August 28, 2005 - September 3, 2005 Archives


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Looks like they’re coming for mathematics now:

Forget about isosceles triangles and the Pythagorean Theorem—they’re square. The hottest trend in high-school math these days is deometry, the study of how the Creator created points, lines, angles, shapes and proofs. While critics decry the entry of religion into math class, fans of the new teaching method maintain that by giving God a primary role in geometry and other fields of mathematics, they are merely restoring balance to an area that has sought to remove all vestiges of religion from the public polygon.

I’m pretty sure this is a parody…

Someone calling himself Homunculus has posted this bit of anti-evolution insanity over at the right-wing website I give it the business in this lengthy post over at EvolutionBlog. Enjoy!

Gene logic

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On Telic Thoughts, Mike Gene presents an interesting but fallacious argument

If MN determined that the Earth was 6000 years old, that evolution could not occur and all living things were fitted into discrete, discontinuous groups, and a global flood once covered the Earth, does MN then mean we must explain this all “without reference to supernatural beings or events?”

What does reference to the supernatural explain? Everything and thus nothing. And notice that MN has not failed here, so unless Mike wants to argue that if in addition to these findings, science cannot explain these data that somehow ‘supernatural design’ becomes more likely then he clearly does not understand the scientific method. Why should our ignorance be seen as evidence for something which we cannot observe?

Some Recent News on ID: September 01, 2005

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1. Marblehead Reporter Letter: Intelligent Design is ‘anti-science’ 2. Indian Country: Mohawk: ‘Intelligent design’ and faith-based science 3. Cleveland Jewish News Intelligent design attacks clear thinking 4. Florida Billboard Supports Teaching ‘Intelligent Design’ in Schools


Since last week’s report, there have been several developments in the Rio Rancho situation, wherein the local school board adopted a new science policy that, according to the Sept. 2nd Albuquerque Journal’s print edition

means teachers will lead discussions on alternative ideas to evolution.

For starters, on Thursday, the Flying Spaghetti Monster (info) has again reached his noodly appendage beyond the internet, into Mainstream Media, or at least to the twice-weekly pages of the Rio Rancho Observer:

And also yesterday (Sept. 1st), several science chairs from the University of New Mexico recommended that Rio Rancho’s Policy 401 should be abolished.

Telic ‘Logic’

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On Telic Thoughts, Salvador makes the following (self defeating) comment, in response to the statement by David Schweingruber that:

David Schweingruber Wrote:

So Iowa State has one thing in common with unaccredited Bible colleges and medieval heresy tribunals – our Bible scholars think they can tell our astronomers how to do their jobs.

And now Sal

Salvador Wrote:

Ouch! That’s about good a slam down as I’ve ever seen!

ID’s minor success

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It seems that ID proponents are at least mildly successful in coaching ID supporters in what to say and not to say and when to say it…

Tim Borseth Wrote:

Well, my arm was twisted. Rather than working hard on campus ministry stuff, I was coerced into writting a letter to the editor of the D.M. Register regarding the Intelligent Design debate. It went through a major revision after Dr. Guillermo Gonzalez himself advised me multiple times as to what to say and what not to say.

At least he puts an end to the myth that Gonzalez was somehow singled out

Tim Borseth Wrote:

I have personally interacted with 15 professors at Iowa State who seriously doubt Darwinism and have offered their assistance in helping college students work through the role of faith in science. Dr. Guillermo Gonzalez is by no means alone.

10,000 and going

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Today, Panda’s Thumb has experienced its highest traffic yet. While the daily hits were growing quite solidly, PT managed to attract over 10,000 visits with over 14,000 page views. [oops make that 11,500 and 16,000. At this rate PT is 3 days away from a million visits]

Congratulations to a fantastic team. Check out the stats for This Month

Reed Cartwright provide the following graphics


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Russell Durbin reports:

Discovery Institute C®SC fellows and friends are fond of citing SETI as an example of intelligent design theory in action. While we at Panda’s Thumb are certain that the CRSC had no intention of implying that SETI endorses their claims to scientific respectability, we thought we might help them avoid any misunderstanding by passing along the following link:

Intelligent Design and Evolution at the White House

Dawkins and Coyne: One side can be wrong

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In One side can be wrong Accepting ‘intelligent design’ in science classrooms would have disastrous consequences, Richard Dawkins and Jerry Coyne express their feelings and findings on intelligent design.

