November 2006 Archives

Microbiology pioneer dies

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Esther Lederberg dies at 83

Stanford University microbiologist Esther Miriam Zimmer Lederberg, a trailblazer for female scientists and the developer of laboratory techniques that helped a generation of researchers understand how genes function, has died at Stanford Hospital.

Professor Lederberg, who lived at Stanford, was 83 when she died Nov. 11 of pneumonia and congestive heart failure.

She discovered the lambda phage, a parasite of bacteria that became a key tool for the laboratory study of viruses and genetics, and was the co-developer with her husband [Nobel prize winner Joshua Lederberg] of replica plating, a technique for rapid screening of bacteria for desired mutations.

“She developed lab procedures that all of us have used in research,” said cancer researcher Stanley Falkow of the Stanford University School of Medicine.

She was also a pioneer of women’s rights, becoming a full professor at a time when women were rare on the faculties of Stanford and other major universities. “She was a real legend,” said Dr. Lucy Tompkins of Stanford.

(Continued at Aetiology)

Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design. Regnery Publishing, Inc. Washington, DC.Amazon

Read the entire series.

The most virulent attacks on evolution tend to come from political conservatives, and many conservatives have argued—as Wells does in The Politically Incorrect Guide to Darwinism and Intelligent Design—that political conservatism and evolution are fundamentally incompatible. Other conservatives, most prominently Larry Arnhart, have argued that conservatism is not only compatible with the lessons of evolutionary science, but that in some ways conservatism fits better with those lessons than do leftist political theories. Although I’m not a conservative myself, and although Arnhart’s writings on the subject contain some significant blind spots, I think he has the better of this argument. But the PIG thinks otherwise, and its attack on pro-evolution conservatives in Chapter 14 is written with the irrational and histrionic tone that many “intelligent design” activists adopt when discussing the subject. Let’s take a look.

Just so stories

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Many of us are familiar with the accusation by Intelligent Design activists that evolution and Darwinism deals in just-so-stories. For example, Behe, after the Kitzmiller ruling, remarked that:

On December 21, 2005, as before, there are no non-design explanations for the molecular machinery of life, only wishful speculations and Just-So stories.

Source: Whether Intelligent Design is Science: A Response to the Opinion of the Court in Kitzmiller vs Dover Area School District By Dr. Michael J. Behe

Similarly, Dembski ‘argues’ that

Evolutionist explanations are just-so stories. They are entirely speculative and do not qualify as evidence.

Source: Dembski, William A., 2002. No Free Lunch, Lanham, MD: Rowman and Littlefield, chap. 6.

If you needed another proof that the Founding Fathers were pretty smart guys when they noted that fights over religion are intractable and produce strife because they involve ultimate questions decided according to dictates of conscience, we have yet another proof. In recent weeks there has been a resurgence of internicine fighting amongst the pro-science blogging community over the issue of religion. The Holy Wars threads involve the debate between two camps: I think the camps are neutrally described as follows (feel free to hurl invective my way if you disagree).

Tyson lecture on YouTube

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Ask and yea shall receive. A kindly tech wizard did stop by and post Neil deGrasse Tyson’s lecture on YouTube (part 1, part 2), so now you can watch it without any tedious downloading. Virtually all of the lecture is there, the last few seconds seem to have been cut off.

The original thread has become yet another holy war thread (my fault, I acknowledge), so I will focus here simply on why Tyson’s lecture turned me into a fawning Tyson fanboy. Highlights:

Tangled Bank #67

The Tangled Bank

Before everyone disappears on their Thanksgiving break, stock up on science at the Tangled Bank #67: Giving thanks for science. And remember: if you have any creationist family members, be sure to get in a good fierce argument about evolution over the turkey day feast.

This is probably not news to anyone who has seen him speak before, but I’m pretty well convinced that Neil deGrasse Tyson, director of the Hayden Planetarium at the American Museum of Natural History in New York City, is the new Carl Sagan.

I watched some of the videos from Beyond Belief 2006 meeting, which as far as I can tell was an attempt by evangelical atheists to convert other academics to be evangelical atheists, so that eventually everyone in the U.S. will become evangelical atheists. (By the way, this plan gives a whole new spin to the term “delusion”, as the skeptical anthropologist Melvin Konner pointed out in his rambling, disorganized, but ultimately wise critique of the get-rid-of-religion folks.) The meeting was written up by the New York Times today, and the ID blogs are all happily clucking with disdain about it.

Neil deGrasse Tyson gave the final talk of the meeting, and thankfully, instead of bitter sniping at academics who have any empathy for religious people, which seems to have been the main activity of this meeting, Tyson took the only realistic route that scientists actually have to increase public support for science, and that is to explain why science is so important, cool, and amazing. I had only previously seen Tyson on PBS a bit, and recently on The Colbert Report, dissing Pluto and other pitiful iceballs.

While mocking iceballs is good fun, that short clip doesn’t get you the full picture of Tyson in action. Give him 30 minutes and a lecture hall, and watch him remind you what science is really about. (Link to huge mp4 file.)

(Note: Tyson’s talk is about the last third of the last mp4 file on this page. The mp4 file is 218 MB, so Right-Click, Save As to download, and give it a good 10-20 minutes. Maybe some friendly tech wizard could stop by, extract the Tyson lecture, put it on YouTube, and link to it in the comments.)

It’s Not Simple, Stupid.

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As many of the Sciencebloggers have already mentioned, Casey Luskin of the Discovery Institute is up to his usual stupidity. In this particular instance, he’s attempting, in a typically inept fashion, to fisk Carl Zimmer’s recent article in National Geographic. So far, I haven’t chimed in, mostly because everyone else has done such a good job that there wasn’t much to add.

Today, though, Karmen pointed out a passage that I’d somehow missed the first time I read Luskin’s piece. In the first part of his “rebuttal,” Luskin wrote:

The article called evolution a “simple” process. In our experience, does a “simple” process generate the type of vast complexity found throughout biology?

Karmen and PZ have both already pointed out the silliness of claiming that simple processes can’t lead to complex results. I’m going to talk about something different, but every bit as silly: the idea that evolution is a simple process.

