Posted by Dave Thomas on October 30, 2004 | Comments (54) | TrackBack (0)

I’ve recently obtained permission from Science and an author of the recent paper “Evolution of Coral Pigments Recreated,” to use the splendid figures in a popular discussion of this important new work.  Permission to post these figures was granted only for the NMSR page, so I can’t post them here, but here’s a link to my new article, “New Work Documents the Evolution of Irreducibly Complex Structures.”

Here’s a snippet:

Recent work on the evolution of pigments in star corals, “Evolution of Coral Pigments Recreated,” by Juan A. Ugalde, Belinda S. W. Chang, and Mikhail V. Matz, (Science 2004 305: 1433 (9/3/2004), Copyright 2004 AAAS) shows conclusively that “irreducibly complex” structures not only can evolve, but that they have evolved. This should lay to rest the “Intelligent Design” assertion that this type of complexity is forbidden to natural evolution.

And Ugalde et. al.’s conclusion:

The more complex red color evolved from green through small incremental transitions (a stepwise accumulation of improvements), each identified in our experiments by ancestral gene reconstruction (Fig 1D). This mode of evolution has been anticipated since Darwin, but has only recently been demonstrated in computer simulation experiments (5, R. E. Lenski, C. Ofria, R. T. Pennock, C. Adami, Nature 423, 139 (2003), “The Evolutionary Origin of Complex Features” )

Continue reading “New Work Documents the Evolution of Irreducibly Complex Structures” (offsite at NMSR)

Posted by PvM on October 29, 2004 | Comments (1) | TrackBack (0)

In his 2004 paper “The Origin of Biological Information and the Higher Taxonomic Categories” Meyer introduces the reader to the concept of Shannon information. Despite the fact that the paper is presented as an ‘extensive review paper’ which ’ argues that no current materialistic theory of evolution can account for the origin of the information necessary to build novel animal forms’ Meyer forgets to add the relevant scientific research showing how variation and selection can increase Shannon information in the genome.

What I find surprising is the number of references omitted in this review paper directly relevant to the origin of biological information.

Continue reading  “Icons of ID: Meyer and the case of the missing references”

Posted by Reed A. Cartwright on October 29, 2004 | Comments (2) | TrackBack (1)

December’s Backpacker Magazine has a long article about rafting the Grand Canyon in ICR style.  The author, an Evangelical-Christian-turned-Agnostic describes his adventures with the group that included Tom Vail, Steve Austin, Andrew Snelling, a doctor, a pathologist, a chiropractor, a home-schooling family of four, and a pair of chicken farmers, among others.  It was a nine day trip that started at Lee’s Ferry with a description of how the layer below the Great Unconformity is the closest to the land Noah walked on.  As the trip continued, the author wondered if Stockholm syndrome explained why he was starting to think that the creationist geology had some sense to it.  The authored described a worship service that took place before they left Marble Canyon and entered the Grand Canyon.  I think it offers a good feel for the article and the trip.

The day before we descended into the canyon, we attended church services on the rim.  After hymns and prayer, a preacher from ICR got to going, and brother, he could bring it.  I like some good preaching, and this was that.  He paced the riser, he found his cadence and he worked it.  He took it up, and he took it down.  He spoke of invisible things, of how man can only define God in the things He has made, which means we have all seen God, which means that we are left no excuse of disbelief.  He got some mm-hmms with that one.  Riffing in the area of Romans 1:22, he spoke of men so full of their own philosophy they become blind to what God has made.  He mentioned Carl Sagan, and did a little billions and billions impression.  Then the preacher came to a full stop, stage right, and looked out at us with his head at an impish tilt.  Stood there silent for two beats, then said, “By the way, ol’ Carl knows what’s goin’ on now!“  The congregation bubbled with chuckles.  The preacher held a smug pose, on hand sucked aw-shucks style in a pants pocket, the other held flat beneath the splayed Bible from which he had been quoting without looking.  As the chuckles spread, the preacher rolled his eyes and gave the Bible a little bounce.  And I’ll tell you, he lost me right there.  You want to lure me back, brother, show some compassion.  Before honor is humility, if you’ll allow me a little Old Testament.  Drop to your knees and pray through tears that our fellow sinner Carl might yet be redeemed.  What you had there was a jig danced on a lost soul.  I’d heard those chuckles before, from people of my own congregation, as they listed to one of our preachers recount how he turned his back on a struggling member after he caught her wearing shorts.  From that day forward, I’ve tried to reconcile the deep goodness of my childhood church with the poisonous little seems of petty certitude.  If found myself doing a similar thing in the canyon, trying to reconcile the chuckles on the rim with the sincere smiles all around me.

