October 2007 Archives

First, I actually agree with Egnor that “Creationism” and “Intelligent design” are ostensibly different things; however, the history behind the Intelligent Design movement puts the lie to the prima facie difference between the two.

So for Egnor to claim that “Intelligent design isn’t a religious belief” is the height of disingenuousness; an accusation he himself levels at Pigliucci.

Egnor made much of the fact that Pigliucci cited a survey result that showed that people with more education were less likely to agree with the statement that “heaven is a physical place”. While Egnor may still believe that Heaven is hiding above the firmament and that Hell is in the depths of the earth, it seems rather ignorant to claim that Heaven is a physical place rather than a spiritual place. In response Egnor exclaimed “Why is Dr. Pigliucci surprised that most people, even well-educated people, believe in Heaven?”, it is clear that the question was about Heaven as a real (physical) place. But Pigliucci’s argument was simply that “In fact, the connection between education (science education in particular) and belief in paranormal phenomena or explanations is an empirical matter”.

Now I understand that not too many people take the musings of Egnor too seriously but I do enjoy a good fisking. Saves me a lot of hard work. For those interested in the excellent and thought provoking essay by Pigliucci, it can be found here. Critical thinking can prevent scientifically vacuous concepts like Intelligent Design and other forms of Creationism from violating St Augustine’s position on science, a position I believe us Christians should take seriously.

In my earlier posting on Johnson, I was reminded by a Ron Okimoto that Johnson in an interview with the Berkeley Science Review had made even more startling claims:

“I considered [Dover] a loser from the start,” Johnson begins. “Where you have a board writing a statement and telling the teachers to repeat it to the class, I thought that was a very bad idea.” The jaw drops further when he continues:

Johnson Wrote:

I also don’t think that there is really a theory of intelligent design at the present time to propose as a comparable alternative to the Darwinian theory, which is, whatever errors it might contain, a fully worked out scheme. There is no intelligent design theory that’s comparable. Working out a positive theory is the job of the scientific people that we have affiliated with the movement. Some of them are quite convinced that it’s doable, but that’s for them to prove…No product is ready for competition in the educational world.

I remain speechless. The real question now becomes, if there is no real competing ‘theory of ID’ then how can ID have been ‘expelled’. It seems to have been flunked.

The Smart Set (a reincarnation of H.L. Mencken’s great magazine from the Twenties) has an article on the creationist museum in Kentucky. Excerpt:

The museum here isn’t the first devoted to a literal interpretation of the Bible’s opening book. There’s also the 7 Wonders Creation Museum near Mt. St. Helens, the Museum of Earth History in Eureka Springs, Arkansas, and the Institute for Creation Research’s Museum of Creation and Earth History in Santee, California. This summer, the Big Valley Creation Science Museum opened to less fanfare in a small, vinyl-sided building in Alberta, Canada.

AiG’s museum in Petersburg, however, is the biggest creationist museum in the country and, AiG boasts, the most “professional.” The ministry brought in Patrick Marsh, the designer behind Universal Studios’ Jaws and King Kong attractions. At Universal, Marsh used special effects to build a fear of killer sharks and giant gorillas. In Petersburg, he’s used the same tools to build a fear of God.

The Creation Museum also draws the most on the conventions of traditional natural history museums, including the rush for interactivity and entertainment as a means of reaching young minds. Qualities like these led believers to pony up the entire $27 million in construction costs, leaving the museum debt-free, according to its builders. They’re also what AiG hopes will attract 250,000 people every year to this sleepy corner of Kentucky.

(Read the rest…)

In other words, the flagellar machine itself indicates that it did not arise by a random and unguided process like Darwinian evolution, but rather arose by a non-random and intelligently directed process such as intelligent design.

Source: Evolution News Blog, Principled (not Rhetorical) Reasons Why ID Doesn’t Identify the Designer (Part 1)

Let’s carefully analyze this statement. What is intelligent design? It is the set theoretic complement of the disjunction regularity-or-chance. In other words, that which remains when science cannot explain how something arose via processes of regularity and chance. In other words, Luskin basically describes the definition of design. However, in order to reach a true design inference, one has to take the step towards agency. It is in that step where ID fails miserably, and even though ID proponents like Dembski warned about confusing design with agency, Luskin seems to not have gotten the memo.

Before I proceed, however, I note that Dembski makes an important concession to his critics. He refuses to make the second assumption noted above. When the EF implies that certain systems are intelligently designed, Dembski does not think it follows that there is some intelligent designer or other. He says that, “even though in practice inferring design is the first step in identifying an intelligent agent, taken by itself design does not require that such an agent be posited. The notion of design that emerges from the design inference must not be confused with intelligent agency” (TDI, 227, my emphasis).

Source: Ryan Nichols, Scientific content, testability, and the vacuity of Intelligent Design theory, The American Catholic Philosophical Quarterly, 2003 ,vol. 77 ,no 4 ,pp. 591 - 611

Well, if Behe can call Miller an intelligent design proponent because of his Christian faith, showing that ID really is all about religion, then it seems that it is not more than fair that we call Behe an evolutionist for his acceptance of common descent, and his somewhat self-contradictory claim that after God set it all in motion, evolution could very well have played itself out via purely natural processes of regularity and chance. But if that is the case then ID, which is based on eliminating such natural processes to infer design seems to have lost its claim to it.

Miller Wrote:

Even more confusing is Behe’s attempt to meld this version of design with science. He tries to argue that his God need not intervene to produce change because “the purposeful design of life to any degree is easily compatible with the idea that, after its initiation, the universe unfolded exclusively by the intended playing out of natural laws.” Really? Bebe has just provided two hundred pages of passionate arguments that natural laws are not sufficient to explain evolutionary change, only to turn around and claim that they are. His core argument is that the natural laws that produce mutations cannot generate the diversity needed to explain evolutionary change. Then he insists that the unfolding of our universe is governed entirely by those same natural laws. And Behe does nothing to dispel this self-contradiction.

Kenneth R. Miller “Faulty Design” Review of “The Edge of Evolution” CommonWeal, October 12, 2007

Just in time for Halloween, the latest edition of Newsweek has a neat article about the psychology of supernatural belief. Here are a couple of excerpts:

The mind also sees patterns in random data, which is why the sky is speckled with bears and big dippers. This drive to perceive patterns—which is very useful in interpreting experimental data as well as understanding people’s behavior—can also underlie such supernatural beliefs as seeing Jesus in the scorch marks and flecks of grain on a grilled-cheese sandwich. “If a stain looks like the Virgin Mary,” says Hood, “then it is a divine sign and not a coincidence. If the wind in the cave sounds like a voice, then it is a voice.” […]

The mind also tends to impute consciousness to inanimate objects (ever yell at a balky computer?). This leads us to believe that natural phenomena are “purposeful, caused by agents with sentient minds,” says Hood, whose book “The Supernatural Sense” is due next year. It’s only a short step to thinking that “ ‘things that go bump in the night’ are the result of some spirit or agent,” not branches brushing against your drainpipe.

Sound like anyone you know?

An important point made in the article is that the tendency to see patters that aren’t there or to impart consciousness to things that aren’t conscious is a normal outcome of the way the human brain functions, due in large part to having to deal with incomplete sensory input. A couple of important lesson to draw from this (to me anyway) is that, first of all, rigorous empirical testing is necessary in science precisely because everyday perception can be so badly misleading. And secondly, the brain’s wiring can make it very difficult for people to disabuse themselves of supernatural beliefs. I still don’t know what the best method of doing that is, but getting them to understand the underlying means by which such beliefs form is probably a useful exercise.

The Association for Science Education adds its voice for evolution

From the NCSE we hear about the Association for Science Education which has issued a statement on science education, “intelligent design” and creationism

The Association for Science Education – a professional association for teachers of science in Britain and around the world, with over 15,000 members – recently issued a statement (PDF) on science education, “intelligent design,” and creationism, reading in part:

it is clear to us that Intelligent Design has no grounds for sharing a platform as a scientific ‘theory’. It has no underpinning scientific principles or explanations to support it. Furthermore it is not accepted as a competing scientific theory by the international science community nor is it part of the science curriculum. It is not science at all. Intelligent Design belongs to a different domain and should not be presented to learners as a competing or alternative scientific idea. As such, Intelligent Design has no place in the science education of young people in school.

In the post about my review of Behe’s The Edge of Evolution, many complained that they couldn’t access the full text without a university subscription or paying a huge fee. I have checked Elsevier’s policies on this. Authors are not allowed to post the published PDF to their websites (you have to get that from Elsevier), but they can put up the unformatted, submitted preprint version of their articles, as long as they include the reference and DOI to the published version. So here is the reference: Nicholas J. Matzke (2007). “The edge of creationism.” Trends In Ecology and Evolution, In Press, Corrected Proof, Available online 24 October 2007. ScienceDirect, doi: 10.1016/j.tree.2007.09.004.

…and the full text is below the fold. Note that the unpublished version has a few minor differences from the published version. For example, it has more emphases which were kind of my way of jumping up and down on the smoking ruins of Behe’s core arguments in The Edge of Evolution.

