December 11, 2005 - December 17, 2005 Archives

THEY HAVE NO SHAME

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Paul Mirecki professor (and former chairman) of the University of Kansas Department of Religious Studies, reported that he was attacked by two men at about 6:30 AM on last Monday, 05/12/05. As one may observe from the link above, Panda’s Thumb has to date not discussed this issue beyond merely mentioning that it occurred. This was the result of considerable debate, hundreds of emails- many very heated, amongst the dozen or so of us who are regular contributors to the Thumb.

The religious right was not so restrained. Within hours, “conservatives” were claiming that Mirecki’s report was false and that his injuries were faked Mirecki hospitalized after beating. Within two days William Dembski promoted the idea that Mirecki had faked the attack. The website Dembski directed his readers to also held the possibility that Mirecki was a drug addict and/or drug dealer;

Comment by Sean — Wed 7 Dec 2005 @ 6:39 am

I think it’s most likely that he was beat up for some completely different reason, which would have been embarrassing, or even incriminating, for him to admit. A drug deal, perhaps.

Without any supporting evidence at all, or time to reflect, right-wing zealots began braying about Tawana Brawley and Al Sharpton, and comparing Mirecki with Kerri Francis Dunn. We have seen the far right employ this technique so often it is now known as “swift boating.” I am reminded of the advice provided to the Army’s Airborne Rangers if captured, “Admit nothing, Deny everything, Make counter-accusations.”

A few recent papers…

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The issue of Nature Reviews Genetics from which I pulled the Homeobox genesis article actually contains a whole series of articles focusing on evolution of the body plan. Here's a brief taste of the good stuff found in the journal:


Garcia-Fernàndez J (2005) The genesis and evolution of homeobox gene clusters. Nature Reviews Genetics 6:881-892.

The crucial function of homeobox genes in patterning the body has been appreciated for decades. This article pulls together existing data to explain how the current clustered organization of Hox genes, and that of the related ParaHox and NK clusters, came about, the forces that preserve gene clustering and the contribution of Hox, ParaHox and NK genes to the major evolutionary transitions in animal body plan.


Pearson JC, Lemons D, McGinnis W (2005) Modulating Hox gene functions during animal body patterning. Nature Reviews Genetics 6:893-904.

The function of Hox proteins in axial patterning and morphological evolution ultimately depends on the effects of these proteins on downstream targets. This article reviews four important lines of research into Hox function - including work to identify the nature of Hox targets and define the structure of target enhancers, and the recent realization that Hox gene expression might be modulated by conserved microRNAs.


Peel AD, Chipman AD, Akam M (2005) Arthropod segmentation: beyond the Drosophila paradigm. Nature Reviews Genetics 6:905-916.

Genetic studies of Drosophila melanogaster have laid the foundations of our understanding of axial development. But just how universal is this fly model? The growing number of experimental methods that have become available for other arthropods is revealing a surprising diversity of pattering mechanisms, and allows us to formulate a model of how segmentation mechanisms might have evolved.


Martindale MQ (2005) The evolution of metazoan axial properties. Nature Reviews Genetics 6:917-927.

Multicellular animals come in many shapes and forms but they owe their body organization to the emergence of three design features - the anterior-posterior and dorso-ventral axes, and the three germ layers. Morphological and, more recently, molecular analyses on four basal metazoan taxa have begun to reveal how such features emerged and evolved, although a consensus model will depend on a stronger phylogenetic framework and a broader sampling of informative taxa.


Keep that all in mind next time a creationist tries to tell you that evolution is superfluous, or that Intelligent Design has a research plan.

Dover and the Future of ID Lawsuits

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The Chicago Tribune had an interesting article last week about the three most likely outcomes of the Dover trial (which, as Nick noted yesterday, is expected to happen next week). It also contained a little nugget about the Gull Lake situation here in Michigan, where apparently the Thomas More Law Center is still planning to sue on behalf of two teachers who were told by the school board they can no longer teach ID in their 7th grade science classrooms.

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

I haven’t yet addressed one error that Judge Carnes made yesterday. Carnes claimed that the disclaimer sticker accurately reflected the opinion of the textbook author, Ken Miller, that evolution is a theory and not a fact. (I believe that this was part of the defense’s argument.)

“I don’t think you all can contest any of the sentences” on the disclaimer sticker, Judge Ed Carnes of the 11th U.S. Circuit Court of Appeals told an attorney arguing for parents who sued.