Read more (at The Questionable Authority):

Australian Lungfish update

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I just received word from Per Ahlberg that the status of the Australian lungfish conservation efforts have reached a critical phase: letters are needed NOW. Here's the situation:

The Traveston Dam proposal has moved into a new and critically important phase: it has been referred to the Federal Environment Minister (Mr Ian Campbell) for consideration under the Federal Environmental Protection and Biodiversity Conservation Act. Ian Campbell has the power to stop the dam, but if he doesn't it is unlikely that any other organisation or individual will be able to do so.

The first hurdle that must be crossed in order to stop the dam is to ensure that the Minister does not allow the Queensland Government to conduct the EPBC assessment of it's own proposal - something that he is entitled to do. This would be a recipy for disaster as they would be certain to conclude that their own proposal is environmentally sound! The assessment must be carried out by the Federal Environment Ministry to ensure a proper process.

The Save the Mary River Campaign is asking supporters to write to Mr Campbell and a number of relevant senators to demand a proper assessment, and provides some very helpful information and instructions. This is URGENT: letters have to be received before 27 November.

You can get details here—start writing!

We tend to focus on the ID creationists here at PT, but it is worth remembering that outside of the public policy sphere, in the conservative evangelical subculture, it is still the young-earth creationist ministries that are the dominant players.

All year there have been rumors and speculation about the causes of a breakup between the USA branch of Answers in Genesis, which is sinking a huge amount of money into their Creation Museum, and the Australia branch. Blogger Jim Lippard is The Official Expert on all of this, and today he has The Big Scoop on a whole bunch of new details about the schism. Follow the links in his post to see his previous posts tracking the issue throughout 2006.

Now It’s Really, Really Over

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As I posted previously, the South Carolina State Superintendent of Education Race had resulted in a narrow sliver of a win by the pro-science candidate Jim Rex. But the creationist candidate, Karen Floyd, had the option of protesting the results. Today however she has finally conceded.

In which I am a prophet

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Five days ago, I wrote about a creationist letter that was published in Nature. At that time, there was a discussion going on in email with the gang at the Panda's Thumb, and someone said we ought to get a pool going on how long it would take before the Intelligent Design creationists would use this to argue that their case was being seriously discussed in the pages of a major scientific journal. Four months was suggested; I said one week.

I should have put some money down on that.

It turns out one of the PhD alumni in biology from Moran's school (University of Toronto), a respected scientist and pro-ID creationist recently had his letter published in the prestigious scientific journal Nature. This is news in itself that creationists and ID proponents are getting airtime now in scientific journals

That was the unctuous clown, Sal Cordova, of course. It was four days before they were trumpeting this crank letter as a triumph for Intelligent Design creationism.

Paul Nelson has developed a liking for ORFans, sequences of DNA that appear to code for proteins, but have (or had) no currently detectable homology to other genes. He feels they represent a difficulty for “Darwinian” accounts of gene origin and common descent. I have previously discussed why ORFans present no challenge to modern evolutionary theory, Dr. Nelson even showed up in the discussion.

More recently, he has been promoting ORFans again, without indicating he has learnt anything at all from our discussion. In particular, in a recent article in the Christian Post he claims that 28% of the genes in Mycoplasma genitalium are ORFans.

Nearly one-third of the protein-coding genes of mycoplasma, the simplest “free-living thing” up until last year, are unknown genes or ORFans.

Unfortunately for him, the actual number is zero. Yes, that’s right, zero. How did he get it so wrong?

Talk.origins' resident curmudgeon and contributor of a number of FAQs in the archives, Larry Moran, has a new blog, the Sandwalk. Interestingly, it seems to have been discovered first by Billy Dembski and Denyse O'Leary, who made a sneering post on it at Uncommon Descent…which means that the comments are filled with the fulminations of the usual creationist suspects. Think about that; they've crept out of the shelter of their heavily censored sanctuary and are out in force at a blog that won't edit and delete and modify your comments. If you want to engage Intelligent Design creationists directly, it's a happy hunting ground!

Oh, yeah…and Moran himself has also put up quite a collection of articles, all in his inimitably opinionated style, so I'm sure the raconteurs of the Panda's Thumb will find much to argue about over there.

Server News

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Well, our server upgrade didn’t go as planned. As a consolation prize, we’ve added another gig of memory to the existing server, and made changes to the server to take advantage of it. We are still planning to upgrade our server and our bandwidth connection. We have enough funds for a new server, but if you feel like donating for the future, give to the Talk.Origins Foundation.

I’ve also reenabled compression for Microsoft Internet Explorer. My tests show me that the previous pt-msie interaction problem has been fixed, probably when I finally fixed the time zone two weeks ago. Let me know if you are having problems with pages not updating correctly.

Evidence of Design?

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by Pete Dunkelberg

The Apologetics Calendar had exciting news for Floridians recently:

Your online source for strategic apologetics events around the U.S. and beyond.

Evidence of Design Conference, November 3–4, 2006 — Clearwater and Tampa, Florida

The C. S. Lewis Society is sponsoring this conference, which will thoroughly equip church members and leaders with generally non-technical, cutting-edge information. It will demonstrate practical steps to use design-evidence as a thoughtful bridge to skeptics who have been taught through Darwinian evolution that God is a myth. This conference will enable Christians and others to use simple evidence to demonstrate there is in fact a designer of life and that he is Jesus Christ. The three main speakers include Dr. Walter Bradley, Baylor University professor, co-author of The Mystery of Life’s Origin and co-founder of the Intelligent Design Movement; Dr. Paul Nelson, leading ID theorist and editor of the journal Origins and Design; and Dr. Tom Woodward, author of Doubts about Darwin and Darwin Strikes Back (October 2006). Their material will be presented in a skeptic-friendly manner, so all skeptics of design are cordially invited. The wonders of living cells will also be portrayed on stage by large models of the “molecules of life,” including a split-open DNA model that is simply stunning. This will be an eye-feast you’ll never forget!

