July 2007 Archives

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People are always arguing about whether primitive apes could have evolved into men, but that one seems obvious to me: of course they did! The resemblances are simply too close, so that questioning it always seems silly. One interesting and more difficult question is how oysters could be related to squid; one's a flat, sessile blob with a hard shell, and the other is a jet-propelled active predator with eyes and tentacles. Any family resemblance is almost completely lost in their long and divergent evolutionary history (although I do notice some unity of flavor among the various molluscs, which makes me wonder if gustatory sampling hasn't received its proper due as a biochemical assay in evaluating phylogeny.)

One way to puzzle out anatomical relationships and make phylogenetic inferences is to study the embryology of the animals. Early development is often fairly well conserved, and the various parts and organization are simpler; I would argue that what's important in the evolution of complex organisms anyway is the process of multicellular assembly, and it's the rules of construction that we have to determine to identify pathways of change. Now a recent paper by Shigeno et al. traces the development of Nautilus and works out how the body plan is established, and the evolutionary pattern becomes apparent.

Continue reading "Cephalopod development and evolution" (on Pharyngula)

Jacob Bronowski used to say that the greatest discovery of scientists was science itself. The scientific method, with its resolute search for causation, its refusal to cower before tradition and authoritarianism was responsible for the great advancement of humanity over the past centuries. Obviously scientists have not always lived up to these standards, but those who have took man to places he could only have imagined before (and not even imagined very well). Central to this accomplishment is science’s refusal to be satisfied with magical explanations of phenomena. Magic, after all, is not an answer—it’s the feeling of satisfaction without answers. It’s the willingness to tolerate a big blank spot in one’s understanding of the universe.

(Read the rest at Positive Liberty…)

I came across a reference to a law review note from last year in the Chapman Law Review. The note was by Stephen Trask, then a student at William Mitchell College of Law and, unsurprisingly, a graduate of Liberty University. It was entitled, Evolution, Science, and Ideology: Why the Establishment Clause Requires Neutrality in Science Classes. Since Chapman is Sandefur’s alma mater, I emailed him to see if he’d seen it and he said no, but he found it and sent me a copy of it. He described it as a “giant, steaming pile of crap”; he was being generous. He’s going to post a full fisking of the article soon, but I wanted to focus on one particular claim Trask makes.

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

Gert Korthof reviews Behe’s latest book “The Edge of Evolution” and shows a level of internal contradiction one has grown accustomed to from ID proponents

Common Descent is based on genetic continuity in the history of life on earth. Design, according to Michael Behe, is based on genetic discontinuities in the Tree of Life. Therefore, Design and Common Descent are not compatible. Make your choice: it is either Design or Common Descent. Contrary to Behe, both cannot be true.

Korthof shows how Behe’s book does little to explain ‘Intelligent Design’, leaving it once again scientifically vacuous.

No, this post isn’t about creationist Ted Haggard and his male escort/methamphetamine scandal.

And it’s not about creationist Kent Hovind, currently serving hard time for federal tax evasion.

It’s not even about the lawsuits and charges of corporate theft that have cropped up between Creation Ministries International (formerly known as Answers in Genesis (AiG)-Australia) and its former partner, AiG-USA, under Ken Ham, nor is it about the on-line porn star who played the role of Adam in a movie made for AiG’s new Creation Supposeum.

No, this new scandal involves Kevin Jackson, whose term as Mayor of Rio Rancho, New Mexico ended prematurely when he was forced to resign over a slew of allegations of financial misconduct.

So, how is Rio Rancho’s ex-mayor involved with creationism? More below the fold.

Quantum Panda Mania!

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I’ve been a busy little bear this summer, and no, I’m not talking about my duty to return Ailuropoda to its once great numbers. I’m referring to my travels around the globe these last few months. I’ve been to so many interesting places that you’d think that I can exist in multiple places at the same time. Call me the Quantum Panda ™ if you want to. My reports from Evolution 2007 will be up later in the week, but I can now give you some links to blog posts done by some of my companions.

But before I do, I want to remind you that you can join my Facebook group, or friend me on MySpace. The Facebook group also serves as the fan group for PT.

Now to the blog posts.

From Sandra Porter at Discovering Biology in a Digital World:

Professor Steve Steve caught experimenting with human subjects!—Don’t look at me like that. I have IRB approval from UE.

Professor Steve Steve bears all at Virginia Tech—Strike a pose. Vogue!

Meanwhile Bora of A Blog Around the Clock and I have been busy in SF:

Professor Steve Steve is helping me work—Is it working hard or hardly working?

Professor Steve Steve at PLoS—PLoS: Pandas Love Open Science

San Francisco—a running commentary—I saw a flock of seagulls in the bay.

San Francisco—a running commentary #2—And I ran so far away.

Professor Steve Steve meets Harry Potter—Not to spoil the ending, but I had no idea that it was all a dream, and Harry would wake up and find Ron in the shower.

Hi, Michelle!—I meet the most interesting people for lunch.

Framing San Francisco—Bamboo frames are my favorite.

Many of you may remember Danica McKellar from her role as Winnie Cooper in The Wonder Years in the late 1980s and early 1990s. What you may not know is that, following the television show, McKellar attended UCLA, where she graduated summa cum laude with a major in mathematics (and published proof to boot). Since graduation, McKellar has maintained an interest in math and science education for girls, and has been active in promoting this. She’s now also published a book on math education for middle school girls (Math Doesn’t Suck: How to Survive Middle-School Math Without Losing Your Mind or Breaking a Nail) that comes out in early August. For those interested, I have a review of the book up here at Aetiology. I also managed to snag an interview with Danica about the book and other topics, including math advocacy for girls that you can check out here.