Don’t forget to check out the November Issue which had a little blurb about Dinosaur Adventure Land.

Posted by Timothy Sandefur on October 28, 2004 | Comments (18) | TrackBack (0)

For those following the Cobb County disclaimer case, the law firm handling the case has informed me that trial has been set for November 8. (Court dates are, of course, always subject to change.)

Posted by PvM on October 28, 2004 | Comments (7) | TrackBack (0)

ID proponents are stumbling over themselves in their haste  to come to the defense of the Meyer 2004 review paper. But rather than defending the paper (given the critiques, an unenviable task now delegated to unnamed ‘DI Staff’), they quickly readjusted their sights and settled for strawmen to shoot down (see for instance the ‘response’ by DI Staff to Meyer’s hopeful monster. Only by creating a strawman argument as to what Gishlick et al were arguing can they even hope to make their case. And I won’t even mention the poor reading comprehension of the papers which were given to Meyer as examples of relevant papers missed by Meyer in his ‘review paper’.

Another example is a recent article by Mark Hartwig.

Although the article itself has received a share of the abuse—mostly in the form of a “critique” published on the Panda’s Thumb blog—the main target has been the editor who published the piece, Richard Sternberg.

(Mark Hartwig in Bitten)

I understand that to ID proponents, peer review can feel like  ‘abuse’ but that is mostly because typical ID ‘research’ tends to be based on appeal to ignorance and a restricted view of science. Unfamiliar with peer review, it may come as a shock when scientists expose the many flaws and shortcomings in what some may have hoped would be a glorious entry of ID into the world of science. But as the critique on Panda’s Thumb has shown, ID cannot really withstand the scrutiny of critical peer review. (A conclusion further supported by the response by the DI staff)

And that must sting…

Continue reading  “Wedgie's World: Stung not bitten”

Posted by PvM on October 27, 2004 | Comments (7) | TrackBack (0)

Historically, the central dogma in molecular biology has been that the genetic information in DNA is transcribed into intermediate RNA which are translated into amino acids to form proteins.  Proteins were seen as the primary regulators of the expression of genes. While this picture appears to be correct for prokaryotes, a different picture arises for eukaryotes.

Mathematical considerations have shown that while generating complexity is simple, controlling it isn’t. The amount of regulation needed tends to scale as the quadratic of the number of genes. The genome size of prokaryotes seems to be limited by these considerations.

Continue reading  “Evolvability: RNA and The Gems of "Junk" DNA”

Posted by PZ Myers on October 27, 2004 | Comments (69) | TrackBack (4)

A long-lost cousin has been discovered, Homo floresiensis, or Flores Man. It's especially dramatic for a number of reasons. It's relatively recent, with the youngest specimen only 18,000 years old, but it is most closely related to Homo erectus. This species was also minute, only 3 feet tall, and tiny-brained. Here we have a group of small, specialized human relatives, living contemporaneously with Homo sapiens, on isolated islands in Indonesia. It's like discovering that Munchkins were real. You can read more here:

• Nature has special online section on Flores Man, with several articles on its discovery free to the public.
• Carl Zimmer has a summary of the significance of the discovery.
• More figures from the paper describing the find can be found on Pharyngula.

Posted by Reed A. Cartwright on October 27, 2004 | Comments (25) | TrackBack (0)

Over at ARN this was proposed as curriculum for Dover, PA new biology policy.

The theory of ID posits the following:

1. High information content (or specified complexity and irreducible complexity constitute strong indicators or hallmarks of past intelligent design.

2. Biological systems have a high information content (or specified complexity) and utilize subsystems that manifest irreducible complexity.

3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (specified complexity) or irreducible complexity.

4. Therefore, intelligent design constitutes the best explanation for the origin of information and irreducible complexity in biological systems.

reference page 92 of Darwinism, Design and Public Education

As far as I can tell, the person who posted this is serious.  From a logical standpoint, the major flaw in this “theory [sic] of ID” is that it relies solely on negative argumentation.  It tries to prove “intelligent design” true by disproving something else.  Such an argument rarely works in science because one has to first demonstrate that both the “proved” and “disproved” explanations together make up the complete set of all possible explanations.  People who rely on negative argumentation seem to always ignore the unknown.

The problems with the proposal go beyond that because number four does not follow from number three even if we grant that there is a complete set.  If hypotheses X and X^c  are a complete set, and X explains 90% of the data, whereas X^c explains 10% of the data, neither is sufficient.  But according to the logic employed in the ID argument above, X^c  would be declared the best explanation because X is not sufficient.  However, X is actually the best explanation on the criterion given despite the fact that it is not sufficient.