Part I: Darwin’s Growing Crisis, will offer presentations by our speakers at Calvary Baptist Church, 110 North McMullen Booth Road, Clearwater, Florida 33759, 727.441.1581 (www.calvarybaptist.org/) at 7:30 pm Friday evening, November 3rd.

Part II: New Evidence of Design, will be presented by the same speakers on Saturday, November 4th at Calvary Baptist from 9 am until noon and at Christ Community Church, 6202 N Himes Ave, Tampa, FL 33614, 813.879.2077 (http://ccct.dallasnewmedia.com/) from 1:30 pm until 4:30 pm. Part II of the conference is presented on both sides of Tampa Bay as a convenience to those desiring to attend. The presentations on Saturday at these two locations are identical.

Had the Discovery Institute had found some startling new evidence just since the Dover trial? Brimming with curiosity, I drove all the way to Clearwater to hear the news. Nelson gave two talks, of which the first turned out to be the best. What follows is little more than my raw notes of that talk. The slides with quotes and citations came quicker than I could take them all down, and as the night wore on my note taking became rather sketchy, but you will get the gist of his presentation. Draw your own conclusions.

The Neandert[h]al FAQ

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The Neanderthal FAQ, by John Hawks, describes the recent DNA analyses as presented in Nature (lots of references and links).

On, Tuesday, November 14th, 2006, Robert Pennock, author of “Tower of Babel, The Evidence Against the New Creationism” presented a lecture titled “The Ground Rules of Science: Why the Judge Ruled Intelligent Design Creationism Out of Court “ on the topic Intelligent Design as part of the Helen Edison Lecture Series [1]. Apparently, the lecture was attended by close to 5000 people, filling the beautiful RIMAC arena

Since the Sixth College sponsored the event, “[a]ll Sixth College students[ we]re strongly encouraged to attend the Convocation, and first-quarter CAT students [we]re required to attend. The 2006-2007 Council of Provosts Convocation Series is also open to the general public. “

As an ironic side note, it seems that Luskin’s confusion as to who was required to attend may have contributed to the full house.

UCSD-TV has scheduled the program for the following dates

12/11/2006, 8:00 PM pacific time zone 12/12/2006, 11:00 PM pacific time zone 12/15/2006, 7:00 PM pacific time zone 12/17/2006, 8:00 PM pacific time zone 12/26/2006, 10:00 PM pacific time zone 1/8/2007, 9:00 PM pacific time zone 1/9/2007, 11:00 PM pacific time zone 1/12/2007, 6:00 PM pacific time zone

Oops, they did it again

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From Premier Christian Radio we learn more about the concept of Intelligent Design.

28 October 2006 Darwin vs. Design

We revisit the subject of Intelligent Design and Evolution with special guest Dr. Tom Woodward from the USA who has written a history of the Design movement. Pete Hearty of the National Secular Society argues for Darwinian evolution. Will the idea of a a “God-like” intelligence behind nature supersede Darwinism?

A “God-like” intelligence behind nature. Good for them, finally some Christians who clearly describe what ID is all about.

Peer Review

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Over at the ARN blog, Denyse O’Leary has a four-part article up attacking the peer-review system. Rob Crowther, of the Discovery Institute’s Media Complaints Division, has chimed in with his own post on the topic. There’s a great deal of humor in watching anti-evolutionists try to dismiss peer review as not worth the effort anyway. It bears an amazing resemblance to this really cute old fable about a fox, but I’ll be kind and pretend that there is actually something more to the O’Leary and Crowther rants than good old sour grapes.

Their major complaint about peer review is, of course, that their stuff, for some bizarre and unaccountable reason, has a really hard time surviving the process. In Crowther’s words:

To sum up, science journals that are wedded to Darwinian evolution refuse to publish authors who explicitly advocate intelligent design. Then Darwinists attack intelligent design as unscientific because it isn’t published in peer-reviewed journals.

O’Leary puts it a bit differently, but the basic concept is the same:

There is a modest but growing number of ID-friendly peer-reviewed publications. But - given the woeful state of peer review - papers that support or undermine ID hypotheses would probably be neither better nor worse recommended if they were never peer reviewed, just published, amid cheers and catcalls..

Of course, they try to justify their criticism of peer review on grounds other than their inability to reach the grapes. Peer review, they claim, doesn’t identify fraud. It’s not that good at catching incorrect findings. It squelches new ideas. It places “intellectual pygmies” in judgement of intellectual giants. It favors consensus. It sucks the life out of people, and is entirely responsible for global hunger and bad hair days. OK, I made the last two up, but you should still get a taste for the basic strategy that’s being employed here - it’s an oldie, but a goodie. Throw as much crap as you can at the wall, and hope that some of it sticks.

In this case, some of it does stick. It should. Peer review is not a perfect system. It is absolutely flawed. It is, in fact, not good at catching fraud. It does not catch many flawed studies. It does make it more difficult to publish new ideas, and it is absolutely capable of sucking the will to live from people. (Just because I made that one up doesn’t mean it isn’t right.) To paraphrase Churchill, peer review is the worst system out there, except for all the others that have been tried.

Read more (at The Questionable Authority):

The results of yesterday’s recount will be certified today by the Elections Commission, and pro-science candidate Jim Rex appears to have edged out ID advocate Karen Floyd by the narrowest of margins – 455 votes out of over 1 million cast. This is being called the closest general election result in South Carolina history. There is a strong chance that the Floyd campaign will protest the result (they have 5 days to do so), but this will be a last ditch desperation move. I don’t think I’m being premature in saying that, barring anything really weird, the race is over and Rex has won.

I would like to be able to say that Floyd’s anti-science posturing did her in, but that’s probably not the case. Her unpopular pro-voucher stance, combined with the fact that Rex was by far the more qualified candidate (Floyd has no educational experience), was most likely her undoing. Still, this is quite an achievement for Rex and a major blow to the Discovery Institute.

South Carolina prides itself on marching to the beat of a different drummer, and last Tuesday was no exception. While Democrats were winning across the country, Republicans were sweeping offices in SC. It appeared that the State Superintendent race would be no different; nearly every poll prior to the election had Floyd up by a healthy margin (polls for such “down ballot” races must be taken with a grain of salt, of course) and she had a huge financial lead, thanks in large part to gobs of money from an out-of-state voucher advocate who used dummy corporations to skirt campaign finance laws. But she still lost.