Although Behe has referred to Miller as an ‘intelligent design proponent’, Miller himself is on the record in many different forms that we should not conflate Miller’s faith with his scientific position.

On November 13^th, 2007 Nova will present Judgement Day: Intelligent Design on Trial” and as part of the experience, Nova is providing an excellent companion website. One of the features involves the perspective of various scientists on defining the concept of science

Miller has two segments in which he explains both the scientific method and religion and addresses what he considers some of the abuses of logic (“a gross mischaracterization to take a scientist in the past … and say that Newton worked based on a hypothesis of design)

On Isaac Newton Running time 1:34
Science vs. Religion Running time 2:29

Miller Wrote:

What Intelligent design pretends to do to be in the tradition in Newton, What intelligent design actually is, to be perfectly honest, is in the tradition of the middle ages where they stop investigation by saying we cannot answer this mystery it is the work of God “the designer”. This is a science stopper

On Amazon, Behe has been making the ‘argument’ that not only Miller is an ‘Intelligent Design’ proponent but also that Miller is (in large part) motivated by theology to embrace Darwinism.

Behe Wrote:

So there you have it. Miller (and Ayala) won’t tolerate life on earth being designed because that would impugn God’s reputation. Too many bad things inhabit the earth. They embrace Darwinism, at least in large part, for theological reasons.

all because Miller observes that

To Behe, these are not byproducts of a fruitful and creative natural world that also gave us the beauty of a sunset, the grace of an eagle, and the talent of a Beethoven. No, each vicious parasite and fatal disease is the direct and intentional work of the designer. This isn’t my conclusion; it’s Behe’s.

Yet in Miller’s scathing review, he clearly states his position

Few may be aware that the State of Florida is revising its educational standards and that a dedicated group of people have been working on the science standards, including evolution. The Orlando Sentinel reports:

Joe Wolf, president of Florida Citizens for Science, called the draft standards a “wonderful” blueprint for science education. Wolf, of Winter Haven, said the evolution debate holds little interest to most scientists, who accept it as fact. That’s why the issue did not become controversial during the standards-writing meetings, he said.

“It’s a PR issue,” he said. “And it’s a religious issue. In the scientific community, it’s not an issue.”

On EvolutionNews.org, the Discovery Institute’s blog site, Robert Crowther manages to spin it as

Florida Citizens for Science Excommunicate Prominent Scientists from “Scientific Community” For Doubting Darwin

So what has happened to Philip ‘the father of Intelligent Design’ Johnson? While some ID proponents have been arguing that ID has nothing in common with religion, Johnson seems to disagree. Since his stroke in 2001, Johnson’s public appearances seem to have been minimal and given his past statements, I am not surprised that ID is keeping Johnson out of the lime-light.

On UcD Tyke explains why the “confusion” by O’Reilly and Stein about the religious nature of ID is due to a fundamental entanglement with creationism. And while some effort is made to manage the message and pretend that ID makes no claims about the designer(s), ID proponents are very clear that the purpose of ID is to introduce the reality of God into the academic world.

Tyke Wrote:

This may be pessimistic, but I very much doubt ID will ever come close to disentangling itself from creationism and religion. By far the largest block of support for ID comes from the conservative Christian community, and they simply see no merit in pretending that they don’t necessarily mean God when they talk about an intelligent designer. In fact, many of them believe it to be disingenuous to do so.

Even Philip Johnson himself is quite open about his religious motives for supporting ID when talking about it on Christian radio shows. While his lawyerly choice of words may allow him to continue claiming that the science of ID is silent on who the creator is, there is no mistaking the message he is sending to the Christian faithful–that ID enables Biblical creationism as a scientific theory.

Jon Blumenfeld on “NOMA”:

Every single [book review in the Reports of the NCSE], in whole or in part, is an attempt to reconcile science and religion – and that’s just one issue of RNCSE.… [C]an’t we dispense with all the book writing, all the mental contortionism, all the close study and redefinition of every word in the bible to somehow rescue God, and just say, “Science good. Faith not subject to reason.” As Hugh Laurie’s character, Dr. House, recently said: “Rational arguments do not work on religious people, otherwise there would be no religious people.”

(Read the rest…)

Update: I’ve corrected an error; Blumenfeld was referring to the reviews section of RNCSE, not to every article.

On UcD Dembski addresses the news that the author of a 52 year old paper has retracted the paper. Dembski makes some claims which are either erroneous or full of irony. So let’s start.

Dembski Wrote:

Below is a fascinating report in the NYTimes about a long-retired professor who found that his work was being cited by “creationists” and THEREFORE decided to retract it.

But in fact the researcher retracted passages of the paper because he had uncovered errors in his paper, errors which were being quote-mined by Creationists.

So not only did the researcher not retract the paper, he asked to retract two passages that contained errors in the claims and which were abused by creationists.

Homer Jacobson Wrote:

In January 1955, American Scientist published my article, “Information, Reproduction and the Origin of Life” (Vol. 43, No. 1). I ask you to honor my request to retract two brief passages, as follows:

Those crazy rascals behind Expelled have some new games they want to play: they’ve put out a casting call for victims of persecution. It’s a pitiful plea, but it will probably net a nice collection of complaints — because it’s true. We do reject Intelligent Design from the academy, from science, and from science education, and there’s a very good reason for that: it’s the same reason we reject astrology, alchemy, creationism, haruspication, necromancy, ornithomancy, and witchcraft from our science courses. Because they aren’t science.

Taylor Kessinger gets it. He’s a junior at the University of Arizona who wrote a nice, lucid opinion piece for the school paper.

Continue reading “The Discovery Institute doesn’t like smart college students” (on Pharyngula)

On Amazon Behe admits that Intelligent Design is nothing more than a code word for Christian faith.

Behe Wrote:

Miller Wrote:

Behe happily notes, as I would, that we live in a universe whose fundamental physical constants are remarkably hospitable to life. To me, and apparently to Behe, these constants may well reflect the will of a creator we would both identify as the God of Abraham.

So let me emphasize: Kenneth Miller is an intelligent design proponent. He believes that the laws of the universe were purposely set up to permit life to develop. Miller thinks that, to accomplish the goal of life, the universe had to be designed to the depth of its fundamental physical constants. I agree with him as far as he goes, but, on the other hand, as I write in The Edge of Evolution, I think design extends further into the universe, past physical constants, past anthropic coincidences, and well into biology. Yet, with respect to design, he and I differ only on degree, not on principle.

Having a hard time finding enough persecution stories, the makers of Expelled! No Intelligence Allowed (background here and here, in case anyone’s forgotten) are now asking students or anyone else they can find to submit their horrible, horrible stories of oppression at the hands of the Dogmatic Darwinist Conspiracy. And if the other persecution stories they’re touting are any guide, little details like being true are not a prerequisite. You too can be a movie star!

Ever sat in class and had your professor straight up challenge your intelligence for suggesting even the possibility of an intelligent design in the universe?

Tired of being labeled merely for questioning aspects of the Darwinian theory of evolution?? Ever been scoffed at or ridiculed in front of your peers?

Well, here’s your opportunity to tell your story on our Website AND possibly be in the movie, “Expelled: No Intelligence Allowed”! Tell the world some of the outrageous things your professors say about your questions.

You and your story just might be chosen by our producers to be in the film, “Expelled: No Intelligence Allowed”! Let your voice be heard!

Oh my, have you been.… scoffed at? Does someone think you’re being foolish? Did they make mean girl faces at you? It’s time to stop taking it like an adult and unleash your inner cry-baby. The tireless defenders of free speech that are the makers of Expelled! will help you denounce those evil professors and anyone else who thinks they have a right to an opinion.

Andy Warhol is now smiling down from heaven (or up from hell) of all the many hours of fame that are about to be created in neat little 15 minute packets. Careful though. Given the loose ethical standards of the filmmakers, you may well end up in an entirely different film than the one you interview for.

On Uncommon Descent Denyse O’Leary asks a question, every ID creationist should ask, and be able to answer: “What exactly is the “design” part of “intelligent design”?”

For an author of a book on Intelligent Design as well as a ‘teacher’ of a pastoral course on Intelligent Design, Denyse seems to be rather unfamiliar with one of the foundational concepts of Intelligent Design. Well, no fear, PvM is here.

I am pleased to announce that Trends in Ecology and Evolution (TREE) has just put up the article-in-press version of my book review of Michael Behe’s The Edge of Evolution. Here is the reference and link:

Nicholas J. Matzke (2007). “The edge of creationism.” Trends In Ecology and Evolution, In Press, Corrected Proof, Available online 24 October 2007. ScienceDirect, DOI.

The DOI link doesn’t seem to be working just yet, presumably that is temporary. And the other link is one of those nasty superlong ones, so if nothing works, go to the TREE website and click on “Articles in Press” to see it (you will have to have a subscription or university access to get the article; I will provide a partial quote below).