It sounds so reasonable, doesn’t it? Such a modest proposal. Why not teach “both sides” and let the children decide for themselves? As President Bush said, “You’re asking me whether or not people ought to be exposed to different ideas, the answer is yes.” At first hearing, everything about the phrase “both sides” warms the hearts of educators like ourselves.

This is a very good article which goes into quite some depth to describe what is wrong with intelligent design while also addressing what is and is not know about the ‘gaps’ so often abused by ID proponents.

It’s good to see how more and more scientists are standing up to defend science. I believe we should thank George W. for his ill-timed remarks.

Diona Carrillo reports on four Cerritos College science instructors who are bravely standing up against intelligent design.

“Intelligent design is a philosophy, it is not a theory, it’s not a scientific theory, it’s not even a scientific hypothesis; it’s a belief,” Constance Boardman, biology instructor said.

The instructors have realized that ID is nothing more than a gap theory

An emphasis on weaknesses or “holes” and gaps in evolution, is the heart of the intelligent-design movement.

Jozsef Ludvig in the Baltimore Sentinel writes

But in reality, by leaving the name and identity of the designer unknown, ID becomes a placeholder for any religion while narrowly escaping the definition of a religion itself. But it can still not pose for science because it starts with the premise that a supernatural force had to be involved in the creation of life from inorganic matter. In order to prove this premise it then invents the non-empirical device of irreducible complexity which is just a typical God-Of-The-Gaps and cannot explain anything by itself. The resulting negative inference of a supernatural force from empirical ignorance is, by definition, neither a scientific subject nor consistent with the scientific method. Thus ID is not science.

Acts Have Consequences

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The recent Kansas creationist kangaroo court hearings on evolution run by three creationist members of the Kansas State Board of Education (see here and here for stories) and the previous (1999) debacle in Kansas are having consquences for higher education in that state. In a story in the Lawrence Journal-World the Provost of Kansas University said

For the state to be portrayed repeatedly in the national press as being anti-science does damage to this university. The frustration is you fight this reputation problem every step of the way.

KU dropped three places in the most recent U.S. News & World Report rankings of universities.

Michael Lynch’s critique of Behe and Snoke (2004) is now available as is a reaction by Behe and Snoke. Don’t forget to read the editor’s message about it as well.

We’re still discussing it, but here is Lynch’s abstract.

Lynch M (2005) Simple evolutionary pathways to complex proteins. Protein Science, 14:2217-2225.

Abstract: A recent paper in this journal has challenged the idea that complex adaptive features of proteins can be explained by known molecular, genetic, and evolutionary mechanisms. It is shown here that the conclusions of this prior work are an artifact of unwarranted biological assumptions, inappropriate mathematical modeling, and faulty logic. Numerous simple pathways exist by which adaptive multi-residue functions can evolve on time scales of a million years (or much less) in populations of only moderate size. Thus, the classical evolutionary trajectory of descent with modification is adequate to explain the diversification of protein functions.

Ricardo Azevedo has some view up on his blog: BS Model Gets Lynched.

Carl Zimmer has the big news: the first draft of the chimpanzee genome is being published in Nature today. This is fantastic news, and it’s difficult to under overstate the importance of this. We want many different organisms sequenced to sample diversity, but having the sequence of two closely related species is going to be incredibly useful. Aren’t you just itching to see what the differences are?

Sadly, I just finished slapping Phil Skell around for his blindness to how evolution informs biology. I suspect he’s going to be dully oblivious to this event, too.

From the Quote Mines: Phil Skell

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In the August 29 issue of the Scientist, Phil Skell writes in his opinion piece “Why Do We Invoke Darwin? Evolutionary theory contributes little to experimental biology” the following:

Phil Skell Wrote:

Despite this and other daculties, the modem form of Darwin’s theory has been raised to its present high status because it’s said to be the comerstone ofmodem experimental biology. But is that correct? “While the great majority of biologists would probably agree with Theodosius Dobzhansky’s dictum that ‘nothing in biology makes sense except in the light of evolution,’ most can conduct their work quite happily without particular reference to evolutionary ideas,”

A.S. Wilkins, editor of the journal BioEssays, wrote in 2000. “Evolution would appear to be the indispensable unifying idea and, at the same time, a highly superfluous one.”