This appears to be the last in a series of massive blows to the Discovery Institute’s political agenda, especially given that South Carolina has been a major focus of theirs. Earlier this year, the state Board of Education rejected DI-backed pro-creationism language in the state curriculum standards (which of course prompted the DI to declare victory based on one obscure line that had been added to the standards during a previous year and was not up for consideration). It seems that they can get no traction at all, not even in South Carolina. Maybe they should just give it up already.

Nature publishes a crank letter

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This week's issue of Nature contains a bizarre letter from a Polish creationist, forester, and member of the Polish parliament. His credentials notwithstanding, it is a very silly diatribe that makes a series of false claims—claims that are trivial to dismiss, but in that fine tradition of the Gish gallop and Hovind's rambling free-association eructations, he makes a lot of them. A whole lot of them; all just plain naked assertions with no evidence to back them up, because the evidence, if he'd bothered to discuss it, contradicts him. Even the title reveals his ignorance of how science works.

Rather than trying to dismantle it piece by piece, I've just added links to his letter that lead to short, simple refutations of his claims.

Continue reading "Nature publishes a crank letter" (on Pharyngula)

Continued random confusion

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Seems that noone has informed Logan Gage of his erroneous interpretations of Darwinian theory, the concept of randomness and the meaning of purpose. In a followup posting Gage argues

Logan Gage Wrote:

If you have not seen it already, you will enjoy playing with this random mutation generator. You will see how wonderful the Darwinian process is at taking your text and moving on to ever-greater levels of complexity.

In addition to failing to comprehend the concept of randomness, Gage now seems to confuse random mutation with ‘the Darwinian process’. Has noone informed him that the Darwinian process consists of two components? In fact, mutations were not even known in Darwin’s days, thus Darwin speaks of variation and selection.

In addition, he also seems to mangle Dawkins’ Weasel example, which seems a common affliction amongst creationists.

In other news, David Opderdeck explores the flawed logic in Logan Gage’s position and argues that Gage’s position “was unfair, and reflects a serious theological problem with some “strong” ID arguments.”

Is there anything redeeming to Intelligent Design?

Server News

We have ordered a new server, and if everything goes according to plan, we will make the switch this weekend. Be prepared for PT to go offline this weekend. We are still exploring our options for improving our bandwidth.

octo_eye.jpg

Ian Musgrave has just posted an excellent article on the poor design of the vertebrate eye compared to the cephalopod eye; it's very thorough, and explains how the clumsy organization of the eye clearly indicates that it is the product of an evolutionary process rather than of any kind of intelligent design. A while back, Russ Fernald of Stanford University published a fine review of eye evolution that summarizes another part of the evolution argument: it's not just that the eye has awkward 'design' features that are best explained by contingent and developmental processes, but that the diversity of eyes found in the animal kingdom share deep elements that link them together as the product of common descent. If all we had to go on was suboptimal design, one could argue for an Incompetent Designer who slapped together various eyes in different ways as an exercise in whimsy (strangely enough, though, this is not the kind of designer IDists want to propose)…but the diversity we do see reveals a notable historical pattern of constraint.

Continue reading "The eye as a contingent, diverse, complex product of evolutionary processes" (on Pharyngula)

Is Life Inevitable?

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The origin of life is one of the most fascinating and controversial of scientific topics. The event occurred so long ago, and left so little clues, that we have struggled in our understanding of it. The basic building blocks of life turn up in meteors, cosmic dust and the gas clouds surrounding stars, as well as being manufactured on Earth in almost every conceivable environment. But how we get from these simple building blocks to metabolism, genes and organisms is not entirely clear, despite several promising lines of attack.

How probable is the origin of life? Creationists and Intelligent Design advocates alike claim that it is highly improbable. Most scientists think we are still at too immature a stage of knowledge to even speculate. However, a recent paper (free PDF here) by Harold Morowitz and Eric Smith in the Sante Fe Institute working papers series , suggests that life might be inevitable on thermodynamic grounds.

… the continuous generation of sources of free energy by abiotic processes may have forced life into existence as a means to alleviate the buildup of free energy stresses.

There is a good over view at Nature News (free online), and you might like to drop in on the Nature NewsBlog on this subject. Myself, I’m not convinced. While they make a good case for a simple autotrophic core of reactions forming the start of life chemistry, there are a range of details missing in their treatment of the thermodynamic aspects. However, this is a promising start from which more formal treatments can be derived. Anyway, read the paper and the Nature commentary, and see what you think. Check out some of the other working papers on the origin of life as well.

Update: Astronomy Now has a very interesting article on new experimental approaches to prebiotic chemistry.

When ignorance applies scientific vacuity

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Just when you think you have seen a new low in scientific ignorance amongst ID activists, Salvador Cordova comes to the rescue by arguing that

Salvador Cordova Wrote:

In information science, it is empirically and theoretically shown that noise destroys specified complexity, but cannot create it. Natural selection acting on noise cannot create specified complexity. Thus, information science refutes Darwinian evolution. The following is a great article that illustrates the insufficiency of natural selection to create design.

In fact, quite to the contrary, simple experiments have shown that the processes of natural selection and variation can indeed create specified complexity. In other words, contrary to the scientifically vacuous claims of Sal, science has shown that information science, rather than refuting Darwinian evolution, has ended up strongly supporting it.

So what causes this significant level of confusion about evolutionary theory, and information theory?

In a recent article in Touchstone Magazine, Jonathan Witt, fellow for the Discovery Institute’s Center for the renewal of science and culture, has written a review of Francis Collins’ book “ The Language of God: A Scientist Presents Evidence for Belief”. Amongst other things in this review he claims that Michael Denton has demonstrated that the “backwards wiring” of the mammalian retina improves oxygen flow and is good design.

Denton of course, has done no such thing. Since I am on a role with things visual, I am reposting an updated version of an earlier article on this topic.

