March 25, 2007 - March 31, 2007 Archives

Three weeks ago I attended the the 2007 Drosophila Conference at the Philadelphia Marriott Hotel. RPM of evolgen was nice enough to allow me to stay in the hotel with him, sleeping on the floor and giving me the bed. RPM took losts of picture and has posted a four part series on his blog.

Steve Steve has the Smarch of his Life – Volume 1: Marriott Hotels Suck

Steve Steve has the Smarch of his Life – Volume 2: Visiting the Poster Session & Grabbing a Beer

Steve Steve has the Smarch of his Life – Volume 3: 12 Drosophila Genomes

Steve Steve has the Smarch of his Life – Volume 4: The Morning After

In 2001, evolution was poised to return to the the Kansas Science Standards. The Intelligent Design Network objected to them and proposed changes that would have left open the door to teaching creationism. Kansas Citizens for Science responded to their proposal, which was sent to all members of the state board. One might suspect the response to have been too parochial for anything other than Kansas creationism; one would be wrong: the response serves as a prototype response for many creationist arguments and works nicely as a reference for letters to the editor even today.

Find it below, after the fold. It is also available in PDF and RTF formats.

In 1999-2000, the Kansas State Board of Education was running their PR machine full-bore, trying to convince the public that the central organizing theory of modern biology and biotechnology was a dead idea. Creationist speaker after creationist speaker was flown into town to put on a dog and pony show. If you were a Young-Earth Creationist, you might have seen Duane Gish/Fred Whitehead nondebate. If you liked ID creationism, you might have seen Johnson or Wells. Back then, it was a very big tent.

Well, KCFS wasn’t going to take things lying down, so we thought we’d prepare a few flyers to inform the audience to help them be ready for the creationists when they arrived. One of those flyers, “Jonathan Wells: Who is He, What is He Doing, and Why?” turned out to be pretty important.

Fast forward to Spring 2005, after the creationists had taken over the state board of education again and ran roughshod over the accepted processes of curricular review. They rejected the recommendations of the experts who developed very good standards and held a show trial, in which evolution would be dragged before them to answer the tough ID creationists’ questions.

The details of the story are described elsewhere, but one of the “witnesses” was Jonathan Wells, who during his testimony claimed that he was not influenced by religion. Within the span of an hour, KCFS was able to print several copies of our Wells flyer to distribute to interested members of the press. The result was that in the following day’s newspapers, Jonathan Wells testimony and his quotations were seen in juxtaposition to each other, making of his credibility to journalists what those in the know had deemed of it for years.

Find the flyer on the flipside. It’s also available in RTF format. Please note that the DI has since changed their name from the Center for the Renewal of Science and Culture to simply the Center for Science and Culture. So clearly it’s no longer religious.

I’m sure you’ve seen the posts here at Panda’s Thumb or over at Scienceblogs about the Discovery Institute’s newest protégé, Dr. Michael Egnor. A professor of neurosurgery at SUNY-Stony Brook, Dr. Egnor has been pontificating on how “Darwinism” has nothing to offer to medicine; and indeed, that evolutionary biology has “hijacked” other fields of study. Mike has already aptly pointed out many of Egnor’s strawmen and intellectual dishonesties, so I won’t review them all. I’ve stayed out of the fray until now because I’ve had limited time and others have been handling it quite ably, but he keeps treading into (and butchering) my territory, so I just wanted to point out a few other things Egnor is waving away when he makes statements like this:

Preventing the emergence of resistant strains of bacteria is important work, but the insight that Darwinism brings to the problem – the unkilled ones eventually outnumber the killed ones – is of no help. We can figure that out ourselves. The tough work on preventing the emergence of resistant bacteria is done by microbiologists, epidemiologists, molecular geneticists, pharmacologists, and physicians who are infectious disease specialists. Darwinism, understood as the view that “chance and necessity” explains all biological complexity, plays no role.

Sigh.

Others have already addressed the blatant ignorance of this statement (spouted following a paragraph wherein he claims that the evolution of antibiotic resistance is just a tautology), so I’m actually going to leave the antibiotic resistance stuff alone for the time being. What I want to address instead are other areas where evolution is critical for insights into many of those fields Egnor mentions, especially since my own research is at the convergence of the first three he lists: microbiology, epidemiology, and molecular genetics.

