March 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):

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!)

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 20^th 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.

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-St[…]asp?ID=15357 ). 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/[…]_teacher.php , and a followup, “What’s the Matter with Colorado?” http://scienceblogs.com/pharyngula/[…]colorado.php ).

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-St[…]asp?ID=15426 ) 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 2/3^rds 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.

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

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.)

Just when you believe that ID activists could not shoot themselves in the foot any further, Casey Luskin comes to the rescue, and Dembski decides to add some fuel to the smoldering fire. So what is going on this time that ticked of our friends at the Ministry of Media Complaints at the Discovery Institute’s Center for the Renewal of Science and Religion? At Red State Rabble, Pat Hayes and at the Austringer Wesley Elsberry explain Casey Luskin’s misplaced ‘outrage’ and show how once again, poor reading and listening skills (see also my previous posting about Dembski mangling Darwin) allow ID activists to create yet another strawman.

While ID is busy with their theological arguments, science is still waiting patiently for ID to present a scientific case ever since ID was found and ruled to be scientifically vacuous.

Enjoy.

On Red State Rabble, Pat Hayes shows the vacuity of Dembski’s ‘arguments’. Dembski had blogged on his Uncommon Descent website a quote from Darwin’s Descent of Man. What follows is Pat Hayes fisking Dembski’s comments.

Dembski Wrote:

Darwin Wrote:

The reckless, degraded, and often vicious members of society, tend to increase at a quicker rate than the provident and generally virtuous members. Or as Mr. Greg puts the case: “The careless, squalid, unaspiring Irishman multiplies like rabbits: the frugal, foreseeing, self-respecting, ambitious Scot, stern in his morality, spiritual in his faith, sagacious and disciplined in his intelligence, passes his best years in struggle and in celibacy, marries late, and leaves few behind him. Given a land originally peopled by a thousand Saxons and a thousand Celts—and in a dozen generations five-sixths of the population would be Celts, but five-sixths of the property, of the power, of the intellect, would belong to the one-sixth of Saxons that remained. In the eternal ‘struggle for existence,’ it would be the inferior and less favoured race that had prevailed—and prevailed by virtue not of its good qualities but of its faults.”

Sounds pretty damning, doesn’t it? But is it?

What has the ID movement been up to, following Kitzmiller and subsequent defeats? Apparently, they are going back to their base. In 2006 and 2007, the ID movement has hosted a number of “conferences” around the country. They call them “conferences” because it sounds scientific, but they are more like weekend revivals, actually, where the ID guys are flown in, give their standard talks to the public, and with a full-time professional apologist like Thomas Woodward (apologetics.org) or Lee Strobel (author of The Case for a Creator, The Case for Christ, etc.) emceeing the event. In fact, the “largest ID conference ever held” was held last September in the Florida Sun Dome, well-known to be a common venue for scientific conferences.

So anyway, this year a series of “Darwin vs. Design” conferences have been set up, apparently in a cookie-cutter format with identical guests and topics, and hosted by Lee Strobel.

The bios of the speakers are online (PDF). This bit is interesting, and shows us another thing that the ID movement has been up to:

Session #3 Dr. Stephen Meyer, director of the Center for Science & Culture, editor of Darwinism, Design and Public Education, and co-author of the forthcoming textbook Explore Evolution, will explain why the information encoded in DNA points powerfully to a designing intelligence.

Oh my, what a clever title for the new Discovery Institute textbook! It’s almost like they picked one of the most common phrases for mainstream evolution education projects and websites, so that they could appear to be teaching science rather than doing religious apologetics.

And as we all know, picking new labels easily solves all conceivable problems with creationist textbooks.

I was recently interviewed by Karl Mogel for his podcast show The Inoculated Mind. Topics include flagellum evolution and Kitzmiller v. Dover, and Casey Luskin’s inability to admit error. Have a listen if you get a chance.

I’m not sure what they are, but there is apparently a site offering free hovinds: FreeHovind.Com. Can anybody tell me what a hovind is before I order a free one?

By this point, the name Michael Egnor should be familiar to readers of this blog - but if you need a reminder, he’s the neurosurgeon who recently signed on to the staff of the Discovery Institute’s Media Complaints blog. Over the last week or two, Egnor has been trying to convince people that evolution is really not important in any way to medicine.

His last attempt, before today, came less than a week ago, with this spectacular piece of inane argumentation. I responded to the arguments that he made, Orac responded to the arguments he made, Afarensis responded to the arguments he made, Mark responded to the arguments he made, and many other people have also chimed in on the topic. A couple of hours ago, Egnor decided to take another swing at the argument.

Read more (at The Questionable Authority):

Over at A Blog Around The Clock, Cortunix has gone to the task of putting together a “brief” list of blog posts where the egnorance of Dr. Michael Egnor has been taken to the woodshed: “Michael Egnor. Who?.”

If you have a few hours to kill, you might want to drop by and read the massive fisking that this man has taken. After all, it looks like he is here to stay as the DI’s new expert on evolution.

A news story today from Oregon (story here) is headlined “Oregon teacher fired after veering from evolution textbook.”

The story says, in part:

During his eight days as a part-time biology teacher at Sisters High School, Kris Helphinstine included Biblical references in material he provided to students and gave a PowerPoint presentation that made links between evolution, Nazi Germany and Planned Parenthood.

That was enough for the Sisters School Board, which fired the teacher Monday night for deviating from the curriculum on the theory of evolution. …

Helphinstine, 27, said in a phone interview with The Bulletin newspaper of Bend that he included the supplemental material to teach students about bias in sources, and his only agenda was to teach critical thinking. “Critical thinking is vital to scientific inquiry,” said Helphinstine, who has a master’s degree in science from Oregon State. “My whole purpose was to give accurate information and to get them thinking.”

