June 2006 Archives

More prion news

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Last fall, Andrea wrote an excellent piece on prions, and how they “contradict century-old biological assumptions and seem to defy the expectations of Darwinian evolutionary theory.” He gives an overview of prions and discusses their potential role in heredity. My interest in them, of course, comes from the diseases they cause. Over at Aetiology, I have a post up discussing a new Lancet paper on the prion disease, kuru, and its potential to act as a model for other human prion diseases (such as “mad cow”). The authors suggest two things: one, that the incubation period of so-called “mad cow” disease may be longer than previously thought, and two, that there may be “waves” of epidemic, determined partly by host genetics.

This is a guest appearance by Jim Downard. Jim’s essays are always thorough, rich in detail, and solidly substantiated. This is his first appearance on The Panda’s Thumb.

There were already several essays posted on this blog addressing the latest book by Ann Coulter. Jim reviews her book from an angle differing from the earlier posts by PT’s regular contributors. His discourse provides a crtitical analysis of essential details of Coulter’s screed.

One third of Ann Coulter’s latest bestseller, Godless: The Church of Liberalism, is devoted to raking “Darwiniac cultists” over the coals for promoting what she is certain is the false science of evolution. Unfortunately her roasting process was hampered by the fact that she forgot to get her fire lit first. Compulsively addicted to secondary sources, Coulter fails to comprehend even those, and exhibits consistent laziness when it comes to checking whether her meagre tinder could ever ignite. In the first part of a series that will examine all the antievolutionary assertions in her book, James Downard explores how Coulter fumbles issues relating to Michael Behe’s Irreducible Complexity claims.

Continue reading Secondary Addiction on Talk Reason

During the symposium on Teaching Evolution, on which I reported recently, someone asked why evolution denial was limited largely to the United States. If you count the Muslim world, then the question is off target; nevertheless, the US is unique among the European nations and their cultural descendants in the strength of its biblical literalist movement. I submitted that the fact may well be traced to the legacy of slavery. That response did not go over well, and someone noted that Europe had its slaves too.

I looked up slavery in the 2003 edition of Encyclopaedia Britannica. Yes, Europe had its slaves, but slavery in western Europe died out during the late Middle Ages. In Germany and Russia, it was replaced by serfdom, which some will consider only a modest improvement. Britain made the slave trade illegal in 1807, and as a direct result much of South America abandoned slavery somewhat afterward. The British abolished slavery in India in 1843 and later moved inland into the continent of Africa specifically to interdict the slave trade. As far as I could learn, no one besides the US fought a civil war over slavery.

I am in the process of leaving Georgia, but Georgia will never leave me. I feel that my time working on science activism with Georgia Citizens for Integrity in Science Education (GCISE) has benefited my state. It was through our efforts that the press learned what was being done to our science standards by the Georgia Department of Education (GADOE), and that the GADOE was lying about it. (My op-ed in the Atlanta Journal-Constitution was the first to bring it to light.) Because of GCISE’s vigilance, public outcry forced the GADOE to pass standards with descent support for evolution.

Over a year or so ago, a teacher came to us at GCISE, asking for help. Her administrators were trying to force her to compromise her teaching, and she was standing up to them. We provided what support we could, but in the end her best support came from the state standards. Now that she has retired, the NY Times is telling her story: Evolution’s Lonely Battle in a Georgia Classroom.

Ms. New was summoned to a meeting with the superintendent, Dewey Moye, as well as the principal and two parents upset about her teaching evolution. “We have to let parents ask questions,” Mr. Moye told her. “It’s a public school. In a democracy people can ask questions.”

Ms. New said the parents, “badgered, got loud and sarcastic and there was no support from administrators.”

Babs Greene, another administrator, “asked if I was almost finished teaching evolution,” Ms. New recalled. “I explained to her again that it is a unifying concept in life science. It is in every unit I teach. There was a big sigh.”

“I thought I was going crazy,” said Ms. New, who has won several outstanding teacher awards and is one of only two teachers at her school with national board certification. The other is her husband, Ward.

“It takes a lot to stand up and be willing to have people angry at you,” she said. But Ms. New did. She repeatedly urged her supervisors to read Georgia’s science standards, particularly S7L5, which calls for teaching evolution. …

Suddenly the superintendent was focused on standards. Mr. Moye called the state department’s middle school science supervisor and asked about evolution. “Obviously the State Department of Education supports evolution,” Mr. Moye said in an interview. …

Ms. New said that from then on, including the entire 2005-06 school year, she had no problem teaching evolution. “What saved me, was I didn’t have to argue evolution with these people. All I had to say was, ‘I’m following state standards.’ “

This is why strong science standards are so important for overwhelmed teachers. They give teachers an easy way to resolve curriculum issues in their favor. Of course, in an ideal world all teachers would have the time and patience to teach their parents and administrators about evolution. However, teachers will be the first to tell you that the world is not ideal.

I am glad that I was a part of the campaign to improve Georgia’s standards. And I hope that you will get involved in your state.

It looks like the case of six private school students against the University of California system will go forward to trial, as reported by Sean Nealon. The UC system sets course standards for admission, and has not approved certain courses, including biology, offered at the Christian private schools that the students attend. The students claim a violation of free speech and religious rights. The judge hearing arguments on UC’s motion to dismiss has said that he is leaning toward sending this one to trial.

Update: See also my post on the Austringer and Ed Brayton’s longer discussion on Dispatches from the Culture Wars.

Are Creationists Anti-Science?

In this recently posted interview, historian of science Ron Numbers said the following:

QUESTION: So, in a certain sense, doesn't this represent some sort of divide between religion and science?

MR. NUMBERS: To me, the struggle in the late 20th Century between creationists and evolutionists does not represent another battle between science and religion because rarely do creationists display hostility towards science. If you read their literature, you'll rarely come across an anti-scientific notion. They love science. They love what science can do. They hate the fact that science has been hijacked by agnostics and atheists to offer such speculative theories as organic evolution. So, they don't see themselves as being antagonistic to science any more than many of the advocates of evolution - those who see evolution as God's method of creation - view themselves as hostile to Christianity.

In this post over at EvolutionBlog, I explain why Numbers is wrong. Creationists are, indeed, anti-science, their perceptions of themselves notwithstanding. Comments can be left there. Enjoy!

This is big.

The world’s leading scientists yesterday urged schools to stop denying the facts of evolution amid controversy over the teaching of creationism.

The national science academies of 67 countries - including the UK’s Royal Society - issued a joint statement warning that scientific evidence about the origins of life was being “concealed, denied, or confused”. It urged parents and teachers to provide children with the facts about the origins and evolution of life on Earth.

This is a nice foil to a recent post on the Discovery Institute’s “Evolution News and Views blog,” noting that their list of “dissenting scientists” has now exceeded 600 individuals, and touting that more international scientists are signing on:

(Continued at Aetiology…)

Joey Campana has developed a site based on the MediaWiki software called ResearchID.org. They made a point of noting that it opened, June 22, 2006.

That’s a mere four years and one day after I announced the opening of TalkDesign.org (TD) at the end of my talk at the CSICOP Fourth World Skeptics Conference. I also pointed out on that day that “intelligent design” had failed to produce on the promised scientific basis for ID, despite the assurances of Wedge document, Rob Koons, and William Dembski that that was priority one for the ID movement.

Let’s consider some of Campana’s welcome letter:

A major priority for ResearchID.org’s administrative team is to provide a place where investigation of intelligent design can take place absent from the tumult of politics and social polemics that surround the issue of ID. A principle focus of this effort to escape the rhetoric is developing a fulcrum of discussion, so that all sides can speak the same language, instead of talking past each other as participants in debates about ID tend to do. This non-polemical environment can allow for some accumulation of some of the “critical mass” that ID theorists mention when they speak of scientific research into a new idea.