I decided to investigate the quote. Guess what?

by Mike Syvanen

[Dr. Michael Syvanen is a professor studying molecular genetics in the Department of Medical Microbiology at the University of California, Davis, and has been an advocate since the early-80s of an idea that has gained considerable support over the last few years - that much evolution is not tree-shaped, but net-shaped. That is, that genes cross taxonomic lineages. Since many attacks on evolution claim we should “teach the controversy”, we at Panda’s Thumb thought it might be nice to present an *actual* controversy in science. Discussion is welcomed. Here, at least.]

It has been over 30 years since the suggestion that horizontal gene transfer (HGT) may have been a factor in the evolution of life entered the literature. Initially these speculations were based on discoveries made in medical microbiology; namely that genes for resistance to antibiotics were found to move from one bacterial pathogen to another. This discovery was so unexpected and contrary to accepted genetic principles that though announced in Japan in 1959 (1,2) it was not generally recognized in the west for another decade. Speculations that HGT may have been a bigger factor in the evolution of life was inviting because it offered broad explanations for a variety of biological phenomena that have interested and puzzled biologist for over the last century and a half. These were problems that had been raised by botanists that have puzzled over the evolution of green plants (3) as well as by paleontologists that recorded macroevolutionary trends (4) in the fossil record that were often difficult to reconcile with the New Synthesis that merged Darwin’s thinking with Mendelian genetics. However, outside of the field of bacteriology this exercise did not really attract that much attention until the late 1990s at which time there was a major influx of data indicating that HGT had been very pervasive in early life. Namely, complete genome sequences began to appear. Simple examination of these sequences showed beyond any doubt that horizontal gene transfer was indeed a major factor in the evolution of modern bacterial, Archael and Eukaryotic genomes.

On Pharyngula, PZ Myers reports how the Lehigh Department of biological sciences has taken a position on intelligent design.

Of particular interest is that this is Michael Behe’s university.

PZ Myers reports that, as was the case with Guillermo Gonzalez, “Behe’s academic freedom is fully supported by his department, but this is a loud vote of no confidence in his work. That sounds like an unpleasantly uncomfortable environment to be in.”

This is off topic, but over on my personal blog I have some low-resolution before and after pictures from New Orleans. The flooding, even at the very low resolution of these images, is simply mindnumbing.

My heart, and I’m sure the heart of everyone here, goes out to all those impacted by this tragedy. People will need lots of time, lots of effort, and lots of assistance before they can begin to recover from this disaster.

The mainstream media is finally coming to terms with the truth of His Lord, the Creator.

One woman even wrote in to say that she had “conceived the spirit of our Divine Lord,” the Flying Spaghetti Monster, while eating alone at the Olive Garden.

”I heard singing, and tomato sauce rained from the sky, and I saw angel hair pasta flying about with little farfalle wings and playing harps,” she wrote. “It was beautiful.” The Spaghetti Monster, she went on, impregnated her and told her, “You shall name Him … Prego … and He shall bring in a new era of love.”

Someone named Emma kindly provided a couple of links to PDF files relevant to the California creationist lawsuit. One of the links is to a propaganda piece written by the Association of Christian Schools International, which is the lead plaintiff in the lawsuit. The second link is to a copy of the actual complaint that has been filed in the case.

The ACSI propaganda flyer is an interesting read, but I’m not going to take the time to criticise it at present. Instead, I’m going to begin by looking at the complaint, which should contain the real meat of the suit. The complaint is over one hundred pages in length, and I have found material that I’d like to comment on very early in the complaint. Since both my time and my tolerance for this type of thing are limited, it will probably take several posts over several days for me to wade through everything. Read More (at The Questionable Authority)

The Faith That Dare Not Speak Its Name

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Jerry Coyne is one of the many contributors to magazines, newspapers, blog sites and so on who have realized that Intelligent Design is not only scientifically vacuous but also theologically risky.

