December 2009 Archives

Of late the IDists have been complaining about the dearth of reviews by ID skeptics of Stephen Meyer’s book Signature in the Cell. I agree, it would be nice if there were more reviews out there, but (a) the arguments boil down to the same old fallacious “improbability of assembly of functional sequence all at once from scratch by brute chance” creationist argument that dates back to at least the 1960s creation science literature, and (b) the book is tedious and repetitive, basically making the same unsupported assertions again and again in slightly different ways. I.e. information comes from intelligence and is too improbable to explain by chance, therefore intelligence! The actual known origin of the vast majority of genetic “information” – DNA duplication followed by mutation and selection is (1) almost completely ignored by Meyer and (2) directly refutes Meyer’s key claim, which is that the only known explanation of new information is intelligence. So in one sense, there is not a heck of a lot to review in Meyer’s book. If you are a sufficient wonk about the ID debate, there is some interesting stuff about Meyer’s highly revisionist account of his own history and the history of the ID movement, and there is an interesting study to be made of the science that Meyer left out of his book, but that makes for a big project, so it will be awhile before I or someone else get it out there.

But, while reading across the book, you do occasionally come across some examples of truly bizarre argumentation. Here an example which I just posted in response to a Telic Thoughts challenge:

Telling apes from humans

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Creationists are always very definite that there are absolutely, absolutely no transitional fossils between apes and humans. For example, according to a 1990 article by Answers In Genesis (AIG)

When complete fossils are found, they are easy to assign clearly as either ‘ape’ or human, there are only ‘ape-men’ where imagination colored by belief in evolution is applied to fragmented bits and pieces.

Very well then. Here are some photos of fossil skulls, all to the same scale. Some are of humans, some of apes. Care to identify which are which?

Fossil 1 Fossil 2
Fossil 3

Answers after the fold.

Darrel Falk is co-president of the BioLogos Foundation and a biology professor at Point Loma Nazarene University in San Diego. He offers a calm review of Signature in the Cell by Stephen Meyer, Director and Senior Fellow of the Center for Science and Culture at the Discovery Institute (Disco). Signature in the Cell seems to be Disco’s main statement of late, but it fails to convince biologist Falk.

Falk begins:

I believe there is a Mind who was before all things and through whom all things are held together (Colossians 1:17): I believe that Mind is the intelligence behind all that exists in the universe. Hence, I believe in intelligent design. Does that by definition then, place me in the Intelligent Design (ID) movement?

Crepuscular rays

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Photograph by Vivian K. Dullien.

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Crepuscular rays in ground blizzard, Boulder, Colorado. Photograph copyright © 2009 by Vivian K. Dullien.

Ornithogalum thyrsoides umbellatum

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Ornithogalum umbellatum – Star of Bethlehem flower. Flower courtesy of Sturtz and Copeland Florists and Garden Center, Boulder, Colorado.

Baraminologists deny ‘hoax’ charges, threaten legal action

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Apparently the charge made on Panda’s Thumb that the Institute for Noachian Studies Fellows Dr. Orbin S. Thicke and Rev. Bob-Bob Lee’s ground-breaking approach to determining the taxonomic level of the Biblical “kinds” on Noah’s Ark is no more than a hoax perpetrated by Dr. Boli has struck a nerve, perhaps even two nerves. According to this story, spotted by Dr. Boli’s clipping service, crack baraminological researchers Thicke and Lee have vehemently denied that their forthcoming book, promised for publication in February 2043, is a hoax.

“We have established a methodology,” Dr. Thicke said. “A top-quality study will take some time, which is why we have given ourselves thirty-four years to complete it. There is no need for critics to weigh in before the study is even finished.”

“We knew we would face opposition from the satanic atheistic communistic Islamofascist spawn of hell,” added the Rev. Bob-Bob. “But a true scientist follows the facts wherever they lead him, as long as they do not lead him outside the pages of Genesis.”

It’s of note also that another set of theoreticians has weighed in:

Meanwhile, a spokesman for Answers in Hesiod, a classical pagan fundamentalist think tank, strongly condemned the projected study for failing to take into account the scientifically valid theory that Chaos, Gaia, and Eros arose spontaneously from nothing.