Writing this review was challenging. There are a great many things wrong with Behe’s book, and attempting to hit the most important points effectively, with just 750 words to work with, was quite a challenge. For example, there was no way to fit in anything about HIV, even though some really good points have emerged on that front in the last few months. Thanks to the PT crew for a great many helpful discussions, comments, etc. I also had Cavalier-Smith’s (1997) TREE review of Darwin’s Black Box, literally the article that got me into ID criticism in a serious way, to inspire me (despite some flaws in that review).

I tried to make every word count, so it is hard to pick a summary quote, but here is a bit from the middle:

Biologist Stephen Matheson describes some cool evolutionary biology experiments:

Even better, though, would be to find an example of evolutionary change in which the new and old forms are still living, so that one could do the before-and-after comparison. It would look something like this: take a species, subject it to evolutionary influences of some kind until the descendants look significantly different from the ancestors, then compare the genomes (or developmental processes) of the descendant and the ancestor, in hopes of discovering the types of changes at the genetic or developmental level that gave rise to the differences in appearance or function of the organisms. That would be a cool experiment.

In fact, that kind of experiment has been done, more than once. The best example, in my opinion, involves an organism far less sexy than a dinosaur or a finch or a whale: Zea mays, better known as corn (or maize).

If that’s got you hungry for more, head on over to his blog and read the entire article.

On UcD, BarryA claims that “Dawkins: “Darwinism Leads to Fascism””

As irksome as Richard Dawkins can sometimes be, one must nevertheless admire his occasional outbursts of honesty. Over at First Things Fr. Ed Oakes refers to an interview Dawkins gave to an Austrian newspaper, Die Presse (July 30, 2005), in which he said: “No decent person wants to live in a society that works according to Darwinian laws. … A Darwinian society would be a fascist state.”

That’s like saying that a Quantum Mechanical society would be an anarchy. I hope that those better versed in logic than our Intelligent Design defender, understands the difference between “A Darwinian society would be a fascist state” and “Darwinism leads to Fascism”?

Kids, you be warned, this is your brain on Intelligent Design…

And what about the ellipsis?

The Ledger reports how “..45-member committee appointed by the state Department of Education began revising the science standards in May in response to a failing 2005 report on Florida’s public school science curriculum by the Thomas B. Fordham Institute, a Washington-based nonprofit group.”

The science side is well supported by an NCSE representative

Jonathan Smith, a Lakeland resident and a representative of the National Center for Science Education, a nonprofit group critical of intelligent design, helped write the new standards.

“It (new standards) closed the door on any ambiguity” about evolution, Smith said. “There isn’t both sides. There is only one side as far as science is concerned.” That side is evolution, he said.

and there are also some creationists who lament that God/Intelligent Design is unfairly excluded

But Mickey Carter, pastor at Landmark Baptist Church in Haines City, said the revisions will be a disservice to students.

He said there should be a balance between both intelligent design and evolution.

“We are denying freedom of ideas, speech and shutting down one side,” Carter said. “The kids ought to be able to study both sides of it so we don’t just turn out a bunch of rubber-stamped robots in the classroom.”

Carter said that science is limited in its ability to determine every fact. “When it’s all said and done, folks just don’t give God enough credit,” Carter said. “Too many things on this world cannot just be an accident. You’ve got to give some credit to some intelligence.”

Why is it that Intelligent Design supporters are honest enough to admit that it ID is all about God while its major activists seem to be denying the obvious fact? Teach the controversy… Despite denials by the Discovery Institute, Intelligent Design is correctly identified as a religious concept. O’Reilly, Ben Stein and many ID supporters could not possible be all wrong :-)

The latest Tangled Bank is online at the Radula — enjoy the diversity of (mostly) biology!

Over on the Ben Stine vs Intelligent Design thread , one Ben Major writes:

…..Behe just placed a major thumping on the head of Sean Carroll on pyrimethamine in a back and forth at Science for the full story see: http://www.amazon.com/gp/blog/A3DGRQ0IO7KYQ2

No, Behe just put together a series of non-sequiturs.

To put this in perspective, here is what Carroll wrote: (which flows on from this article )

“With respect to the latter, the passage he quotes in his Letter about how “[a]dding more mutations …. can increase the level of resistance” is immediately followed in his book by the disclaimer that “[h]owever, as usual there’s a hitch. Some of those extra mutations (but not the first one) seem to interfere with the normal work of the protein” (p. 75). Behe is clearly seeking to convey the message that there is some impediment to Darwinian evolution via multiple intermediates, both in this specific case and in general (hence the phrase “as usual”). However, this is not the case. Careful inspection of the data in the reference I cited (2 (Sirawaraporn et al., 1997)) reveals that, in fact, certain mutations (e.g., Cys59->Arg) increase specific parameters of the enzyme’s performance. Structural studies suggest that this mutation, found at very high frequency in drug-resistant parasites in nature, improves enzyme binding to substrates in the context of otherwise adverse mutations (3(Yuvaniyama et al., 2003)). Furthermore, pyrimethamine resistant dihydrofolate reductase enzymes actually have activities equal to or better than the wild-type enzyme (4(Sandefur et al., 2007)). Behe also neglects to note the fact that such triple and quadruple mutant enzymes have been found in isolates from India, Southeast Asia, Eastern Africa, and South America, including areas where pyrimethamine use has been limited. The latter suggests that mutant parasites may be as fit as wild-type parasites.”

This is the funniest thing I’ve read all week. Yes, it’s even funnier than young-earth creationist and Discovery Institute fellow John Mark Reynolds attempting to argue that J. K. Rowling is wrong about Dumbledore being gay. (It’s fascinating to watch Reynolds blithely employ interpretive principles derived from the doctrine of Biblical inerrancy and apply them to the Harry Potter texts to argue against the very ‘deity’ that created them, J. K. Rowling. It’s a short circuit in Reynolds’s brain, just like young-earthism. But that’s another story.)

Anyway, here’s the funniest thing: First the DI tells everyone to watch Ben Stein on the O’Reilly Factor. But apparently neither Stein nor O’Reilly got the memo about how ID isn’t about religion or God creating things. They both think it is for some reason. And yet they clearly are not part of the evil Darwinist liberal media. Wherever could they have gotten the idea? I mean, it’s not like hundreds of clear statements from ID advocates connecting ID to God, creationism, and conservative evangelical apologetics should have lead them astray.

Here’s the actual text of the latest missive from the Discovery Institute Media Complaints Division:

The next episode of NOW on PBS will report on a trip by scientists and evangelical Christians to Alaska “with open minds to learn about the effects of global warming.”. Earlier this year, the ScienceDaily blog reported on this unique trip.

The Scientists-Evangelical Alaska Expedition grew out of a collaboration that began at a two-day private retreat in December 2006 attended by 30 leaders from the scientific and evangelical communities. The retreat led to close relationships of mutual trust and understanding among the participants and to the release in January 2007 of an “Urgent Call to Action,” a pledge that these leaders would speak with one voice in their shared commitment to protect life on Earth.

On October 22, Anika Smith, posted the following announcement on EvolutionNews.org

Ben Stein, star of the new movie “Expelled,” is going to be on the O’Reilly Factor tonight, talking about his involvement in “Expelled” and the suppression that’s taking place in our nation’s academic and scientific communities. Be sure to tune in and learn more about the movie, which we first noted here.

After Ben KlStein’s disastrous appearance in which both he and the host emphasized the religious foundation of Intelligent Design, the posting seems to have been expelled from the website. But evidence remains

Teach the controversy seems to have its limits. But design inferences are fun.

It’s only taken 30 years, but information about Ebola in nature is finally starting to snowball. First, after almost 15 years of disappearing from the human population, Ebola returned with a vengeance in the mid 1990s, causing illness in 6 separate outbreaks in Gabon, Ivory Coast, Democratic Republic of Congo (DRC), and South Africa (imported case) between 1994 and 1996. As doctors and scientists rushed in to contain the outbreaks, they were also able to collect viral samples, and trap animals and insects in the area, searching for a reservoir for the virus. In this decade, there have been almost yearly outbreaks of Ebola and/or the closely related Marburg virus in Africa, resulting in the discovery of both Ebola and Marburg infection in species of fruit bats–suggesting these animals may be a reservoir species for filoviruses (though more work remains to be done to confirm this).

As I blogged about previously, prior work has suggested that the most deadly Ebola subtype, known as Ebola-Zaire (EBO-Z) after its initial site of isolation, has been spreading steadily eastward across the central African continent. This was tracked by examining isolates of the virus obtained during human epidemics, which introduces a bias into the sample. However, viral isolates from other sources have been quite difficult to obtain, despite many years of searching. A new paper examines viral isolates collected from dead gorillas and reconstructs their phylogeny in an effort to fill in some of these gaps.

(Continued over at Aetiology).

For those who find it too painful to watch the video of Bill O’Reilly interviewing Ben Stein on his show last night, I have taken the liberty of posting a transcript over at EvolutionBlog. Read it and weep. (And believe me, I do mean weep.) Comments can be left there, but please keep in mind that I am only the messenger!