In The Faith That Dare Not Speak Its Name Coyne writes

Coyne Wrote:

Intelligent design, or ID, is the latest pseudoscientific incarnation of religious creationism, cleverly crafted by a new group of enthusiasts to circumvent recent legal restrictions. ID comes in two parts. The first is a simple critique of evolutionary theory, to the effect that Darwinism, as an explanation of the origin, the development, and the diversity of life, is fatally flawed. The second is the assertion that the major features of life are best understood as the result of creation by a supernatural intelligent designer. To understand ID, then, we must first understand modern evolutionary theory (often called “neo-Darwinism” to take into account post-Darwinian modifications).

Intelligent Design described

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In “Letters to the Editor” of the Cornell Daily Sun Adam Moline makes the following statement which captures much of what is wrong with ID

The problem with intelligent design is not that the background assumptions are bad but that the method employed by Intelligent Design’s advocates is not the scientific method. They use God in the same way that the ancient Greek dramatists did: to circumvent an otherwise insoluble problem in the final act. Just as deus ex machina is an improper means to conclude plays, intelligent design is an improper means to advance knowledge.

My native state hasn’t had headlines go nationwide over antievolution lately. But there are indications that Florida may be one of the next big targets of the antievolution advocates.

Ron Matus at the St. Petersburg Times wrote about this in today’s paper:

Ron Matus Wrote:

Nationally, it’s a raging debate. President Bush weighed in this month. Time magazine devoted its cover story to the subject two weeks ago.

But in Florida, the teaching of intelligent design - the newest, faith-based counterpoint to Darwin’s theory of evolution - is not an issue.

At least, not yet.

Some observers expect the other shoe to drop next year, when Florida education officials revisit state science standards as part of a routine review of what should be taught in Florida schools.

Update: Ex-Minnesota antievolutionist Cheri Pierson Yecke has been appointed Florida’s K-12 Chancellor for education. It looks like the antievolution forces have been at work already in Florida.

(Continue reading… on The Austringer)

More on the Iowa situation

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As PvM already mentioned, It’s hitting the fan here in Iowa. For those of you who have been paying attention to the Smithsonian/Privileged Planet controversy, you may recognize the name Guillermo Gonzalez. He’s the co-author of the book by the same name, a DI fellow, and just happens to be a faculty member of the Astronomy department at Iowa State University. Hector Avalos, an associate professor of religious studies at ISU, and colleagues at ISU drafted a letter opposing the teaching of ID as science; 124 faculty signed it. Now, predictably, Gonzalez says he’s being “viciously attacked,” “intimidated,” and it’s created a “hostile work environment” (sound familiar, anyone?).

My Evening with Kent

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My colleague, Steven Mahone, a board member of Colorado Citizens for Science and an engineering professional with the largest utility in southern Colorado, agreed recently to debate the well-known creationist Kent Hovind on evolution vs. creation. As Mr. Mahone describes below, he was snookered into leaving his visual aids at home, whereas at the last minute Mr. Hovind was allowed to present his. As I write, it is still unclear why Mr. Mahone and another debater were prohibited from bringing their visual aids, but it seems likely that the Campus Crusade for Christ, a sponsoring organization, was not at fault, and they have sent Mr. Mahone an elegant and sincere apology, which is reproduced below.

Here is Mr. Mahone’s account of the debate.

Intelligent Design in the news

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Leon Satterfield descibes in The president and ‘intelligent design’ a goofy id(ea):

Leon Satterfield Wrote:

What a goofy idea President Bush had earlier this month when he said that public schools should teach both “intelligent design” and evolution, as if they were academically equal.

The president apparently doesn’t know — or more likely doesn’t care because he can sniff out votes from halfway across the country — that evolution is a scientific notion and that intelligent design is a religious belief and therefore has no place in our secular public schools. He also apparently doesn’t know — or more likely doesn’t care — that we were founded as a secular nation. No national church, no religious creeds we had to pretend to subscribe to.

Shannon Information and Biological Fitness

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For Neurode…

Bergstrom (Department of Zoology University of Washington Seattle, WA, USA) and Lachmann (Max Planck Institute for Mathematics in the Sciences Leipzig, Germany) have published a paper titled “Shannon Information and Biological Fitness”.

They conclude that

In this paper we have shown that two measures of information, Shannon entropy and the decision-theory value of information, are united into one single information measure when one looks at the strategies that natural selection will favor, namely those that maximize the long term growth rate of biological organisms. Furthermore, we have shown that in evolving biological systems, the fitness value of information is bounded above by the Shannon entropy. These results suggest a close relationship between biological concepts of Darwinian fitness and information-theoretic measures such as Shannon entropy or mutual information.

