It looks like the trial in Coppedge v. JPL has finally started after many, many delays. The Discovery Institute appears to be attempting to milk it and spin it for all it’s worth – and of course they are accusing the “Darwinists” of doing this. The reality, though, is that we don’t know anything more than what can be gleaned from the news reports and DI propaganda (and the court filings, if anyone is brave enough to dig through that tedium), and the various evolution folks have said relatively little about it as a result. JPL hasn’t released very much information – probably a good plan. But links, discussion, etc. welcome in this thread.

A recent article in Natural History magazine does not exactly advise eating dirt, but rather examines what the author calls “the hygiene hypothesis,” that is, the hypothesis that the increasing prevalence of asthma and other autoimmune diseases is the result of excessive cleanliness. Along the way, the author, Druin Burch, illuminates in some detail just how good science works.

The recent kerfuffle over the intelligent design creationism movement’s effort to publish the proceedings of a secret conference held (it appears) in a rented room at the Cornell School of Hotel Administration should remind us of an earlier Disco ‘Tute conference run along the same lines. In June 2007 an apparently secret [struck because it’s not clear it was to be secret] conference that was called the “Wistar Retrospective Symposium” was held in Boston. That one included a number of the same participants as the “Cornell” conference: Dembski, Marks, Meyer, Behe, and Axe among them. The main difference is that the 2007 meeting included some genuine experts in information theory and evolutionary biology who raised embarrassing questions for the ID pushers. Daniel R. Brooks of the University of Toronto was one such expert in attendance, and he guest-authored a post on it for the Thumb. The take-home message from Brooks was

ID dooms itself. In their own words at this conference, IDers espouse a program in which the scope and power of the Designer is restricted to purely human dimensions, in which the effects of the Designer on biological diversity have left no discernible trace that can be detected scientifically, in which the effects of Darwinian processes are the only biological phenomena that can be studied scientifically, and in which Darwinian processes are overwhelmingly more powerful than those of the Designer (because they inevitably cause the Designer’s creations to degenerate). For example, it must be evil Darwinian processes that produce emerging infectious diseases, otherwise each pathogen would remain associated only with the host for which it was designed. This is all just too silly.

Interestingly, immediately following the 2007 conference the organizers emailed participants

… stating that the ID people considered the conference a private meeting, and did not want any of us to discuss it, blog it, or publish anything about it. They said they had no intention of posting anything from the conference on the Discovery Institute’s web site (the entire proceedings were recorded). They claimed they would have some announcement at the time of the publication of the edited volume of presentations, in about a year, and wanted all of us to wait until then to say anything.

So like the recent “Cornell” conference, the organizers of the 2007 meeting planned to publish a proceedings volume, but as far as we can tell it has never appeared. While the year until publication mentioned is now approaching five years (shades of Paul Nelson’s ontogenetic depth!), there’s still nothing visible in prospect. Is the recent “conference” no more than the offspring of the earlier one, this time held sans critics so as to generate a propaganda book minus the embarrassing questions of genuine experts that Brooks described? Wouldn’t surprise me a bit.

I strongly recommend Brooks’ takedown to Thumb readers.

Hat tip to Joe Felsenstein for the reminder of Brooks’ post.

The 45^th Carnival of Evolution is up at Adrian Thysse’s Splendour Awaits in a new and interesting format, with (at least) one bug per page guaranteed.

Intelligent design news, commentary and discussion from the 20^th of February to the 7^th of March, 2012. 

Semester 1 of my 3^rd year of university started last week, so I’ve suddenly found myself with coursework to pore over. Likewise, the Discovery Institute seems to have kicked itself into a high gear, publishing a larger-than-average number of articles about numerous different topics, all of which just so happen to be rather important and weighty. Ah well, someone’s got to cover them, my own studies of evolutionary genetics be damned.

This week I’ll be looking at how the ID movement views the relationships between science, religion and politics, how it operates with respect to criticising evolutionary biology and supporting its own ideas, and how it deals with the “bad design” objection from critics of ID.

Recall that John Freshwater appealed the Knox County Common Pleas Court’s affirmation of the Board of Education’s termination of his teaching contract. (See also here.)