Sounds nice. What I’d like to know is where these nicely-behaving non-polemical ID “theorists” are going to come from? I can see that it will be easy to simply say that any known ID critic is off-limits on the site (forgoing any argument about individual commitment to polemics) and you would still have a lot of possible people to step in and take up a skeptical stance. But what about ID advocates? If you exclude the polemical ones, then you have pretty much eliminated the well-known names of the ID movement. Who is going to step in and provide that measured, mature, and non-rhetorical voice for ID?

Anti-ID groups are now parasitical on the claims of ID for their existence. Unwittingly, they have become pawns and foils for ID theorists and researchers. The intelligent design community is in a position where we are setting the agenda, now all we have to do is to continuing bringing more meat to the table.

I think that there is a nugget of truth here: scientists are primarily reacting to anti-science movements. I’d love to do my job well enough that I would be looking for something else to do. And I can find plenty of other stuff to write about here on PT. But other than the nugget of reaction rather than pro-active measures on the part of the scientific community, this bit of text from Campana is completely out in the weeds. One cannot “continue” to do what one has never done before.

Hi, everyone! This is Prof. Steve Steve blogging the Evolution 2006 meeting here on Long Island at SUNY-Stonybrook, home of Douglas Futuyma, Massimo Pigluicci, and other muckety-mucks of evolutionary biology like me. I am a special guest for the spiffy day-long symposium on the Kitzmiller v. Dover case that showed that the ID movement had no clothes, which of course I helped to win. Many of the experts and lawyers, as well as a plaintiff and reporter, are going to be speaking at the symposium.

My buddy Nick Matzke is also here, unfortunately that idiot forgot to bring a camera so this will be a picture-free blog by Prof. Steve Steve. If anyone else has a camera, don’t bother trying to find me at the meeting, because I am currently practicing my invisibility superpower and hanging out with the Invisible Pink Unicorn. Don’t believe me? Invisible Pink Unicorns and Invisible Prof. Steve Steves are not testable hypotheses, you say? Well, do you hold a B. Amboo Chair in Creatoinformatics at the University of Ediacara? Are you a J.D.-M.D.-quintuple Ph.D., seven-time Nobel nominee, often called the Izaak Walton of information theory and the Ulysses S. Grant of drinking contests? I didn’t think so. It takes special training, like mine, to understand IPU and IPU-like phenomena.

In case anyone is interested, there is an interview and article with and about Ron Numbers, historian of science and author of The Creationists, available at the U of Wisconsin. He offers a fairly standard perspective on the creationism wars, one that is commonly expressed here…but I have to confess, I disliked it intensely, and think it represents much that is wrong in the usual conciliatory approach too many people favor.

(Yes! That is an invitation to argue!)

Harriet, Sweet Harriet

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The last known living acquaintance of Charles Darwin, Harriet the Galapagos Tortoise, died recently after a short illness. She was only 176. Some IDists are so desperate for good news – and evidently so superstitious – they are hopefully interpreting Harriet’s passing as an omen (see “A presage of another death?”). Others might note that the fact that Darwin’s pet tortoise was an international celebrity, whose death was widely mourned, is not exactly encouraging news for the evolution-deniers out there.

Old spiders

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web_in_amber_tease.jpg

Two short articles in this week's Science link the orb-weaving spiders back to a common ancestor in the Early Cretaceous, with both physical and molecular evidence. What we have is a 110-million-year-old piece of amber that preserves a piece of an orb web and some captured prey, and a new comparative study of spider silk proteins that ties together the two orb-weaving lineages, the Araneoidea and the Deinopoidea, and dates their last common ancestor to 136 million years ago.

Araneoids and Deinopoids build similar looking webs—a radial frame supporting a sticky spiral—but they differ in how they trap prey. Deinopoids spin dry fibers that they fluff into threads that adhere electrostatically to small insects; Araneoids secrete glue onto the the strand, which takes less work (no fluffing), and is much more strongly adhesive. The differences are enough to make one question whether there was a single origin of orb weavers, or whether the two groups independently stumbled on the same efficient form of architecture.

Continue reading "Old spiders" (on Pharyngula)

On Wednesday, June 14, 2006, the Episcopal News Services reported that the bishops had approved Resolution A129 Affirm Creation and Evolution. The Resolution reads as follows:

Resolved, the House of_____ concurring, That the 75th General Convention affirm that God is Creator, in accordance with the witness of Scripture and the ancient Creeds of the Church; and be it further,

Resolved, That the theory of evolution provides a fruitful and unifying scientific explanation for the emergence of life on earth, and that an acceptance of evolution in no way diminishes the centrality of Scripture in telling the stories of the love of God for the Creation and is entirely compatible with an authentic and living Christian faith; and be it further

Resolved, That Episcopalians strongly encourage state legislatures and state and local boards of education to establish standards for science education based on the best available scientific knowledge as accepted by a consensus of the scientific community; and be it further Resolved, That Episcopal dioceses and congregation seek the assistance of scientists and science educators in understanding what constitutes reliable scientific knowledge.

For those of you who may be unfamiliar, over at Scienceblogs.com they have a weekly feature: Ask a Scienceblogger. Previous questions have included topics as diverse as “brain drain” and the future of the human race (you can view the archives here). This week’s question is one that I thought might interest folks here, as I and others regularly write about science education (and how to improve it). The question is (as noted in the title), “What makes a good science teacher?” I have my thoughts up over at Aetiology, and you can find other musings posted at this link for the next week.

Tangled Bank #56

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The Tangled Bank

While I was out playing all day yesterday, a new Tangled Bank appeared at Centrerion. I'm so late in my announcement that you've probably all read it already, but if you haven't, there's much science writing to occupy you for a while.

PZ Myers has posted a well written article on deep homologies in the pharyngeal arches which link the thyroid/parathyroid glands in humans to the gills in fish.

This is an excellent example of how science contributes to our scientific understanding. Could someone remind me: How again does Intelligent Design explain all this? ‘Poof’?…

Random Search and No Free Lunch

In his book “No Free Lunch”, Dembski argues that, based upon the No Free Lunch Theorems, finding an optimal solution via “random search” is virtually impossible because no evolutionary algorithm is superior to random search. And while various authors have shown the many problems with Dembski’s arguments, I intend to focus on a relatively small but devastating aspect of the No Free Lunch Theorems.

First I will explain what the No Free Lunch Theorems are all about, subsequently I will show how Dembski uses the No Free Lunch Theorems and finally I will show that the No Free Lunch Theorems show how a random search, perhaps counterintuitively, is actually quite effective.

A little while ago Sitemeter recorded PT’s three millionth visit. We are seeing a bit of a fall-off in traffic since the Kitzmiller v. DASD case time, as are many sites that deal with the creation/evolution issue. KvD was an extraordinary spur to interest, which makes it all the more important to raise awareness afterward.

Following the Scopes trial in 1925, popular belief held that the antievolutionists had suffered a defeat and were in retrenchment. This was not so. In the next few years, over twenty other states passedproposed legislation similar to Tennessee’s Butler Act, with the effectintent of banning the teaching of evolutionary biology in public schools in those states.(*) Two states, Mississippi and Arkansas, actually passed the antievolution measures, making the intent take the force of law.

We need to keep in mind that the anti-science threat has not been rendered impotent by the outcome of the KvD trial. The contributors to PT will continue to keep you informed of developments as we see the new strategies for opposing effective instruction in evolutionary biology emerge.

(*)Thanks to Nick Matzke for pointing out my error of recall concerning proposed and passed.

Argento v. Coulter

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York Daily Record columnist Mike Argento, who some say is H.L. Mencken reincarnate, takes on Ann Coulter here.

The BBC is reporting that a Cardiff University study is revising the numbers of pandas left in the wild upward – and it all has to do with panda poo.

“A panda can defecate 40 times a day so there’s loads of poo to find,” said Prof Bruford.

“They also secrete a mural layer which gives an insight into the cells in their guts and we can extract their DNA from it.

