a simple prop

It appears that Dembski and Marks (and a student of Marks by the name of Winston Ewert) have a third paper [pdf] which Dembski describes as “a thorough deconstruction” of the AVIDA program. Unsurprisingly, it was presented at an engineering conference, the 2009 IEEE International Conference on Systems, Man, and Cybernetics. I’m unsure as to how much peer review was involved for this one and I’m unqualified to comment on the content, so I’ll leave that to others.

Update (12/14): See here for further comments on the IEEE International Conference on Systems, Man, and Cybernetics.

As is traditional, I like to take some time at the end of the year to look back on some of the triumphs of the ID movement (see 2008, 2007, and 2006). Frankly, not much really happened and if you look at the scribblings over at Uncommon Descent or Evolution News and Views (both surely the pulse of the movement), you’d think that ID has something to do with global warming denialism.

Let’s start with what probably will be seen as the highlight – Steve Meyer was named World Magazine “Daniel of the Year” (following in Phil Johnson’s footsteps who received the award in 2003). Meyer produced a big book that received a crush note from (that well known scientist) Thomas Nagel in the Times Literary Supplement but is unlikely to have any impact on the biological community. Equally as unlikely to have an impact on biology are the two papers published in engineering journals by Dembski & Marks. The Biologic Institute – now with additional YEC goodness – appears to have not produced any research. In fact, that whole research thing is continuing to be a bit of an embarrassment for the movement. If anything, the year was marked by ID forays into rewriting history (see here, here & here), bad pedagogy, science envy, publishing nine year old conference proceedings, abject stupidity, and using the bible to make scientific points. Oh and defeat … lots of defeat.

So as always, this gives me an excuse to post my annual list of things we didn’t see from the main players of the ID movement. I’ve had to modify it a little given Dembski’s tremendous success publishing in engineering journals:

• A peer-reviewed paper in the relevant literature by Dembski, Wells, Nelson, Meyer …
• Or for that matter, a single peer-reviewed article offering either (a) positive evidence for design, (b) a method to unambiguously detect design, or (c) a theory of how the Designer did the designing, by any fellow of the DI.
• An exposition of Nelson’s theory of “ontogenetic depth” (promised in March 2004)
• An article by Nelson & Dembski on problems with common descent (promised in April 2005).
• Nelson’s monograph on common descent (currently MIA since the late 90’s).

See you next year for an update!

Update (12/11): Looks like D&M have done it again and gotten a third engineering paper published. Exciting times for ID. It really is a new science for a new century. A revolution, even.

Dembski “uses the Bible” to illustrate a scientific point. From here:

After a time of musical praise and worship, Dembski took the stage and began a clear, concise analysis of the necessity for Intelligent Design studies. He highlighted the similarities and differences between Intelligent Design and Creation Theory and explained why there was a need for both and how science and religion go hand in hand. Dembski’s investigative research and insightful lecture was met with appreciative applause as he concluded with prayer. … The topics that Dembski discussed at The Baptist College of Florida were grounded in Biblical faith and doctrine ranging from Darwinism to Information Theory.

HT to John Pieret

From a review of Stephen Meyer’s latest attempt at science-by-popular-book:

Meyer’s book, if he can successfully carry the burden of proof, is probably one of the most important books since Copernicus challenged the prevailing scientific notion 566 years ago that the Earth was the center of the universe.

A tad hyperbolic, don’t you think?

*head explodes*

Hugh Miller was a Scottish stonemason and popularizer of geology who wrote a number of excellent books in the 1800′s that argued against scriptural geologists and sought a truce between science and religion. You can read a little more about him here. There is a modern Hugh Miller who apparently is a “research chemist” (BS in chemistry) in Colombus OH who believes that “[l]ong before Answers in Genesis’s museum and its director Ken Ham were born major museums were aware that dinosaurs and man coexisted“. He’s a Catholic young earther who has produced a paper that used radiocarbon dating on dinosaur remains:

RECENT C-14 DATING OF FOSSILS INCLUDING DINOSAUR BONE COLLAGEN. Are the results a confirmation of rapid formation of the geologic column as modern sedimentology studies have predicted?

The discovery of collagen in a Tyrannosaurus-rex dinosaur femur bone was recently reported in the journal Science. Its geologic location was the Hell Creek Formation in the State of Montana, United States of America. When it was learned in 2005 that Triceratops and Hadrosaur femur bones in excellent condition were discovered by the Glendive (MT) Dinosaur & Fossil Museum, Hugh Miller asked and received permission to saw them in half and collect samples for C-14 testing of any bone collagen that might be extracted. Indeed both bones contained collagen and conventional dates of 30,890 ± 380 radiocarbon years (RC) for the Triceratops and 23,170 ±170 RC years for the Hadrosaur were obtained using the Accelerated Mass Spectrometer (AMS). Total organic carbon and/or dinosaur bone bio-apatite was then extracted and pretreated to remove potential contaminants and concordant radiocarbon dates were obtained, all of which were similar to radiocarbon dates for megafauna.