Cosmic Soup

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Here’s an interesting article from Nature News (subscription may be required):

Organic compound found in the stars

Astronomers have found the largest negatively charged molecule so far seen in interstellar space. The discovery, of an organic compound, suggests that the chemical building blocks of life may be more common in the Universe than had been previously thought.

The molecule is a chain of eight carbons and a single hydrogen called the octatetraynyl anion (C8H¯). Two teams of scientists have spotted it near a dying star and in a cloud of cold gas.

The discovery, along with that of three smaller organic molecules in the past year, opens up a suite of potential chemical reactions and products. It suggests that ‘prebiotic’ molecules such as amino acids, the building blocks of protein, could form all over the Universe, says Tony Remijan, an astronomer at the National Radio Astronomy Observatory (NRAO) in Charlottesville, Virginia.

Way cool.

Luskin Being Silly

Over at the Discovery Institute's blog, Casey Luskin thinks he's caught evolutionists wanting it both ways:

Question: What do you do when a theory logically predicts both (a) and not (a)? Answer: Apparently you heavily promote it.

MSNBC recently published two articles promoting Darwinian just-so stories to the public. The first article about the evolution of Waterfowl genitalia contends, “Scientists had speculated that male waterfowl evolved longer phalluses to give them a competitive edge over those not as well-endowed when it came to successfully fertilizing females.” That makes sense, I suppose. But the article makes one admission that strikingly contradicts that little just-so hypothesis: “Most birds lack phalluses, organs like human penises. Waterfowl are among the just 3 percent of all living bird species that retain the grooved phallus...” If long phalluses are so advantageous for reproduction, why did so many birds supposedly lose them? Darwinists will look back retroactively and claim that under the environmental conditions or sexual selection pressures experienced by most bird species, long phalluses weren't advantageous. The problem in so doing is that they now have a theory which can explain both (a) long phalluses, and also not (a).

You might enjoy listing all the reasons why that is a silly criticism. My list is available over at EvolutionBlog. Comments can be left there. Enjoy!

Tripoli Six: Home and Free

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It’s over in Libya. Nick previously blogged about the Tripoli Six: a Palestinian doctor and five Bulgarian nurses, working in Libya, who were accused of infecting hundreds of children with HIV. The group have been imprisoned since 1999–despite the fact that an analysis of the HIV isolates from the children confirmed that the epidemic began before the medical workers arrived in the country (and continued even after they were jailed). After a long battle, mostly legal and political rather than scientific, they’ve been freed and sent back to Bulgaria. More on the story at the BBC and the New York Times.

I should note that though the science ultimately wasn’t the determining factor in their release, the science blogosphere and Nature (with journalist/blogger Declan Butler leading the charge) were important in keeping this prominent in the scientific community. And while we celebrate their freedom, there are still hundreds of HIV-infected children in Libya, and grieving parents who missed out on justice in this case.

Mind Your Businesses

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The Southwestern Baptist Theological Seminary, William Dembski’s current employer, has something rather curious on its website. If you look at their page of upcoming conferences, here is what they have listed in the left-hand sidebar:

  • The Practice of Biblical Counseling
  • Certification in Biblical Counseling
  • The Family: Reclaiming a Biblical View
  • Intelligent Design in Business Practice

Can you spot the one that appears out of place? Me neither.

But anyway, yes, they really are having a conference called, Intelligent Design in Business Practice. The flier for the conference comes complete with an obligatory ape-typing-at-keyboard graphic. Unfortunately, it does not say which of the speakers this is intended to represent.

If you’re wondering what the heck ID could have to do with business practice, when it doesn’t even have anything to do with science, then you’re thinking what I’m thinking. All the pretense about ID being some dispassionate scientific theory – not exactly believable to begin with – is rather hard to maintain with them holding conferences that try to apply ID to things that have little or nothing to do with science. (Not to mention that even their supposedly “scientific” conferences tend to resemble tent revivals.) As the Wedge Document has promised us, ID is supposed to have “cultural implications” for “sex, gender issues, medicine, law, and religion”. Business isn’t listed there, but once you’ve declared that your theory makes sweeping dictates over all facets of human society, it’s hardly a stretch to add business practices to the list.

Nevertheless, one has to wonder, given the history of the ID movement, exactly what useful advice the ID movement could possibly have to offer business. As luck would have it, I’ve gotten my hands on a preliminary schedule – the only copy in existence as a matter of fact – which I will post below the fold.

Reality 1, Behe 0

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Or …

T-urf13 redux

A few months ago I posted an essay about a remarkable example of the evolution of Irreducible Complexity from scratch, via natural, unguided mechanisms. While the reaction to this essay has been pretty muted (precious little to take note of, save for one well-hidden reference on Uncommon Descent to “No Free Lunch”, citing pages that make arguments clearly refuted in the PT essay), I had no idea that a much bigger response, or target, would emerge from the Halls of ID. This would, of course, be Mike Behe’s recently-released follow-up to “Darwin’s Black Box”, entitled “The Edge of Evolution”.

More follows beneath the fold, but here’s the short version for those of us with miniscule attention spans -the previous essay refutes (or, better said, refuted) the EoE in no uncertain terms, showing that the centerpiece of the EoE, the value Behe assigns to the “probability” of occurrence of a protein interaction or binding site, does not agree with what we can and do know about the history of a bonafide multiple simultaneous mutation.

Well, at least someone is taking the recent threats against the Colorado biologists (http://www.pandasthumb.org/archives[…]logists.html ) seriously. (See also “Creato-terrorism update,” http://www.pandasthumb.org/archives[…]orism_1.html .) Today’s Boulder Daily Camera carries a signed editorial, “Fundamentalist threat not an isolated event” (http://www.dailycamera.com/news/200[…]olated-event ), by Jennifer Platte. Ms. Platte notes

The packages containing veiled threats that were slipped under the doors of labs at the department of evolutionary biology at the University of Colorado appear to be part of a larger campaign being waged by one man against the department.