Let a thousand flowers bloom for a moment and then die and be woven into leis for … um. Oh. Sorry. Wrong fantasy. What was it someone once said about open minds and falling brains?

Panda’s Thumb spokesbear Professor Steve Steve was unavailable for comment due to a prior commitment with some bamboo stalks in eggnog. But I heard him exclaim as he trundled out of sight, “Happy holidays to all, and to all a good night!”

α-actinin evolution in humans

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Blogging on Peer-Reviewed Research

Perhaps your idea of the traditional holiday week involves lounging about with a full belly watching football — not me, though. I think if I did, I’d be eyeing those muscular fellows with thoughts of muscle biopsies and analyses of the frequency of α-actinin variants in their population vs. the population of national recliner inhabitants. I’m sure there’s an interesting story there.

In case you’re wondering what α-actinin is, it’s a cytoskeletal protein that’s important in anchoring and coordinating the thin filaments of actin that criss-cross throughout your cells. It’s very important in muscle, where it’s localized in the Z-disk at the boundaries of sarcomeres, the repeated contractile units of the muscle. This diagram might help you visualize it:

sarcomere.jpeg

Actin (green), myosin (red). Rod-like tropomyosin molecules (black lines). Thin filaments in muscle sarcomeres are anchored at the Z-disk by the cross-linking protein α-actinin (gold) and are capped by CapZ (pink squares). The thin-filament pointed ends terminate within the A band, are capped by tropomodulin (bright red). Myosin-binding-protein C (MyBP-C; yellow transverse lines).

(Creation) science marches on!

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Dr. Boli’s Celebrated Magazine has been in my reader for some time, and his advertisements, news articles, and answers to questions are both amusing and often satirically pointed. Today he notes a work in preparation called “A New Approach to Baraminology” by Dr. Orbin S. Thicke, Ph.D., and the Rev. Bob-Bob Lee, D.M., Fellows of the Institute for Noachian Studies. It promises great things:

One problem, however, has until now remained intractable: the question of which taxonomic rank properly represents the baramin, or original created kind, beyond which it is not permissible to search for common ancestors.

Read the rest there, and be sure to pre-order your copy for anticipated delivery in February 2043. It will make a lovely gift. For someone. Right? Right?

Slab avalanche

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Slab avalanche – showing starting zone, track, and runout.

That’s the headline of a short blurb in yesterday’s issue of Science. According to Science, the National Research Council (CNR) of Italy helped to fund and promote a creationist book that was edited by a vice-president of CNR. I have not investigated CNR, but I assume it has properties in common with the US National Science Foundation.

The book, Evolutionism: the decline of an hypothesis, was edited by a historian of Christianity at the European University of Rome and was based on the proceedings of a meeting at which scientists and philosophers argued, in the words of Science, “that conventional dating methods are wrong, that fossil strata resulted from the Deluge, and that dinosaurs died 40,000 years ago,” not to mention “why evolution is unscientific.”

Ben Goldacre reviews the year …

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in bad science in the UK. Surely the U.S., the country with Senator Jim “climate change is a hoax” Inhofe, the anti-vaccination movement, and, of course, the ever-popular Center for the Renewal of Science and Culture, can out-do those stodgy Brits in the bad science department! Post your best examples in the comments.

The Onion‘s “Top 10 Stories of The Last 4.5 Billion Years” includes this instant classic.

When anti-reason inspires terrorism

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Literary agent Andy Ross was the owner of a bookstore in Berkeley that was bombed in 1989, apparently for carrying Salman Rushdie’s Satanic Verses after the fatwa was issued condemning Rushdie to death. Here and here are his memories of that day and its aftermath. They are well worth reading and deserve wider circulation. They remind us that those who would have us abandon reason on religious grounds do not always stop at words, and it is always worth opposing them.

Hat tip to The Friendly Atheist.

Dolichovespula maculata

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Photograph by Kevin Klein.

Photography contest, Honorable mention.