Last week the first draft of the complete genome of the Sea Urchin was announced. In amongst the wealth of data were new clues to the evolution of the immune system, and the discovery that Sea Urchins express both rhabdomyeric and cilliary opsins, without having specialised eyes, gives us new clues to the evolution of the eye.

But several months ago, a paper was published with far less fanfare. In this paper, the photosensitive pigment from an alga was inserted into the retinal ganglion cells of blind mice, and their visual responses were restored (Bi et al., 2006). This paper may lead to the treatment of certain kinds of blindness, but also blows away one of Behe’s arguments.

Random confusion by design?

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These days it’s hard to visit the few pro-ID sites and not be greeted by a level of scientific ignorance matching and in some cases even exceeding the level of scientific vacuity of ID itself. Point in case is a recent contribution by Logan Gage titled Francis Collins on Square Circles

If the Discovery Institute’s Center for the renewal of Science and Culture were serious about its quest to improve science education, especially evolutionary biology, then it should spend some time educating its spokespeople.

Gage objects to Collins’ position on evolution and Christianity, ‘arguing’ that an unguided and random process could not possibly involve a deity. Let’s count the many confusions:

The sea urchin genome

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sea_urchin_sm.jpg

Oh happy day, the Sea Urchin Genome Project has reached fruition with the publication of the full sequence in last week's issue of Science. This news has been all over the web, I know, so I'm late in getting my two cents in, but hey, I had a busy weekend, and and I had to spend a fair amount of time actually reading the papers. They didn't just publish one mega-paper, but they had a whole section on Strongylocentrotus purpuratus, with a genomics mega-paper and articles on ecology and paleogenomics and the immune system and the transcriptome, and even a big poster of highlights of sea urchin research (but strangely, very little on echinoderm development). It was a good soaking in echinodermiana.

Continue reading "The sea urchin genome" (on Pharyngula)

My day was spent in the Twin Cities attending the inaugural public meeting of the Minnesota Citizens for Science Education (MnCSE), and I can safely say now that Science Education Saturday was a phenomenal success: a good turnout, two top-notch talks, a stimulating panel discussion, and an involved audience that asked lots of good questions. You should have been there! I expect that, with the good response we got today, that there will be future opportunities to attend MnCSE events.

I'll just give a brief summary of the main points from the two talks today. I understand that outlines or perhaps even the powerpoint files will be available on the MnCSE page at some future date, but give the organizers a little time to recover from all the effort they put into this meeting.

Continue reading "A summary of the MnCSE Science Education Saturday" (on Pharyngula)

This Worm Has Turned

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Imagine that you are a Ph.D. candidate in biology. You aren’t doing anything with charismatic megafauna; your focus is on invertebrates. Worms, really. But you’ve done some work on figuring out how worms move through substrate. It is good work, and you’ve been published in Nature on the topic. That’s all pretty cool.

Then, you find out that your research has been used as a prime exhibit in a political campaign to advance “intelligent design” and “teach the controversy” positions. That’s not cool.

Kelly Dorgan, though, has her own message about the misuse of her work, one that she has sent to the Ohio Board of Education, and that she has graciously given permission to be published here. Read it below the fold.

One would hope that politicians seeking to understand science education would turn to people who know what they are talking about, and avoid propaganda outlets. In Ohio, the propaganda has been dished out in large quantities by SEAO and the Discovery Institute. Fortunately, there are many science faculty at Ohio’s universities who have taken the time to advise non-scientists on the Ohio State Board of Education; they have made themselves available as a resource. There are professional scientific organizations in Ohio whose goal is better science education for students. Between these resources, a politician who wants to get serious about improving science education in Ohio has many choices in getting good advice.

Witt reviews Collins

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Jonathan Witt, fellow for the Discovery Institute’s Center for the renewal of science and culture, has written a review of Francis Collins’ book “ The Language of God: A Scientist Presents Evidence for Belief”.

Witt objects to Collins’ interpretation of Intelligent Design, arguing that like many before him, Collins just does not get it… Or does he?

A few weeks back, I posted a rebuttal to the Casey Luskin/Michael Behe interview, which itself rebutted the Pallen/Matzke Nature Reviews Microbiology paper on flagellum evolution.

As I posted previously, there is a new organization in Colorado called the Colorado Evolution Response Team, or CERT. James DiGregori, a founding member of CERT and a senior colleague of mine, was interviewed on NPR’s Colorado Matters. The direct link to the audio file is here. It’s an excellent interview.

In other news, if anyone wants to know who won the South Carolina State Superintendent of Education race, tough potatoes. We will have to wait until at least next week to get closure on that. But the pro-science candidate currently has the lead, and that’s encouraging.

Desperate times for ID

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On UcD our dear friend Salvador Cordova shows how the recent political, scientific and legal disasters to Intelligent Design have made the movement desperate for some ‘good news’. According to Sal, the good news comes in the form of 30% of community college professors considering ID to be science.

So let’s look at the study in question:

The study was done by two sociologists, Neil Gross of Harvard University and Solon Simmons of George Mason University. They contacted 1,471 professors at religious and secular colleges and asked about politics and faith.

Source: Praying for an ‘A’ might not impress your prof

Honest Science Wins in Ohio

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As readers of the Thumb no doubt already know, honest science won big in the Ohio State Board of Education elections yesterday. Four of the five candidates endorsed by Ohio HOPE won their races. In the fifth race, Ohio HOPE endorsed two of four candidates who unfortunately split 51% of the vote between them, allowing a third candidate to win with 38% of the total vote. Ohio HOPE was organized by scientists in Ohio a few months ago to support teaching honest science in K-12.

The most striking result of the SBOE election was the overwhelming defeat of Deborah Owens Fink. Owens Fink first brought Intelligent Design Creationism to the Ohio Board in 2000, offering a “two models” motion: teach both evolution and intelligent design. Later she followed the Disco Institute party line in advocating “critical analysis of education” (= Wells’s trash). When that was finally nuked in February 2006, Owens Fink commenced pushing a so-called “Controversial Issues Template” that in its original incarnation included global warming, stem cell research, cloning, and evolution as its targets. That effort was resoundingly rejected by the SBOE in October.