“When we found the same profile in a number of different locations at different times, it showed how mobile the pandas are,” he said.

The good news is that there are apparently more pandas left to leave those poo samples behind than was previously known. But who knew that it could be so dangerous to hunt the wild panda poo?

“The mountains are an absolutely wonderful place but it can be cold and difficult in winter.

“Our PhD student nearly fell off a cliff trying to gather samples, he was having to hike up 2,500 metres.”

Oh, those ubiquitous, anonymous, and expendable Ph.D. students! Where would science be without them?

jefferts_schori.jpg

They've elected a new presiding bishop, Katharine Jefferts Schori. You have to look at her biography to see why I'm even mentioning a new religious leader:

As a scientist and an Episcopalian, I cherish the prayer that follows a baptism, that the newly baptized may receive "the gift of joy and wonder in all God's works." I spent the early years of my adulthood as an oceanographer, studying squid and octopuses, including their evolutionary relationships. I have always found that God's creation is "strange and wonderfully made" (Psalm 139). ...

The vast preponderance of scientific evidence, including geology, paleontology, archaeology, genetics and natural history, indicates that Darwin was in large part correct in his original hypothesis.

I simply find it a rejection of the goodness of God's gifts to say that all of this evidence is to be refused because it does not seem to accord with a literal reading of one of the stories in Genesis. Making any kind of faith decision is based on accumulating the best evidence one can find what one's senses and reason indicate, what the rest of the community has believed over time, and what the community judges most accurate today.

It's a good thing that article is loaded with Bible quotes and other religious nonsense, or I'd be tempted to become an Episcopalian. Oh, well, even with all the wacky mythological stuff, she still looks like one of the good ones. Congratulations, Dr Jefferts Schori! While I'm not about to join a church, you do exhibit the kind of sensible perspective on the real world I'd like to see much, much more of in religious leaders…although, looking at the comments here, some Christianists are less than thrilled with the election of a rationalist to head a church, while others seem to be enthusiastic.

(via Kynos)

Seattle Adventures

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Dr. Reed and I are at the University of Washington, Seattle this week attending the Summer Institute in Statistical Genetics.

Anybody got suggestions for what we can do with our down time? We are staying on campus and don’t have a car.

Random Nonsense

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Over at Uncommon Descent William Dembski is linking to the random mutation site with approval. Claiming to be a “ Darwinian Evolution Experiment”, all it is is a simple random mutation generator. To be “Darwinian”, a system has to have selection as well. No selection, as in this case, well, it’s a waste of space. So why is Dembski linking to a site that he knows is a attacking a strawman version of evolution? Maybe its a bit of street theatre to distract people from the fact that he is happy with Ann Coulters appalling book, you know, the one where she falsley accuses honest scientists of fraud?

If you want to see a real Darwinian Evolution Experiment pop over to Zachriel’s Word Mutagenation and Phrasenation pages, where mutation and selection is used. Not only only do you get to evolve plain English words and phrases (the thing that the random mutation site claims you can’t do), you get to look at the code and see how it is done! Extra cool. If you are hankering for an old style Dawkins Weasel program, I maintain an archive here.

The following posting is based on a response I provided to Allen MacNeill on his excellent blogsite. In addition to much needed checking of grammar and spelling, I also have added additional content and/or revised the argument for clarity.

Avid readers of Pandasthumb may remember that Allen MacNeill is a Cornell professor who will be teaching an Intelligent Design course this summer. The course in question is: BioEE 467/B&Soc 447/Hist 415/S&TS 447: Seminar in History of Biology, and has a blogsite. The first class will start June 27, 2006.

In the posting, to which I responded, Allen shows the many problems in one of Salvador Cordova’s postings. Sal is an avid ID activist and defender of Dembski and his postings can be ‘admired’ at Uncommon Descent. Sal stated that ““There are many designed features in biology that make no sense in terms of natural selection but make complete sense in terms of design.””

As Allen shows, this is a very flawed statement. In my response I make an attempt to explain in straightforward terms why Intelligent Design’s approach is flawed and makes ID scientifically vacuous or in other words, void of content.

PvM Wrote:

Excellent points Allen. ID proponents seem to be quick to claim that science is using ID’s approach to detect design but on closer scrutiny these claims fall apart quickly.

ID is inherently a claim based on ignorance (elimination) and while it uses some ‘fancy sounding’ terms like complex specified information, the terms are used in a manner which conflates ID’s terminology with how science uses such terminology.

Ann Coulter: Clueless

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Ann Coulter is a “provocative” American conservative columnist (more what we Australians would call a “Shock Jock”) who has written a book titled “Godless: the Church of Liberalism”. Four of her chapters (8-11) are on evolution. Now, we know Coulter is going to be provocative, and no-one expects these chapters to follow the guidelines of the Journal of Molecular Evolution, but within the limitations of a popular book by someone who is not a biologist, how does she handle evolution?

Badly; really, really badly. As PZ Myers has just posted, she basically repeats every Creationist canard ever produced (she does the no transitional fossils argument on page 216), and even some that the creationists themselves have since abandoned such as the tautology argument (page 199). What she doesn’t get wrong is badly misrepresented. Behe, Dembski and Berlinksi are thanked fulsomely for their help with the evolution section (see Acknowledgments, page 303); they should hang their heads in shame.

I've now read all of the science-related (that's applying the term "related" very generously) stuff in Ann Coulter's awful, ghastly, ignorant book, Godless, and it's a bit overwhelming. This far right-wing political pundit with no knowledge of science at all has written a lengthy tract that is wall-to-wall error: To cover it all would require a sentence-by-sentence dissection that would generate another book, ten times longer than Coulter's, all merely to point out that her book is pure garbage. So I'm stumped. I'm not interested in writing such a lengthy rebuttal, and I'm sure this is exactly what Coulter is counting on—tell enough lazy lies, and no one in the world will have time enough to correct them conscientiously. She's a shameless fraud.

What to do? Well, we can't take apart the whole thing, but what we can do is focus on individual claims and show that Coulter is outrageously wrong—that she has written things that indicate an utter lack of knowledge of the subject. Some of us at the Panda's Thumb are going to be doing just that—look there later for more—and what I'm going to do here is address one very broad claim that Coulter has made repeatedly, and that is also common to many creationists.

That claim is that there is no evidence for evolution. I know, to anybody who has even a passing acquaintance with biology, that sounds like a ridiculous statement, like declaring that people can live on nothing but air and sunlight, or that yeti are transdimensional UFO pilots. Yet Coulter baldly makes the absurd claim that "There's no physical evidence for [evolution]", and insists in chapter 8 of her new book that there is "no proof in the scientist's laboratory or the fossil record." This is like standing outside in a drenching rainstorm and declaring that there is no evidence that you are getting wet.

Continue reading "Ann Coulter: No evidence for evolution?" (on Pharyngula))

A few days ago, on June 12, 2006, I attended the second, more-or-less annual symposium on “Teaching Evolution: Meeting the Challenge” at the University of Colorado at Boulder. The symposium was organized by Sarah Wise, a teacher turned graduate student in the Ecology and Evolutionary Biology Department (EEB), along with fellow graduate student Mike Robeson and Cathy Russell of the university’s Science Discovery unit. It was aimed at public school and college teachers, including elementary-school teachers. The symposium’s purpose was to “feature a full day of practical one-hour workshops and panel discussions on Teaching Evolution, interspersed with opportunities to interact informally with other participants. Additionally, resources for teaching evolution will be available to look at, including books, posters, software and other products to facilitate the teaching of evolution.” You may find information on the workshops here http://www.colorado.edu/eeb/EEBproj[…]rkshops.html and many of the materials presented here http://www.colorado.edu/eeb/EEBproj[…]sources.html

Approximately 70 people attended the symposium. Of those, approximately 50 % were high school teachers, 15 % were teachers from middle or elementary levels, 25 % were university faculty, staff, or students, and 10 % were from other scientific organizations such as the Denver Zoo and the Boulder Open Space department. In a survey given in conjunction with the symposium, 57% of respondents reported that they self-censor their teaching of evolution at least somewhat and/or receive indirect pressure to avoid teaching evolution from their school or community. I do not have any further information, but we may note that only 65 % of the respondents were school (noncollege) teachers, so the fraction that self-censors or receives pressure not to teach evolution may be as high as 85-90 %.