Content on the blog www.pandasthumb.org suggests that e-mails that preceded the packages threatened to “take up a pen to kill the enemies of Truth,” and stated that the writer would file charges of child molestation against the professors for teaching evolution. The writer believes that these professors are “the source of every imaginable evil in our society: drugs, crime, prostitution, corruption, war, abortion, death…” He appears to have been inspired by the words of Pastor Jerry Gibson, who allegedly spoke at Doug White’s New Day Covenant Church in Boulder, saying that “every true Christian should be ready and willing to take up arms to kill the enemies of Christian society.”

Update 30 July 2007. A letter in today’s Boulder Daily Camera claims that Mr. Gibson “never said this or anything like it” and directs us to the New Day Covenant Church’s Web site.

A looong time ago, I mentioned that I spent St. Patrick’s Day weekend in Wartburg College in Waverly, Iowa, at a symposium I helped to plan (but neglected to blog! Oops). Along with other scientists, theologians, philosophers, and generally interested persons, we worked for a bit over a year to put this symposium together. Why?

The principal aim of the conference is to clarify the causes of the conflict between science educators and those who wish to have Intelligent Design taught in public schools. We do not claim to be neutral on this issue. We are convinced that ID is not good science and should not be presented as such. Our position is consonant with that of the National Center for Science Education and the Iowa Academy of Science. We believe that the polarization of opinion on this issue has created misunderstanding and confusion and that a clarification of terminology and concepts is essential for productive dialogue and decision making.

How did it turn out? I have the write-up over at Aetiology

Over at the Discovery Institute’s Media Complaints Division, Casey Luskin is keeping himself busy trying to fudge assert that the notion of “junk DNA” (which ID advocates consider erroneous, despite the fact that strong, independent lines of evidence indicate that a large fraction of genomic DNA in most eukaryotic organisms is phenotypically non-functional) was the result of application of Darwinian principles.

Several people (e.g. T. Ryan Gregory, Larry Moran and Steve Reuland, as well as myself ) have already pointed out that, on the contrary, a strict application of the Darwinian paradigm, also known as “panselectionism” or “adaptationism”, led many prominent evolutionary biologists to initially resist the idea that some DNA may be non-functional, an opposition which was later mostly lifted (sometimes partially, as we will see) by the progressive acceptance of neutralist views.

It’s another day, and Casey “The Energizer Bunny” Luskin is at it again, claiming that ID successfully predicted that “junk DNA” would be found to have a function. He has yet to explain how and why he believes that “Darwinism” somehow stifled research into those areas of the genome, and ignores the fact that scientists routinely use our understanding of evolution, common descent, and natural selection to identify areas of the genome to identify non-coding regions that are likely to have function. He does, however, provide us with an explanation for why he thinks that Intelligent Design somehow “predicts” function for all of the so-called “junk” DNA:

Intelligent design begins by studying the types of complexity produced by intelligent agents. We observe that intelligent agents produce things for a purpose, that is, to fulfill some function. This leads ID proponents to an expectation—yes, a prediction—that DNA will not tend to contain meaningless junk but will contain structures that have (or once had) a function for the organism. ID does not lead us to the expectation that our cells’ DNA will be largely non-functional garbate. The hypothesis—that “junk”-DNA will have function—is obviously experimentally testable. In fact, I know pro-ID biologists studying the function of junk-DNA who were inspired to do such research due to intelligent design. One biologist in particular is not yet tenured, and so I will not disclose his/her name. Suffice it to say, for this biologist, finding function for non-coding DNA was directly inspired by intelligent design.

If that explanation looks familiar to you, it should. It’s pretty much the same one he gave last month. This leads me to my two challenges - one that’s addressed to most of you, and one just for Casey:

Read more (at The Questionable Authority, where comments may be left):

Tangled Bank #84

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The Tangled Bank

Sorry. I just couldn't resist. This week's Tangled Bank has an ancient Greek theme, so I think it's entirely appropriate to have King Leonidas summon you to Tangled Bank #84. Don't worry, there isn't much carnage involved.

In a recent Panda’s Thumb comment thread, Pam asked (among other things) about our human species genetic Adam and Eve:

I have been reading for the last few years now, that there is a consensus among the majority, that humans have been genetically traced to a two human ancestory: A genetic “Adam and Eve”.

This is a relatively common misconception, and a very understandable one. There have been published studies that have looked at the most recent common mitochondrial DNA ancestor of all humans, and other studies that have looked at the most recent common Y-chromosome ancestor of all humans. Since mitochondrial DNA is only inherited from the mother, the most recent mitochondrial DNA ancestor is frequently referred to as “mitochondrial Eve.” Similarly, since the Y-chromosome is passed on exclusively from father to son, the most recent Y-chromosome ancestor gets called “Y-chromosome Adam” a lot. The use of those two terms is not entirely inappropriate, but it can be very misleading - particularly for those who haven’t taken a bunch of college-level biology.

Let’s start with the biggest misconception, and move on from there. When it comes to Adam and Eve, there’s good news and bad news. The good news is that I can unequivocally state that they never got divorced. The bad news is that they never married. That’s understandable, of course, since Eve died more than 50,000 years before Adam was born.

Right about now, I’m guessing that we’re hitting the point when confusion sets in. After all, if every man on earth is descended from Y-chromosome Adam, and if we’re all descended from our fathers, and if Y-chromosome Adam was married, why wasn’t his wife “Eve?” We all clearly must be descended from her, too, right? (And if confusion hadn’t set in already, it almost certainly has now that I wrote that.) Let’s see what (if anything) I can do to clear things up.