(Continued over at Aetiology).

As I mentioned earlier, there’s a really interesting paper on mammal evolution in the latest issue of the journal Nature. The authors of the paper compiled a really fantastic sampling of molecular data that included data from about 99% of all currently known extant mammals. The data was then used to conduct an analysis that was by far the most comprehensive look at the molecular evolution of mammals ever undertaken. The researchers concluded, based on this analysis, that mammals diversified a lot earlier then was previously believed - so much so, in fact, that it seems to cast some doubt on how important the K-T mass extinction really was to mammal evolution.

The nature article is behind the subscription wall, unfortunately, but if you have access it’s a good read. (You can find the full citation at the bottom of the post.) They did some cool stuff, and got some cool results. How the results should be interpreted, on the other hand, is much more complex and will take a lot longer for scientists to work out.

Read More (at The Questionable Authority):

The mammalian tree is rooted deeply and branched early!

mammal_tree_sm.gif
(click for larger image)

All orders are labelled and major lineages are coloured as follows: black, Monotremata; orange, Marsupialia; blue, Afrotheria; yellow, Xenarthra; green, Laurasiatheria; and red, Euarchontoglires. Families that were reconstructed as non-monophyletic are represented multiple times and numbered accordingly. Branch lengths are proportional to time, with the K/T boundary indicated by a black, dashed circle. The scale indicates Myr.

That's the message of a new paper in Nature that compiled sequence data from 4,510 mammalian species (out of 4,554) to assembly that lovely diagram above. Challenging the 'conventional wisdom' that mammalian diversity is the product of an opportunistic radiation of species after the dinosaurs were wiped out at the end of the Cretaceous 65 million years ago, the authors instead identified two broad periods of evolutionary expansion among the mammals: an early event 100-85 million years ago when the extant orders first appeared, and a radiation of modern families in the late Eocene/Miocene. A key point is that there is no change in rates of taxon formation across the Cretaceous/Tertiary (K/T) boundary—mammalian diversity was rich before the dinosaurs disappeared.

Continue reading "Don't blame the dinosaurs" (on Pharyngula)

What did evolution have to do with the deciphering of the genetic code?

According to the Discovery Institute’s [Egnorant] News and Views, nothing.

According to the actual research, everything.

This is interesting:

Creationists welcomed their new leaders to Knoxville last weekend for a convention held by the Discovery Institute, a Seattle non-profit that acts as a publishing house and endowment for proponents of intelligent design (ID). The institute supports a dozen senior fellows and more than two dozen other scientists. Staff scientists are working to develop an intelligent design curriculum, and advance copies of Explore Evolution, a biology textbook soon to be released by the organization, were available at the convention. Program Director Stephen Meyer told the crowd it is “premature” to teach intelligent design in public schools. Meyer said, “We encourage people not to push this in schools right now.”

The science of ID isn’t fully developed, and it shouldn’t be pushed in schools, but the revolutionary research movement founded with a textbook is producing another textbook! (and another!)

There's a very good reason I reposted an old reply to a creationist today. It's from 2004, way back shortly after I'd started this blog, and it addresses in simple terms the question of how ordinary biological mechanisms can produce an increase in information. I brought it up because Casey Luskin is whining again. He says the "Darwinists" have not answered any of the questions Michael Egnor, their pet credentialed creationist du jour, has asked.

Yet for all their numbers and name-calling, not a single one has answered Egnor's question: How does Darwinian mechanisms [sic] produce new biological information?

I had an op-ed in the Albuquerque Tribune a couple of weeks ago, on the topics of a rash of creationist bills in the New Mexico Legislature, and the super-sneaky tactics of the New Mexico Science Foundation.

Of course, in this “Tit-for-tat” world of ours, our local Intelligent Design Creationists finagled an op-ed response. Joe Renick, Executive Director of the Intelligent Design Network, is the author of Fear of exposure: The fight against academic freedom is rooted in the worry that Darwinism’s weakness will be revealed. It’s quite a ramble, but this little tidbit is what caused me to have a coffee spit-take:

Joe Renick Wrote:

The greatest threat to the Darwinian dogma today is science itself.