Last year, I wrote a post called From Darwin to Hitler, or not? This post discussed the book From Darwin to Hitler by historian Richard Weikart, who just happens to be a Discovery Institute fellow. The thesis of the book is that Darwin and his ideas – common ancestry and natural selection – somehow led to Hitler and Naziism, although the logic connection between the two sets of ideas is extremely murky. Weikart’s book has been used by the Discovery Institute (see e.g. here), ARN (see the description of the new video – also look carefully at the tasteful video cover, posted at left), and other creationist groups to promote exactly this idea, which creationists had already been promoting for decades anyway, just without an official historian behind them.

While it is tempting, and I think legitimate, to dismiss the whole thing as a severe expression of Godwin’s Law, there are more sophisticated criticisms. My major points in my post were that (a) Weikart goes out of his way to bash and dismiss the “Haeckel to Hitler” thesis promoted by an earlier historian (Daniel Gasman), noting among other things that Haeckel was a pacificist, but (b) Haeckel has much more direct links to Naziism than does Darwin – Haeckel was closer in time, location, idealogy, promotion of eugenics, influence on Germany in the early 1900s, etc; therefore (c} Weikart’s Darwin-to-Hitler thesis is even sillier than the Haeckel-to-Hitler thesis that Weikart himself criticizes. But I’m just a blogger.

Cordova Steps In It

Over at Uncommon Descent, Salvdor Cordova offers this amusing essay about why ID is a far more useful framework than evolution for scientific research. I'm sure everyone will be shocked to learn that his argument is, well, not correct. I've posted a full reply over at EvolutionBlog. Comments can be left there. Enjoy!

Never underestimate the ID advocates’ propensity for wishful thinking. Bill Dembski has just informed his acolytes that “International interest in ID is growing.” (bold in the original). The reason? Well, according to Dembski, Australians search for “intelligent design” via the Google engine at 6 times the rate per person of their American counterparts. The Danes, a whopping 20 times as much!

Before you start thinking that something is rotten in Denmark, and planning a moral boycott of delicious jelly-filled pastries by relabeling them “Darwin rolls” or something, think again. The only rotten thing here is Dembski’s understanding of how the comparative Google searches are tabulated, despite the fact that the information is clearly shown on the Google site.

dentalium_polar_lobe.gif
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The diagram above shows the early cleavages of the embryo of the scaphopod mollusc, Dentalium. You may notice a few peculiarities: the first cleavage is asymmetric, producing a cell called AB and a larger sister cell, CD. Before the second division, CD makes a large bulge, called a polar lobe, and it almost looks like it's a three-cell stage—this is called a trefoil embryo, and can look a bit like Mickey Mouse. The second division produces an A, a B, a C, and a D cell, and there's that polar lobe, about as large as the regular cells, so that it now resembles a 5-cell embryo. What's going on in these animals?

Continue reading "Polar lobes and trefoil embryos in the Precambrian" (on Pharyngula)

An AP story this morning discusses a new fossil find in China of an early bird, Gansus, from about 100 million years ago. The headline reads “Bird fossils in China called a missing link in evolution.”

Now this is a neat find, and I urge you to read the story, but I’d like to discuss the headline as an example of the way the popular press mischaracterizes science sometimes, and adds to public misconceptions about evolution.

Over at Darwin Central, some impressively-obsessed blogger has attempted to rate 50 creationist websites on their propensity to use commonly-mined quotes. Methods: (1) start with the quotes in the Talkorigins.org Quote-Mine Project; (2) search for those quotes on the creationist websites; (3) somehow put it all in a relational database; (4) tabulate.

The winner, with 75 of the 158 quotes listed at Talkorigins, was Anointed-one.net/. It is followed by a couple of sites that are primarily creationist quote-mine collections (studying the evolution of such collections would be an interesting project). Answers in Genesis (#9), the ICR website (#8), and Harun Yahya (#5) make the top ten list, but the famous Velikovskian Ted Holden, aka The Inimitable One, beats them all with his website bearfabrique.org (#4). The Discovery Institute comes out at a disappointing #30, but there is a lot of competition out there, and they spend a lot of their time trying to dumb down the education of U.S. children.

All in all, this is a rather impressive effort, and another example of the kind of “creoinformatics” that the web and modern technology makes possible.

Creationist amorality

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Here's a gorgeous educational site, The Virtual Fossil Museum. It has a nicely organized set of fossil galleries, all intended for use by the education community, and all appropriately credited. This is the way it is supposed to be done.

Unfortunately, that's not the way creationists do it. Here's a case of creationists caught red-handed in blatant theft.

Continue reading "Creationist amorality" (on Pharyngula)

Today’s lesson is about publishing. Not writing. Not scholarship. Just the act of getting words out in front of other people without any sort of tedious labor behind them. Oh, and most important, these words will have your name in the byline. The case study is Creationism - How Entropy challenges Evolution Theory by B. G. Ranganathan. It went up on the “Best Syndication” weblog on the 13th. Along with the featured article, you get the opportunity to buy Ranganathan’s book offering, Origins?, from Amazon, as it is prominently displayed in the left sidebar.

The first step is to pick your topic. When it comes to antievolution, there are three things going for you. First, there is a plethora of material to be recycled without risk. As antievolution advocates sometimes point out, their ideas have deep roots, tracing back at least to certain Greek philosophers. Recognizable material of somewhat more recent vintage (and thus easier to incorporate into a pseudo-essay that passes as modern) comes from authors like the Reverend William Paley. Authors such as George Macready Price and Henry M. Morris assembled many of the arguments together in various books. And, as I said, nobody cares if you steal it. In fact, others will be confused if you provide complete references and trace back claims to sources. That just isn’t done as a matter of course in this field, and, of course, it pays to pick up the social gestalt of your new career.

Second, there is a market. As Harvard Lampoon noted, it’s the sort of market whose pant’s pockets display the sort of scorch marks produced only by large quantities of spontaneously combusting cash. Antievolution, if it accomplishes nothing else, moves money around the marketplace from folks who read the same material over and over to those who, like you, are now learning how to be the sort of person who transfers material from old sources and puts your name over the top.

Third, the mere act of repeating various hoary old chestnuts will give you a solid sense of community. Others who are doing just as you do will welcome the opportunity to come to your defense if someone criticizes you. It gives them something to do other than look for more things to recycle. You will quickly learn to do this, too. Of course, the stances taken are also all borrowed from earlier writers, so it just comes down to copying slightly different parts of the usual sources in order to label and dismiss critical forays.

Babu Ranganathan has this down pat. Let’s take a look at his effort and see where he got his material.

(Continue reading… on the Austringer)

PT readers may recall Jack Krebs’s post from May that recounted the behavior of Kansas State Department of Education Director of Communications David Awbrey at the Kansas City Press Club on May 4, 2006. To summarize, Krebs caught Awbrey asserting that evolution and science were just atheistic metaphysics, and, according to Awbrey, so were dinosaurs:

Anyone see the origin, anyone see the Big Bang, anyone see the dinosaurs? These are all metaphysical speculations by people who look at the same evidence and disagree with what they see.

Krebs later challenged Awbrey at the forum, and Awbrey denied these statements, but Krebs taped the whole thing and posted the quotes and recordings here on PT.

Well, fast forward a month, and now Awbrey has resigned after only six months on the job. Coincidence? We report, you decide.

Hat tip to Red State Rabble.