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Dolichovespula maculata–Bald-faced hornet larvae.

Evolution: Education and Outreach vol 2 issue 4 online

I missed this earlier, but T. Ryan Gregory reminds us that the new issue of Evolution: Education and Outreach is now online. There’s a broad range of articles and reviews in the issue, and one stands out for me. It’s Douglas Allchin’s article on resources for teaching the evolution of morality. All the articles are linked from Gregory’s post here. I heartily commend it to your attention. That journal is a valuable resource for us all.

by Joe Felsenstein http://evolution.gs.washington.edu/felsenstein.html

In a discussion here of the views of the creationist Cornelius Hunter I posted a comment with a summary of his views about Bad Design arguments. I argued that

what he has just done is to admit that the hypothesis of a Designer is not science, as it predicts every possible result. If you predict every possible outcome, the ones that are seen and the ones that are not, then you have not predicted anything!

At his own blog Hunter objected strongly, saying that

Unfortunately these misrepresentations are typical of evolutionists. Not only are evolution’s metaphysical arguments from dysteleology, or bad design, perfectly valid, they can also be quite powerful. Felsenstein’s strawman that we say otherwise would be bizarre if it wasn’t so common.

Was I wrong?

Freshwater: Dec 8, 10, & 11, 2009

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Added in edit: This is a very condensed summary (three days of testimony in a bit over 2,000 words). If you have questions about specific issues or topics please ask them in the comments and I’ll respond as I can.

This last week saw us creep nearer to the conclusion of Freshwater’s case to keep his job as a middle school science teacher. He was the main witness for the greater part of three days on direct examination by R. Kelly Hamilton, his attorney. In late December when the hearing resumes he will be cross-examined by David Millstone, the Board of Education’s attorney. Unless Hamilton has other witnesses to call (not a negligible possibility), we should get to the Board’s rebuttal case (if one occurs) in January. There’s no telling how long that may take nor how long Freshwater’s rejoinder (if any) to the rebuttal might take.

Freshwater’s testimony this week had four main components:

1. Denial: He denied many of the allegations, attributing the contradicting testimony from other witnesses to misperceptions, misunderstandings, or flat lying.

2. Appropriate Use: He claimed whatever ID and/or creationist material he might have used was to illustrate bias and lack of objectivity in the interpretation of good science and was consistent with the Academic Content Standards.

3. Confusing Directives: He claimed that he received confusing instructions from the administration concerning religious materials in his classroom, and to the best of his understanding complied with administrator’s directives.

4. Incomplete Report: He claimed that the HR OnCall investigators’ report was incomplete and misleading, did not fully investigate the allegations, did not comply with the terms of the master contract between the Board and the bargaining unit, and did not keep a promised appointment for a second interview for which Freshwater had prepared a comprehensive report.

More below the fold.

Comment on access to publicly funded research

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I got this announcement from AAAS today:

Make your voice heard!

We have been asked to relay to the broad scientific community the following opportunity to advise US government policymaking deliberations.

You can read the latest updates at: www.whitehouse.gov/open

The Obama Administration is seeking public input on policies concerning access to publicly-funded research results, such as those that appear in academic and scholarly journal articles. Currently, the National Institutes of Health require that research funded by its grants be made available to the public online at no charge within 12 months of publication. The Administration is seeking views as to whether this policy should be extended to other science agencies and, if so, how it should be implemented.

The Office of Science and Technology Policy in the Executive Office of the President and the White House Open Government Initiative are launching a “Public Access Policy Forum” to invite public participation in thinking through what the Federal government’s policy should be with regard to public access to published federally-funded research results.

To that end, OSTP will conduct an interactive, online discussion beginning Thursday, December 10. The discussion will focus on three major areas of interest:

* Implementation (Dec. 10 to 20): Which Federal agencies are good candidates to adopt Public Access policies? What variables (field of science, proportion of research funded by public or private entities, etc.) should affect how public access is implemented at various agencies, including the maximum length of time between publication and public release? Add your comments

You will want to read the Terms of Participation and will need to register a new account and log in using the link at the bottom of the page to comment. Tips on how to comment and moderate posts are listed in the right-hand column. * Features and Technology (Dec. 21 to Dec 31): In what format should the data be submitted in order to make it easy to search and retrieve information, and to make it easy for others to link to it? Are there existing digital standards for archiving and interoperability to maximize public benefit? How are these anticipated to change?

