June 10, 2007 - June 16, 2007 Archives

Over at Uncommon Descent, Dembski wonders how the NCSE will deal with "the growing number of non-religious ID proponents" and links to this blog which is something called ICON-RIDS "an international coalition of non-religious ID scientists & scholars." Turns out ICON-RIDS is a one-man coalition, and that the man in question is an "ID Pleasurian ... a non-religious amalgam of ID science and Hefnerian Playboy philosophy."

Read more at Stranger Fruit, where comments can be made.

A recent paper (free access) by Associate Professor Susan Dudley, published in the Royal Society journal Biology Letters argues that some plants recognize their kin.

Kin recognition is important in animal social systems. However, though plants often compete with kin, there has been as yet no direct evidence that plants recognize kin in competitive interactions. Here we show in the annual plant Cakile edentula, allocation to roots increased when groups of strangers shared a common pot, but not when groups of siblings shared a pot. Our results demonstrate that plants can discriminate kin in competitive interactions and indicate that the root interactions may provide the cue for kin recognition. Because greater root allocation is argued to increase below-ground competitive ability, the results are consistent with kin selection.

Although it were gardeners who knew this all along:

The Discovery Institute’s Casey Luskin contends in this post that librarians in public schools are “censoring” Intelligent Design by refusing to put copies of Michael Behe and Philip Johnson books on their shelves. Of course, Luskin cites the famous Supreme Court decision Board of Education v. Pico, 457 U.S. 853 (1982), claiming that it holds that the First Amendment is violated when school districts refuse to stock certain books on their library shelves.

As y’all know, a frequent topic of conversation here is communicating science to the public. While many of us do it directly via sites such as this one, the bulk of science writing that the public will read is done by the pros–people writing for the magazines and newspapers, among other outlets. Often, their stories include interviews with research scientists. However, we’re not always so easy to get in touch with, and we blow reporters off altogether–apparently, pretty frequently.

On a listserv I subscribe to, there recently was a discussion amongst writers regarding how to get academics (and business-types; don’t feel the question is limited *only* to academics) to respond to interview requests. However, given the wording of the question and some of the responses, I think the question itself highlighted a bit of the gulf between journalists and academics, so I’m putting some of my own thoughts on why academics don’t respond first at Aetiology (and particularly when they are at conferences or on business travel, which was the topic of one comment), and I welcome any suggestions you have on how you prefer to be contacted–and what might improve response rates for writers. (It would be great if any writers out there added their additional comments as well–imagine, a dialogue!…)

Science journalism is a business filled with a few bright shining stars standing amidst a lot of writers whose stars are… let’s just say, they don’t shine as bright. Concerning the latter, there is a recent article in Wired magazine titled, One Scientist’s Junk Is a Creationist’s Treasure. It’s your standard attempt at journalistic “balance” that puts crackpots on an equal playing field with actual scientists whose work the former group misrepresents. There’s no excuse for this when a little background knowledge and a little more attention to what the real scientists are saying should show why the creationists are spouting nonsense.

As the title should tell you, the article has to do with so-called “junk DNA” and a recent paper concerning the opossum (Monodelphus domestica) genome. The authors of the paper found that a small fraction of transposable elements shared by the opossum and human genomes appear to contribute to host fitness, apparently by contributing to gene regulation. (Update: That particular paper isn’t involved with the opossum genome project; the conserved sequences are found within “boreoeutherians” which include primates, rodents, and carnivores – not the opossum.) This is a highly interesting if not exactly Earth shattering find.

Unfortunately, every time a new study comes along showing that some small fraction of so-called “junk DNA” turns out the have a function, the ID people do a strange sort of victory dance, as if this somehow proves that they’ve been right all along. In fact this is starting to become a frequent talking point with them. As with most creationists myths it’s taken on a life of its own, and I’m sure we’ll see it wandering around like a zombie for years to come in spite of the fact that it was DOA from the get-go. The new paper of course doesn’t support ID by any stretch of the imagination, nor do any recent findings concerning junk DNA, but the author of the Wired piece, Catherine Shaffer, just credulously repeats claims made by Michael Behe and Stephen Meyer as if they had some measure of legitimacy. Which is why it’s got Paul Nelson crowing about it. Below I will do the work that Shaffer didn’t and explain just how wrong these guys are.

Behe Blows It (in other news, dog bites man)

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The iconic image of the Kitzmiller v. Dover trial in Pennsylvania was Michael Behe sitting on the witness stand, a pile of papers and book chapters on the evolution of the vertebrate immune system on his lap, steadfastly denying the existence of research on the evolution of the vertebrate immune system. In his new book, The Edge of Evolution, Behe continues his practiced denial, minimizing or ignoring a pile of research in order to maintain his claim that evolution can’t produce this or that biological structure because it is “irreducibly complex”. While I didn’t get a review copy, I know a friendly bookstore owner who encourages customers to read in the store.

I will leave it to others to evaluate Behe’s claims about the various specific biological systems (and many have: see Science after Sunclipse for a complete listing). I will return to a piece of research that demonstrates that Behe’s conception of how evolutionary processes produce complicated structures is amazingly over-simplified and empirically false, and that his conception of what evolutionary processes are capable of is pure caricature.

Mark Chu-Carroll has already dissected Behe’s misuse of probability and his utter ignorance of the properties of high-dimensioned and plastic fitness landscapes and ERV nicely illustrates the point. As Nick Matzke has remarked,

My first take is that The Edge of Evolution is basically an incompetent attempt to provide a biological foundation for the silly assumptions that were made in Behe and Snoke’s (2004) mathematical modeling paper in Protein Science.