“It is a theory, not a fact; the book supports that,” Carnes said.

(AP)

Judge Ed Carnes of the U.S. 11th Circuit Court of Appeals said that the lower court judge had misstated facts in his ruling, overstating the influence religious protests had on the school board’s actions. He also said the words on the sticker are “technically accurate,” and that the Cobb County school board was justified in singling out the theory of evolution for comment.

“From nonlife to life is the greatest gap in scientific theory,” Carnes said. “There is less evidence supporting it than there is for other theories. It sounds to me like evolution is more vulnerable and deserves more critical thinking” than other subjects.

Here is part of Ken Miller’s testimony during the trial phase:

Hox genesis

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One of the hallmark characters of animals is the presence of a specific cluster of genes that are responsible for staking out the spatial domains of the body plan along the longitudinal axis. These are the Hox genes; they are recognizable by virtue of the presence of a 60 amino acid long DNA binding region called the homeodomain, by similarities in sequence, by their role as regulatory genes expressed early in development, by the restriction of their expression to bands of tissue, by their clustering in the genome to a single location, and by the remarkable collinearity of their organization on the chromosome to their pattern of expression: the order of the gene's position in the cluster is related to their region of expression along the length of the animal. That order has been retained in most animals (there are interesting exceptions), and has been conserved for about a billion years.

Think about that. While gene sequences have steadily changed, while chromosomes have been fractured and fused repeatedly, while differences accumulated to create forms as different as people and fruit flies and squid and sea urchins, while continents have ping-ponged about the globe and meteors have smashed into the earth and glaciers have advanced and retreated, these properties of this set of genes have remained constant. They are fundamental and crucial to basic elements of our body plan, so basic that we take them completely for granted. They determine that we can have different regions of our bodies with different organs and organization. Where did they come from and what forces constrain them to maintain their specific organization on the chromosome? Are there other genes that are comparably central to our organization?

Continue reading "Hox genesis" (on Pharyngula)

GCISE Press Release

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Today Georgia Citizens for Integrity in Science Education issued a press release concerning confusion that arose, yesterday, during the appeal of Cobb County’s disclaimers.

December 16, 2005

Crucial Evidence Left Out at Cobb County Appeal, Says Georgia Science Advocacy Group

GCISE (Georgia Citizens for Integrity in Science Education) consists of parents, clergy members, K-12 faculty, higher education faculty, and other concerned citizens. GCISE is committed to improving science education in the state of Georgia, and therefore is deeply concerned about inaccuracies in the scientific information and legal evidence discussed at the 11th Circuit Federal Appeals Court today. We hope to educate the public on this matter in advance of the Court’s ruling.

An erroneous conclusion was drawn in court today that the evolution disclaimer stickers were placed in Cobb science textbooks before parental complaints about the evolution content. As reported on 3/29/2002 by the Atlanta Journal Constitution however, the Cobb County School Board received complaints about new biology textbooks at a very contentious public school board meeting on 3/28/2002. During that meeting Cobb parent Marjorie Rogers informed the board that she had a petition signed by 2,300 people “dissatisfied with science texts that espouse ‘Darwinism, unchallenged.’” It was reported at that time that the Board would appease these parents by asking their lawyers to draft disclaimers “caution[ing] students that evolution is only a theory.” The Board testified in federal district court that they were addressing concerns from a group of conservative Christian parents with objections to teaching evolution.

To make matters worse, it was abundantly clear that confusion still reigns in Georgia about the meaning of the terms “theory” and “fact” as used by scientists. The National Academy of Sciences, organized by President Lincoln in 1863 to advise the nation on scientific matters, defines a scientific fact as “an observation that has been repeatedly confirmed.” Furthermore, they define a scientific theory as “a well-substantiated explanation of some aspect of the natural world that can incorporate facts, laws, inferences, and tested hypotheses.” With these definitions in mind, biological evolution can be considered both a fact and a theory. The readily observable “Fact” of Evolution is that populations of organisms change over time. Even creationist think tanks are on record accepting this idea. For example, no one denies that bacteria are rapidly evolving resistance to antibiotics and insects to pesticides. The “Theory” of Evolution uses several natural mechanisms including natural selection to explain quite well how the fact of evolution has occurred. Contrary to statements made in Court, evolution is probably our most thoroughly validated scientific theory, with hundred of years of supporting evidence.