Read more (at The Questionable Authority, where comments can be left):

By now, regular readers will probably be familiar with The Clergy Letter Project spearheaded by Michael Zimmerman. Formulated in part to respond to the framing of the evolution controversy as a battle between science and religion, the letter now boasts more than 10,700 signatures from clergy, and have sponsored Evolution Sunday events for the past 2 years.

Well, Zimmerman has a new project now:

Our latest initiative is to create a list of scientists around the world who are willing to answer scientific questions posed by clergy who are supportive of modern science in general and evolution in particular (Link). In just a bit over three weeks, we already have over 200 scientists signed up to help out. I hasten to add that the information these scientists will be providing will be solely of a scientific nature and thus their personal religious inclinations are absolutely irrelevant.

In addition to creating a useful resource for clergy, I am hoping for the list to make a major political statement: religious leaders and scientists can work together – despite what religious fundamentalists claim. I also would very much like to have more names on this list than the number of scientists the Discovery Institute has on a list it trumpets of scientists claiming to “question” evolution.

(Emphasis mine). If you’re interested, drop an email to Michael ([Enable javascript to see this email address.]) and include your name, title, address, area(s) of expertise, and email address–and spread the word!

(Cross-posted at Aetiology).

Let’s Talk Junk (Again).

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Back in the middle of last month, I had a few things to say about Casey Luskin (DI flak) and his understanding of so-called junk DNA. It’s now the middle of the month again, and Casey is again talking a lot - and understanding very little - about “junk” DNA. Larry Moran has a post up where he tries to educate Casey about the fact that a hell of a lot of DNA is still, at least as far as we know, junk. I’m going to take a look at something a little bit different - one of the methods scientists use to identify areas of “junk” DNA that have important functions. It’s a pretty cool way of doing things, but it’s not one that Casey likes to talk about - because it’s really one of the finest examples of how our understanding of Darwinian evolution has lead to new discoveries about living things.

Read more (at The Questionable Authority):

Barbara Forrest and Paul Gross have a paper titled Biochemistry by design published in TRENDS in Biochemical Sciences Vol.32 No.7 , 2007. (10 pages including 1.75 pages of references) I am not surprised why the defense in the Kitzmiller trial tried to get Forrest removed as an expert witness.

Creationists are attempting to use biochemistry to win acceptance for their doctrine in the public mind and especially in state-funded schools. Biochemist Michael Behe is a major figure in this effort. His contention that certain cellular structures and biochemical processes – bacterial flagella, the blood-clotting cascade and the vertebrate immune system – cannot be the products of evolution has generated vigorous opposition from fellow scientists, many of whom have refuted Behe’s claims. Yet, despite these refutations and a decisive defeat in a US federal court case, Behe and his associates at the Discovery Institute continue to cultivate American supporters. They are also stepping up their efforts abroad and, worryingly, have achieved some success. Should biochemists (and other scientists) be concerned? We think they should be.

After a group of ultra-Orthodox rabbis issued a “fatwa” forbidding Jews even to touch books by Rabbi Nathan Slifkin, he became kind of a celebrity. The popularity of his books jumped dramatically. A number of reviewers (and blurb writers) proceeded to extol the merits of Slifkin’s literary output, and specifically of his latest book titled The Challenge of Creation. Slifkin asserted in this book that scientific theories including evolution theory, not only are fully compatible with the tenets of Judaism, but that all science is in fact rooted in the Torah. The list of blurbs for Slifkin’s book includes those by Professor Michael Ruse, and by a number of other university professors, and prominent rabbis.

There is, though, at least one reviewer whose opinion of Slifkin’s opus is quite different from the acclaims by Slifkin’s admirers. His review, titled “When Quote Mining Becomes Quote Mania” can be read at Talk Reason..

Gordy Slack interview

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Gordy Slack was on the radio in the Bay Area yesterday and the show is now online. I haven’t listened to the whole thing yet but I’m sure it was good, since Gordy is quite a thoughtful guy. Gordy is also doing a reading at Books Inc. Opera Plaza, 601 Van Ness Ave. SF, CA, on Monday, 7/16. 7:00 pm – I might go myself if I get the chance…

Fri, Jul 13, 2007 – 10:00 AM Author Gordy Slack Listen (RealMedia stream) Download (MP3)

(Windows: right-click and choose “Save Target As.” Mac: hold Ctrl, click link, and choose “Save As.”)

The show welcomes author Gordy Slack for a conversation focusing on his book, “The Battle over the Meaning of Everything: Evolution, Intelligent Design and a School Board in Dover, PA.

Host: Dave Iverson

Guests: Gordy Slack , author of “The Battle over the Meaning of Everything: Evolution, Intelligent Design and a School Board in Dover, PA.”

SCANDAL AT THE PANDA’S THUMB!

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Professor Steve Steve, how could you?

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He will be going into rehab, and promises never to do it again.

(via Zeno)

Creato-Terrorism Update

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Today’s Denver Post and Colorado Daily have articles on the threats made to the CU Boulder faculty. The perpetrator has been identified as one Michael Korn, a former Messianic Jew who has converted to Christianity. And he’s been up to this for awhile it seems.

Evolution of a sex ratio observed

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If you've been reading that fascinating graphic novel, Y: The Last Man(amzn/b&n/abe/pwll), you know the premise: a mysterious disease has swept over the planet and bloodily killed every male mammal except two, a human named Yorick and a monkey named Ampersand. Substantial parts of it are biologically nearly impossible: the wide cross-species susceptibility, the near instantaneous lethality, and the simultaneity of its effect everywhere (there are also all kinds of weird correlations with other sort of magical putative causes, which may be red herrings). On the other hand, the sociological part of the story seems very plausible. There is no feminist utopia, the world goes on in a traumatized and rather complicated way, and the reactions everywhere vary from crazed euphoria to a more common despair. One thing that isn't at all implausible, and actually has been observed, is a plague that selectively exterminates males.