The ID crowd was all giddy about Ben Stein appearing on Bill O’Reilly’s show, little did they know that Bill would introduce ID as follows:

“intelligent design, that is, a deity created life”

Seems that Bill and Ben never got the Discovery Institute’s talking points. I am almost starting to accept the hypothesis that Ben Stein is doing this all to expose ID with “Expelled”. Surely this belongs in the category of humor.

On Bill O’Reilly, Ben Stein made the following claim:

Ben Stein Wrote:

ID is an effort to fill in the gaps, and is a sincere effort to add new knowledge to the theory.

(paraphrased)

Nice to know that ID is in the business of filling the gaps, seems that Ben Stein does realize that ID is just a variant of God of the Gaps. However, like so many other ID proponents, Ben has been misled to believe that ID adds new knowledge to the theory. It doesn’t. Did he not get Bill’s memo? Did Ben not get a copy of the Wedge document?

Bill Dembski Wrote:

As for your example, I’m not going to take the bait. You’re asking me to play a game: “Provide as much detail in terms of possible causal mechanisms for your ID position as I do for my Darwinian position.” ID is not a mechanistic theory, and it’s not ID’s task to match your pathetic level of detail in telling mechanistic stories. If ID is correct and an intelligence is responsible and indispensable for certain structures, then it makes no sense to try to ape your method of connecting the dots. True, there may be dots to be connected. But there may also be fundamental discontinuities, and with IC systems that is what ID is discovering.”

Since ID proponents argue, without much merit, that they are being censored, I invite them to explain on this thread to us what knowledge ID has added to science. Ideally, this would be knowledge which would not have been added to science were it not for Intelligent Design’s “revolutionary approach” which involved avoiding to deal in ‘pathetic levels of detail’.

Read more at Pharyngula

The National Geographic shows how intelligence can be reduced to simpler processes and rules. The work is important as it shows, contrary to ID’s assertions, that intelligence can in fact be reducible to processes of regularity and chance. From ants to bees to fish to caribous, the researchers found that “swarm intelligence” is based on simple creatures following simple rules based only on local information. In other words, none of the creatures sees the bigger picture and yet the swarm “responds” in an intelligent way.

Several researchers have used the concept of swarm intelligence to find solutions to similar problems. For instance, Southwest Airlines used the principle to find an optimal schedule for its planes leaving and arriving at gates. In another instance a company optimized its profits by scheduling which plants were to deliver to which customers.

WIkipedia explains:

SI systems are typically made up of a population of simple agents interacting locally with one another and with their environment. Although there is normally no centralized control structure dictating how individual agents should behave, local interactions between such agents often lead to the emergence of global behavior. Examples of systems like this can be found in nature, including ant colonies, bird flocking, animal herding, bacterial growth, and fish schooling.

In the comments section of an earlier posting in which I explored the “arguments” from an ID proponent as to why the suckling behavior of whales shows evidence of Intelligent Design, Duncan posted the following rebuttal by Dr Colin D MacLeod

Duncan Wrote:

The comment about whales and their nipples being evidence of Intelligent Design was published in a letter to the Scottish newspaper The Herald, and seems to derive from a 1938 book by the Creationist Douglas Deraw, entitled “More Difficulties of the Evolution Theory”. The claim received a pretty terminal rebuttal on 20 October, with the publication of the following letter:

Dear Dr. Behe

I have recently read your response to Abbie Smith’s article on the HIV-1 protein VPU. Ms Smith showed how Vpu’s recently evolved viroporin activity directly contradicts your statement that HIV has evolved no new biding sites since it entered humans (Edge of Evolution, page 143 and figure 7.4, page 144 ). I was greatly disappointed in your response. I must admit to having a special involvement in this case. Firstly, I drew the illustrations for Ms Smith’s article, and its follow up. But secondly, as a member of my professional association’s education committee, I am directly concerned with the support and nurturing of the new generations of enquiring minds, those that we will pass the torch of enquiry on to when we retire. It is in this regard that your response very disturbing. It is almost the exact opposite of what a concerned scientist and science communicator should have done.

It was bad enough that you chose to ignore her for over two months and then did not do her the courtesy of replying on her blog (1). It was bad enough that you chose to start by belittling her and playing the “I’m a Professor and she is a mere student” card (conveniently ignoring the fact that she actually works on HIV). This is particularly egregious in science, where we pay attention to the evidence and logic of an argument, rather than the letters after an author’s name. Doubly so if we wish to guide young scientists into a demanding profession.

But by far the worst, you ignored her core argument. That in the space of a decade HIV-1 Vpu developed a series of binding sites that made it a viroporin, a multisubunit structure with a function previously absent from HIV-1. Dr. Behe, it is not enough to cite a generalist review and claim that the differences between HIV-1 strains are “not all that great”. You actually have to show why Vpu developing binding sites to form a multi-subunit structure with a novel function does not falsify your claim that HIV has developed no new binding sites. Ironically, the very paper you cite to dismiss Ms Smith contains evidence of at least two new binding sites in HIV. I will not dwell on this any further, as Ms Smith is producing her own response.

Compare the efforts by Denyse O’Leary to teach about the so-called “controversy” surrounding Intelligent Design with the efforts by the McGill Journal of Education to instruct teachers as to the topic of evolution.

The former strictly belongs in a category of “Pastoral Care” while the latter focuses on science teachers. Not surprisingly since Intelligent Design is mostly a religious controversy over a the distinction between materialism (read atheism) and theism (read Intelligent Design). However science is not materialistic but rather uses the very successful method of “methodological materialism” or “scientific method” to study the world around us.

The impact of ID’s position on science is immediately noticeable as it refuses nay is inherently unable to provide any scientific explanations beyond proclaiming that our ignorance is evidence of something called “design” where “design” is nothing more than the “set theoretic complement of regularity and chance”. If science cannot yet explain a particular feature, ID is quick to fill the gap, often very temporarily, with “design” rather than accepting the scientific position of “we don’t know”.

ERV has gotten around to reading the paper quoted by Behe in his previous defense of ERV’s essay. She reports that “He isn’t pubjacking! He’s commandeering a publication!”

ERV Wrote:

Hmmm. Now that statement looks funny. I mean it lacks the tell-tale “…” that usually mark Creationist quote-mines, but something just looks fishy about Behes choice of quote. Hmmm. Wonder what comes right after the portion Behe chose to quote?

Read more at He isn’t pubjacking! He’s commandeering a publication!

In Florida, we have just finished writing new science standards for all grades of public schools. The standards are intended to be a core of fundamentals that will be taught and tested. I am commenting on an email sent to a number of the standards writers by Fred Cutting of Florida. Cutting has some suggestions for the new Florida School Science Standards, and concludes a longish email with these two proposed additions:

1. Standards requiring students to learn about the anomalies to all theories (standard models) including standard models for the origin and evolution of life;

2. Standards requiring students to learn about the abuses and misuses of science in America’s recent history.

Update: now crossposted to Florida Citizens for Science

The first of these is supposed to accomplish many things:

I think that most people would agree that the terms Religion, Scripture, Spirituality describe quite accurately the context for Denyse O’Leary’s “teaching” of a non-credit course in Pastoral Care about “Intelligent Design”. I hope she can find a suitable textbook which accurately describes Intelligent Design.

Who would have thought that Intelligent Design was so intertwined with religion :-) Thanks Denyse.

The course is described as

RSS7-F By Design or By Chance? An Introduction to the Intelligent Design Controversy The intelligent design controversy is best understood as a conflict between materialist and non-materialist views of the origin and nature of the universe. Reputable scientists can be found on both sides. Because the two sides proceed from different assumptions, they do not agree, as Thomas Kuhn would say, on what would constitute a falsification of their premises. The controversy continues to grow because, while the materialism is prevalent in academia and the media, it is widely discredited in the population at large, including the professional classes.

I wonder if Denyse is familiar with St Augustine when she presents her materialist versus non-materialist views or worse, her claim that “reputable scientists are found on both sides”.

Hat Tip: PZ Myers

It looks like the makers of the Expelled! documentary have some competition. There’s a new film soon to be released titled Einstein Wrong: The Miracle Year. Unless you’re denser than a black hole, it’s obvious from the title alone that it’s an anti-relativity piece. The “Miracle Year” refers to Einstein’s Annus Mirabilis of 1905, which just had its 100^th anniversary. So naturally, the time is ripe for it to be destroyed.

The filmmaker is a man by the name of David de Hilster, whom I had never heard of before. He has no background in physics or any other natural science, though his bio proudly states that “his science skills [were] recognized in elementary school”. He also runs or is at least the major contributor to a site called Science Watchdogs, where he humbly places himself as arbiter of all that is or isn’t science.

In order to explain all of the problems with the theory of relativity, de Hilster employs members of his family, particularly his mom. This is certainly a step up from Ben Stein, but the “everyday person” technique is unlikely to convince most skeptics. After all, relativity is conceptually hard, and seeing an elderly lady sit around the living room doing her knitting doesn’t exactly smack of cutting edge science. There is the implied argument that if a theory can’t be made sensible your average suburban mom, then something must be wrong with it. Nuts, says I.