Finally, the disclaimer sticker placed in Cobb textbooks calls evolution a theory about “the origin of life.” This is incorrect and makes the sticker extremely misleading to students. Evolution does not explain the origin of life on earth; it explains how that life has changed over the millennia since its origin. Thus the sticker is incorrectly representing scientific understanding.

Our children deserve complete, scientifically accurate textbooks, unadulterated by politically motivated, obfuscating messages. The success of Georgia students in college and in a global economy depends on science literacy. GCISE pledges our full support to parents and teachers wishing to provide the best possible education in modern science for their students.

Georgia Citizens for Integrity in Science Education P.O. Box 4642 Marietta, GA 30061 http://www.georgiascience.org Email: [Enable javascript to see this email address.] Tel: 770-825-8002 Additional contact: Sarah Pallas, GSU Biology professor, 404-651-1551

More on Cobb

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You may remember that yesterday a conservative judge in the Cobb County Disclaimer appeal accused the ACLU of lying. Specifically, Judge Carnes claimed that the ACLU had its timeline wrong about the case. The Judge was wrong as the AJC says this morning, “Appeals judges skeptical about Cobb ruling“.

In an interview after Thursday’s court hearing, Rogers, a self-avowed six-day biblical creationist, said she gave the petitions to the board before it decided to buy new science books with chapters on evolution.

“There wouldn’t have been any reason to give it to them in the fall,” she said. “They were done to try and persuade them not to buy the books.” One of the petition’s three options, she said, was for the board to put disclaimers in the new books.

Daniel Morgan has written a very thorough review of the entire Richard Sternberg situation and it’s well worth reading. Sternberg, you may recall, was the editor of a journal who went outside the normal peer review process to insure that a very badly written paper by DI fellow Stephen Meyer would get published. Morgan debunks the whole Sternberg-as-martyr myth that has grown up around it.

Summit Lists Ways–but Not Means–to Strengthen Science

In an unusual show of unity, 50 business, academic, and legislative leaders came to Washington, D.C., last week to proclaim what they believe is obvious: The United States should be paying more attention to science and engineering. But although there was a rousing consensus on the need to improve teaching, graduate more science majors, and boost spending on research and translating the results to the workplace, there was mostly silence on how these changes might come about and who would pay for them.

***

The group’s series of recommendations, announced before the meeting began, include more federal spending on basic research and set-asides for high-risk research, a doubling over the next 10 years of the number of undergraduates earning science and engineering degrees, changes in immigration laws to make it easier for foreign-born graduates to remain in the United States, and greater support for advanced manufacturing technologies.

VEN.jpg A class of bipolar neurons, known as Von Economo neurons (VEN), are found in layer Vb of human neocortex. VEN morphology is very simple: they have a large apical dendrite as do cortical pyramidal neurons but lack the collection of basal dendrites. They possess the high-volume, elongated cell body that is typical of fast-conducting projection neurons, and preliminary tract-tracing indicates that they are such, although the array of their projections has not been elucidated. Interestingly, VENs are found in a select few cortical areas that receive inputs from numerous brain regions; the fronto-insular cortex (FI) and anterior cingulate cortex (ACC). Thus, VEN morphology and anatomical location suggest that these cells are positioned to receive an array of diverse information in parallel and then compress it for speedy processing.

Continue reading at Neurotopia…

An Atlanta Blogger, The Sanity Inspector, attended the appeal of the Cobb County Case today and has posted his notes of the hearing: “ Cobb County Evolution Stickers Have Their Day In Court.”

During the hearing the judges criticized the plaintiffs for errors in their brief. Judge Carnes claimed that Marjorie Rodger’s petition didn’t occur until after the stickers were enacted, and the ACLU’s attorney was not prepared for this spin.

Looking at the archives of the AJC, we have confirmed that Judge Carnes is wrong, the Cobb County School Board was clearly aware of the petition before they enacted the disclaimer:

plosRobinson0511.jpg In my last post I mentioned in passing the feature article appearing in November’s issue of PLoS biology.

In that paper, Richard Robinson describes some of the difficulties faced by researchers into the Origin of Life. The origin of replicating molecules is a question of intense interest to biologists because replication is the required (and perhaps sufficient) condition for subsequent evolution. (“Give biologists a cell and they’ll give you the world” is how Robinson puts it.)

The fundamental breakthrough in Origin of Life (OoL) research came, of course, from the famous Miller-Urey experiment, in which it was shown that energy applied to mixtures of inorganic compounds could lead to the formation of biologically significant molecules. Despite problems that later emerged in Miller and Urey’s model, the fundamental point always remained that some conditions exist that can result in the spontaneous origin of organic molecules.