Miller’s work is to appear in “the proceedings of an international conference on evolution” featuring Catholic scientists from Germany, Italy, US, Poland and France. Other papers in the volume titeld “Evolutionary Theory: A Critical Analysis” include:

• The second law of thermodynamics excludes evolution
• Experiments in stratification do not support evolution
• Is radiometric dating reliable?
• The concept of evolution in biology
• Race formation and mutations do not constitute steps in evolution
• Critical reflections of evolutionism as a scientific or pseudo-scientifc theory and as an atheist ideology
• Philosophic-theological prerequisits of the evolution theory
• The Negative Impact of the evolutionary hypothesis on scientific research.

There’s a summary of the meeting here but suffice it to say that it includes such folks as Guy Berthault and Maciej Giertych.

The real fun is that Behe is talking at another meeting with Miller and other YEC Catholics. I wonder if he will take the time to publicly set the YECs straight? Probably not.

Update (10/14): John Pieret has more details on Miller.

Jonathan Wells claims:

Illustra Media interviewed [Simon] Conway Morris and [James] Valentine for this project in October and November of 2006—less than three years ago. Both Morris and Valentine knew they were being interviewed by Illustra Media, which was well known for having previously produced two pro-intelligent design films, Unlocking the Mystery of Life and The Privileged Planet. They were not deceived in any way.

Jim Valentine says:

I wish to clarify my role in the new film Darwin’s Dilemma. When I was interviewed about a decade ago for the material used in this movie, I was unaware that this interview might appear in a film promoting intelligent design. My appearance should not be misconstrued as support for any creationist agenda.

Now who are you going to believe?

Valentine did an interview in 1993 regarding the origin of phyla for a DVD sold by ARN.  I wonder whether that footage is the same one being re-used for Darwin’s Dilemma, the latest Illustra Media piece. (Strangely, the YouTube sample of the older Valentine interview is no longer available.)

Valentine goes on to state:

I disagree with the view that the best explanation for the Cambrian record is the action of an “intelligent designer” instantaneously creating phyla. Had the filmmakers bothered to read my book On the Origin of Phyla, they would have understood that I do not support a creationist interpretation of the Cambrian explosion or the fossil record. Scientific findings in many fields, including my own (paleobiology) as well as geology, geophysics, geochemistry, developmental biology, and systematics, have led to a synthesis of the events surrounding the Cambrian explosion that is in full accord with well-established evolutionary principles.

Yet another case of an expert being misused by denialists.

Jonathan Wells thinks that “duplicating a gene doesn’t increase information content any more than photocopying a paper increases its information content.” Wells is, of course, wrong. Is anyone surprised?

Update: And while on the topic of Wells … he’s apparently telling folks he is a Presbyterian. Father would not be happy.

John Pieret has a nice piece up on the latest DI missive. In it he points out further egregious use of Darwin’s own words in Origins. Witness the DI’s quotation:

Few scientists understood the importance of critical thinking better than Charles Darwin. When he first proposed his theory of evolution in Origin of Species in 1859, Darwin faced intense intellectual opposition from both the scientific community and the culture of his day. To help restore objectivity to the debate over evolution, Darwin wisely counseled, “A fair result can be obtained only by fully stating and balancing the facts and arguments on both sides of each question.” [Emphasis in DI original]

And now look at the original:

This Abstract [Origin], which I now publish, must necessarily be imperfect. I cannot here give references and authorities for my several statements; and I must trust to the reader reposing some confidence in my accuracy. No doubt errors will have crept in, though I hope I have always been cautious in trusting to good authorities alone. I can here give only the general conclusions at which I have arrived, with a few facts in illustration, but which, I hope, in most cases will suffice. No one can feel more sensible than I do of the necessity of hereafter publishing in detail all the facts, with references, on which my conclusions have been grounded; and I hope in a future work to do this. For I am well aware that scarcely a single point is discussed in this volume on which facts cannot be adduced, often apparently leading to conclusions directly opposite to those at which I have arrived. A fair result can be obtained only by fully stating and balancing the facts and arguments on both sides of each question; and this cannot possibly be here done.

As John points out, Darwin is not claiming that all sides are equal – and should thus be given equal time – in the debate regarding evolution. Instead he is noting that he had been unable to include all his relevant “facts and arguments” (because of the rushed nature of Origin) and that a “fair result” (i.e. acceptance of his theory) can only result when all the evidence is examined. The DI intentionally omit both the context of the quote and the complete sentence because, let’s face it, it would make their argument untenable.