Now, it’s tempting to attribute Owens Fink’s defeat to the overall Democratic landslide in Ohio. She is closely identified with the religious right and has used their mailing lists to strong effect in her election campaigns and in the anti-science effort in the SBOE in 2002 and 2004. But I think that does not account wholly for her defeat. To give one counter-example, Sam Schloemer, a strong and outspoken defender of honest science on the Board and a Republican, won in District 4 with 67% of the vote, more than reversing the overall Democratic margin. The average Democratic margin in the statewide offices for which I have data at the moment was 55%-44%. Owens Fink got just 29% of the vote in her SBOE district, substantially less than the statewide average vote for Republicans and less than even Ken Blackwell’s meager 37%.

An important aspect of this win for Ohio is that it was a decisive statement by voters who knew what they were voting on. Owens Fink has been outspoken in her contempt for scientists. She told the NYTimes that the notion that there is scientific consensus on evolution was “laughable”. She and Chris Williams, a creationist biochemist ally, spent two hours on a young earth creationist’s radio program in the weeks before the election maligning mainstream science. When the “Controversial Issues Template” was finally deep-sixed by the SBOE, Reverend Michael Cochran, the other prominent ID advocate on the Board, complained that declaring an emergency and voting at the same meeting as the motion was made was merely a tactic to prevent careful consideration. Well, the voters had plenty of time for careful consideration and they resoundingly rejected ID creationist efforts to subvert the teaching of honest science in Ohio.

RBH

There has been a lot of competition, but here is one of the silliest things I’ve read this week on the ID blogs:

And who is Leshner to judge what will promote science?

In case you didn’t know, Alan Leshner is the CEO of the American Association for the Advancement of Science (AAAS).

Randy Neanderthals?

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In population genetics, the influx of new genetic variants from one population to another after a period of genetic isolation is called introgression. One of the most intriguing questions in anthropology is the possibility and role of introgression along the Homo sapiens lineage, that is, in more mundane terms, the extent to to which our H. sapiens ancestors were willing and able to mate with other coexisting human species (such as H. neanderthalis, and possibly even H. erectus), and whether such exchange of genetic material played any role in our evolution.

Molecular evidence from available Neanderthal mitochondrial DNA, which is transmitted to the progeny by females alone, has suggested that Neanderthal gals did not contribute to H. sapiens‘s current mitochondrial genetic diversity. Whether any trace of sapiens-Neanderthal interbreeding can be detected in nuclear genes, however, is still an open question. A paper appearing online yesterday in PNAS (free access, for once!) reports strong evidence of introgression for a variant of the microcephalin gene, known to be involved in brain development and size. To make a very long story short, it appears that a common human variant of the microcephalin gene originated on a chromosomal region that separated from the human lineage over 1 million years ago, only to come back (“introgress”) into H. sapiens about 37,000 years ago. John Hawks’s Anthropology blog has a couple posts with an excellent explanation of the story, so I’ll just send you there to read about it. John also hints at more evidence coming out in the near future for sapiens-Neanderthal hanky-panky, and of course Svante Paabo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, the whiz of ancient DNA analysis, has recently announced his goal to clone and sequence the Neanderthal genome, which is likely to yield more information in this regard, so stay tuned…

Tangled Bank #66

The Tangled Bank

This week's Tangled Bank covers everything from spacewomen to cavemen in The Tangled Bank - The Future, Present, and Past at easternblot.net. The election news is all over, so it's time to read some science!

Go Forth and Vote

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The 2006 Weblog Awards

The Panda’s Thumb has been lucky in past elections, with Dover, Kansas, Ohio, and South Carolina coming out on the side of science. Once more our readers need to get out and vote. This time vote for us for Best Science Blog of 2006.

  • Polls close at 11:59 PM (US - Eastern) December 15, 2006.
  • You may vote once every 24 hours in each poll.
  • After voting in an individual poll you will be locked out from voting again in that poll (on the computer you voted from) for 24 hours.

If you are for pandas and sunshine, vote for Panda’s Thumb. If you like root canals and creationists, vote for the other guys.

Remember, vote early and vote often.

This thread is for discussing the 2006 Midterm Election. Make sure you watch the Daily Show’s Midwestern Midterm Midtacular series (archives available on the Comedy Central website, 1 hour special tonight) to get in the right frame of mind.

It will be interesting to watch the results, because there is a fair bit of evidence that politicians have been running from “intelligent design” this year, at least when they are trying to appeal to voters in the middle (get-out-the-base efforts, e.g. phone calls to likely supporters, seem to be different).

And the press has been paying attention in a number of races. See the NCSE news summary on Kansas, and the story about the Ohio Board of Election race between Deborah Owens-Fink and challenger Tom Sawyer: “Evolution Debate at Center of Ohio Board of Education Race.” There is little polling for such elections, and voter turnout is typically very low for (a) midterm elections and (b) local races. So it is very hard to predict how things will turn out.

State-wide races are also important to watch – notably, Pennsylvania Senator Rick Santorum is facing a tough challenge, and has been running from ID ever since the Kitzmiller v. Dover loss (before that, he was the biggest friend the ID movement had in Congress). The issue has also come up in Michigan and dozens of other states.

I know that the official Kansas election returns are here. But please post links to the returns for other races, news stories on the issue, etc.

Last week’s Chronicle of Higher Education carries an excerpt (note: subscription required) from Blind Faith: The Unholy Alliance of Religion and Medicine, a book by Columbia University Professor Richard P. Sloan on the relationship between medical science and religion. Obviously a very hot topic, especially after the loud salvo coming from Dawkins’s The God Delusion, and the sharp reverberations it generated in both printed and online form (not to mention the reverberations on the reverberations).

I have not read Sloan’s book, but from its reviews and other writings by him, it is clear that he is no faith-healing enthusiast - on the contrary. Still, I strongly hope his book’s arguments are less naive than what this excerpt makes them look like, because unless the piece was meant more as a provocation and a teaser than a summary, they just fall flat Regardless, I think the excerpt is worth discussing here, and thinking about, because of its relevance not only for the general relationship between science and religion, but also because some of the issues it covers relate to the evolution/Creationism controversy.