More than just a pretty face

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Staphylococcus aureus. The name means, literally, “golden grape clusters.” Upon staining, these round bacteria are visualized in clumps that resemble bunches of grapes. Every microbiology student is familiar with the most notorious member of the Staphylococcus species, S. aureus, which often produces a distinct yellow pigment when grown on agar plates containing blood. This bacterium itself causes a wide range of illnesses, ranging from food poisoning to deadly skin infections. Of great concern is the fact that strains that resist a number of antibiotics–including methicillin–have been increasingly isolated no only in hospital settings, but also in the community. Vancomycin-resistant strains have also been isolated, but are not yet widespread. It was recognized almost 25 years ago that the S. aureus yellow pigment consists of a number of carotenoids, similar to those produced in carrots and other fruits and vegetables. Studies of these carotenoid pigments have revealed their free-radical scavenging properties, protecting cells and tissues from the damaging effects of free radicals and singlet oxygen. (In other words, they’re antioxidants). Interestingly, one mechanism by which phagocytic cells of the host immune system destroy pathogenic invaders is via release of reactive oxygen species. Do these bacterial carotenoids protect S. aureus against damage initiated by the host immune system?

(Continued at Aetiology)

plosMarques.jpg Review of: Marques et al., “Emergence of Young Human Genes after a Burst of Retroposition in Primates.” PLoS Biology 3(11):1970-1979.(Synopsis on PLoS Biology)

November’s issue of PLoS biology has several papers of evolutionary relevance.

  • Richard Robinson gives a nice review of some current thinking about abiogenesis.
  • The evolution of “genetic robustness” is explored in a paper from Paul Turner’s lab.
  • A paper by Sabeti ET al. demonstrates that the evolution of a disease resistance locus in humans, thought to have been under strong recent selection, cannot actually be distinguished as non-neutral.
  • Mating preferences in fruit flies were shown by Rundle ET al. to evolve as a side effect of selection in divergent environments.

In addition, this very elegant paper describes some surprising results relating to the evolution of new genes in humans.

The ACLU-PA blogSpeaking Freely” is reporting that Judge Jones is probably going to hand down his decision next week. Trust me, those ACLU guys are close to the source.

Over on the NCSE Kitzmiller website, I have finally gotten a chance to OCR and upload Barbara Forrest’s supplementary expert report in the Kitzmiller case. This document was originally filed under seal, but became public when introduced into evidence in open court. See the experts folder for all expert reports.

kong.jpg

“King Kong” opens today (Weds. Dec. 14th). While it would be gratuitous good fun to jump on the “Kong” bandwagon simply to ride the giant gorilla’s coattails, there is actually an on-topic reason to discuss this brutish Hollywood megastar today.

Tangled Bank #43

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With the appeal of the Cobb County disclaimer sticker being heard on Thursday, the Discovery Institute is trying to spin the case. Their spin contains obvious lies.

“Contrary to claims from the ACLU, the district court judge actually ruled that the sticker fulfilled a legitimate secular purpose,” said Dr. John West, Associate Director of the Center for Science and Culture at Discovery Institute.

I’m not going to beat around the bush. West is lying. As I documented earlier in the year, Judge Cooper in no way found that the sticker fulfilled a secular purpose. Judge Cooper ruled that the board had legitimate secular purposes, but he also ruled that the sticker did not fulfill those purposes, e.g.

the Sticker appears to have the purpose of furthering critical thinking because it tells students to approach the material on evolution with an open mind, to study it carefully, and to give it critical consideration. The other language on the Sticker, which states that evolution is a theory and not a fact, somewhat undermines the goal of critical thinking by predetermining that students should think of evolution as a theory when many in the scientific community would argue that evolution is factual in some respects.

(Selman v Cobb p24)

the Sticker also has the effect of undermining evolution education to the benefit of those Cobb County citizens who would prefer that students maintain their religious beliefs regarding the origin of life.

(Selman v Cobb p38)

See “For every setback, spin spin spin.” for more information.

Of course Casey Luskin can’t help but raise the polemics:

The decision is dangerous to democracy and has chilling implications for the free speech rights of scientists, educators, and citizens who are skeptical of Darwin’s theory. It needs to be overturned.