The early word is that PT contributor Reed Cartwright (real webpage) (alter ego) has, despite being a PT poster, helping to construct the PT blog, and spending his time annoying creationists, managed to PASS his dissertation defense. Watch out world, here comes Dr. Cartwright.

I believe Prof. Steve Steve is planning the all-night bash in Athens as we speak. I wonder how spatially explicit population genetics sounds after a few pints of bamboo beer?

Media alert!

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We have some interesting events coming up on TV and radio: two interviews that pit the wise against outrageous fools.

  • Tonight (Wednesday), Jay Leno is having two special guests on his show. Ann Coulter, who is plugging her new anti-evolution, anti-freethought, anti-thought book of hate, is going to be on, and most wonderfully, with her will be George Carlin, of the famous irreverent irreligiousness and sharp, searing wit. Let's hope for fireworks.
  • Friday, at 3:15 ET, on NPR's Science Friday…it's Chris Mooney, author of The Republican War on Science and advocate of good science, will be paired up with Tom Bethell, author of The Politically Incorrect Guide to Science, who most infamously said, "Darwin's theory, I believe, is on the verge of collapse…Natural selection was quietly abandoned, even by his most ardent supporters, some years ago."

These could be great fun. Tune in!

Updated with some missing text and edited for content June 15

A recent article in Physics Today discusses the search for SETI using optical detectors. On Uncommon Descent, Dembski claims that OSETI shows how the explanatory filter is used in sciences. Since Robert Camp already has shown why such a claim is inappropriate for SETI, I would like to explore Dembski’s latest claim as it applies to OSETI.

I will quote from the article to show how OSETI mimics the explanatory filter in the sense that it can generate false positives. Ironically, Dembski quotes the same passage, which suggests that Dembski accepts false positives for his explanatory filter, and which would render the filter useless.

OSET is, like SETI, an attempt to detect intelligently designed signals but unlike SETI ,which focuses on narrow band signals, OSETI relies on nanosecond optical pulses which it claims are more likely generated by intelligent sources because of the lack of known natural mechanisms that would generate such pulses.

Because no known astrophysical source could put out a bright nanosecond optical pulse, some SETI searchers have concluded that looking for signals from technologically advanced aliens is more promising with optical telescopes than with radio telescopes

If we find nanosecond pulses, we can’t lose,” says Horowitz. “If it’s not from an alien civilization, at least we will have discovered an astrophysical phenomenon that no one anticipated. Not a bad consolation prize.

Source: Physics Today, June 2006, http://www.physicstoday.org/vol-59/[…]-6/p24.shtml

In other words, if nanosecond pulses are found, science will be in a a ‘win-win’ situation since either the pulse indicates intelligent design or the pulse indicates a new astrophysical phenomenon. In other words, a design inference in OSETI, unlike the Explanatory Filter, still leaves open a natural explanation.

Over at Scientist, Interrupted there is an excellent review of a new book by Smithsonian paleontologist Doug Erwin. The review speaks of “the PT boundary” and “the PT mass extinction”, but, sadly for creationists, it is speaking not of the Panda’s Thumb, but the Permian-Triassic boundary. The PT mass extinction is the largest and most severe mass extinction recorded in the fossil record, and (unlike the KT boundary, due to a bolide impact), scientists have not reached consensus on what the the primary cause(s) were.

Erwin’s book is entitled Extinction: How Life Nearly Ended 250 Million Years Ago. Check out the review and the book.

From a post on KCFS News today: (You can listen to the actual speech there, if you wish - it’s only three minutes long.)

Today I spoke at the Kansas BOE meeting during the Open Forum about KCFS’s letter to the superintendents. My main points were:

  • The Board’s standards are seriously flawed.
  • The Writing Committee’s Recommended standards have been completed, and are much better than the Board’s standards.
  • KCFS believes that, based on the Dover criteria, the Board’s standards could be declared unconstitutional.
  • The state BOE and their standards can’t be directly challenged because the state standards are non-binding, but if a district adopts and implements the state standards, then they are the entity that is at legal risk.

Therefore, KCFS urges districts to reject the Board standards and adopt the Committee’s Recommended standards.

The last bulleted point above caught the attention of some reporters and audience members, who told me later they appreciated having this distinction pointed out: it is the local district who could pay for the Board’s constitutionally flawed standards, not the Board itself.

My colleague in Ohio, Dick Hoppe, calls this the “Dover trap.” The Board standards may embolden districts with creationist leanings to bring ID creationist material into the classroom and to invoke the Board standards as their justification. At that point, the local district will become a potential target for a lawsuit - a potential Dover situation for the district. Districts should be aware of this danger.

Evolution by gene loss

Sometimes it’s amazing just how little we know about the microbes around us. For precious few microbes, we know a good deal about virulence factors–genes and proteins that, when present, increase the severity of disease either in animal models or in humans (or both). However, much of this research has been done investigating acute infectious diseases, where one is infected, becomes ill, and gets better in the course of a few weeks to a month. Much less is known about factors that affect long-term (or chronic) infection. A recent study addressed one gap in this research, tracking the evolution of the bacterium Pseudomonas aeruginosa in chronically infected cystic fibrosis patients.

(Continued at Aetiology)

Today, June 13th, is primary day in South Carolina. Most of the would-be Democratic nominees are running unopposed, but the Republican slate is packed full for a number of races.

The race for state Superintendent of Education has no fewer than 5 candidates running for the Republican nomination. The SCSE page has the response of each candidate during a recent debate to the question of what they thought about teaching “alternatives” to evolution. Read the responses and see what you think. The two front-runners in the race are supposedly Karen Floyd and Bob Staton, and the winner of the nomination will be heavily favored to win the general election. You can read more about Floyd’s opinion on teaching evolution here. Staton is a bit harder to pin down. Most agree that he doesn’t feel strongly about the issue, and therefore his answers tend to be tactfully vague.

Also on the ballot today is Oscar Lovelace challenging incumbent Governor Mark Sanford.

There are three candidates running for Lt. Governor. Incumbent André Bauer is being challenged by Mike Campbell and Henry Jordan. The views on teaching evolution among the first two are not a matter of public record as far as I know, but Jordan has, shall we say, a rather unsubtle opinion. He also has complementary views on religious diversity.

Anway, if you are from South Carolina, please get out and vote. There are obviously other issues to consider, so choose your candidates carefully.

Antievolution, Nevada style

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Apparently the petition to amend the Nevada constitution to include various creationist objections to evolution is going to die for lack of signatures. Petition author Steve Brown, a Las Vegas masonry contractor, has stopped the signature gathering effort a week before the June 20 deadline. See the NCSE news story for more. Hat tip to Red State Rabble.

If you haven’t seen the text (PDF) of the petition, I have posted it below the fold. It is…unique in several ways:

Larry Laudan, philosopher of science and Senior Investigator at the Instituto de las Investigaciones Filosóficas, National Autonomous University of Mexico, is often quoted by ID activists in support of their claims about the demarcation problem. The demarcation problem basically is a philosophical argument about how to define what is and is not science. Larry Laudan strongly criticized the ruling by Judge Overton in McLean v. Arkansas Board of Education. Laudan argued that contrary to Overton’s decision creation science is in fact testable, tentative and falsifiable.

Laudan is also the author of “The Demise of the Demarcation Problem”, printed in Michael Ruse’s “But Is It Science?”. The Discovery Institute and its various contributors have made extensive use of Laudan’s position on the demarcation problem. Ironically, it seems that Larry Laudan holds some very strong opinions in this area. In an article called On Methodological Naturalism and Intelligent Design (or Why Can’t Lawrence VanDyke Leave Well Enough Alone?) Brian Leiter simply went down the hallway to talk to his colleague Laudan.

