July 16, 2006 - July 22, 2006 Archives

The State of ID Research

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How bad have things gotten for the ID folks? Well, they used to brag about all of the great discoveries waiting to be made by any biologist willing to take an ID perspective. Since that hasn't quite panned out, to put it kindly, they've lowered their standards a bit. If William Dembski's latest blog entry is to be believed, now you need only use a phrase like “sophisticated design principles” in a biology paper to have the ID folks claim you as one of their own.

I have the full details in this post, over at EvolutionBlog. Comments can be left there.

Myspace

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head.jpg Butterstick, my youngest, was talking the other day about this new website he found, Myspace. After checking out the site and seeing all the cool people I can be friends with, I decided to sign up.

So if you want to become my friend, an official Pandit, you can do so on Myspace.

Darwin writes -I think- above his first notebook sketch of an evolutionary treeDue to the Darwin Correspondance Project, the Darwin Digital Library of Evolution at the American Museum of Natural History Library, modern Darwin scholarship by people like James Moore, the AMNH Darwin exhibition, together with the web, amazing things are now possible if journalists get interested in taking a serious look at Darwin and reactions to Darwin.

An example is an hour-long program entitled “Evolution and Wonder – Understanding Charles Darwin” that is being broadcast on many public radio stations on Sunday and Monday. It is also available for online download in streaming or mp3 format at the program website, which includes a large amount of additional material.

Rather than re-invent the wheel I will quote the summary from NCSE news:

New Judge Jones Interview

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There is a new interview with Judge Jones in the July/August edition of the Pennsylvania Lawyer. The article is not available online, but I wanted to share some of the more interesting bits. As he did at the close of the trial and many times since, he offered a great deal of praise to the attorneys, particularly from the plaintiffs team:

In this case, however, it wasn’t simply a matter of everyone just doing their jobs. In Jones’ view, the lawyers performed exceedingly well.

”I think that some of the cross-examination was absolutely fabulous,” said Jones. “It will endure, and I think it will be excerpted for advocacy classes…. I would say, in particular, Eric Rothschild’s cross-examination of Professor [Michael] Behe – the intelligent design proponent – that might be as good a cross-examination of an expert witness as I have ever seen. It was textbook.”

That it was. If you want to read it, it begins here. I said at the time that it was one of the most devestating cross examinations I had ever seen. Aside from the testimony of Barbara Forrest, I thought that the Behe cross was the single most important turning point in the trial. It was during that cross that it was established, beyond a doubt, that ID is primarily an argument from ignorance. Behe continuing to assist that the scientific literature contains nothing to explain the evolution of the immune system even after admitting that he had not read an enormous portion of that literature could not have looked worse.

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

Gallagher gets it?

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The name “Richard Gallagher” may be familiar to some readers. Gallagher is the editor of The Scientist, and last year, somewhat naively suggested that the evolution/creation “debate” was actually a good thing (you can find the text of his editorial at this site). Both PZ and Jason Rosenhouse took him to task for the editorial (and Gallagher replied, and PZ shot back). The next month, New Scientist then published a number of letters responding to the editorial, and Gallagher also wrote a reply (republished here by the Discovery Institute). Gallagher ended that piece with this quote:

Critical thinking has no place in science class? Really? That bodes incredibly poorly for the future of science teaching. We’re shelving our best weapon against intelligent design, and I find it incredibly sad that scientists who support evolution so strongly would have us shield growing young minds from the “dangers” of critical thinking.

If that’s not dogma, I don’t know what is.

…which of course doesn’t really address the arguments PZ and Jason had put forth–no one wants to “shield minds” from critical thinking at all.

So, of course it’s a bit depressing to see an editor of a life science magazine make strawman mischaracterizations of his fellow scientists who approach the issue differently (and, perhaps, have spent a bit more time in the trenches than Gallagher has). But Gallagher’s editorial in the July issue (“Zealots for Science”) makes me think that, maybe, hopefully, he’s starting to get it.

(Continued at Aetiology)

In Chapter 6 of Darwin's Black Box, Michael Behe listed several immune subsystems that he considered irreducibly complex (IC), and therefore (according to him but no one else) unevolvable. One incredibly complex immune subsystem that Behe neglected to mention was the system that genetically modifies antibody genes during the course of an immune response. This system is largely responsible for our ability to generate stronger and faster resistance to subsequent infections, and is integral to why vaccines work. 3 recent papers used concepts in evolution to help characterize one of the most interesting and novel immunological genes discovered since the RAGs in the late 80s, a gene called activation induced deaminase (AID, pronounced as initials), a gene pivotal to antibody modification. Not only did these papers reveal interesting functional insights into AID, but also helped solidify a model for the origin and evolution of this system. Two of the articles come from labs instantly recognizable to most molecular immunolgists, but are totally unknown in ID/evolution circles. The third comes from a lab that most of the regulars here at the Panda's Thumb would immediately recognize, PT's own Andrea Bottaro.