Marc Hauser: Moral Grammar

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In earlier postings of mine, I mentioned the term “moral grammar” without providing the full references as to where the term originates and what it means. The term “Moral Grammar” was coined by Marc Hauser to describe a universal set or rules and principles to be used to build moral systems:

The core idea is derived from the work in generative grammar that [MIT linguist Noam] Chomsky initiated in the 1950s and that the political philosopher John Rawls brought to life in a short section of his major treatise A Theory of Justice in 1971. In brief, I argue that we are endowed with a moral faculty that delivers judgments of right and wrong based on unconsciously operative and inaccessible principles of action. The theory posits a universal moral grammar, built into the brains of all humans. The grammar is a set of principles that operate on the basis of the causes and consequences of action. Thus, in the same way that we are endowed with a language faculty that consists of a universal toolkit for building possible languages, we are also endowed with a moral faculty that consists of a universal toolkit for building possible moral systems.

Source: American Scientist The Bookshelf talks with Marc Hauser by Greg Ross

Jonathan Wells, the creationist who makes shoddy claims about developmental biology, has deigned to respond to my criticisms…but only indirectly, on another blog. It's an interesting response, in that it once again reveals Wells' misunderstandings of biology, and his sneaky way of inserting phony claims.

Continue reading "Well, well, Wells: Jonathan Wells reacts" (on Pharyngula)

It certainly has been a rough few days for disgraced Rev. Ted Haggard, quoted by AP/MSNBC as saying

The fact is I am guilty of sexual immorality. And I take responsibility for the entire problem… I am a deceiver and a liar. There’s a part of my life that is so repulsive and dark that I have been warring against it for all of my adult life.”

Why mention this on the Thumb? Because Haggard is also a barnstorming “Goo to you by way of the Zoo”-style creationist. As proof, I submit this 6-minute YouTube video that looks to be part of Richard Dawkins’ BBC television series “The Root of All Evil.” The appearance of Rev. Haggard in this series was mentioned on the Thumb waaaay back on Jan. 12th, 2006 by commenter Dean Morrison.

Anyway, watch this 6-minute YouTube clip to see just how really smarmy and oily Haggard can be when he’s not trying to explain his sexcapades.

Hat Tip: Thanks to Raw Story

Time: God vs. Science

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Time has an interesting article on God vs. Science which includes an interview with Francis Collins and Richard Dawkins.

The article points out how the Intelligent Design movement may have inadvertantly given science a much needed boost, as more and more scientists express their frustrations with the level of scientific vacuity of this new form of creationism. Even more ironically, ID may have provided atheists a much needed boost.

Like Freudianism before it, the field of evolutionary psychology generates theories of altruism and even of religion that do not include God. Something called the multiverse hypothesis in cosmology speculates that ours may be but one in a cascade of universes, suddenly bettering the odds that life could have cropped up here accidentally, without divine intervention.

Few may have noticed that recently the Natural History Museum of the University of Oslo opened an exhibition on homosexuality in the animal kingdom

The exhibit puts on display a small selection among the more than 1500 species where homosexuality have been observed. This fascinating story of the animals’ secret life is told by means of models, photos, texts and specimens. The visitor will be confronted with all sorts of creatures from tiny insects to enormous spermwhales.

The website shows some interesting examples of gay animals and provides some useful references.

Republican State Superintendent of Education candidate Karen Floyd, a strong supporter of Intelligent Design, helpfully tells us what we’ve known all along:

“I support the Education Oversight (Committee)’s premise that we should have critical analysis so that the discussion of intelligent design is not prohibited and could be part of the classroom discussion,” Floyd said.

The Discovery Institute must not be pleased. After having bent over backwards to insist that their “critical analysis of evolution” plan in South Carolina isn’t the same thing as teaching ID, here Floyd goes and lets the cat out of the bag. As we’ve seen time and time again, it’s hard for them to maintain their position that “critical analysis” has nothing to do with ID when their own supporters understand it as teaching ID.

And here’s something else that may have them spinning for damage control:

Forbidding teachers, even science teachers, to broach the subject of life’s origins creates an atmosphere of fear that’s unfair to children, [Floyd] said. Students are smart, she said, “and they connect the dots: Some will wonder “how many dinosaurs boarded Noah’s Ark.”

Uh-oh, here comes Young Earth Creationism. And to think that the Discovery Institute has spent all that time trying make people think that ID had nothing to do with creationism in general, much less the extreme YEC position.

I have more to say about Karen Floyd and the race for State Superintendent of Education over at Sunbeams from Cucumbers.

Dear everybody,

I have braved the intellectual desert that is philosophy in order to bring enlightenment to these poor philosophers of science at the Philosophy of Science Association conference in Vancouver. I allowed the lovely Janet Stemwedel to host my report and the photos she took of me instructing various people in the real truth about science.

Here is me avoiding that Wilkins guy and having fun, before it went downhill, as these things do, but it has some famous philosophers (if that’s not a contradiction in terms) with me. And here is some more of me with other philosophers, who are only famous to other philosophers. That Wilkins guy keeps getting into the shot, though, so close one eye to avoid seeing him.

Strange worm, Xenoturbella

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xenoturbella.jpg

This odd marine worm, Xenoturbella bocki, is in the news right now, and I had to look it up in Pechenik's Biology of the Invertebrates(amzn/b&n/abe/pwll) to remind myself of what it was. Here's the complete entry:

Xenoturbella bocki

This marine worm, first described in 1949 as an acoel flatworm and later claimed as either an early metazoan offshoot or a primitive deuterostome, has recently been affiliated with primitive bivalve molluscs, based upon a study of gamete development (oogenesis) and an analysis of sequence data from both 18S rRNA and mitochondrial genes. Little is known about its reproductive mode, and developmental studies that might help to resolve the phylogenetic issues are just starting to be reported. A second species was described in 1999.

The animals are up to 4 cm long, vermiform (worm-shaped), and covered by locomotory cilia. They have no digestive tract, and indeed no organs at all. Their only conspicuous morphological feature, other than their cilia, is a statocyst for determining orientation. To date, they have been collected only off the coasts of Sweden and Scotland, in sediments at depths of 20 m to 100 m.