Continue reading "Evolution of a sex ratio observed" (on Pharyngula)

And they say evolution isn’t predictable. Ever since ID went down in flames in the Kitzmiller v. Dover case, creationism watchers have predicted that creationism would evolve yet again, this time into something called “critical analysis of evolution” or “teach the [made-up] controversy”. For the last month or two I have been warning about the Discovery Institute’s new crypto-creationist textbook, which is sneakily entitled Explore Evolution: The Arguments For and Against Neo-Darwinism (yes, take a good hard look at the spiffy website). The book is clearly another shot at the Of Pandas and People strategy, namely, “when a court case goes against you, change the label and try again.”

We already knew that the first official big promotional conference for Explore Evolution was going to be at an event for teachers held at Biola University. (Formerly known as the Bible Institute of Los Angeles, the only institute in the U.S. that has graduate courses in “intelligent design”, and pretty literally the place that put the fundamentals in fundamentalism. Oh yes, how could anyone ever think that Explore Evolution is crypto-ID/creationism?)

Now it looks like the Discovery Institute has engineered a cover story in World Magazine, a leading conservative evangelical magazine. The magazine has an interview with Behe about his new book, but more importantly has a story about a plan to insert Explore Evolution into a public school in Tacoma, Washington:

Over on UD, Paul Nelson claims that he is representing the “Darwinian tree of life” position correctly when he asserts that the tree must trace to a single cell, not just a single species:

From NOVA Upcoming Summer & Fall 2007 Programming:

NOVA shows on PBS on Tuesdays @ 8 pm ET/PT (check local listings):

Judgment Day: Intelligent Design on Trial (w.t.) November 13, 2007 at 8 pm ET check local listings

One of the latest battles in the war over evolution took place in a tiny town in eastern Pennsylvania called Dover. In 2004, the local school board ordered science teachers to read a statement to their high school biology students. The statement suggested that there is an alternative to Darwin’s theory of evolution called intelligent design, the idea that life is too complex to have evolved naturally and therefore had to have been designed by an intelligent agent. The science teachers refused to comply with the order, and alarmed parents filed a lawsuit in federal court accusing the school board of violating the separation of church and state. Suddenly, the small town of Dover was torn apart by controversy, pitting neighbor against neighbor. NOVA captures the emotional conflict in interviews with the townspeople, scientists and lawyers who participated in the historic six-week trial, Kitzmiller, et. al. v. Dover School District, et. al., which was closely watched by the world’s media. With recreations based on court transcripts, NOVA presents the arguments by lawyers and expert witnesses in riveting detail and provides an eye-opening crash course on questions such as “What is evolution?” and “Does intelligent design qualify as science?” For years to come, the lessons from Dover will continue to have a profound impact on how science is viewed in our society and how to teach it the classroom.

Produced by NOVA WGBH Science Unit and Vulcan Productions, Inc. Additional production by The Big Table Film Company.

Reinventing the worm

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Sometimes, I confess, this whole common descent thing gets in the way and is really annoying. What we've learned over the years is that the evolution of life on earth is constrained by historical factors at every turn; every animal bears this wonderfully powerful toolbox of common developmental genes, inherited from pre-Cambrian ancestors, and it's getting rather predictable that every time you open up some fundamental aspect of developmental pattern formation in a zebrafish, for instance, it is a modified echo of something we also see in a fruit fly. Sometimes you just want to see what evolution would do with a completely different starting point — if you could, as SJ Gould suggested, rewind the tape of life and let it play forward again, and see what novelties arose.

Take the worm. We take the generic worm for granted in biology: it's a bilaterally symmetric muscular tube with a hydrostatic skeleton which propels itself through a medium with sinuous undulations, and with most of its sense organs concentrated in the forward end. The last common ancestor of all bilaterian animals was a worm, and we can see that ancestry in the organization of most animals today, even when it is obscured by odd little geegaws, like limbs and armor and regional specializations and various dangly spiky jointed bits. You'll even see the argument made that that worm is the best of all possible simple forms, so it isn't just an accident of history, it's a morphological optimum.

But what if we could rewind the tape of life a little bit, to the first worms? Is it possible there are other ways such an animal could have been built? It seems nature may have carried out this little experiment for us, and we have an example of a reinvented worm, one not constructed by common descent from that initial triumphal exemplar in the pre-Cambrian — an alternative worm.

Continue reading "Reinventing the worm" (on Pharyngula)

Obsessively barking up the wrong tree

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I apologize to James Hall for using his phrase in describing what Robert Crowther, and other Intelligent Design proponents, seem to be involved in when they are objecting to the simple fact that Intelligent Design is a straightforward argument from ignorance.

The problem is that ID proponents have used equivocating language which has led to much confusion amongst its followers. I cannot blame Crowther for taking serious the claims of his DI fellows, but merely claiming that ID is not an argument from ignorance is merely begging the question.

While it is relatively straightforward to reach the conclusion that ID is an argument from ignorance, it does require some careful analysis of how various terminologies are being used by ID proponents.

My colleague, Michael Grant of the Ecology and Evolutionary Biology Department, was one of the victims of the recent harassment, reported by Steve Reuland here. Professor Grant tells me that he has “been receiving these histrionic emails and books and packages for a year; he even comes into my office when I’m not here. He started with me and Jeff Mitton [chair of EEB] but expanded to the rest of the department and may have crossed a legal line with the rest. I have a huge stack of emails and packages and even a big fat paperback book from him.” I think that, by legal line, he means the threatening tone of the last e-mail below.