Mark analyzed Behe’s argument from teeny-weeny numbers, showing that it is based on fundamentally flawed assumptions about the topography of fitness landscapes and the supposed inability of evolving populations to escape from local maxima. I’ll show that Mark’s analysis has empirical corroboration – Behe’s probability model generates wholly absurd results. In addition, I’ll describe data, some of it from new analyses, that flatly contradict Behe’s claims about what evolutionary mechanisms allegedly cannot do. To put it in the most direct terms possible, Behe is either ignorant or actively ignores evidence that contradicts his fundamental assumption about what evolutionary mechanisms can do. I’ll show that in addition to producing entities that are irreducibly complex by Behe’s original Darwin’s Black Box definition, computer models of evolution also produce those entities via evolutionary pathways that are irreducibly complex by Behe’s second so-called “evolutionary” definition, pathways that contain multiple unselected mutational steps. Neutrality lives! Then I’ll make a few remarks on Behe’s probability calculations in the light of computer evolutionary simulation runs, and make a few remarks on Behe’s notion of fitness landscapes.

More below the fold.

Reed Cartwright just forwarded me (and a few others) an email that was just sent out to an evolutionary biology mailing list. I’m going to quote it in full below. Don’t worry if you don’t understand the technical terms in there - you don’t need to know what Bayesian methods are, or how they’re used in phylogenetics, or even what phylogenetics is to understand why this email is important, and why all concerned should be proud of themselves.

Read more (at The Questionable Authority):

featured in openlab 2006

The OpenLab 2006 has been reviewed for Nature by nuclear physicist and PT reader Paul Stevenson: “Blogger’s Unite.” (Don’t miss the editor’s summary as well: “Brought to blook”).

The review is pretty positive for something that was put together at the last moment using material that wasn’t made for print media.

The entries highlight the great variety of styles that can thrive in the blogosphere. Most of the pieces are a little chattier than the usual book or magazine article, but those chosen are formal enough not to grate on the printed page. Occasionally, the prose is loftier than a typical popular science book. Some even veer too much towards the tone of a research article — leaving terms like suprachiasmatic nucleus or a zygomaticomaxillary suture unexplained.

The book works well enough as a standalone anthology of science writing, but I share the editor’s hope that it will prompt eager print readers hitherto unfamiliar with the vibrant young medium that is science blogging to have a look, and maybe even have a go.

I am serving as the editor for the 2007 edition and Bora serves as series editor. As the Nature review mentions, we are already accepting nominations for next year. Click the image below to submit something. We’ll probably be making an early cut in July, so get your favorite posts from the first half of the year in.

Openlab 2007

Note that you can put this banner on your own blog.

(Hat Tip: Neurophilosophy)

Jason Rosenhouse has already noted that Tom Woodward opined that "in the next six to twelve months, Darwinism will go into a steep nose dive as the result of Behe’s new book." How is this "tremendously important" book going to change the landscape of ID? Early indications appear to say ... not at all.

Read more at Stranger Fruit where comments can be left.

Jerry Coyne educates Behe about a few common misconceptions about evolution and shows why Intelligent Design, especially ‘at the edge’ is fully scientifically vacuous.

Coyne reviews Behe’s latest book ‘the Edge of evolution’ and like many before him finds the book unconvincing and ‘rather pathetic’.

What has Behe now found to resurrect his campaign for ID? It’s rather pathetic, really. Basically, he now admits that almost the entire edifice of evolutionary theory is true: evolution, natural selection, common ancestry. His one novel claim is that the genetic variation that fuels natural selection–mutation–is produced not by random changes in DNA, as evolutionists maintain, but by an Intelligent Designer. That is, he sees God as the Great Mutator.

Egnor and ignorance

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Egnor Wrote:

It’s clear that Dr. Gonzalez was denied tenure for only one reason: he stated publicly that he believes there is evidence for design in the universe. As I observed in a previous post about Georges Lemitare, the Catholic priest who is the father of the Big Bang theory, many of the most prominent astronomers in history have shared Dr. Gonzalez’s opinion about the evidence for design in the universe. Nowadays, it is very dangerous to state such beliefs in science departments of many universities, including Iowa State University.

In spite of the evidence to the contrary, the Discovery Institute insists that Gonzalez was denied tenure for believing that there is design in the universe. Even Hauptman was clear that it was not an issue of belief but an issue of science and that Intelligent Design is scientifically vacuous.

Hauptman Wrote:

Intelligent design is not even a theory. It has not made its first prediction, nor suffered its first test by measurement. Its proponents can call it anything they like, but it is not science.

and

Hauptman Wrote:

I believe the comment that somehow this decision had something to do with the feelings of the community was also reprehensible, as are statements that this tenure decision is a denial of free speech.

It is purely a question of what is science and what is not, and a physics department is not obligated to support notions that do not even begin to meet scientific standards.

Source: Des Moines Register: Rights are intact: Vote turns on question, ‘What is science?’ John Hauptman, letter to the editor, June 2, 2007

In other words, its all about the science not the belief.

There’s a very interesting post on the Newsweek blog by science journalist Sharon Begley about the existence of genes for synapses in the sea sponge, which has no need for such structures. Begley is discussing an article in PLoS One that found that the same genes that code for synapses are present in sea sponges, one of the most primitive multicellular organisms on the planet, which have no nervous system and therefore no need for synapses.

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

You may have noticed that the Montana Law Review let the DI folks have the last word in their symposium on the Dover trial; I’m going to fix that. Pete Irons has graciously sent me his full reply to the “rebuttal” written by Luskin, West and DeWolf and given me permission to post it here. The first article can be found here. Irons’ first reply is found here. The DI’s response is found here. You can read Irons’ final reply to their rebuttal, go to Dispatches from the Culture Wars. Comments may be left there.

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