Leiter: I’ve not only perused Beckwith’s book, I’ve read large parts of it, and it might be said on VanDyke’s behalf that the book is, in many respects, as misleading as VanDyke’s review (Beckwith is a bit more careful on certain crucial points than VanDyke, to be sure–but a competent book reviewer might have noted, rather than parotting, Beckwith’s misleading claims). My colleague Larry Laudan is, needless to say, well beyond being amazed anymore by the gross misrepresentations of his views–and of issues in the philosophy of science–in law reviews and by proponents of ID. (Didn’t it occur to VanDyke that I might walk down the hall and point out his nonsense to Laudan? He just rolled his eyes and chuckled.)

Leiter continues to explain:

Sometimes serendipity presents you with an opportunity to educate those who are confused by the claims of Intelligent Design and somewhat unfamiliar with evolutionary theory. So let me start with the answer and then look at the question.

Genetic Programming (GP) has a proven capability to routinely evolve software that provides a solution function for the specified problem. Prior work in this area has been based upon the use of relatively small sets of pre-defined operators and terminals germane to the problem domain. This paper reports on GP experiments involving a large set of general purpose operators and terminals. Specifically, a microprocessor architecture with 660 instructions and 255 bytes of memory provides the operators and terminals for a GP environment. Using this environment, GP is applied to the beginning programmer problem of generating a desired string output, e.g., “Hello World”. Results are presented on: the feasibility of using this large operator set and architectural representation; and, the computations required to breed string outputting programs vs. the size of the string and the GP parameters employed.

Genetic Evolution of Machine Language Software Ronald L. Crepeau NCCOSC RDTE Division San Diego, CA 92152-5000 July 1995

The Results?

From Figure 5 it can be seen that this run achieved a correct output (fitness = 352) at about 150,000 spawnings (100 to 1200 generations). By about 450,000 spawnings, the agent was composed of less than 100 instructions. Ultimately, the agent size reduced to 58 instructions before the process was terminated.

Next question?

Nick in New Mexico

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We in New Mexico are honored to have PT’s own Nick Matzke as our guest this weekend.

Nick was in-studio on the NMSR Science Watch radio show today, and gave a gripping rundown of the Dover ID Trial from the inside… matzke.jpg KABQ 1350 AM Board Op Lindsey sets levels for Nick on the Science Watch radio show (Sat 10th)

AND, Nick is giving a FREE SPEECH tomorrow (Sunday, June 11th) at UNM’s Anthropology lecture hall.

COME ON BY!

It’s sponsored by CESE.

Singer and teleology

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Dembski argues, without supporting evidence, that when the natural processes of chance and regularity have been eliminated, that which remains should be called ‘Intelligent Design’. This definition presumes that ‘Intelligent Design’ is not reducible to natural processes, leading to the inevitable conclusion that Intelligent Design is about the supernatural.

In the early 20th century, Edgar Singer presented his thesis on mechanism and teleology. Krikorian read the following paper during the 1955 memorial meeting for Edgar A. Singer, Jr., at the University of Pennsylvania.

Since living beings are defined in terms of teleology, the laws that apply to them can be called teleological laws. These laws, as earlier noted, are statements of averages. It is because the laws are of this character that we may describe the behavior of living beings in terms of chance, spontaneity, and variability, and in some cases even of freedom.

Since behavioral sciences captures the behavior of intelligent, living beings in teleological laws which are expressed as a ‘law of averages’ or in other words, expected behavior, combined with chance, variability and spontaneity. Or to use Dembski’s terminology: reducible to regularity and chance. In fact, advertising, Amazon’s suggestions, all are based on predictable characteristics of intelligent life. In other words, the claim that intelligent design cannot be reduced to regularity and chance seems to go against common sense knowledge.

I wrote recently how evolution and phylogenetic analysis of HIV isolates has provided evidence that the progenitor to HIV jumped into humans in Cameroon or a nearby area. Obviously it’s a topic that’s interesting to me, but may seem a bit esoteric to some. RPM over at Evolgen has a new post showing another application of phylogenetic analysis to HIV that may be of interest to readers here, where infectious disease epidemiology meets CSI.

As I reported awhile ago, the Discovery Institute’s attempts to add “critical analysis” language to the parts of the South Carolina biology curriculum that deal with evolution have failed. The Board of Education did not add those changes, and the Educational Oversight Committee, led by creationist Sen. Mike Fair, finally conceded on that front and decided to accept the standards without the creationist language. Fair and his ally Bob Walker, who is a representative in the lower house, are apparently banking on a budget proviso requiring all textbooks adopted by the state to contain no less than 10% material be given up to 10% weighting for the promotion of “higher-order thinking skills”. In the Bizarro world inhabited by the Discovery Institute, where words mean the precise opposite of what they normally mean, this apparently implies creationism. Walker tried to get the House Education and Public Works committee to add an amendment to a bill to codify this somewhere other than in an obscure budget proviso, but that attempt failed miserably.

So that’s where things stand. But remember: The Discovery Institute exists on Planet Bizarro. In their world, things are the opposite of what they seem:

South Carolina Set to Join Four Other States Calling for Critical Analysis of Evolution.

Columbia, SC – The South Carolina Education Oversight Committee (EOC) will vote Monday, June 12, on whether to give final approval to science standards for biology that require students to summarize how scientists “investigate and critically analyze aspects of evolutionary theory.” The standards were approved unanimously by the South Carolina Board of Education on May 31. Four other states (Minnesota, Pennsylvania, Kansas, and New Mexico) already have science education standards encouraging critical analysis of evolution.

Back here on Planet Earth, the Board of Education did not add the “critical analysis” language to the curriculum standards, and the EOC cannot accept standards containing that language without the Board of Education adding them first. But when declaring victory, why let a little thing like defeat get in your way?

Edited to add: It was brought to my attention that the science curriculum does actually contain one sentence about “critical analysis” that was added a year ago, so the DI press release isn’t technically untrue. It is, however, grossly misleading in that the changes they lobbied for all throughout the first half of this year, which included adding “critical analysis” language to each and every indicator dealing with evolution, were rejected. It was these changes, not the one from last year, that created the impasse between the EOC and BOE. The EOC’s June 12th vote is noteworthy in that it will end this impasse with the Discovery Institute failing to get the changes they wanted.

While Intelligent Design remains unable to explain much of anything in science, evolution has identified another mechanism. PZ Myer already discussed this example of Genetic Accommodation and I would like to use this as another example of the scientific relevancy of evolutionary science versus the scientific vacuity of Intelligent Design.

PZ Myers Wrote:

Here’s some very cool news: scientists have directly observed the evolution of a complex, polygenic, polyphenic trait by genetic assimilation and accommodation in the laboratory. This is important, because it is simultaneously yet another demonstration of the fact of evolution, and an exploration of mechanisms of evolution—showing that evolution is more sophisticated than changes in the coding sequences of individual genes spreading through a population, but is also a consequence of the accumulation of masked variation, synergistic interactions between different alleles and the environment, and perhaps most importantly, changes in gene regulation.

The schedule for the special symposium on “Intelligent Design on Trial: Lessons from the Kitzmiller v. Dover creationism case,” on Monday, June 26, 2006 at the Society for the Study of Evolution meeting at SUNY-Stony Brook has been updated (see below).

Further update: Rob Pennock informs me that the symposium will be videotaped, with the intention of putting it on the internet after the meeting.

In other news, although some helpful suggestions have been made, I am still seeking housing for June 24-27, since I was invited only after dorm housing had closed. Like I said, I’ll pay my share and bring a sleeping pad or something. Surely there is a penniless grad student out there somewhere. Email me: matzkeATncseweb.org. (Update: found housing and received several kind offers. Thanks very much.)

Also, I just noticed that in just one day PT became the top google hit for “SSE 2006”, while the actual meeting website is ranked #6.

Tangled Bank #54

Remember the “we’re-creationists-and-proud-of-it” creationists? Well, despite the press that ID has been getting, the older sort are still around. Today, they’re discussing not the beginning of the universe, but the end. Evidently they don’t like “dark matter” and “dark energy”, explanations that astrophysicists have proposed to explain certain puzzling phenomenon like the fact that galaxies spin faster than the gravity from their observed stars seems to allow.