While it is not yet posted It is now posted to the Ohio 5^th District Court of Appeal’s Opinions page. I received a copy of the Court’s decision that was filed just this morning and is signed by the three-judge panel that considered the appeal. It denies Freshwater’s appeal in its entirety, affirming the decision of the Knox County Court of Common Pleas that the Board of Education’s termination of Freshwater was justified. One quotation to give the flavor:

(32) During the proceedings [the administrative hearing] appellant [Freshwater] was represented by a competent attorney, he was permitted to fully explain his actions, he presented witnesses on his behalf, and he had a full opportunity to challenge the Board’s key witnesses. R.C. 3319.16 does not contain any requirement that a teacher be afforded an opportunity to refute the contents of a referee’s report in the period between the filing of the report and its acceptance or rejection by the board of education, nor does it provide for an additional hearing before the board if the teacher does not like the results of the hearing before the referee.

Given what I saw in the administrative hearing, I might take issue with the “competent attorney” phrase, but let that be.

The Appeals Court ruled that

For the reasons stated in our accompanying Memorandum-Opinion, the judgment of the Court of Common Pleas, Knox County, is affirmed. Costs to appellant.

The Appeals Court did not address several of the questions Freshwater’s appeal raised. For example, it did not address Freshwater’s claim that he was just “… informing students of various alternative theories without regard to those theories’ religious or anti-religious implications.” The appeals court did not mention Freshwater’s claim that his termination violated his right to free speech and what his appeal called “the subsidiary right of academic freedom.” The Appeals Court confined its ruling to the question of whether the Court of Common Pleas “abused its discretion” in affirming the Board’s decision, and rejected Freshwater’s appeal on that basis.

The next step, should Freshwater and the Rutherford Institute take it, is an appeal to the Ohio State Supreme Court. I cannot predict whether that will happen. My intuition is that the Rutherford Institute would like to find a case invoking academic freedom, free speech, and free exercise on the part of a public school teacher that could make its way to the U.S. Supreme Court, but while IANAL, I suspect that Freshwater’s case is way too weak for them to risk it on that case.

There is still mostly an eerie silence from the creationists/IDists on the Springer/Cornell issue (previous PT posts: 1, 2, 3). Basically all we have in terms of official response are the comments given to Inside Higher Ed. But much of the evidence of the details of the conference that originally existed has been taken down. Here are the examples of which I am aware:

This meme has been going around. Recently someone did What Scientists Do, so…it’s time for evolutionary biology. Obviously YMMV if you’re not an evohacker, but even you field biologists end up coming to us in the end anyway when you have to turn your pet hypothesis into a statistically testable model. (Insert maniacal laughter.)

HT: What I do generator

The following article is a draft of a review by Paul R. Gross of Freaks of Nature: What Anomalies Tell Us about Development and Evolution, by Mark S. Blumberg. The review will be published in Reviews of the National Center for Science Education.

An important subtext of Freaks of Nature, by the developmentalist Mark S. Blumberg, is the central importance, indeed the necessity, of monsters. To appreciate them is important, the argument goes, not only for progress in developmental biology, but also for solving the most challenging contemporary problems of evolutionary mechanism. A concomitant of this subtext is pleadings for an unmistakably more positive view, at least within those two sciences, of monsters and – as per the title – freaks of nature.

Those following the controversy about the ID/creationist volume that was scheduled for publication by Springer that is being further peer-reviewed by Springer should make sure to check out the piece by reporter Kaustuv Basu at Inside Higher Ed. (See previously: PT post #1, PT post #2.)

Here, we get the first reactions from the creationists involved with the project:

This week’s furor broke along predictable lines, with the editors of the book criticizing the attitude of the supporters of evolution. John Sanford, one of five editors of the book and a courtesy associate professor at Cornell University’s Department of Horticulture, said in an e-mail that he was amazed that anyone could think that the “Darwin Dissidents” were trying to take over academe.

“Obviously we are only trying to exercise academic freedom and freedom of speech, and are challenging a sacred cow,” he wrote. “Where are the academics who profess tolerance and open dialog? Where are the academics who would confront ‘hate speech’ on their own campus?”