The never ending stream of articles critical of Intelligent Design have appeared since Bush made his ill-timed statement.

Daniel C. Dennett, a professor of philosophy at Tufts University, is the author of “Freedom Evolves” and “Darwin’s Dangerous Idea”, joins the virtual fray.

In Intelligent Design: Show me the science Dennett explores Intelligent Design.

Dennett Wrote:

Is “intelligent design” a legitimate school of scientific thought? Is there something to it, or have these people been taken in by one of the most ingenious hoaxes in the history of science? Wouldn’t such a hoax be impossible? No. Here’s how it has been done.

Response to slanderers

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A couple of weeks ago, after I posted on Panda’s Thumb a brief response (see here) to Dembski’s amusing dismissal of my essay published in Skeptic, v. 11, No 4, 2005 (without his saying a word about the substance of my critique), on the website maintained by Dembski appeared a comment whose author accused me of false claims regarding my publication record.

As I had mentioned before, the last time I updated my list of publication was in 1985, when I applied for a position at CSUF. At that time the list already contained over 200 items, even though it did not include many of my published papers which were outside my professional work (many such papers were published in several languages in magazines such as Partisan Review, Midstream, Present Tense, Kontinent, Possev, Ukrainian Quarterly, Samtiden, Vremya Iskat [Et Levakesh], Vremia I My, and others).

Confronted with the libelous post on Dembski’s site, which Dembski chose to keep without rebuttals, thus in fact joining the author of the calumny, I searched my files and found my List of publications which I submitted to CSUF in 1985. It contained 211 items, even omitting many publications outside my professional research.

Dr. Wesley R. Elsberry kindly offered to scan and OCR the text of that list of publications (many thanks, Wesley). Thanks to Wesley’s generous assistance, this list, which is more than 20 years old, although containing a few OCR errors, can now be seen here.

I don’t think I need to prove that I did not abruptly stop publishing in 1984. Were the list updated after 1985, its size would grow by more publications, and more so if, besides my research papers, it included also papers dealing with pseudo-science in its various disguises. If my papers and the book which are not about my research in physics were added, the total would be now over 300 items, in tune with what I claimed in my response to Dembski’s post.

I apologize for taking space on Panda’s Thumbs by posting these remarks, but I feel it is proper to post them after the libelous comment appeared on Dembski’s site, where, as it is known, no comments are allowed which are short of either praising Dembski or attacking his critics.

Evolving motors

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As we are so often reminded by proponents of Intelligent Design creationism, we contain molecular “machines” and “motors”. They don’t really explain how these motors came to be other than to foist the problem off on some invisible unspecified Designer, which is a poor way to do science—it’s more of a way to make excuses to not do science.

Evolution, on the other hand, provides a useful framework for trying to address the problem of the origin of molecular motors. We have a theory—common descent—that makes specific predictions—that there will be a nested hierarchy of differences between motors in different species. Phylogenetic analysis of variations between species allows us to reconstruct the history of a molecule with far more specificity than “Sometime between 6,000 and 4 billion years ago, a god or aliens (or aliens created by a god) conjured this molecule into existence by unknown and unknowable means”.

Richards and Cavalier-Smith (2005) have applied tested biological techniques to a specific motor molecule, myosin, and have used that information to assemble a picture of the phylogenetic history of eukaryotes.

Continue reading “Evolving motors” (on Pharyngula)

Intelligent Design Theories

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While ID itself remains silent on the nature of the designer, some real scientific theories are sprouting up around the country which do not shy away from identifying the nature of the intelligent designer.

The tooth fairy, the easter bunny, Santa Claus and the stork…

Hat tip to Gerald Nachman of the San Francisco Chronicle

Teach the controversy I say…

The Seattle Post Intelligencer has an opinion piece where it asks the following burning question:

Chapman and company acknowledge that intelligent design is underdeveloped as a testable scientific theory. Nevertheless, they believe their ideas deserve inclusion in science curricula. A number of states already have opted for just such a requirement. Soon, we all may be facing this Burning Question:

Should intelligent design be part of science education?

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