Now, I think it is perfectly reasonable to criticize these explanations on their merits – it is conceivable, for example, that dark matter doesn’t exist and that instead we need some new physics to describe gravity at the very coarse scale – see for example the latest on MOND (Modified Newtonian Dynamics) in New Scientist (plain text). And the answer to this question could impact our view of the eventual fate of the Universe – i.e., will we get a “Big Crunch” or not?

But I think the creationist solution to the problem leaves something to be desired:

Evolutionists accuse creationists of inventing a “God of the Gaps” to cover for their ignorance of true science. It would appear that the high priests of astrophysics have their own Gods of the Gaps, namely dark matter and dark energy. What will happen to the universe? It won’t be the Big Crunch or the Big Chill, but the Big Furnace: “But the day of the Lord will come like a thief, in which the heavens will pass away with a roar and the elements will be destroyed with intense heat, and the earth and its works will be burned up. Since all these things are to be destroyed in this way, what sort of people ought you to be in holy conduct and godliness, looking for and hastening the coming of the day of God, because of which the heavens will be destroyed by burning, and the elements will melt with intense heat! But according to His promise we are looking for new heavens and a new earth, in which righteousness dwells” (2 Peter 3:10-13).

Astrophysics, schmastrophysics!

Darwin and Medicine, redux

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The summer 2006 edition of Stanford Medical Magazine has devoted their issue to “The evolutionary war.” Being the alumni magazine of a medical school, of course they have an article on “Darwin in medical school.” It’s a nice overview, discussing a bit of the history of “Darwinian medicine” and the pros and cons of teaching it in an already over-scheduled medical school curriculum.

(Continued at Aetiology)

The mighty Kent Hovind has struck out.

On June 5th 2006, Hovind pled nolo contendere as charged to three counts: constructing a building without a permit, refusing to sign a citation and violating the county building code. Hovind was ordered to pay $225.00 per count. The plea brings to an end a 5-year battle over a $50.00 building permit. Hovind estimates he spent $40,000 in legal expenses on this case. Meanwhile, the property taxes for Dinosaur Adventure Land are in arrears in an amount of $10,338.36 ($4,955.23 for 2005 and 5,383.13 for 2003 and 2004).

In both criminal and civil trials in the United States, a plea of "nolo contendere" means that the defendant neither admits nor disputes the charge or no contest. It literally means "I do not wish to contend." Spiro Agnew famously approximated it as "I didn't do it, but I'll never do it again." This plea is only recognised in the U.S. No formal plea is required in civil matters where paper pleadings are used.

ID Legislation in Michigan

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We’ve got a sudden rash of ID activity here in Michigan. The MCFS board got word yesterday that the House Education Committee in Michigan was going to hold a hearing this morning on HB 5251, a bill that would require the teaching of all the major ID arguments in public school science classes. We had thought this bill was dead in light of HB 5606, which was signed into law in April. But the pro-ID language had been taken out of that bill, so the sponsors of 5251 have revived it.

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

In Is Intelligent Design Testable: A response to Eugenie Scott Dembski tries to defend ID against the observation that ID does not present any testable hypotheses. Eugenie Scott responded to Dembski in The Big Tent and the Camel’s Nose

Eugenie Scott Wrote:

In my talk, I wasn’t deploring the untestability of ID per se but the fact that its proponents don’t present testable models. I was referring to the fact that ID proponents don’t present a model at allin the sense of saying what happened when. At least YEC presents a view of “what happens”: the universe appeared within thousands of years ago, at one time, in its present form, living things are descended from specially created “kinds” from which they have not varied except in trivial ways, there was a universal flood that produced the modern geological features, and humans are specially created apart from all other forms. So what happened in the ID model?

If ID is interested in ‘teaching the controversy’ and informing students about good science, then why is it that ID activists have so far refused to take much of any stance on the ‘scientific’ claims by the young earth creationists?

Eugenie ends with the following observation and question

SSE 2006 meeting

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Update: just see the newer post for the revised schedule. (Update: I have added the info on the keynote speakers for June 26, and we are going to try and get the event recorded.) Alrighty, who is coming to the 2006 meeting of the Society for the Study of Evolution (SSE), the Society of Systematic Biologists (SSB), and the American Society of Naturalists (ASN), aka SSE 2006, aka Evolution 2006 at SUNY Stony Brook?

Well, it looks like I am going (Note: I may need to bring a sleeping bag and crash on someone’s floor, housing looks fully booked – see my note and contact info) – because someone or other recently realized I ought to be there for this:

Monday, 26 June – Sessions. Symposium title: Intelligent Design on Trial: Lessons from the Kitzmiller v. Dover creationism case. Organizers: Robert T. Pennock, Michigan State University and Brian Alters, McGill University List of Speakers

* Robert T. Pennock , Michigan State University, “The Ground Rules of Science” * Barbara Forrest, Southeastern Louisiana University, “On Being a ‘Hybrid Expert’: Detailing the Intelligent Design ‘Wedge Strategy’ in Federal Court” * John F. Haught, Georgetown University, ŸEvolution and Faith: “What is at Stake?” * Brian Alters, McGill University, “But is it Good Pedagogy?” * Brian Rehm, Kitzmiller Plaintiff & Current Dover School Board member, “From parent and teacher to plaintiff and director” * Kenneth R. Miller, Brown University, “Fossils, Genes, and Mousetraps - The 21st Century Case for Evolution” * Lauri Lebo, Lauri Lebo, Lead Local Reporter in Dover, “Beyond ‘He said, she said:’ How to be fair when the debate isn’t balanced.”

Format: Morning Session: 60 minute slots (45 minute talks / 15 min Q&A). Afternoon Session: (30 min, 60 min, 30 min talks, then 30 min joint Q&A). This will be a full day event.

Monday, June 26, 7:00-8:30 pm – SSE Education Committee Public Outreach Lecture

Speakers: Eric Rothschild & Steve Harvey, Pepper Hamilton LLP. Title: “In Defense of the First Amendment: An Up-Close Look at the Landmark ‘Intelligent Design’ Case of Kitzmiller v. Dover Area School District”

In other words, we’re getting the band back together!

Yesterday (June 5, 2006) Kansas Citizens for Science sent an open letter to the superintendents of Kansas public schools explaining why the current 2005 KBOE standards are seriously flawed, and suggesting that districts adopt the Recommended Standards developed by the science standards writing committee instead. We have asked that each superintendent distribute the letter to the district’s Board members also. I have included the whole letter below: see Recommended Standards on the KCFS News site for related information.

Read more of the story here.

A while ago I discussed the relevance of motive in determining whether or not something may have been designed. A good example of how this can be turned into a scientific concept is given in a paper submitted to Arxiv called “Message in the Sky”:

“It’s a crazy assumption that there’s a supreme being that wants to send us a message,” said Steve Hsu, an associate professor at the University of Oregon, admitting that believing in a message involves a leap of faith. “But, if you could create a universe in your laboratory, wouldn’t you want to leave a message inside?”

(Seed Magazine article)

Remarkably (or perhaps not) this ‘tongue in cheek’ paper has attracted Dembski’s attention. Remember that Dembski is still struggling with how an Intelligent Designer could inject information into our universe with zero energy:

Won for All

Last night, I had to read this book RPM mentioned. It's not very long—about 100 pages, counting a preface, an epilogue, and an afterward, and it has lots of pictures—but be warned: it's very inside baseball.

The book is Won for All: How the Drosophila Genome Was Sequenced(amzn/b&n/abe/pwll) by Michael Ashburner, and its subject is the rush to sequence the Drosophila genome in 1998-1999. It's a rather strange twist on what I expected, though. While the subtitle says "How the Drosophila Genome Was Sequenced," there is almost no science at all in the body of the book; instead, it's all about the people and the politics, with Ashburner flitting about from place to place, yelling at people and eating sushi. It's phenomenally entertaining.