There is apparently a lot of confusion about what “free speech” means in the creationist community. Just this week I experienced this with Casey Luskin. I recently emailed him to express my worry that he might have trouble sleeping at night, after he abandoned his oft-stated claims to be environmentalist and pro-science when he wrote this post: “A Friendly Letter to the Heartland Institute and Other Advocates of Free Speech on Global Warming”. The post gave all kinds of love to the global-warming deniers, and didn’t bother to raise a single finger of criticism for the deniers’ numerous shenanigans, even though Luskin agrees with the mainstream that global warming is happening and humans are causing it. Luskin replied that he was just defending freedom of speech, to which I replied:

For the addicts, my article on the Freshwater affair was published online today in Reports of the National Center for Science Education. Table of Contents of the issue, and PDF of the article.

Note: This topic is outside of my specialty, so it may be that I have missed some important points. I think I’ve got the basics correct, but this is a very complex topic. I will be interested in critical but constructive posts in the comments.

Update: required reading, which basically confirms my points I think:

Weiss, K. M. and J. C. Long (2009). “Non-Darwinian estimation: My ancestors, my genes’ ancestors.” Genome Research 19(5), 703-710.

Nievergelt, C. M., O. Libiger and N. J. Schork (2007). “Generalized Analysis of Molecular Variance.” PLoS Genetics 3(4), e51.

On Monday, Jerry Coyne at Why Evolution is True posted on “Are there human races?” While acknowledging the very bad history of the race concept in human history, and noting some of the problems with applying the concept to humans, Coyne concluded, basically, that the answer was yes, there are human races. While reviewing Jan Sapp’s piece which concluded that human races did not objectively exist, Coyne wrote:

As those who have followed the comment thread on the previous post know, the link to the webpage for the forthcoming creationist/ID “Biological Information: New Perspectives” volume on the Springer website went dead yesterday, approximately 24 hours after the PT post went up. This may mean that the volume had already been identified as problematic, and the webpage was put up due to some oversight or failure to update a database.

Surprisingly for the ID movement, which normally cries “oppression” and “freedom of speech” at the first sight of criticism, there has been virtually no reaction so far. The only creationist reaction is from Todd Wood, who is a lone wolf in the creationist movement in several ways. David Klinghoffer at the Discovery Institute (DI) did put a post up at the DI Media Complaints Division soon after my post, but it was taken down before anyone saw it, except apparently for Google blog aggregators.

I added some new features to Red Lynx recently. So go check it out. Now.

http://scit.us/redlynx/

Note: The Springer webpage for the book was taken down about 24 hours after this post; see update post.

It looks like some creationist engineers found a way to slither some ID/creationism into a major academic publisher, Springer. The major publishers have enough problems at the moment (e.g. see the Elsevier boycott), it seems like the last thing they should be doing is frittering away their credibility even further by uncritically publishing creationist work and giving it a veneer of respectability. The mega-publishers are expensive, are making money off of largely government-funded work provided to them for free, and then the public doesn’t even have access to it. The only thing they have going for them is quality control and credibility – if they give that away to cranks, there is no reason at all to support them.

(A note: even if you bought the ridiculous idea that ID isn’t creationism, they’ve got John Sanford, a straight-up young-earth creationist for goodness sakes, as an editor and presumably author!)

Here’s the summary:

Biological Information: New Perspectives

Series: Intelligent Systems Reference Library, Vol. 38

Marks II, R.J.; Behe, M.J.; Dembski, W.A.; Gordon, B.L.; Sanford, J.C. (Eds.)

2012, 2012, XII, 549 p.

Hardcover, ISBN 978-3-642-28453-3

Due: March 31, 2012 $179.00

The deepest spot in the earth’s oceans is the Challenger Deep in the Marianas Trench in the western Pacific, at 10,994 meters. The BBC has a magnificent interactive graphic of the Trench. Pause as you descend to play the clips at various depths. (And yes, you’ll see the same CIO dating commercial at every stop!)

Hat tip to Talking Points Memo.