Bob mentions that one of his son’s is in Freshwater’s class

Bob: And from day 1, John, he has been telling me what a wonderful teacher you are and the fact that you present both sides to issues and which is just wonderful and unfortunately kind of rare in the schools today.

So what do you guess, did Freshwater tell about the two sides of homosexuality? Or was this a topic in which John decided to tell only one side of the story?

From CNN we learn that

The report also cites evidence that Mr. Freshwater told his students that “science is wrong because the Bible states that homosexuality is a sin and so anyone who is gay chooses to be gay and is therefore a sinner.”

Listen to the rest for more foolishness.

Couple of interesting stories about the efforts of Turkish Muslim creationist Harun Yahya (nee Adnan Oktar). From the New Humanist:

Oktar is a figure fairly well known to Darwinists and despite his claims to scientific competence is clearly little more than a crank. However what had changed, according to the report, was the scale and ambition of Oktar’s pseudo-scientific message. Since 2006 copies of a substantial, glossy and smartly packaged book called Atlas of Creation, credited to Harun Yahya, had been arriving at schools and universities across Europe. In Spain, France, Switzerland and Denmark clear evidence of the growing resources and confidence of European Muslim creationism was thudding on to the mat. The book is the first of a projected seven-part series, and parts two and three have already begun arriving at educational institutes Europe-wide.

(via NF)

And from Reuters:

Well-illustrated and free of theological jargon, they preach that Islam is the one true faith and Darwinism, by undermining religious belief, has led to the discord, atheism, terrorism and extreme political ideologies plaguing the world.

Reader-friendly, the books appeal to Muslims trying to square modern science with their faith in an inerrant Koran, much like Christian evangelicals who read the Bible literally and support creationism or intelligent design theories.

(via LGF)

After the attempts by Coach Daubenmire to defend Freshwater have failed miserably, most recently on Geraldo, an “official site” named “ Bible on the Desk” has been created which claims to be the official site for Freshwater. Its most visible attribute is a Donate button and a FoxNews interview.