Points one, two, and three are popular talking points of “intelligent design” activists but are not supported by any scientific research.  (If you disagree, feel free to provide references to the peer-reviewed scientific papers that demonstrate any of these things.)  As such they are entirely inappropriate for a secondary school science curriculum that treats them as anything other than the pseudoscience they are.

Another obvious flaw is that “information” is not defined in any biologically meaningful way (or at all).  Under some definitions of “information,” high information content is the hallmark of a completely random process.  “Information” as a formal concept is butchered by “intelligent design theorists” almost as badly as the Second Law of Thermodynamics is butchered by Young Earth Creationists.

If this represents what “intelligent design” activists think counts as science, then its only use in a science classroom is to point out how to not do science.

Posted by PvM on October 26, 2004 | Comments (2) | TrackBack (0)

In an opinion column for the Iowa State Daily, Scott Rank, a senior in journalism and mass communication from Knoxville, addresses intelligent design, and the recent lecture where two ISU professors addressed the fallacies and problems with Guillermo Gonzalez’s and Jay Richard’s “The privileged planet” ^[1].

Scott Rank’s comments show some excellent examples of the shoddy research of the issues as shown in detail by two Panda’s Thumb regulars: Richard B Hoppe and Gary Hurd. With permission of the authors I am reproducing their responses here since they show clearly what is wrong with Intelligent Design and its proponents. Richard B Hoppe has already posted his comments on Panda’s Thumb so I will focus on the comments by Gary Hurd and  comments by the “Faculty and Graduate Students of Ecology, Evolution and Organismal Biology”.

Continue reading  “Icons of ID: Is intelligent design science or creationism 2.0?”

Posted by Richard B. Hoppe on October 26, 2004 | Comments (11) | TrackBack (0)

The parade of those whose qualifications to knowledgeably evaluate a scientific theory are non-existent continues.  Last week it was real estate agents, this week a student journalist at Iowa State.

Scott Rank, Opinion Editor of the Iowa State Daily, published a column describing a recent on-campus forum in which Guillermo Gonzalez’s The Privileged Planet was critiqued by Professors Hector Avalos and John Patterson of Iowa State.  Avalos is characterized as “Iowa State’s most beloved atheist,” while Patterson, a retired faculty member, is a long-time critic of creationism.  (Jim Foley discusses TPP briefly here.)

I’ll not discuss in detail most of the errors in Rank’s column — they’re familiar to anyone with some passing acquaintance with IDist bloviations.  Three specific aspects of the column, though, are of interest given that Rank is allegedly a senior journalism major.  It’s not just that Rank is scientifically ignorant: his column displays a careless disregard for both accuracy and journalistic ethics.  It’s in the best tradition of hack propaganda, complete with a fictitious quotation.

Continue reading  “Journalists Against Evolution”

Posted by Nick Matzke on October 26, 2004 | Comments (0) | TrackBack (0)

Remember Cassini, the multibillion dollar spaceship we put in orbit around Saturn back in July?  (If not, see the PT posts Say hello to Phoebe and First decent views of the surface of Titan, and the Cassini website).

Well, it has taken awhile for Cassini to do its first full orbit, but it is back in the inner Saturnian system, and today it completed its first flyby of Titan, the solar system’s largest moon and only moon with a thick atmosphere made of nitrogen and organic compounds.

Cassini will pass within 746 miles of Titan — a mere 10 hour drive on the freeway — and snap up close photos, and image the surface in detail with atmosphere-penetrating radar.

Continue reading  “Titan flyby #1 today”

Posted by PvM on October 26, 2004 | Comments (2) | TrackBack (0)

In a Letter to Nature, Vladimir Svetlov makes the following observations talking about the Meyer 2004 paper:

Your News story Peer-reviewed paper defends theory of intelligent design” (Nature 431, 114; 2004) suggests that getting an intelligent-design paper into a peer-reviewed journal is a huge achievement for creationism. I am more surprised it took so long to get one in.

Dr Svetlov continues to observe:

The paper in question presents no new arguments and is unremarkable in any way except in that it has been published. It appeared in a journal that, until this particular editorial decision, enjoyed much-deserved obscurity. Proponents of intelligent design would have us believe that this publication is a testament to the scientific legitimacy of their theory — although the editor has since left and the journal has disowned the paper as “inappropriate” (see Nature, 431, 237; 2004).

In my opinion it is yet another testament to the rampant proliferation of scientific publications, resulting in a flood of inconsequential papers appearing in those thousands of journals that exist on the fringes of scientific publication.

(The real dirty secret of academic publishingNature 431, 897 (21 October 2004))

Continue reading  “ID: The real dirty secret of academic publishing”