Now I am not a physicist either, and my knowledge of relativity theory extends no further than that of most otherwise scientifically literate people (which is to say, slightly above Star Trek level). But looking at the movie’s website and watching its trailer, I can’t help but feel that I’ve seen this somewhere before. Yep, it uses the exact same tactics as Expelled! and other ID/creationist propaganda. And that seriously pegs my BS meter.

As reported by NCSE, Sen. David Vitter (R-LA) has withdrawn his $100,000 earmark for anti-science education: Vitter earmark withdrawn. During yesterday’s session Vitter asked that the money in the earmark be directed to other projects, insisting that he never intended—yeah, right—for the money to go towards teaching creationism.

Joshua Rosenau of “TfK” has the full exchange on his blog.

Mr. VITTER Madam President, I rise today to discuss a project I sponsored in the fiscal year 2008 Labor, Health, Human Services and Education appropriations bill. The project, which would develop a plan to promote better science-based education in Ouachita Parish by the Louisiana Family Forum, has raised concerns among some that its intention was to mandate and push creationism within the public schools. That is clearly not and never was the intent of the project, nor would it have been its effect. However, to avoid more hysterics, I would like to move the $100,000 recommended for this project by the subcommittee when the bill goes to conference committee to another Louisiana priority project funded in this bill.

Mr. HARKIN Madam President, I appreciate the sentiments by the Senator from Louisiana and accept this proposal to move the funding for this project to other priority projects for the State of Louisiana in the bill when it goes to conference committee.

Mr. SPECTER Madam President, I concur with my colleague and will agree to move these funds in conference committee.

Congratulations to everyone who contacted their senators about this earmark. The students of Louisiana owe you a debt of gratitude. You not only got the earmark withdrawn, you also got the sponsor to do it.

Kudos all around.

Things are not going well for Michael Behe. First his concept of Irreducible Complexity is shown to be full of holes, then he publishes a paper with Snoke (so much for the claim that ID proponents do not get to publish) to argue that there are limits to evolution, only to be shown to be wrong soon thereafter by another publication which points out some of the unreasonable assumptions made by Behe. And more recently, after a very “successful” defense of ID in the Kitzmiller trial, Behe has published a book in which he, mostly ad hoc, claims that there are limits to evolution. Needless to say, scientists were once again not very impressed.

In one example, ERV took on Behe’s claim about HIV. It took Behe several months to respond and his response both lacked in civility as well as in scientific content. Perhaps by mistake, perhaps by design, Behe left commenting enabled and soon comments filled his blog page. While several of these comments show once again the problems with Behe’s familiarity with science, it is the lack of scientific content of Intelligent Design which I would like to point out.

Last January Prof. Steve Steve, Bora, and I met Congressman Brad Miller (D-NC) at the NC Science Blogging Conference. We took the opportunity to explain to him NCSE’s Project Steve and our Project Steve Steve.

Rep. Miller is the Chairman of the House Science and Technology subcommittee on Oversight and Investigation and promised us that he’d ask science skeptics that testify before him “How many are named Steve?”.

Today, he did it:

Do you all know any climate skeptics … named Steve?

During a hearing about the impact of global warming on the arctic he unexpectedly asked the panel if they knew any Steves that agreed with them. The global warming skeptics couldn’t name any off the top of their head, while the global warming researchers named two.

Miller also gave the Panda’s Thumb a plug for good measure.

The discussion about Steves begins a bit before one hour, fourteen minutes (1:14) in the RealPlayer clip of the hearings. It continues for a few minutes.

I’d love to see the clip on youtube if anyone can extract it. If not, a transcript would be nice. (A lot of people don’t like dealing with RealPlayer.)

I guess that Miller had a good time bringing up Project Steve because he directed his staff to email us about it.

Hopefully, more politicians will follow his example when dealing with “expert” testimony.

Just when you think that you have heard it all, an Intelligent Design supporter makes the claim that Whales illustrate intelligent design. I kid you not.

We are surrounded by evidence of intelligent design. Take but one example: the suckling mechanism of the whale. The whale is a mammal which suckles its young underwater. It does so by means of a watertight cap around the mother’s nipple which fits tightly around the baby’s snout so as not to allow the entrance of sea water. Such a mechanism does not allow of a transitional form which adapts slowly to its environment. It does not allow for a gradual evolutionary process. It must exist perfectly formed for the purpose or the baby whale dies. How else could such a mechanism exist if not brought about by an intelligent and purposeful creative force?

Nick Matzke documented a likely origin for this claim

What is even more funny is how people at UcD respond to this news… Check out Born Again’s flawed understanding of vestigial organs:

…. some modern whales have a pair of bones embedded in their tissues, each of which strengthens the pelvic wall and acts as an organ anchor.

Carl Wieland- 1998

Seems like the useless leftover legs actually have purpose in the whale!

With the appendix finding purpose in humans it seems the Evolutionists seem to be running out of vestigial parts to point to as proof for their cherished lie!

Is this the best ID has to offer? Well, it can get worse, just check out Dembski and Denyse O’leary’s comments about eugenics and Darwinism at UcD.

Children you have been warned, this is a ‘brain on ID’…

Creationism to be banished from Swedish schools

The Swedish government is to crack down on the role religion plays in independent faith schools. The new rules will include a ban on biology teachers teaching creationism or ‘intelligent design’ alongside evolution.

“Pupils must be protected from all forms of fundamentalism,” said Education Minister Jan Björklund to Dagens Nyheter.

Some Christian schools teach biology students that the world and the organisms on it were created by a supreme being. This is often presented as another valid scientific theory alongside evolution - something most scientists reject.

Religious Education will remain on the curriculum and it will still be allowed to start the school day with prayers. But in classes teachers will be expected to stick to the curriculum.

In his talk “Molecular Machines/Death of Darwinism”, Dembski makes the following observation:

Dembski Wrote:

what do they do. Darwinian mechanisms is a divide and conquer strategy. You take a system and if you can find a sub system of that system which performs some function then you have divided the problem . Clearly the global system evolved from the system that is embedded in it. End of story. No need to do any engineering work or any design work or anything, that’s enough. Enough to point to these intermediate systems. but not give any detailed testable step by step scenario for how point A could have evolved by gradual means into point B. Nevertheless that is enough to convince them because from their perspective design is a non-starter, it’s unthinkable

In order to understand the scientific argument, it is important to remember how ‘design’ is defined by Intelligent Design. Design is the “set theoretic complement of regularity and chance”. In order to reach a design inference, Intelligent Design needs to show that of the countless possible paths, none remain plausible, quite an unenviable task. Behe has attempted to circumvent the hard work by arguing that systems that are Irreducibly Complex cannot have evolved (well, he does accept the possibility of evolution of such systems but considers them improbable). That position by itself has turned the certainty argument of ID into a probability argument and thus undermines the ID position. But science has done more, it has shown that so-called Irreducibly Complex systems can exist as smaller parts with a different function. In other words, the system is only irreducibly complex as to a single function. Science is pointing out that simpler systems with a function do exist and thus the IC argument fails. Does this mean that science rests? Of course not. Let’s take the bacterial flagella as an example and compare what science has done versus what ID has done. Well, I have provided science’s progress in this area, and I am hoping that an ID proponent can fill in the details as to what ID has added to explain the bacterial flagella. Needless to say, Dembski’s words show that he clearly does not comprehend the concept of ‘design’ and the scientific response to it.

I believe it was a famous French philosopher who said that everybody can make mistakes but only a fool stubbornly adheres to them. The story I am going to tell now may serve as an illustration of the above maxim, with a small modification: although the term “fool” may still (arguably) reflect the situation, the term “incompetent” is applicable unarguably. The hero of the story is William Dembski.

Read Errors not corrected for three years point to incompetence at Talk Reason.

Irony alert:

William Dembski Wrote:

People sometimes ask me why I encourage posts on global warming here at UD, whose focus is ID. The reason is that global warming exhibits many of the same abuses of science that we see in the ID debate. Science has become a wonderful tool for social control. This role of science in modern secular culture is destructive and needs to be broken.

Can anyone say Wedge

Ignorance begets ignorance.

I finally got around to reading Paradigms on Pilgrimage, by Stephen J. Godfrey and Christopher R. Smith. Godfrey and Smith began their careers as young-earth creationists. Godfrey became a paleontologist, and Smith, a Baptist minister. Each underwent what they call a “pilgrimage” as the acquisition of compelling, new knowledge forced them to reevaluate their literalist religious belief. Both, however, remained devout Christians.

Godfrey is now Curator of Paleontology at the Calvert Marine Museum in Maryland. In the 1980’s, he enrolled in graduate school, where he studied vertebrate paleontology. One of his first jobs was to search for fossils in sedimentary rocks. These rocks are layered, so the deeper you dig, the older are the fossils you find. Godfrey was most impressed by fossilized footprints and other markings, known as trace fossils, left in the sandstone by earlier organisms. As a young-earth creationist, Godfrey had thought that the sedimentary rocks and the fossils within them had been laid down by the Flood. If that was so, then how could terrestrial vertebrates have left footprints in the sand (which was presumably under water)? Godfrey researched trace fossils and found that they appear at many levels in many sedimentary rock formations all around the world. He could not account for the appearance of trace fossils in rocks that had supposedly been left behind by a flood that killed all the animals that might have made the footprints. Godfrey also found cracked and fossilized mud flats, which he recognized immediately had been baked by the sun and could not have been deposited by a flood. The earth suddenly became much older than Godfrey had imagined.