There is a revolution underway in the biological sciences. A whole new field of biology called “Systems Biology” has emerged during the past 10 or 15 years. This revolution is just as profound for the biological sciences today as the transition in physics was from classical physics to quantum physics and relativity in the early part of the 20th century.

In this exciting new field, research is guided not by Darwinian principles but by design principles because design principles are needed to explain design-like features.

Now hold on just a minute! Sure, “Systems Biologists” use words like “design” occasionally, but that doesn’t automatically mean they think “designs” in nature must be “poofed” into existence by an un-named magical being.

I would like to see a few (or even a dozen) letters from bonafide Systems Biologists setting Renick straight in the Albuquerque Tribune. It’ll be a quality Lesson for New Mexico Creationists: completely misrepresent an entire discipline, and you might just get chewed out.

Some comments on “Systems Biology,” along with information on writing the Trib, appear below the fold.

The Tangled Bank

The latest edition of the Tangled Bank is online at Balancing Life. I hope you like mangos.

Last night (March 26), a friend in Longmont, Colorado, sent me an e-mail in which she told me of a science teacher who had run a debate on global warming – among sixth graders (see the story in the Longmont Times-Call at http://www.longmontfyi.com/Local-Story.asp?ID=1535… ). I was in class all day today, but fortunately PZ Myers was on the job and posted 2 articles on the subject (“Another Bad Teacher,” http://scienceblogs.com/pharyngula/2007/03/another… , and a followup, “What’s the Matter with Colorado?” http://scienceblogs.com/pharyngula/2007/03/whats_t… ).

I will therefore just alert our readers to Mr. Myers’s essays and also add that the Times-Call today ran another article (“Debunking Darwin,” http://www.longmontfyi.com/Local-Story.asp?ID=1542… ) to the effect that the teacher will retire at the end of the year to devote himself to writing and opposing “Darwinism.”

The teacher noted that the district “might breathe a sigh of relief when I’m gone.” So will I.

Answers In Genesis is getting set to open their new Creation Museum, the one that is so well placed it’s miraculously within a 6-hours’ drive of 2/3rds of the American population.

But it’s not all fun and games. Trying to figure out how to cram Earth history into 6000 years, how to cram thousands of species onto a wooden Ark, and how to cram all this nonsense down people’s throats can be hard work. That’s why they’ve called in a team of crack scientists to resolve some of the hairier issues. One of the museum’s scriptwriters explains:

In designing a museum for the next generation, we clearly understood from the start that we had to be forward thinking, to gather the latest research, and to imagine where science will be five years from now. We needed a science reference board, made up of some of the very best experts in every field.

And what are these best experts working on?

“Based on genetics, I think Adam’s chest hair needs to be short, like Sean Connery’s.”

The conversations with scientists were never dull. In one memorable discussion, a sixty-something college professor threw back his chair, jumped up, then started lumbering about like an ape to explain how a monkey walks.

Decades of education and research have clearly paid off.

Prof. Steve Steve has a new job: producing raw material for paper production.

Researchers at a giant panda reserve in southern China are looking for paper mills to process their surplus of fiber-rich panda excrement into high quality paper.

Liao Jun, a researcher at the Chengdu Giant Panda Breeding Base in Sichuan province, said the idea came to them after a visit to Thailand last year where they found paper made from elephant dung. They thought panda poop would produce an even finer quality paper, he said.

I can see it now: Prof. Steve Steve’s Old Fashioned Panda-Processed Paper.

A Field Guide to Design Detection

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Via John Wilkins, a law student’s dissection of his professor’s insistence that the universe displays evidence of design. It’s an excellent analysis of the emptiness of the intelligent design movement’s argument for detecting design in the world. An extract:

I said that in order to infer intelligence from something, you would need an analytical framework. For example, “These particular factors, present in a given phenomenon, are indicative of intelligence for these reasons. Etc. Those factors are present in this phenomenon, therefore we can conclude that this phenomenon is the result of intelligence.” It seems like a simple framework; no more than instructions on how to recognize something, a sort of “Field Guide to Discerning Intelligence in the World.”