That's it. Part of that is now known to be wrong: the data showing an affinity to the molluscs is an artifact, caused by the fact that it somehow eats bivalves, and partly digested clam material contaminated the samples. Otherwise, not much is known; I've found papers describing the presence of oocytes inside the animal, but no one as far as I know has actually observed its development. It's a strange, mysterious blob of a worm.

Continue reading "Strange worm, Xenoturbella" (on Pharyngula)

Stand Up for Science this Tuesday

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In a post entitled, “Where are They Now,” RedStateRabble points out a difference between the Kansas BOE creationist political message during the primary (when they were fighting for votes between Republicans) and their message during the runup to the general election. Take a look at it, then come back here, because there’s more below the fold…

Frankenvirus

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It was All Hallows Eve when the paper came out in Genome Research, and although there wasn’t the crackle of lightning bolts or a hunchbacked assistant called Igor, the announcement that researchers had resurrected an ancient human endogenous retrovirus (HERV) brought enough of the “how dare you resurrect an unknown virus” kind of response to warm the heart of Frankenstein devotees everywhere. I won’t discuss these aspects of Frakenvirus, it’s done better elsewhere. However, the whole HERV resurrection issue has interesting implications for Intelligent Design advocates.

The latest from the Pensacola News-Journal is that Kent Hovind is in jail until sentencing in January, and the jury ordered the Hovinds to forfeit over $400k to the government:

Haeckel on gastrulation

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This morning, the ID guys were embarrassed – once again – when it was revealed that they didn’t know what they were talking about when they accused PZ Myers of lying by misquoting Wells in PIGDID. PZ dealt with this pretty darn convincingly over here.

But looking at the Haeckel/embryos chapter of PIGDID reminded me of something that has always bugged me about Wells’s claims. Here it is:

Yet only after cleavage and gastrulation does a vertebrate embryo reach the stage that Haeckel labeled the “first.” If it were true (as Darwin and Haeckel claimed) that vertebrates are most similar in their earliest stages, then the various classes would be most similar during cleavage and gastrulation. (Wells, PIGDID, p. 30)

There you have it: Darwin and Haeckel were ignorant of diversity in embryo gastrulation! What boobs!

Imagine my surprise when I actually took a look at Haeckel’s Anthropogenie (1891 edition):

On Evolution News Casey Luskin makes the following claim:

“North Korean Nuclear Test Forces Seismologists to Make a Design Inference”.

Luskin is correct to point out that seismologists have made a design inference. What Luskin fails to tell you is that the design inference has little relevance to Intelligent Design’s “Design Inference”.

Let me explain why Luskin’s claim shows that Intelligent Design has failed to address some of the many criticisms raised, and that ID’s concessions have rendered it to be scientifically vacuous.

See also SETI, archeology and other sciences at Skeptico’s blog for why Luskin’s arguments fail.

PZ Myers is such a LIAR!

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In my review of the embryology of Jonathan Wells in PIGDIG, I made a specific example of the abuse of a quote from Bill Ballard; I pointed out that he selectively edited the quote to completely distort Ballard's point in the cited paper, and used that to show how dishonest all of Wells' work was.

Now Tim McGrew of Kalamazoo wants to accuse me of intentionally distorting Wells' words. I didn't just selectively edit, he thinks I actively changed Wells' words to make my point.

Let me rephrase that: Myers has changed Wells's wording and then has the temerity to accuse Wells of misleading the reader at the very point where Myers himself has made the change in Wells's words.

Let me put that more bluntly: Myers is lying through his teeth. Literally. He is actually that dishonest. And not a single commentator on Panda's Thumb for the past two months could be bothered to check Myers's quotation against Wells's actual words to see whether Myers was telling the truth.

Sal Cordova, sycophant of the ID movement, has of course leapt upon this claim at Uncommon Descent as well. Let's see how accurate McGrew and Cordova are.

Continue reading "PZ Myers is such a LIAR!" (on Pharyngula)

This just in from the Pensacola News-Journal:

‘Dr. Dino,’ wife guilty

Jury deliberations took about three hours.

A federal jury has convicted Kent Hovind and his wife, Jo, of tax fraud.

Hovind faces a maximum of 288 years in prison. His wife faces up to 225 years. Her charges include aiding and abetting her husband with 44 counts of evading bank-reporting requirements.

And at the end:

Defense lawyers for the Hovinds rested their case on Wednesday without presenting evidence or calling witnesses.

My question: if the Hovinds weren’t going to put on a defense, why didn’t they just make a plea bargain agreement, avoid the ordeal of a trial, and get reduced sentences?

Server Issues

When we switched to our new server software, it appears to have screwed up how some browsers manage their cache. This means that some browsers are stuck on outdated pages.

To fix this issue, you need to clean out your cache (or temporary internet files).

De Rerum Natura Changes

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I’ve made some layout changes to my personal blog. Why am I telling PT readers about it?

Well, depending on how the new layout works on my blog, I’m going to update the layout of PT. So let me know what you think about the new layout on De Rerum Natura.

http://dererumnatura.us/

The SciPhi Show, IslamOnline.net

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Last week, I did an interview on the podcast program called The SciPhi show (Science Fiction and Philosophy), run by Jason Rennie. It has now been posted (direct link to mp3 – 16 MB). The show previously did interviews with Michael Shermer, and ID guys Salvador Cordova and Michael Behe. I was somewhat annoyed with what the latter two were getting away with in their interviews, so on the spur of the moment I dropped Rennie an email, and boom, he had me on.

In addition to pointing out all the usual ID mistakes, there was an interesting discussion about Star Trek: Remember that Star Trek episode where they discover that the suspiciously coincidental bipedal, humanlike form of all of the Star Trek aliens was (somehow) encoded into bacteria seeded across the galaxy billions of years ago, by an ancient bipedal race, a fact revealed when a 3-D holograph recording is deciphered out of the ancestral DNA genome (somehow!). The only thing the episode left out was an explanation for human-klingon-vulcan interfertility. Great episode, typically ludicrous science, but does it help the ID guys make their case? Listen to find out.

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