Over at Quintessence of Dust, Steve’s got a nice post (and the first of a series) on the “absurdity of the ID fixation on the Weasel program” in which he contextualizes what Dawkins was trying to achieve with an illustration that he himself described as “misleading in important ways.”  

1. Close comments on post complaining about censorship
2. Play Stalin card
3. ??????
4. Profit

Jeff Shallit has more.

My talk yesterday to the Humanist Society of Greater Phoenix went well (I think). Apparently the crowd, nearly 120, was the largest they have even had. It was my fourth talk to HSGP (apparently also a record) – no doubt, I will be back in the future. The slides are available here.

It seems I will have to change my LOL Dembski. Teh mathz haz appeared – their relevance to evolutionary biology, however, remains zero. Dembski’s latest (and much bally-hooed) attempt at being taken seriously has finally appeared in print: a joint paper with engineering professor Robert Marks titled “Conservation of Information in Search: Measuring the Cost of Success.” You may remember that Dembski was unwilling to say where the paper was to appear lest the Evil Atheist Conspiracy^tm cause the paper to be pulled. In wonderful news for for the ID movement, it has appeared in that noted journal of evolutionary biology, IEEE Transactions on Systems, Man & Cybernetics. You will be familiar with the journal because it is where most to the breakthroughs in 20th century biology were published.

The paper is available here and the lovefest over at Uncommon Descent has already gone sour with the master himself closing comments (a mere nine comments – and just over an hour – in) after he was called on errors and misrepresentations. Sayeth Bill, “I’m growing weary of these quibblings and thus shutting the comments off.” This is somewhat ironic for a professor who sends his students onto the internet to drive-by comment on sites that oppose ID. For Dembski, valid criticisms are mere “quibbles” and Darwin’s work on barnacles mere “puttering”. It must be tough being such a great (and unrecognized) philosopher, theologian, mathematician, and historian. He truly is the Isaac Newton of our times. But I’m willing to predict that this paper will do nothing to disprove or problematize the abundant evidence for natural selection and its efficacy.

That aside, other critiques have begun to appear:

• Mark Chu-Carroll at Good Math, Bad Math
• Joe Felsenstein at the Panda’s Thumb
• The Metropolis Sampler
  

I will add more as I find them.

Bill Dembski is attempting to justify his pedagogical technique of sending students to “hostile” websites to drop comments. For example, in this syllabus we see:

At least 10 posts defending aspects of the Christian worldview totaling at least 3,000 words on “hostile” websites

For another course (AP 410), students have to

provide at least 10 posts defending ID that you’ve made on “hostile” websites, the posts totalling 2,000 words, along with the URLs (i.e., web links) to each post (worth 20% of your grade).

Now what’s problematic here isn’t that Dembski is encouraging students to post on “hostile” sites, it is that the assignment doesn’t force the students to engage with their critics in any way. Instead, all the student has to do is cut and paste some text, save the url, and pass it on to Dembski. Money in the bank.

Those of us who use discussion forums and webboards in our teaching know that if any value is to be gained from the exercise students must engage with each other and respond to claims while defending their own through a series of engagements. It is such long-term engagement that is profitable not “drive-by posting”.

In short, my objection is not that Dembski’s students are posting on “hostile” sites, it’s that he is not doing anything pedagogically useful by encouraging them to do so. Dembski appears to be as good a teacher as he is a mathematician or theologian.

Update (8/11): Joel Borofsky, Dembski’s former TA, tries to defend his master but completely ignores the sort of argument I’m making and instead wikers on about what he sees as argumentative fallacies. Come on Joel, defend Dembski’s pedagogy …

So looks like pili and flagella can appear without a designer’s action. No doubt the ID brigade will either argue that the change doesn’t represent an increase in information or that it represents front-loading by the Designer That Shall Not Be Named.

[Geobacter] sulfurreducens bacteria were cultured on a graphite electrode under a 400 mV applied bias. The goal was to force the bacteria to adapt to conditions inside the MFC [microbial fuel cell] with the hope that they would evolve greater functionality in the process. Several colonies were isolated after five months in the MFC environment and re-cultured under normal conditions. When placed in an MFC cell, the specially cultured bacteria grew much more rapidly—current saturated after 50 hours as opposed to 400 hours—and they provided twice the current density of normally cultured bacteria.

Analysis of the enhanced bacteria showed that there were two primary adaptions. First, pili, fine, thread-like structures that connect neighboring cells, dramatically increased in the new bacteria. These structures are thought to be responsible for electronic conduction in bacterial films. Also, unlike their precursors, the enhanced bacteria all had flagella that allowed both motility and enhanced attachment to anode surfaces. It is unclear which adaptation is primarily responsible for the enhanced performance.

From here with a hat-tip to RBH.

Reference: Biosensors and Bioelectronics DOI:10.1016/j.bios.2009.05.004

Image: G. sulfurreducens biofilm (source)