Laurence Moran at Sandwalk comments on a video excerpt with Bill Dembski, recently touted by the Discovery Institute’s Robert Crowther. What is fascinating that despite more than a decade of Intelligent Design ‘research’ this is the best ID has to offer.

Ironically, Dembski starts of by stating that “what darwinists have done is hidden behind complexities of living systems”. How ironic can this be… While science, as I have shown in several examples, deals in explanations, pathways and hypotheses, Intelligent Design has contributed exactly zero to our scientific understanding of these systems. Worse, while Dembski mentions some complex systems, he also avoids some examples of complex systems science understands quite well how they may have evolved.

My thanks to Robert Crowther for presenting the “best’ response ID has to offer. You be the judge.

The NCSE reports on Paul Gross’s book review of Behe’s “The Edge of evolution”. Like so many other scientists, Gross is not impressed.

Reviewing Michael Behe’s latest book, The Edge of Evolution (Free Press, 2007), in the October 2007 issue of The New Criterion, the biologist Paul R. Gross is anything but impressed. After observing that Behe’s argument from irreducible complexity in Darwin’s Black Box (Free Press, 1996) was quickly recognized to fail, he comments (PDF), “In response, Behe and the [“intelligent design”] movement shifted ground, first redefining I.C. in an effort to meet the flood of negation, finally (in effect) by scanting it in favor of more general claims. The Edge of Evolution is Behe’s heroic effort to snatch victory from the jaws of defeat.” Gross adds, “The clear goal is to justify his original claim that the purposeful complexity of life cannot be a product of ‘random mutation,’ that there must be intelligent design, and (en passant) that I.D. is the great scientific discovery of our age.”

Noting that Behe’s arguments have already taken a pounding (in review after review after review), Gross identifies two kinds of scientific flaws: “errors of the model itself and in the associated calculations, and … ignoring important conflicting material in the primary literature.” He gives three examples: Behe’s misunderstanding of a report on the frequency of spontaneous resistence to a drug in the malaria parasite; his unwarranted assumption that mutations in the relevant gene would have to be simultaneous; and his neglect of the experimental and theoretical literature on protein evolution – “the book’s grand argument ignores the known, frequent appearance, by Darwinian pathways, of protein-protein interactions in small populations. There is a vast experimental and theoretical literature on protein evolution.”

Paul R. Gross is University Professor of Life Sciences, emeritus, at the University of Virginia, and holds honorary degrees from the Medical College of Ohio and Brown University. He is a Fellow of the American Academy of Arts and Sciences. With Norman Levitt, he authored Higher Superstition: The Academic Left and Its Quarrels with Science (Johns Hopkins University Press, 1994); with Nick Matzke, he wrote “Analyzing Critical Analysis: The Fallback Antievolutionist Strategy” for Not in Our Classrooms: Why Intelligent Design is Wrong for Our Schools; and with Barbara Forrest, he authored Creationism’s Trojan Horse: The Wedge of Intelligent Design (Oxford University Press, 2004; reissued in paperback with a new chapter on Kitzmiller v. Dover, 2007).

Now some comments on the review

Taner Edis (author of An Illusion of Harmony: Science and Religion in Islam , Prometheus Books, 2007), writes in an essay about the sitiuation with intelligent design vs. evolution in Muslim countries:

“Muslim populations have not been very hospitable to Darwinian evolution, supporting some of the most successful versions of creationism in the world. Lately, some Muslim intellectuals have been showing interest in intelligent design as well.”

Taner Edis argues that this is a mistake, and that enthusiasm for intelligent design can only harm the already weak state of science in Muslim lands.

Read Intelligent design: a blind alley by Taner Edis at Talk Reason.

I recently attended a show by Roy Zimmerman. Roy has some very funny songs on political topics such as Dick Cheney, the sexiest man in the world and Intelligent Design and Saddam Shame and “Defenders of Marriage” and the very touching “Thanks For the Support”

Enjoy

The Nobel Committee announced that this year’s Nobel Peace Prize has been awarded to Vice-President Gore and the scientists of the IPCC Committee. My congratulations to Gore for his work to popularize the science behind global warming and increase public awareness and to the IPCC for collecting the necessary data and achieving a consent on the science of global warming.

“for their efforts to build up and disseminate greater knowledge about man-made climate change, and to lay the foundations for the measures that are needed to counteract such change”

There is much commonality between those who deny the science behind evolution and the science behind global warming and it should not come as a surprise that there exists a strong overlap between the two categories.

The full press release below the fold

Shelley Batts, the promising young scientist behind the Retrospectacle blog and a friend of the Panda’s Thumb, is up for a $10,000 blogging scholarship. She’s currently in 2^nd place, but is 1000 votes behind first place. So let’s all get behind her and push her to a victory. You’ll be helping a brilliant young neuroscientist do what all scholars need to do - pay off their student loans! Click on the button below and cast your vote.

The Los Alamos Monitor announces a presentation starting at 7PM in the Fuller Lodge, Los Alamos. The presentation will address intelligent design and the scientific method and has been sponsored by the New Mexico Academy of Science and the Coalition for Excellence in Science and Mathematics Education.

Efforts exist to make the scientific method evolve into something different, specifically in regards to the theory of evolution. During a presentation at 7 p.m. Tuesday in Fuller Lodge, Francis Slakey of Georgetown University will work to spread awareness about these efforts.

The presentation is free to the public and the New Mexico Academy of Science and the Coalition for Excellence in Science and Mathematics Education are sponsoring the lecture.

Slakey, in his presentation, will address Intelligent Design and its effect on the scientific method.

Alan Hurd, director of the Lujan Neutron Scattering Center at Los Alamos National Laboratory, explained the scientific method involves creating a hypothesis and testing it. If something cannot be verified, then it is not covered by the scientific method, he said.

Intelligent Design was created to circumvent the scientific method in order to resolve questions about humans’ origins. If evolution is happening, Intelligent Design suggests that it is being guided by a supernatural intelligence.

The ID blogosphere is much agog, and has been for some time, about recent (and not so recent) results that suggest some sort of functionality in what has long considered to be nonfunctional (junk) DNA in eukaryotes. The most recent buzz centers on studies (such as ENCODE ) that indicate that large swaths of so-called junk DNA are “expressed” by RNA polymerase II. Apparently, the fact that RNA polymerase transcribes alleged junk DNA is a blow to Darwinism, and a feather in the cap of ID. Their excitement in this regard, I suspect, will wane greatly once they learn some of the true implications of these results. For the matter of “expression” in junk DNA is one wherein ID meets, and gets swallowed by, the Garbage Disposal.

What follows is a discussion of a relatively recent report that rains on the ID parade. As is my habit, I’ll summarize the essay for those with short attention spans – the bottom line is that the so-called “function” that so excites the ID proponents may be little more than manifestations of quality control in gene expression, and that the supposed functional swaths of non-coding junk DNA may be nothing more than parts of the genome that encode, and lead to the production of, “junk” RNA (if I may so bold as to coin a phrase). In a nutshell, junk piled on top of junk.

My second example in this very educational series is how science explains the origin of the bacterial flagella.

Science Explains

Erv asks and Science explains. First of all thanks to Erv for providing us with a ‘transcript’ of Dembski’s lecture

“Evolution in (Brownian) space: a model for the origin of the bacterial flagellum” Nick Matzke 2003

Background to “Evolution in (Brownian) space: a model for the origin of the bacterial flagellum” Nick Matzke

Pallen MJ, Matzke NJ. “From The Origin of Species to the origin of bacterial flagella.” Nature Reviews Microbiology, 4(10), 784-790. October 2006. (pdf)

Intelligent Design Explains

William Dembski, 2007 in Dembski v the masked man

Nova PBS has announced the special “Judgement Day: Intelligent Design on Trial” to be aired on November 13, 2007. Nova and Paul Allen’s “Vulcan productions” of PBS Evolution fame, bring us

One of the latest battles in the war over evolution took place in a tiny town in eastern Pennsylvania called Dover. In 2004, the local school board ordered science teachers to read a statement to their high school biology students. The statement suggested that there is an alternative to Darwin’s theory of evolution called intelligent design, the idea that life is too complex to have evolved naturally and therefore had to have been designed by an intelligent agent. The science teachers refused to comply with the order, and parents opposed to intelligent design filed a lawsuit in federal court accusing the school board of violating the separation of church and state. Suddenly, the small town of Dover was torn apart by controversy, pitting neighbor against neighbor. NOVA captures the emotional conflict in interviews with the townspeople, scientists, and lawyers who participated in the historic six-week trial, Kitzmiller, et. al. v. Dover School District, et. al., which was closely watched by the world’s media. With recreations based on court transcripts, NOVA presents the arguments by lawyers and expert witnesses in riveting detail and provides an eye-opening crash course on questions such as “What is evolution?” and “Does intelligent design qualify as science?” For years to come, the lessons from Dover will continue to have a profound impact on how science is viewed in our society and how to teach it in the classroom.