Some people, whose intellectual honesty is as questionable as my professor’s, have actually tried to posit “particular factors” that should be indicative of intelligence. Popular methods include Michael Behe’s “irreducible complexity” and William Dembski’s “specified complexity.” Neither is satisfactory. Behe’s idea has been shown wrong by experiment and Dembski’s idea assumes that we can know the probability of the occurrence of any phenomena. (“Specified complexity” is supposed to be anything that is both highly complex and highly unlikely. Except how do you know if it is unlikely? What is the probability of trees? Impossible to say.)

Nobody has yet come up with a convincing “Field Guide to Discerning Intelligence in the World,” but that did not stop my professor from insisting that I have no basis for failing to see intelligence in “natural” phenomena. Apparently it did not occur to him that since he (via Cicero, or vice versa) was making the proposition that “Intelligence is evident in natural phenomena,” it was up to him to explain why exactly that proposition should be accepted, not up to me to demonstrate why it is incorrect.

Just so. ID creationists endlessly assert that they have a methodology for detecting design in biological things, but when push comes to shove, they never ever actually apply it. Has anyone ever seen systematically gathered validation or reliability data on any of their design detection methods? I haven’t. So why is the methodology so difficult to apply? Because it rests firmly (and solely) on the claim “I know it when I see it”. And who is doing the “seeing” is the main variable, not the “it”. It’s an entirely subjective notion.

RBH

Go on over to his place and leave a birthday greeting, and be sure to check out the multimedia collection of good wishes.

We wondered what we could do to express our appreciation, and had a hard time figuring out what would be appropriate … until a student asked to borrow one of my copies of The God Delusion because he couldn't find one anywhere in town. Instead of giving Dawkins a present directly, the Myers family is donating a copy of his book to the local library, where we hope some receptive minds will discover it.

The Dallas News reports that at the Southern Methodist University, several science professors have objected to a planned presentation on “Intelligent Design”. Acutely familiar with the history of Intelligent Design, the science professors state that:

“These are conferences of and for believers and their sympathetic recruits,” said the letter sent to administrators by the department. “They have no place on an academic campus with their polemics hidden behind a deceptive mask.”

The SMU quickly clarified its position

“Although SMU makes its facilities available as a community service, and in support of the free marketplace of ideas, providing facilities for those programs does not imply SMU’s endorsement of the presenters’ views,” the statement said.

The concern is real namely that

Many SMU science professors say they are worried that merely allowing “Darwin vs. Design” on campus could give the public impression that Intelligent Design has support from scientists at the school.

Which led the departments of Anthropology, Biological Sciences and Geological Sciences to respond as follows:

“In this case, the Departments of Anthropology, Biological Sciences, and Geological Sciences in SMU’s Dedman College of Humanities and Sciences wish to reaffirm their commitment to applying rigorous scientific principles to teaching and research on the subject of evolution.”

During my time in Kansas Citizens for Science, I was privileged to work with science supporters of all walks of life as I developed flyers and pamphlets on evolutionary topics or criticizing aspects of the intelligent design creationism movement. When some ID creationism speaker would come to town, KCFS would be there, passing out flyers that informed the audience what they would be hearing from the creationist and why it was wrong or disingenuous. (When Phillip Johnson came to Lawrence, it was fun to see everyone in the hall reading our brightly colored pamphlets prior to his talk. Everything he said, we already had written down in our pamphlets.)

I’m now out in Pennsylvania. While KCFS is still going strong (and about to host Monkey Girl author Edward Humes’s lecture at JCCC this Thursday), one thing I have missed from KCFS is the availability of easy-to-find pamphlets or flyers on ID creationism or evolution. I’d like to fix that.

So, I’ve updated “A Word About Intelligent Design Creationism.” Its text appears below as the extended entry as well as in PDF and RTF formats. Please feel free to adopt the text of this flyer to your own purposes, though appropriate attribution with a plug for the Thumb would be appreciated.

I’ve added a new “Category” of Flyers/Pamphlets under which we’ll hopefully amass quite a library of pro-science literature broadsides and pamphlets. Alternatively, if you have flyers that you’ve made, let us know via comments below. (We might be able to make those available here or on other archive sites as well.)

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