* Management (Jan. 1 to Jan. 7): What are the best mechanisms to ensure compliance? What would be the best metrics of success? What are the best examples of usability in the private sector (both domestic and international)? Should those who access papers be given the opportunity to comment or provide feedback?

Each of these topics will form the basis of a blog posting that will appear at www.whitehouse.gov/open and will be open for comment on the OSTP blog at blog.ostp.gov.

Sincerely, Alan I. Leshner, CEO, AAAS and Executive Publisher, Science

A pen-pal of mine sent me the following message regarding Stephen Meyer’s Signature in the Cell:

The Dishonesty Institute is mounting a campaign in support of Meyer’s book over at Amazon.com. In the past day there have literally been scores of new positive 5 star reviews posted by those who have seen the Dishonesty Institute’s e-mail appeal. Please vote Nay on each of these reviews and Yea on the negative ones, especially mine and Donald Prothero’s, since ours are the most comprehensive negative one star reviews posted at Amazon.com.

Freshwater: December 8, 2009

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I won’t have a writeup of the Dec 8 tonight or even very soon. Power was out this evening due to a windstorm, and the contractors came today to work on the house. Pam Schehl has a good summary in the Mt. Vernon News.

Heliconia

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Heliconia, Bella Vista Cloud Forest Reserve, Ecuador.

Freshwater: Dec 3 & 4, 2009, sessions

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The administrative hearing on the termination of John Freshwater as a middle school science teacher in Mt. Vernon, Ohio, resumed on December 3, with truncated sessions both the 3rd and 4th. The sole witness heard on the 3rd was Ellen Button, a middle school science teacher, and the sole witness on the 4th was William White, the middle school principal. I’ll put it all below the fold.

Cornelius Hunter says he isn’t a young-earth creationist, so I have edited that part of my previous blog post. However, he admits he has never written about his position on the age of the earth. This is pretty incredible for anyone who books and blogs on the evolution/creationism debate.

Aron-Ra in the flesh

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Back when I was a little baby creationism debater, back in the day when the world wide web was young, there were several gladiators who, every day on the talk.origins newsgroup, sallied forth and took on all comers. These were names like PZ Myers, Wes Elsberry, John Wilkins…that’s right, these guys, now famous, all were originally newsgroup junkies. Eventually I got to meet them all in person. But another gladiator there was, by the name of Aron-Ra, who wielded his challenge to great effect. I never got to meet him…but now there is YouTube.

No Longer Sleeping in Seattle

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Note: Another guest post from Don Prothero. I have added links, and the references section, where I put some graphics so that readers can see what Prothero is describing. – Nick Matzke

Update: Shermer’s review is now online here, and the audio of the debate is here.

I guess my interview with National Geographic News online last week, and last Monday’s debate with Stephen Meyer and Richard Sternberg must have really wounded them, because this week I’m the new bete noire of the IDists over at the Discovery Institute. For two years, they completely ignored my 2007 book, Evolution: What the fossils say and why it matters even though it pulled no punches in criticizing them, has been on the best-seller list for most of that time, and greatly outsells Meyer’s new book. (Incidentally, they bragged at the debate about how his book had won an award from the Times Literary Supplement. This is false. It turns out that there was a favorable review by Thomas Nagel, a maverick philosopher of morality, not an award by the TLS. My book, on the other hand, DID win the Outstanding Book in Earth Science Award for 2007 from the American Association of Publishers).

In any case, they’ve been attacking me with everything they have this week, with Casey Luskin and Jonathan Wells both weighing in. Normally, it is not worth dignifying their garbage with a response, but in case any of the readers of Pandasthumb.org want to get the straight facts (and not their distorted version), here’s what you should know:

Stephen Meyer on Bad Biological Designs

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As long as we’re piling on Stephen Meyer, there are a number of arguments for which Don Prothero was prepared that Meyer apparently didn’t make in the recent debate. A couple are worth posts of their own.