That was the title of an article by Stephen Prothero in the Boulder Daily Camera this morning (March 19). Professor Prothero is the chairman of the religion department at Boston University, and his article was run on the Web site (latimes.com) of the Los Angeles Times under the title, “We live in the land of biblical idiots: Public school courses that promote Bible literacy can enhance our civic life.” Professor Prothero argues in favor of teaching the Bible as literature and the Bible in history. His primary argument is as follows:

In part 1, I showed how GilDodgen’s concerns about computer models show how Intelligent Design is scientifically vacuous, but since evolution deniers often also tend to be global warming deniers (often for very similar reasons), it may be helpful and beneficial to explore in more depth the value of computer models in science.

Let’s first explain how computer simulations of global warming take place and why we can indeed trust the results. We often hear arguments from global warming deniers which take shape as follows:

We all know that the weather is unpredictable beyond a certain time frame of 7-10 days so how can climate models be trusted?

This fallacious argument is based on a confusion of weather and climate. Climate is a statistical concept based on the outcome of many computer runs with slightly different models, conditions, weather is a local (and real) phenomenon (I already pointed out these differences when discussing Bill Dembski’s flawed understandings of these basic concepts.

Definition of climate (Edward Lorenz): “Climate is what you expect, weather is what you get.”

Updated for the 21^st century (Myles Allen): “Climate is what you affect, weather is what gets you.”

Climate modelers use what is commonly known as General Circulation Models (GCM) which differ from weather prediction models in several important aspects.

The Michael Egnor article that I blogged about earlier today was a response to an article written by Scienceblogger Mark Chu-Carroll. Mark has has written his own response to Egnor’s latest post (Pigheaded Egnorance, Antibiotic Resistance, and Tautologies). It’s absolutely worth going over there and giving it a read.

While you’re there, you might also want to take a look at this post by Afarensis and this one by Orac, both of which address the Egnorance of yesterday.

Comments may be left at the home blog for each of those posts.

Dr. Michael Egnor is, once again, trying to explain why evolution isn’t important to medicine. This time he’s responding to Mark Chu-Carroll’s post on Tautology. In his latest post, Egnor continues to challenge the conventional wisdom that an understanding of evolution in general and natural selection in particular is essential to understanding and dealing with the phenomenon of bacterial resistance to antibiotics.

Here’s his latest statement along those lines:

Mark, your dad’s illness didn’t happen because his doctor didn’t know enough about random mutation and natural selection. Our battle against bacterial resistance to antibiotics depends on the study of the intricate molecular strategies bacteria use to fight antibiotics, and our development of new antibiotics is a process of designing drugs to counter the bacterial strategies. We use molecular biology, microbiology, and pharmacology. We understand that bacteria aren’t killed by antibiotics that they’re resistant to. We understand tautologies. Darwin isn’t a big help here.

Thus far, Dr. Egnor has only discussed the phenomenon of bacterial resistance in general. I’m going to present a pair of real, specific, and relatively recent scenarios where I think an understanding of evolution by natural selection has played an important role in public health debates involving appropriate uses of specific antibiotics. My question - and challenge - to Dr. Egnor is this: can you explain why an understanding of evolution by natural selection was really not important in these specific cases? If you cannot, can you please explain why you still believe that an understanding of evolution by natural selection is irrelevant to medicine?

Read more (at The Questionable Authority):

On Uncommon Descent we learn why global warming deniers share so much with evolution deniers and why people should be wary of Intelligent Design:

Gildodgen Wrote:

Computer simulations of global warming and Darwinian mechanisms in biology should not be trusted, because they can’t be subjected to empirical verification. In these two areas, computer simulations and models can degenerate into nothing more than digital just-so stories — in one category about the future, and in the other about the past. The programmer can produce whatever outcome he desires, by choosing initial assumptions and algorithms, and weighting various factors to produce a desired output.

First of all GilDodgen explains why one should be critical about Intelligent Design when he ‘argues’ “Don’t Trust Computer Simulations And Models That Can’t Be Tested Against Reality”. In other words, the scientific vacuity of ID should be a major source of concern. But there is more and I will address this in my second installment.

Neurosurgeon and recent addition to the Discovery Institute’s Media Complaints Division blog Dr. Michael Egnor is at it again. He’s responded to Burt’s latest response to his prior response to Burt’s earlier response to his - you get the drift. Burt’s been doing a great job of responding to Egnor, and I don’t want to step on his toes, but Egnor says a couple of things this time that I think would benefit from the perspective of someone who is studying evolutionary biology.

First, though, I’d like to address this delightful bit of less-than-honest rhetoric:

Read more (at The Questionable Authority):

A new species of leopard has been described from Borneo and Sumatra. Read more over at Stranger Fruit.

When we think of the spread of antibiotic resistance between animals and humans, we tend to think of it going from Them to Us. For example, much of the research over the past 20 years on the sub-clinical use of antibiotics in animal feed has looked how this use of antibiotics as a growth promotant breeds resistant organisms in animals, which can then enter the human population via the food we eat. Along a similar line, I just mentioned Burt’s post post on cephalosporin use in cattle and the evolution of antibiotic resistance, where the worry is that use of these broad-spectrum antibiotics in animals will select for resistance that can then spread to humans. However, spread of resistant organisms is not a one-way street. For example, it has been suggested that transmission of methicillin-resistant Staphylococcus aureus (MRSA) has been transmitted both from horses to humans and vice-versa (see, for example, this Emerging Infectious Diseases paper). A new paper suggests that this phenomenon can happen even in animals that aren’t in such close contact with humans: chimpanzees.

(Continued at Aetiology)