“Among other things,” writes Professor Grant, “he identifies me as a ‘child molester’ for teaching evolution and threatens to get me fired plus he threatens legal action on that front. In the most recent communications, he writes words many of my colleagues consider death threats.”

Update, 13 July 2007, 3.55 MDT. The Colorado Daily has released the name of the alleged perpetrator here .

His full name is Michael Philip Korn. He sometimes goes by his Hebrew name, Menachem (not Menacher). He lives in Nederland, a small mountain community west of Boulder. His Web site is http://www.jesusoverisrael.blogspot.com/, but it has not been updated in months. He says about himself,

I was born in America, moved to Israel after graduating from Harvard, enlisted in the Ba’al Teshuva movement, and joined a Messianic Chassidic cult (Breslov) from 1990-1999. Through the help of South African missionaries, I came to see that Jesus is the Jewish Messiah and Saviour of the World. I was baptized in a natural spring in the Israeli Galilee outside of the famous mystical city of Safed on 20 June 2000, and now I seek to introduce Jewish people to Jesus Christ, their Messiah whom they don’t yet know.

Michael Philip Korn is also cited at Southern Exposure here.

Further, as Steve Reuland notes, the story has been reported in the Denver Post as well as the Colorado Daily. The Associated Press has also picked up the story, as has Salon. You may find an earlier Panda’s Thumb report with comments here.

The affair is cited at Red State Rabble here.

It looks like somebody either never heard of Dover, or refused to learn from their lesson. It seems the local ID supporters of Chesterfield County aren’t happy:

So far, the official actions of the CCSB have been limited to issuing a rather vague and confusing statement. ID proponents had hoped to influence the selection of science textbooks, but they started their campaign too late, and the CCSB approved the selection of standard biology texts. But there is still much concern about the situation in Chesterfield. ID supporters, backed by a local conservative group called the Family Foundation, are energetic and well-organized, as evidenced by their ability to deliver a petition with more than 1,100 people who questioned the use of “evolution-only” science texts.

Energetic and well-organized supporters of pseudoscience… sounds like a one-way ticket to another budget-busting, unwinnable multimillion dollar lawsuit. Virginia, you can do better than these guys.

The Alliance for Science has the full story. If you are a Virginia resident and want to get involved, please contact them. Also, visit the link to learn much more about the story, and also about Shawn Smith’s blog that tracks the Intelligent Design Creationism movement in Chesterfield County. Let’s keep sound science in Virginia science classes and get the jump on things before they can stir up trouble.

Crossposted at Neurotopia

Creato-Terrorism

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It was only a matter of time. The creationists, frustrated at continued legal losses and the complete lack of respect they receive from scientists, have finally past the threshold from trying to distort science in schools to attacking science in a more direct fashion. Today’s Denver Post contains a very short piece about an unnamed “religious group” leaving threatening packages at the CU Boulder ecology and evolutionary biology department, just up the road from where I work. (I’m a little disappointed that our campus didn’t receive this honor – but then again I could do without security crawling all over the place, making sure we have our ID badges displayed properly, etc.)

The messages included the name of a religious-themed group and addressed the debate between evolution and creationism, CU police Cmdr. Brad Wiesley said. Wiesley would not identify the group named because police are still investigating.

“There were no overt threats to anybody specifically by name,” Wiesley said. “It basically said anybody who doesn’t believe in our religious belief is wrong and should be taken care of.”

The first threat was e-mailed to the labs - part of CU’s ecology and evolutionary biology department housed in the Ramaley Biology building - on Friday. Wiesley said Monday that morning staff members found envelopes with the threatening documents slipped under the lab doors.

Unfortunately, the article is short on details. More about this as it develops. Update: In what should come as a surprise to no one, Rob Crowther of the Discovery Institute, on the basis of no evidence at all, implies that the biologists who received these threats lied to the police about them. He also has a hard time with basic reading comprehension:

But where’s the evidence that the perps are actually creationists, or religious at all?

Read the second sentence of the article (i.e. the first sentence I quoted above). The policeman investigating this incident informed the Post that the group is “religiously-themed” and that they made references to creationism. Then again, maybe Crowther thinks the police are lying too. It gets worse:

As one colleague pointed out, that is hardly the way religious believers refer to their own belief system. Rarely do Christian groups refer to their own “religious beliefs” — it is mainly secularists who refer to beliefs with the modifier “religious.”

Except the person who used the modifier “religious” was the policeman, not the perpetrators. We do not know at this point what exactly the perpetrators said. We don’t even know for sure that they’re Christian (methinks Rob doth protest too much…)

We now have a draft of the sea anemone genome, and it is revealing tantalizing details of metazoan evolution. The subject is the starlet anemone, Nematostella vectensis, a beautiful little animal that is also an up-and-coming star of developmental biology research.

nematostella.jpg
(click for larger image)

Nematostella development. a. unfertilized egg (~200 micron diameter) with sperm head; b. early cleavage stage; c. blastula; d. gastrula; e. planula; f. juvenile polyp; g. adult stained with DAPI to show nematocysts with a zoom in on the tentacle in the inset; h, i. confocal images of a tentacle bud stage and a gastrula respectively showing nuclei (red) and actin (green); j. a gastrula showing snail mRNA(purple) in the endoderm and forkhead mRNA (red) in the pharynx and endoderm; k. a gastrula showing Anthox8 mRNA expression; l. an adult Nematostella.

A most important reason for this work is that the anemone Nematostella is a distant relative of many of the animals that have already been sequenced, and so provides an essential perspective on the evolutionary changes that we observe in those other organisms. Comparison of its genome with that of other metazoans is helping us decipher the likely genetic organization of the last common ancestor of all animals.