One of the problems intelligent design proponents face is how to deal with bad biological designs. There are lots of examples–Oolon Colluphid of The Secular Cafe has a handy annotated list of 96 of them.

In his doorstop Signature in the Cell, Stephen Meyer has an appendix with 12 alleged predictions of intelligent design “theory.” One of his purported predictions concerns putatively bad or suboptimal designs in biological processes and structures. First a little background.

Intelligent design creationists in general use three basic arguments in dealing with the issue of suboptimal designs. First, they argue that the suboptimality results from “devolution.” What were once optimal designs have degenerated due to the vicissitudes of time and the second law of thermodynamics, or for some, Adam and Eve’s screw-up in the Garden–those of the YEC persuasion commonly attribute that degeneration (along with predation and parasitism) to the Fall. This is one of AIG’s approaches. Meyer also has used the “design decay” argument–see here.

A second argument is to claim that a given design really isn’t suboptimal. For example, in an interview attributed to Lee Strobel’s The Case for a Creator, Meyer reportedly claimed that the inverted vertebrate retina was “a tradeoff that allows the eye to process the vast amount of oxygen it needs in vertebrates” [p.87] (and also see AIG’s argument to this effect).

The third approach is to wave off questions about purportedly bad design as a theological issue, not a scientific one: Who are we to make assumptions about the Designer’s unknowable (to science) intentions and motives? ‘ID is real science and we don’t do theology.’ See here and here for examples.

By Don Prothero http://faculty.oxy.edu/prothero/index.htm

Don Prothero is a paleontologist and Professor of Geology at Occidental College in Los Angeles, and Lecturer in Geobiology at the California Institute of Technology in Pasadena, and author of Evolution: What the Fossils Say and Why it Matters, in my opinion the very best book on fossils and evolution for the general reader. Last night, Monday, November 30, Prothero debated (along with Michael Shermer) ID advocates Stephen Meyer (longtime head of the Discovery Institute’s Center for the Renewal of Science and Culture) and Richard von Sternberg (the former editor who in 2004 published Meyer’s pro-ID article in the last issue of the Proceedings of the Biological Society of Washington (D.C.) which Sternberg was scheduled to edit, despite the article being wildly off-topic for an alpha taxonomy journal, substantially copied from other Meyer publications, badly inaccurate, and just weird in several ways). Sternberg is now, I believe, an employee of the Discovery Institute.

Prothero wrote these remarks directly after the debate and emailed them to me. I have added links where relevant. — Nick Matzke

My mind is a bit fuzzy from the loss of sleep, and the two hours of “debate” went by very quickly, so I cannot recall all the details, let alone recount them. Here are my morning-after thoughts about last night’s “Battle in Beverly Hills.” I don’t know when they’ll release the video recording of the event, but when it does come out, hopefully it will be possible to post it so you can all see for yourself how it went. My subjective summary of it is that our side did very well: I caught them off-guard with new arguments they had no answer for; Shermer pushed them hard repeatedly to state who the “Designer” was (and Meyer finally conceded it was God), while we both pushed them hard on the fact that neither of them ever addressed the topic of the debate, “Origins of Life.” I could tell that they were rattled a number of times, and I definitely shook up Meyer and got under his skin with my answers. Several times Meyer and Sternberg were arguing with each other, leaving the moderator, our side, and the audience wondering who runs their show. The best sign of my effect on them was Meyer trying to challenge MY credentials, or dodging a tough question by playing the sympathy card and calling me “condescending” — and the virulent post on the Discovery Institute site this morning, full of lies and spin. Of course, the event is staged so that no one will really “win”. Their supporters turned out and dominated the audience, but I had a LOT of people come up to me during the book signing (we sold a LOT of books) and congratulate me, or discuss points further with me. And we got just as much applause and sympathetic laughter at our well-turned phrases as they did.

Wes on Opderbeck and Dover

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This is a good read: Wes on Opderbeck and Dover.

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