“Judgment Day: Intelligent Design on Trial” is produced by NOVA and Vulcan Productions, in association with The Big Table Film Company. © 2007 WGBH Educational Foundation and Vulcan Productions, Inc. Funding for NOVA is provided by David H. Koch, the Howard Hughes Medical Institute, the Corporation for Public Broadcasting, and public television viewers.

In a recent paper, authors Yuri Wolf and Eugene Koonin present a hypothesis on the origin of the translation system and show how science proceeds. I am encouraging ID proponents to present a similarly detailed explanation based on the foundational concepts of Intelligent Design.

The authors explain how the problem is neither trivial and yet can be resolved:

The origin of the translation system is, arguably, the central and the hardest problem in the study of the origin of life, and one of the hardest in all evolutionary biology. The problem has a clear catch-22 aspect: high translation fidelity hardly can be achieved without a complex, highly evolved set of RNAs and proteins but an elaborate protein machinery could not evolve without an accurate translation system. The origin of the genetic code and whether it evolved on the basis of a stereochemical correspondence between amino acids and their cognate codons (or anticodons), through selectional optimization of the code vocabulary, as a “frozen accident” or via a combination of all these routes is another wide open problem despite extensive theoretical and experimental studies. Here we combine the results of comparative genomics of translation system components, data on interaction of amino acids with their cognate codons and anticodons, and data on catalytic activities of ribozymes to develop conceptual models for the origins of the translation system and the genetic code.

In other words, any hypothesis needs to address the catch-22 scenario as well as incorporate the scientific knowledge gathered so far.

I have been appointed “links curator” for The Panda’s Thumb. My job will be to scour the web for the best websites and blogs related to the mission of The Panda’s Thumb. To that end I have already added some links to the new links page. I will be adding more as time permits, but in the meantime I though I would throw the question open to the readers. What websites and blogs should be included? To get an idea of the type of websites I am looking for you can consult the links page. Finally, a number of scientists have made pdf’s of their papers freely available on the web here, for example. I assume they have the necessary permission to do so, but since I don’t want to get anyone in trouble for copyright issues I am somewhat reluctant to link to them. What do you think?

Comments may be left at Afarensis: Anthropology, Evolution, and Science.

In biology, genetics, biochemistry, and molecular biology classes, one of the things that we used to learn that distinguishes prokaryotes from eukaryotes is the “fact” that eukaryotes have polyadenylated mRNAs, while prokaryotes do not. This morphed rather easily into a distinction – eukaryotes do polyadenylation, prokaryotes do not. For years, this was standard fare in class. However, even as generations of students (beginning with the discovery of polyadenylate tracts in hnRNA in eukaryotes) were learning of this distinction, we knew that all was not right with this. Among the lurking pieces of conflicting data was that the first biochemical entity that was shown to add poly(A) tracts to RNAs in vitro was a bacterial one, isolated and purified from E. coli (1).

Speaker lectures on evolution, intelligent design controversy on historical and local level at Ohio University

The controversy between evolution and intelligent design does not come down to whether a person is religious, but is a matter of sound scientific evidence, said a speaker who was on campus last night as part of Ohio University’s scientific lecture series.

“Evolution is the only scientific game in town,” said Dr. Eugenie C. Scott, executive director of the National Center for Science Education, a nonprofit organization based in Oakland, Calif., that promotes teaching evolution in public schools.

Seems that the successes of NCSE and its supporters has become a thorn in the eye of the Discovery Institute.

I think that I’ve fixed most of the encoding issues that I am aware of. I had to edit a few lines of MT code and add some new logic to my MT-Dispatcher.

Parts of the database are still “corrupted” because of the bug. I can fix most of it, but I won’t do it right away.

Shelley Batts, a PhD student at the University of Michigan, is up for a $10,000 scholarship based on the amazing quality of her blogging at Retrospectacle.

You may remember her as the student who took on abusive publishers (and won) and who let Prof. Steve Steve get kidnapped.

Go vote for her; she wins the scholarship if she gets more votes than any of the other 20 finalists.

By Douglas L. Theobald, Assistant Professor of Biochemistry, Brandeis University

“Its major importance would appear to be financial support of the surgical profession.”
—Alfred Sherwood Romer and Thomas S. Parsons, The Vertebrate Body (1986), p. 389.

A recent science news article from the Associated Press reports on a novel hypothesis (Bollinger et al. 2007 JTB in press) concerning the possible function of the human vermiform appendix. Given how much creationists dislike all things vestigial, the Bollinger paper will undoubtedly be paraded on anti-evolution websites with grandiose claims about how “researchers are declaring that they have found a purpose for the human appendix”—and the paper itself unfortunately provides several tasty quote-mines ready to be plucked.

The new hypothesis, to be published in the Journal of Theoretical Biology, was proposed by a group of immunologists and surgeons from Duke University Medical Center. Bollinger et al. suggest that the structure and location of the human appendix has been specifically modified for an adaptive function, namely for housing and preserving beneficial gut bacteria during certain pathogenic infections that otherwise would clear the bowel of all enteric bacteria. Evidently, individuals who had an appendix would have a selective advantage over those individuals who had either no appendix or who had a larger appendix with a larger opening. Presumably after, say, an epidemic of amoebic dysentery, individuals with such an optimally sized appendix would be better able to repopulate the gut with good bacteria and to recover (this is an adaptationist paraphrase; the authors don’t use explicit evolutionary terms). The authors were led to this hypothesis after they noticed that human appendixes (yes, that’s the proper plural for the anatomical structure) contained significant bacterial biofilms, which are notorious for allowing bacteria to withstand all manner of malign assaults, including vigorous mechanical cleaning and chlorine bleaching.

Back over the summer, William Dembski was talking up “Baylor’s Evolutionary Informatics Laboratory”, and one of the features there was a PDF of an essay critiquing the “ev” evolutionary computation program by Tom Schneider. Titled “Unacknowledged Information Costs in Evolutionary Computing”, the essay by Robert J. Marks and William A. Dembski made some pretty stunning claims about the “ev” program. Among them, it claimed that blind search was a more effective strategy than evolutionary computation for the problem at hand, and that the search structure in place was responsible for most of the information resulting from the program. The essay was pitched as being “in review”, publication unspecified. Dembski also made much of the fact that Tom Schneider had not, at some point, posted a response to the essay.

There are some things that Marks and Dembski did right, and others that were botched. Where they got it right was in posting the scripts that they used to come up with data for their conclusions, and in removing the paper from the “evolutionaryinformatics.org” site on notification of the errors. The posting of scripts allowed others to figure out where they got it wrong. What is surprising is just how trivial the error was, and how poor the scrutiny must have been to let things get to this point.

Now what remains to be seen is whether in any future iteration of their paper they bother to do the scholarly thing and acknowledge both the errors and those who brought the errors to their attention. Dembski at least has an exceedingly poor track record on this score, writing that critics can be used to improve materials released online. While Dembski has occasionally taken a clue from a critic, it is rather rarer that one sees Dembski acknowledge his debt to a critic.

In the current case, Marks and Dembski owe a debt to Tom Schneider, “After the Bar Closes” regular “2^ndclass”, and “Good Math, Bad Math” commenter David vun Kannon. Schneider worked from properties of the “ev” simulation itself to demonstrate that the numbers in the Marks and Dembski critique cannot possibly be correct. “2^ndclass” made a project out of examining the Matlab script provided with the Marks and Dembski paper to find the source of the bogus data used to form the conclusions of Marks and Dembski. vun Kannon suggested an easy way to use the Java version of “ev” to quickly check the claims by Marks and Dembski.

(Also posted at the Austringer)

In an earlier posting, I promised to provide an overview of alternative codes in DNA. Such examples include alternative splicing and alternative reading frames (ARFs) which I will discuss here

The classical view of DNA was straightforward, DNA gets transcribed into RNA, introns get removed and the resulting exons form a protein. Exons are coding sequences in genes, introns are pieces of DNA/RNA that interrupt exons. The first step involves RNA synthesis (transcription) where the DNA is transcribed into RNA and exons and introns are still present, the next step is RNA splicing where introns are being removed. Alternative splicing causes different exons to be combined into messenger RNA (mRNA). These mRNA are translated into proteins in a step called protein synthesis.

From “This Modern World,” a brilliant cartoon on Intelligent Design (hat tip: Noodle Food):

This is a guest appearance of Erik Tellgren.

I (Mark Perakh) have not contributed anything to this essay and am posting it as a courtesy to Erik.

Here starts Erik’s text:

William Dembski has been one of the most influential contributors to the Intelligent Design (ID) movement. Among other things, his work has added the terms specified information, specified complexity, and complex specified information to the basic vocabulary of the ID movement. These terms are all directly related to the logarithms of special types of probabilities, e.g. the probability of a pattern of interest given that it was produced in some way that excludes the foresight and guidance of an intelligent agent.