Continue reading "Common elements of eumetazoan gene organization in an anemone" (on Pharyngula)

The Alliance for Science, a wonderful group of which I am a member, has a link about a survey that examines public perception of the new Creation Museum. Having recently visited the Propoganda Ministry Museum myself, I was very underwhelmed. I will report my experiences there in a future post replete with pictures over at Neurotopia. I feel bad because I haven’t been keeping up on the evolution/science activism side of my life for a very long time now, aside from this post and pushing the Alliance for Science’s Evolution Essay Contest, I have done very little this year to even address the issue. Might have something to do with my dad dying and whatnot, I’m not sure.

The interesting part of the survey is that “white evangelicals” or “fundamentalists” weren’t particularly approving of the intellectual travesty Museum either. Maybe there is hope for America after all. Or, maybe the “Museum” really is such a shoddy, transparent attempt at evangelizing that nobody is fooled.

Do stop by and check it out.

First Calvert now Luskin?

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I have always found it fascinating how ID proponents try to avoid dealing with the real issues and instead focus on strawmen. For instance, Calvert and now Luskin are obsessed with the idea that:

Darwinian logic often contends that because a given proportion of ID proponents are creationists, ID must therefore be creationism. It’s a twist on the genetic fallacy, one I like to call the Darwinist “Genesis Genetic Argument.” As noted, it implies that each any and every argument made by a creationist must be equivalent to arguing for full-blooded creationism.

Much is wrong with this claim. If it were only so simple.

ID neither explains nor predicts

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Dembski, quoting Moorad Alexanian:

Dembski Wrote:

One can similarly say of Darwinian Theory of evolution, “I see evolutionary theory as not a theory–only a set of curious conjectures in search of a theory. True, it has great explanatory power, but a viable theory must have more than that. It must make predictions which can be falsified or confirmed.”

I am glad that at least Dembski is accepting the explanatory power of evolutionary theory, so now the question is merely, does evolutionary theory make predictions which can be falsified or confirmed.

However, a more urgent issue has been raised, namely, ID not only lacks explanatory power but also fails to make any non-trivial predictions.

We all remember Dembski’s admission that

As for your example, I’m not going to take the bait. You’re asking me to play a game: “Provide as much detail in terms of possible causal mechanisms for your ID position as I do for my Darwinian position.” ID is not a mechanistic theory, and it’s not ID’s task to match your pathetic level of detail in telling mechanistic stories. If ID is correct and an intelligence is responsible and indispensable for certain structures, then it makes no sense to try to ape your method of connecting the dots. True, there may be dots to be connected. But there may also be fundamental discontinuities, and with IC systems that is what ID is discovering.”

Nuff said

This video is one of the most effective criticisms of Ham's horrible little monument to ignorance in Kentucky — it's a geological tour of the rocks the “museum” is built upon. It seems the creationists chose to build on some beautifully fossil-rich Ordovician layers.

It convinces me that if I were in the Cincinnati area I'd rather kick around in the hills around the area than to waste my time in a pile of bunk.

A very interesting report

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A book-length report of the Committee on the Limits of Organic Life in Planetary Systems (commissioned by NASA) based on today’s best science is available free online here (It also can be purchased in a printed form from National Academies Press - see the above link).

Robert Crowther Wrote:

Critics of intelligent design theory often throw this question out thinking to highlight a weakness in ID. Richards shows that the theory’s inability to identify the designer is not a weakness, but a strength. ID does not identify the designer is because ID limits its claims to those which can be established by empirical evidence.

This is yet another example of why ID is scientifically vacuous. Indeed, if the designer could be established by empirical evidence, it would immediately eliminate the ‘Intelligent Designer’ as proposed by ID, namely a supernatural designer called ‘God’. In fact, in order to establish a ‘designer’ and in fact ‘design’ science inevitably uses such concepts as means, motives, opportunity, capability and so on. In addition, science uses eye witness accounts, physical evidence and more to support its thesis.

So how does ID infer design? Simple by arguing that a particular system or event cannot be explained by natural processes and thus should be seen as evidence for design. While ID also requires a specification, such specification is trivial, all that is required is some imagination about function.

ID faces a real problem: Either it insists that it cannot determine much of anything about the Designer which makes the ID inference inherently unreliable and thus useless (Dembski) or it attempts to become scientifically relevant but then it can at best conclude ‘we don’t know’.

So why do ID proponents still insist on such a flawed premise? Kitzmiller and Judge Jones explain.

Tangled Bank #83

PT needs a video…

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…as you can see by looking at the cool video of science bloggers at the American Society of Microbiology meeting. You do get to meet fellow PT blogger Tara Smith there, as well as our buddy Larry Moran.

This just in. Current Biology has published a short dispatch piece reviewing the flagellum evolution issue:

W. Ford Doolittle and Olga Zhaxybayeva (2007). “Reducible Complexity - The Case for Bacterial Flagella.” Current Biology, 17(13), R510-R512. July 3, 2007. DOI

I recently expressed some discouragement about the capabilities of blogs for critiquing scientific papers. I still have those reservations, but here is a data point that leans the other way:

Panda Prison Break

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Prof. Steve Steve’s buddy breaks out:

In the comments section of another thread over at Pandas’ Thumb, I asked leading ID proponent Paul Nelson to explain why he thinks the differences between humans and chimps represent macroevolution and not microevolution. Dr. Nelson responded to my question. The terms microevolution and macroevolution are so frequently used in the context of creationism, Intelligent Design, and evolution, so I thought it might be a good idea to move the topic to a new thread.

In addition to linking to Paul’s comment, I’ll also reproduce it in full at the end of this post. That should make it easier for people to see what he said in its entirety, without my commentary.

My question to Dr. Nelson was this:

While you’re here, and this is genuine curiosity on my part, could you take a couple of minutes to elaborate on exactly why you believe that human-chimp divergence is macroevolutionary rather than microevolutionary?