The conservative pundit Peggy Noonan today published an opinion piece in the Wall Street Journal in which she blames confusion over global warming on – wait for it – climate scientists.

She writes:

…how sad and frustrating it is that the world’s greatest scientists cannot gather, discuss the question of global warming, pore over all the data from every angle, study meteorological patterns and temperature histories, and come to a believable conclusion on these questions: Is global warming real or not?

Yes, how sad. Except that the vast majority of scientists with any credibility have in fact come to the conclusion that global warming is real, and that it has a likely anthropogenic origin.

Coming to Life

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Books from Nobel laureates in molecular biology have a tradition of being surprising. James Watson(amzn/b&n/abe/pwll) was catty, gossipy, and amusingly egotistical; Francis Crick(amzn/b&n/abe/pwll) went haring off in all kinds of interesting directions, like a true polymath; and Kary Mullis(amzn/b&n/abe/pwll) was just plain nuts. When I heard that Christiane Nüsslein-Volhard was coming out with a book, my interest and curiousity were definitely piqued. The work by Nüsslein-Volhard and Wieschaus has shaped my entire discipline, so I was eagerly anticipating what her new book, Coming to Life: How Genes Drive Development(amzn/b&n/abe/pwll) would have to say.

It wasn't what I expected at all, but I think readers here will be appreciative: it's a primer in developmental biology, written for the layperson! Especially given a few of the responses to my last article, where the jargon seems to have lost some people, this is going to be an invaluable resource.

Continue reading "Coming to Life" (on Pharyngula)

.. and why you should care.

KCFS invites Panda’s Thumber’s from all over to visit us next week and get your fill of discussion of the science standards. Here’s what we’ve got planned so far:

“What’s the Matter With Kansas’ Science Standards, And Why Should You Care?”

A presentation by Jack Krebs President of Kansas Citizens For Science and Member of the Science Standards Writing Committee

Jack Krebs will speak on the meaning of the changes made to the Kansas science standards by the creationist majority on the Board of Education. You’re invited to attend the following talks. All are free and open to the public

If you can help advertise, download the appropriate flier and distribute it in any way that will help. Thanks.

Monday, July 24, 7-9 PM, at Johnson County Community Center, Carlsen Center, Room 211, College Blvd. & Quivira, Overland Park, Kansas flier

Thursday, July 27, 7-9 PM,, at Hutchinson Community College & Area Vocational School, Shears Technology Center, 1300 N. Plum, Hutchinson, Kansas flier

NEW - Friday, July 28, 7-9 PM, at St. Thomas Episcopal Church, 710 N Main St, Garden City, Kansas flier

NEW - Saturday, July 29, 1-3 PM, at Tomanek Hall, Room 106, Fort Hays State University, Hays, Kansas flier

Monday, July 31, 7-9 PM at Kansas City Kansas Community College - Performing Arts Center, 7250 State Avenue, Kansas City, Kansas. flier

See here for additional resources associated with these talks.

Sponsored by Kansas Citizens For Science www.kcfs.org

Information: Jack Krebs – 785-840-5113 [Enable javascript to see this email address.]

How do you make a limb? Vertebrate limbs are classic models in organogenesis, and we know a fair bit about the molecular events involved. Limbs are induced at particular boundaries of axial Hox gene expression, and the first recognizable sign of their formation is the appearance of a thickened epithelial bump, the apical ectodermal ridge (AER). The AER is a signaling center that produces, in particular, a set of growth factors such as Fgf4 and Fgf8 that trigger the growth of the underlying tissue, causing the growing limb to protrude. In addition, there's another signaling center that forms on the posterior side of the growing limb, and which secretes Sonic Hedgehog and defines the polarity of the limb—this center is called the Zone of Polarizing Activity, or ZPA. The activity of these two centers together define two axes of the limb, the proximo-distal and the anterior-posterior. There are other genes involved, of course—this is no simple process—but that's a very short overview of what's involved in the early stages of making arms and legs.

Now, gentlemen, examine your torso below the neck. You can probably count five protuberances emerging from it; my description above accounts for four of them. What about that fifth one? (Not to leave the ladies out, of course—you've also got the same fifth bump, it's just not quite as obvious, and it's usually much more tidily tucked away.)

Continue reading "Generic bumps and recycled genetic cascades" (on Pharyngula)

I wrote here that pili–long, filamentous surface molecules involved in adhesion and bacterial “sex”–had recently been discovered in gram positive organisms; pecifically, in group A and B streptococci (Streptococcus pyogenes and Streptococcus agalactiae, respectively), using a genomics approach. Though this publication is quite recent, this is a fast-moving area of research, as evidenced by two new papers which extend this earlier research into pili in the group B streptococcus (GBS).

(Continued at Aetiology)

Tangled Bank #58

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The Tangled Bank

The newest, niftiest, most fascinating edition of the Tangled Bank is now available online at Salto Sobrius.