No one’s free speech is at stake here. The Cobb County School District and the Cobb County School Board are being sued in the case. Since both are entities of the government, neither have free speech rights. Private citizens do have free speech rights, and the only private citizens in this case are Jeff Selman and the other plaintiffs. Only in tin-foil-hat-land would the question of Selman v. CCSD affect the free speech of anti-evolutionists.

The blog of CourtArtist: going where cameras cannot has just put up a sketch of Day 2 of the Kitzmiller case. In the scene, the lead plaintiffs’ witness, Kenneth Miller, is being cross-examined by Robert Muise of the Thomas More Law Center. The CourtArtist blog is the blog of Art Lien, who says he is the NBC courtroom artist who usually covers the U.S. Supreme Court.

I just have to add that I think that is probably me in the background in the upper right-hand corner, with the glasses and red tie…

1924-07-22_textbook_row_near.pngAt some point during the last year I realized that nothing really ever changes in creationism, except perhaps the labelling. This probably occurred in-between the discovery that “intelligent design” originated in 1987 as a new label for the creationism just that year ruled unconstitutional in Edwards v. Aguillard, and watching William Buckingham testify at how personally offended he was that the Dover teachers dare teach just a little bit of the evolution that the Pennsylvania state standards required.

Sometimes, though, not even the labels change. Take the Cobb County “theory not fact” sticker which was stuck in every Cobb County biology textbook as a warning label against evolution. It is on my mind because, while it was been ruled unconstitutional in the January 2005 district court decision Selman v. Cobb County, the hearing for the appeal is scheduled for this week, Thursday, December 15.

Now, “theory not fact” policies are sometimes described as a “new” creationist tactic. But I recently came across some information which dates such policies straight back to good-ol’ days of the Scopes Era, the mid-1920’s, when men were men, monkeys were monkeys, evolution was in effect banned from the textbooks, no one was pretending that protecting Biblical literalism wasn’t the key issue, and William Jennings Bryan was barnstorming around the country decrying the evils of evolution.

The first “theory not fact” policy was in fact passed by the California State Board of Education in 1924-1925. The policy was adopted as – guess what – the Board’s accommodation to fundamentalists protesting the teaching of evolution in California. In 1925, the Board took this policy and applied it to textbooks, turning down those that dared treat evolution as anything more than a (colloquial) “theory.”

The newspaper stories from that day read like they are from The Onion. But they’re for real. Via the Historical Archives of the Los Angeles Times in the ProQuest database (subscription required – go visit your local university library), here is a quote from the July 22, 1925 issue of the Los Angeles Times:

I have posted a bunch of new material on the NCSE Kitzmiller v. Dover website. Almost all of the post-trial filings, responses, etc., are now online in the post-trial directory or the amicus directory. The shortest and sweetest filing is probably the Plaintiffs’ Response to the amicus briefs (PDF) of the Discovery Institute and the Foundation for Thought and Ethics. I quote the good bits here.

Also, on the NCSE front page there is a summary of Margaret Talbot’s excellent long review of the trial published in last week’s New Yorker. The drawing at left is the preview graphic for the full-page drawing that accompanies the print article; it depicts plaintiffs attorney Eric Rothschild cross-examining the star ID witness, Michael Behe. As the caption put it, Behe was cross-examined “with cheerful mercilessness.” I imagine that one will be going on Eric’s door.

Saletan on ID, Take 4.

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William Saletan of Slate writes occasionally about ID, and usually has some good insights. Here’s his latest:

Fantasy Island

The money shot:

This, more than monkey ancestors, is what alarms creationists. Larson lists the social ills they blame on the teaching of evolution: abortion, eugenics, homosexuality, effeminacy, divorce, communism, long hair. He’s been told that Phillip Johnson, the founder of the intelligent design movement, brought up cross-dressing three times in his most recent book. “And those are important issues,” Larson adds, trying to sound even-handed, but the journalists laugh. “It is important,” a colleague next to me whispers. “There’s a lot of shopping involved. You have to buy for two.”

Cross-dressing? I was taught all those other things in my homo-abortion evolution classes, including the fact that evolution leads inexorably to both socialism and laissez-faire capitalism at the same time, but I was never taught how to cross-dress. How could my home state of South Carolina ever have received an “A” while leaving out the cross-dressing?

Anyway, this is the fourth article that Saletan has written on ID in the last few years. Here are the earlier ones in chronological order:

Unintelligible Redesign

What Matters in Kansas

Grow Some Testables

I didn’t care much for the second one, but he makes up for it with the third one.

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