August 2008 Archives

Steve Steve in London

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Steve Steve is having the time of his life at the Nature Network conference. Right now, he’s slumped over on the podium, recovering from yesterday’s festivities. A picture is found below.

The question for you is this: Who is Steve Steve explaining evolution to?

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(The following is a slight adaptation of this essay. Readers may post questions and/or comments there as well as here.) As this series of essays has explained, the polyadenylation of messenger RNAs is a vital aspect of gene expression in eukaryotic cells (and a not-so-unimportant facet of RNA metabolism in other contexts). Polyadenylation is mediated by a sizeable complex that includes various RNA-binding proteins, nucleases, and other interesting activities. Genetic studies in yeast indicate that virtually every subunit of the core complex is essential - for viability and for pre-mRNA processing and polyadenylation in vitro and in vivo. (This review is freely available and serves as a good starting point for readers who wish to explore the subject further.) Biochemical and/or immunological depletion studies reveal a similar scenario in mammals, and a less-expansive set of studies suggests that a similar rule of thumb will apply in plants. The bottom line of all of this is that almost all of the subunits of the polyadenylation complex seem to be essential - remove one, and the complex cannot function. In the vernacular of a proponent of intelligent design, the polyadenylation complex would seem to be irreducibly complex.

It is in this context that the recently-completed genome of the parasitic organism Giardia lamblia enters the fray. Last year, the complete sequence of G. lamblia, some 12 million base pairs, was determined and analyzed. The authors of the study published in Science noted a number of interesting things - a preponderance of genes encoding protein kinases, evidence for substantial horizontal gene flow from bacteria and archaebacteria, and a streamlined core gene expression machinery (transcription and RNA processing). This streamlining is especially notable in the case of the polyadenylation machinery. Remarkably, of all the subunits in the yeast complex, genes for only three* can be found in G. lamblia (see the figure that follows this paragraph - adapted from Fig. 1 of Morrison et al.).

In a Comment in the journal Genome Biology Gregory Petsko, Professor of Biochemistry and Chemistry Protein Crystallography at Brandeis University discusses the latest shenanigans of the Intelligent Design movement. ( Gregory A Petsko It is alive Genome Biology 2008, 99::106)

They’re at it again. Armed with another new idea from the Discovery Institute, that bastion of ignorance, right-wing political ideology, and pseudo-scientific claptrap, the creationist movement has mounted yet another assault on science. This time it comes in two flavors: propaganda and legislative.

What is Petsko talking about?

Tangled Bank #112

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The Tangled Bank

The latest edition, Tangled Bank #112, is now available at Science Notes.

This issue was delayed because I neglected to ride herd on it while I was off in the Galápagos, but the next edition, at En Tequila Es Verdad, will be on schedule next week, on 3 September. So get inspired by the latest and send in links to your science writing pronto!

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? “.

The AAAS responds to “Expelled”

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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.

New Features

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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.

Padian’s Takedown of “Of Pandas and People.”

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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 20th 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).

The Sixth Intenrational Conference on Creationism was held from August 3-7, in Pittsburgh, PA. That being a mere five hour drive from my digs in Harrisonburg, I naturally attended.

Unlike the revival tent atmosphere that prevails at Ken Ham's ubiquitous gatherings, the ICC's represent an attempt at a serious scientific conference on creationism. If you flip through the conference proceedings and just give it a quick skim, you could easily be impressed by the professionalism of the volume and the level of technical detail in the papers. It's a side of creationism we rarely see, and serves as a reminder that these folks honestly believe what they are saying, and at least attempt to do science with their idiosyncratic interpretaion of the Bible as their starting point.

Alas, combining the scientific legitemacy of creationism with the turgid style of academic prose is not the formula for a pleasant conference. I will be reporting on my experiences at the conference over at EvolutionBlog. The first two installments are already up: Part One and Part Two. Comments can be left there. Go have a look, and stay tuned for further installments.

The evolution of Jeffrey P Schloss

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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

Human & Dino footprints, and Dating strata & fossils?

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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.

Channel 4: The Genius of Darwin

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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.

Tangled Bank #111

The Tangled Bank

You can now read Tangled Bank #111 at the denialism blog. It's poetical!

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

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