I asked that because he had just written a blog post in which he classified (more than once) the divergence of chimps and humans as “macroevolutionary.” The beginning of his response to my question is somewhat dismissive:

Micro, macro, tomato, tomahto…”I am apt to suspect there enters somewhat of a dispute of words into this controversy” (Hume 1779).

I’ve spent the last two years studying evolutionary biology, molecular ecology, speciation, and related subjects at the graduate level. My interest in evolution started well before that, and I’ve been following the various creation-evolution controversies for a solid decade now. I have absolutely no problem with the idea that the distinction between macro- and microevolution is nothing more than a dispute over words.

The thing is, they’re not my words.

Read More (at The Questionable Authority):

When an anti-evolutionist attempts to publicly “explain” a scientific paper, it usually signals two things: you should read the paper for yourself, and you should not be surprised to find that the creationist “explanation” misrepresents what the paper really says. A new blog post by Paul Nelson is no exception. Nelson, descending from the (relative) intellectual heights of the Discovery Institute to join the crowd at Dembski’s Whine Cellar, tells his readers that scientists did not grasp the true point of a 1975 paper because they did not read it all the way through.

The paper in question is a relatively famous one - it’s a paper in Science by Mary-Claire King and Allan Wilson that compared the available measures of genetic difference between humans and chimps with what was known about the morphological, behavioral, and cultural differences between the two species. King and Wilson, in this paper, calculated that there was a 1% genetic difference between humans and chimps, and that this difference is not enough to account for how different the two species really are. Nelson claims that scientists focused on the first finding because it was reported early in the paper, and missed the second part because it came later, after us lazy lab boys had given up on reading. (Nelson apparently believes that scientists share his work ethic.)

Read more (at The Questionable Authority):

Help out PT 2.0

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As some of you may know, I’m working on a new layout for the Panda’s Thumb and updating our backend at the same time. I’ve decided that this might be a good opportunity to delegate my work load to other experienced programmers.

I have a list of several projects that I’d like to complete before the role out of PT 2.0. So if you are interested in helping, send me a email at [Enable javascript to see this email address.]. I am looking for people who have lots of experience with Perl, MoveableType, MySQL, PostgreSQL, AJAX, JSON, Prototype, and/or Javascript.

Over at Uncommon Descent, the blog of William Dembski and friends, a contributor has a post up discussing Peter Duesberg’s aneuploidy hypothesis for cancer (which Orac discussed here for more background). The post itself is a bit confusing–it’s titled “When Darwinism Hurts,” and according to the author’s clarification, it’s about “Darwinism” leading us down the wrong path as far as cancer research goes. (Though whether cancer would be due to mutations in specific genes or in chromosomes, it’s still an evolutionary process, but I digress…) To me, anyway, the more interesting portion was in the comments section, where both DaveScot and Sal Cordova imply also that HIV might not cause AIDS; more over at Aetiology.

The UK government has followed in the footsteps of the Dover ruling by confirming that “intelligent design”, aka “neo-creationism” will not be taught in schools as part of the National Curriculum, reports VNU Net.

“The government is clear that creationism and intelligent design are not part of the science National Curriculum programmes of study and should not be taught as science.”

Recently the Council or Europe released a report addressing their concerns with “Intelligent Design”.

Haldane’s non-dilemma

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Quick, before I start the post proper, guess how many beneficial mutations separate us from the last common ancestor of humans and chimpanzees. Write your guess on a bit of paper, then read on.

Over at Uncommon Descent, Dave Scott opines

“Coyne and his chance worshipping peers are stuck between a rock and a hard place. The rock is gradualism and the hard place is Haldane’s Dilemma (http://en.wikipedia.org/wiki/Haldane’s_dilemma) . As gradualism gets more gradual Haldane’s Dilemma gets more difficult to overcome – there’s a limit to the number of mutations that can become fixed. As gradualism gets less gradual then the improbability of simultaneous beneficial mutations becomes more difficult to overcome. A truly classic example of being stuck between a rock and a hard place!”

The “simultaneous beneficial mutations” argument is a relatively new (or at least rejigged) argument that is dealt with elsewhere (see also here). However, Haldane’s dilemma has been a favoured argument in anti-evolution circles for a long time. Unfortunately for the anti-evolutionists, Haldane’s dilemma has never been a barrier to evolution, despite their misrepresentations. Recent work from the Human, Chimpanzee and Macaque genome projects underlines the fact that Haldane’s dilemma does not prevent evolution, and it is worthwhile revisiting one of the core anti-evolution arguments relating to it in the light of these results.

Although the line above says that this is a post by Mark Perakh, in fact I only served as a conduit for posting Professor Jerry Coyne’s material.

Professor Coyne has published a review (see here ) of Michael Behe’s new book titled The Edge of Evolution. Along with other reviewers, such as Mark Chu-Carroll, Sean Carroll, Richard Dawkins, and others, Jerry Coyne views Behe’s new book as Behe’s poorly substantiated (and vain) attempt to somehow pull up Behe’s status from the deep pit he finds himself in after the Dover trial, and thus to be re-admitted to the scientific community as a genuine scientist.

Behe responded to Coyne’s review on an Amazon blog (see here).

Now Professor Coyne offers a rebuttal of Behe’s response, which rebuttal I have the privilege of posting.

I can add to Jerry Coyne’s rebuttal just a few words. As it could be expected, Behe’s “response” to Coyne’s critique is typical of Behe’s supercilious style wherein he does not shy away from a self-gratifying delusion regarding his fiasco as an expert witness at the Kitzmiller vs Dover Board of Education trial. Professor Coyne in his brief rebuttal shows the dismal failure of Behe as the author both of his new book and of his “response” to critics.

Read Jerry Coyne’s rebuttal at Talk Reason.

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