Well, I’ll give Dr. Dino this: at least he is consistent in his wackiness. The latest from the Pensacola News-Journal:

Hovind’s attorney, Assistant Public Defender Kafahni Nkrumah, told U.S. Magistrate Judge Miles Davis at a hearing Monday that his client did not want to enter a plea because he does not believe the United States, the Internal Revenue Service and the U.S. Attorney’s Office “have jurisdiction in this matter.”

When pressed by Davis to enter a plea of either guilty or not guilty, Hovind said he wished to enter a plea of “subornation of false muster.”

”Subornation,” according to Webster’s Dictionary, means instigating another to do something illegal. “Muster” is an assembly, often for inspection or roll call.

When pressed by Davis, Hovind said he was entering a not guilty plea “under duress.”

First, I would just like to say that everyone here at PT would like to express their sympathies to the public defender assigned to Hovind. I suppose public defenders see all sorts of weird things, but Hovind will be a handful.

I attempted to gain a little more insight on what “subornation of false muster” is supposed to be – the poor reporter was obviously struggling. The Pensacola News-Journal‘s columnist, who was at the hearing, said it was “a defense I haven’t heard in 30 years of hanging around courtrooms.”

Over at Uncommon Descent, Dembski has quoted from a Times of London article titled "How man's best friend overcame laws of natural evolution." Over at Stranger Fruit (where you can leave comments) I wonder what all the fuss is about.

Listeria monocytogenes is a gram-positive, rod-shaped bacterium. It can be found in the environment as a soil inhabitant. However, it also can be a frequent contaminant of our food supply. As the latter, the bacterium is a significant public health concern, as it is capable of causing serious infections. Listeriosis (infection with Listeria) causes ~2500 serious illnesses and 500 deaths each year in the United States, and the hardest-hit are those with poor immune systems due to age (the very young and old), other immunocompromsing conditions (such as chemotherapy, organ transplant, or AIDS), and pregnant women. Once ingested, the bacterium is able to cross the intestine and spread throughout the body via the bloodstream, where it can attack organs and cause serious damage.

The very fact that it’s typically an environmental organism (rather than a solely pathogenic agent) likely accounts for some of its virulence and transmission. It’s able to survive a number of environmental stresses, including low temperature and high salt concentrations. Indeed, its ability to grow at relatively low temperatures is one way it evades our efforts to control it: it can grow in food even at refrigeration temperatures.

Listeria is particularly insidious as a cause of fetal death or other complications during pregnancy. Intrauterine infection can lead to preterm labor, spontaneous abortion, stillbirth, or serious–and potentially deadly–infection of the neonate. However, fairly little is known regarding exactly how this condition develops, or the mechanisms that lead to infection of the fetus. It has been thought that the increased susceptibility to infection with Listeria during pregnancy is largely due to a decrease in cell-mediated immunity that occurs as a result of pregnancy. This is a particularly attractive hypothesis for Listeria, which is an intracellular pathogen. A new paper in PLoS Pathogens examines this phenomenon in greater detail, using a guinea pig model of infection.

(Continued at Aetiology)

The primary election for the Kansas Board of Education is coming up on August 1. Everyone is following the election closely, because the creationists currently have a 6-4 majority on the board, but 4 of the creationists are up for reelection, while only 1 of the pro-science candidates is up for relection. Furthermore, in many places in Kansas, the Republicans are so dominant that the real fight is not between a Democrat and a Republican in the general election, but between a moderate Republican and a conservative Republican in the primary.

So, you can expect that the Kansas news will be heating up for the next two weeks. We here at PT will do our best to keep you in the loop, but here are some webpages and blogs based in Kansas that you should follow for the latest firsthand accounts:

Stand Up for REAL Science. This website, which I just found out about, is run by Kansas biology teacher Jeremy Mohn. He appears to be somewhat annoyed at the Discovery Institute’s irony-meter-busting “Stand Up For Science” campaign. It’s a nice looking site, and comes with his blog, An Evolving Creation, where he has already debunked one of the fables that the ID advocates are telling about the group Kansas Citizens for Science.

Earlier this week the Kansas state Board of Education unveiled a glossy pamphlet on the changes made to the Kansas science standards. Even though they claimed to just be including direct quotes from the standards, they in fact did some significant editorializing that supports the Discovery Institute and the Intelligent Design network’s campaign position that Intelligent Design is not included in the standards.

But the Kansas science standards do say that students should learn about ID, and that ID content ought to be in the standards.

If you want to read more about this new KBOE pamphlet, see State BOE aligns itself with Intelligent Design campaign in saying “No ID in standards at KCFS News.

However, here I would like to repost from KCFS News my analysis of the Board’s Rationale statement showing that indeed the Board does call for students to learn about ID. I know Nick Matzke posted on this topic earlier, but I wanted to present my take on the matter also.

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