Continue reading "Won for All" (on Pharyngula)

Zachary Moore, who describes himself as “ just an average Scientist-At-Large, specializing in molecular biology” and who “… dabble[s] in many interests, including religion, jeet kune do, the outdoors, cinema, tolkien, sasquatch, and homebrewing beer. “ has an interesting website called Evolution 101 with many excellent podcasts which can be downloaded from freethoughtmedia.com. Check also the transcripts of the shows as Zach’s blogsite

Creationists have considered the ‘mystery’ of the chirality of life a problem inaccessible to scientific explanation. Of course, science as usual takes little notice of claims to ignorance and has provided yet another explanation for the chirality of life.

Point in case, a recent paper in Nature shows that:

Chirality, the molecular version of right- and left-handedness, has intrigued chemists ever since Pasteur found mirror-image tartaric acid crystals. The synthesis of molecules in a single chiral form is usually achieved by using a chiral entity from the outset. But in some reactions the formation of a chiral product seems to be further amplified. Most current explanations implicate autocatalysis as the source of this asymmetry. An alternative mechanism is demonstrated this week. This new approach generates a strong bias towards one chiral form from a small initial imbalance, based on the equilibrium solid–liquid phase behaviour of amino acids. As this takes place in aqueous solution, the process might explain how a prebiotic world, with left- and right-handed molecules present in equal numbers, could turn into a living world where biomolecules favour one chiral form.

Editor’s Summary ‘Chemistry mirrors life’

The paper in question is:

Martin Klussmann, Hiroshi Iwamura, Suju P. Mathew, David H. Wells, Jr Urvish Pandya, Alan Armstrong and Donna G. Blackmond Thermodynamic control of asymmetric amplification in amino acid catalysis Nature 441, 621-623 (1 June 2006)

Based on the work by Dembski, this ‘researcher’ concludes that

So we are left to conclude that homochirality came about by some directed, non-stochastic mechanism

So let’s look at the ‘design inference’ in more detail

The Anti-Defamation League has put up the transcript of a fantastic speech given by Judge Jones back in February. Jones gives his perspective on what it was like to be the judge in the Kitzmiller case, and then uses it as a platform to talk about the larger issues of judicial independence, legal precendent, and separation of powers. It’s quite a read – I don’t think the creationists have yet realized how much they marginalize themselves with kneejerk attacks on a class act like Jones.

It’s always risky business to divine what the founding fathers might think about current developments, but I’m certain, I’m entirely certain, that by deciding the Dover case the way that I did, I performed my duties as a district judge in exactly the way that the founding fathers had in mind when they created the Federal Judiciary in Article III of the Constitution.

In fact, I will submit to you that had I decided the Dover matter in a different way, I would have then engaged in just the kind of judicial activism which critics decry. That is, to have ruled in favor of the School Board in this case based on the facts that I had before me at the conclusion of the trial, I would have had to have overlooked precedents entirely and thus impressed upon the facts of the case my sense or the sense of the public concerning what the law should be, and not what it is.

This is ad hoc justice based upon either my preferences or biases or the perceived will of the majority. Taken to its extreme, it is anarchy at any level that to rule in such a fashion represents the true work of an activist judge. And so the real criticism of my decision, and this is one which I will readily accept, is that I did not render an activist decision.

See also the NCSE news story summarizing other recent news coverage on Jones.

With the recent find of various additional transitional fossils, it may be relevant to revisit a ‘golden oldie’ written by Wesley Elsberry title Missing links still missing!? Talkorigins Post of the Month: February 1998. Although, given the number of transitional fossils, I doubt that many creationists feel brave enough to still make the argument that such transitionals are lacking.

Based on the arguments by Darwin, Elsberry derives an estimate for the expected number of transitional fossils:

Elsberry Wrote:

Let’s derive an expectation of ratio of transitional to non-transitional fossils from what Darwin actually said, shall we? Darwin stated that natural selection would work intermittently, and often only at long intervals.

On the other hand, I do believe that natural selection will always act very slowly, often only at long intervals of time, and generally on only a very few of the inhabitants of the same region at the same time. (CR Darwin, Origin of Species, 1st ed., p.153)

In Creationism by Any Other Name, Charles G. Lambdin reviews the Privileged Planet film and describes it as ‘a contemporary classic of pseudoscience’.

I have written many postings on the Privileged Planet. Lambdin is similarly not very impressed by the correlation of ‘one’ or coincidences argued to be ‘evidence for design’.

Lambdin Wrote:

The thesis of The Privileged Planet is no different than the classic case of Presidential coincidences: Abraham Lincoln was elected to congress in 1846. John F. Kennedy was elected to congress in 1946. Lincoln was elected President in 1860, Kennedy in 1960. Both of their last names have seven letters. Both of their wives experienced the loss of child in the White House. Both were shot in the head on a Friday. Both were assassinated by Southerners and succeeded by Southerners. Lincoln was succeeded by Andrew Johnson, who was born in 1808. Kennedy was succeeded by Lyndon Johnson, who was born in 1908. Lincoln’s assassin, John Wilkes Booth, has 15 letters in his name. Kennedy’s assassin, Lee Harvey Oswald, has 15 letters in his name. Both assassins were known by three names. Booth was born in 1839, Oswald in 1939. As I am unable to imagine otherwise, these coincidences are too great to have occurred due to chance alone, so there must be some Intelligent Assassin behind it. Thus runs the reasoning throughout The Privileged Planet.

Since Evolgen recognizes the importance of evo-devo, I'll return the favor: bioinformatics is going to be critical to the evo-devo research program, which to date has emphasized the "devo" part with much work on model systems, but is going to put increasing demands on comparative molecular information from genomics and bioinformatics to fulfill the promise of the "evo" part. I'm sitting on a plane flying east, and to pass the time I've been reading a very nice review of the concept of modularity in evo-devo by Paula Mabee (also a fish developmental biologist, and also working in a small college in a small town in the midwest…but rather deservedly better known than yours truly). In addition to summarizing the importance of the concept of modularity to evolution and development, the paper also does something I always appreciate: it summarizes the key questions that the modern evo-devo research program is working to answer.

Continue reading "Modules and the promise of the evo-devo research program" (on Pharyngula)

Casey Defines Creationism

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Casey Luskin, over at the Discovery Institute’s Center for the Renewal of Science and Culture, has taken the time to redefine creationism for us:

Despite Holden’s editorializing, ID is not creationism because creationism always postulates a supernatural creator, and/or is focused on proving some religious scripture. But intelligent design does neither.

I’d like to thank Mr. Luskin for taking the time to clarify that point. I’ll try to remember to keep in mind the non-religious nature of the Discovery Institute in the future.

Oh, and by the way, Casey, whatever happened to that old logo you folks had? It was a lot cooler looking than the new one. I’ve got a copy, in case you lost it:

Lawyer who helped win Dover case dies

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Lawyer who helped win Dover case dies

Joseph M. Farber was committed to civil liberties, an associate said.

Jun 1, 2006 — Joseph M. Farber, 34, of Narberth, who was a member of the team of lawyers who won a court decision barring the teaching of intelligent design, died of a brain tumor May 22 at home.

It can’t be said often enough that “nothing in biology makes sense except in the light of evolution.” Moving from physical characteristics–color, bone shape, the form of bacterial cells–to genetic characteristics in order to classify organisms–and infer phylogenies–was a giant advance. That the molecular characteristics confirmed what was known using physical characteristics was a breakthrough, and allowed for more sophisticated analyses of organisms that don’t have bones or other easily-observable physical features that allow for simple classification into groups: microbes. I’ve previously pointed out the utility of phylogenetic analysis in tracking the spread of pathogens. A new study on the origin and evolution of HIV employs a similar approach in order to elucidate the history of the virus in Africa.

(Continued at Aetiology).

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