In a recent draft manuscript, Dembski and his coauthor Marks extend the vocabulary with three new terms [1]: endogenous information, exogenous information, and active information. They consider as given a search space and a fixed subset, called a target, that makes up some fraction ps of the search space. An issue of interest to them is how to measure how well a search algorithm [2] exploits the structure of the search problem. Two possible candidates are the probability p that a search algorithm is successful and the ratio p/ps. Readers of Dembski’s previous writings will not be surprised to discover that Marks and Dembski prefer to log-transform their probabilities and rename them ‘information’. In equations, their definitions are

endogenous information = -log₂(p_s),

exogenous information = -log₂(p),

active information = -log₂(p_s/p).

Continue reading Comments on Active Information at Talk Reason

On a few occasions Dembski lamented that his critics are usually not mathematicians and hence are not really qualified to debate his mathematical exercise. Recently two professional mathematicians - Olle Häggström and Peter Olofsson, both highly qualified experts in math statistics and related fields, published essays showing serious faults in Dembski’s mathematical output. Dembski and Marks responded with an article where they attempted to refute Olle’s arguments. While some replies to Dembski and Marks have already been posted, a reply from Olle himself was expected. I am glad to inform PT visitors that Olle’s reply to Dembski and Marks has appeared here. I think Olle succeeded admirably to reveal the emptiness of Dembski-Marks’s arguments.

Compare the following article in the Christian Post and the Discovery Institute ‘spin’ with the actual statement by the National Council for the Social Studies on Intelligent Design

In the Christian Post article, Crowther is quoted suggesting that the NCSE and other supporters of evolution education have flip-flopped on the topic of whether or not Intelligent Design should be allowed to be taught as a scientific alternative to evolution in social science classes.

Crowther cited several examples from previous articles in which the NCSE and other supporters of evolution education proposed social studies as an appropriate forum for discussing non-Darwinian thoughts such as Creationism and Intelligent Design. Furthermore, Crowther suggested that critics of Intelligent Design have strategically misrepresented the scientific claim as synonymous to Creationism to exclude it from being taught in science classes.

While Crowther is still misrepresenting Intelligent Design as presenting scientific claims, it is clear that for all practical purposes Intelligent Design has been found to be lacking in scientific content (Kitzmiller) and that given its historical foundations, Intelligent Design is linked with Creationism

Judge Jones Wrote:

In making this determination, we have addressed the seminal question of whether ID is science. We have concluded that it is not, and moreover that ID cannot uncouple itself from its creationist, and thus religious, antecedents.

Having corrected this minor confusion amongst ID proponents, I will now explore if the NCSE has flip flopped on the topic of teaching Intelligent Design in social science classes.

Denyse O'Leary Wrote:

I have ordered a copy of Harun Yahya’s Atlas of Creation, which (some say) has got the Council’s shirts in a knot, and will tell you what I think after I have read it.

Seems that Denyse is quite forthcoming about Intelligent Design being nothing more than Creationism. Seems that the Council was right after all.

Guardian Online

The ‘controversy’ about teaching Intelligent Design Creationism in schools may have an unexpected side-effect, namely that schools will more strongly emphasize the teaching of the scientific theory of evolution while also pointing out how Intelligent Design and other forms of creationism are not scientific and in many cases even anti-scientific and misleading.

Growing numbers of pupils believe in creationism, and science teachers should be prepared to cover the topic in their classes, education experts said today.

On UcD, the lack of scientific research seems to have gotten to Dembski who seems to be attempting to include much of anything as being relevant to ID’s ‘design inference’

Dembski Wrote:

Need it be added that digital forensics consists in drawing design inferences.

Need it be added that this would constitute a common problem of conflation. While the terms may sound similar, an ID ‘design inference’ is very different from how one commonly uses the term.

Press Release - 656(2007)

Council of Europe states must “firmly oppose” the teaching of creationism as a scientific discipline, say parliamentarians

Strasbourg, 04.10.2007 “Parliamentarians from the 47-nation Council of Europe have urged its member governments to “firmly oppose” the teaching of creationism “which denies the evolution of species through natural selection” as a scientific discipline on an equal footing with the theory of evolution.

In a resolution passed by 48 votes to 25 during its plenary session in Strasbourg, the Council of Europe Parliamentary Assembly (PACE) declared: “If we are not careful, creationism could become a threat to human rights.”

David Lampe, Associate Professor at the Department of Biological Sciences at the Duquesne University, provides some interesting data: A comparison between Michael Behe and Sean Carroll.

Certain people seem attracted to “intelligent design” creationism because some (actually, very few) people with real Ph.D.’s advocate it. One of these is Michael Behe, a biochemist from Lehigh University. I have heard him described as “a scientist of the first rank.” People can argue over “rankings” but there exist some objective measures as to how influential a scientist is and how good their ideas actually are. These measurements are generally of two kinds:

• Number and kind of publications of the scientist;
• Citations of these works (which show that the scientist’s ideas are being used to do productive work).

An interesting exercise which shows how ID can quickly become a ‘science killer’.

It seems that the posting on horse fossils attracted some ID creationists who quickly dispersed when called to defend their ignorant claims. Not surprisingly, creationists have abused a perceived weakness to undermine evolution when in fact the full story (as well as the simplified story) both present an excellent overview of evolution in action.

In Beating fossil horses: Creationists take on an “Icon of Evolution”, Brian Switek describes his somewhat painful introduction to ID ‘science’

The book that introduced me (albeit painfully) to intelligent design and critics of evolution was the infamous Icons of Evolution by Jonathan Wells, and in it Wells spends an entire chapter attempting to discredit the idea that horses evolved. This is not surprising, especially given that horse evolution was so triumphantly heralded by none other than “Darwin’s Bulldog” Thomas Henry Huxley in 1876. Indeed, the rich amount of fossils uncovered, plus public interest and prestige allowed horses to take on an iconic status, caused the transitions among fossil horses to become one of the most widely-cited examples of evolution, the change from small, multi-toed ancestors to large, one-toed descendants making for a very compelling scientific narrative.

Brian, continues to outline ‘the rest of the story’, so often found missing in creationist resources.

Unless this is yet another one of those Dembski ‘parodies’, Dembski has ‘apologized’ and conveniently removed the offending postings which showed the depths to which Dembski had gone.

The only redeeming part of Dembski’s “apology” is that he references an excellent paper by Paul Gross

PZ Myers, in his wisdom, observes that

After his recent rampage against the Baylor administration, Bill Dembski now claims to be offering an apology to Baylor…only not really. I don’t think he knows what ‘apology’ means — a statement loaded with reservations like “I mean in no way to mitigate the gravity of Baylor’s wrong in censoring the research of Robert Marks and his Evolutionary Informatics Lab” and “I hurt my family and lost about three weeks of productive work by being consumed with anger about the injustice against Robert Marks” is not an apology — it’s an opportunity to reiterate your grievances. And closing with the injunction to “leave justice in the hands of a God” is just a standard Christian passive-aggressive threat.

What is ironic to me is that if Dembski had apologized after his ill-timed “Waterloo” email, he would still have been in charge of the ID Friendly Institute at Baylor. Now Bill laments that his ill temper caused him to lose 3 weeks of productivity. Somehow, many may see this as a three week gain.

PZ Wrote:

This wasn’t an apology. It was an opportunity for Dembski to flush several embarrassing posts down the UD Memory Hole™.

So what do PT readers think, was this a real apology or if not, what was it?

At Laelaps, Brian Switek, a soon-to-be-graduating student at Rutgers University who is studying ecology and evolution describes the oft misunderstood evolution of the horse

The story of the evolution of the horse shows how science incorporated new data to update what was originally a overly simplified view of horse evolution and reveals an exciting example of evolution in action.

The author ends with an important lesson namely that simplification, an oft used tool in education, can also provide creationists with opportunities to spread “doubts”. What surprises me is that one seldomly hears creationists complain about how our science classes ‘linearize’ “laws” when in fact, everyone knows that much of the world around us is quite non-linear.

Still, our current understanding is incomplete, and further fossil finds will continue to rustle the branches of the evolutionary bush. In fact, I would not be surprised if more early forms came to light, and I would be especially interested to see if the “Oligocene Bottleneck” is real or merely a factor of fossil collecting bias. There should be no mistake about the amazing entanglement of branches horses represent, however, and it is somewhat surprising that the public does not often hear about the true form of horse phylogeny. While I did not do an in-depth study of how horse evolution was portrayed in the popular media, from what I have seen it seems that past scientists and authors have often opted for simplicity, getting the public to accept evolution has occurred being more important than giving them an accurate depiction of how evolution works. This is a harsh lesson that we are still learning, as inaccuracies in books, museum displays, and other outlets can leave the door open for creationists to spread distrust of science.

On Quintessence of Dust, associate professor of Biology Stephen Matheson (yes a Steve Steve), treats us to a fascinating trip through morphospace. He discusses a recent paper by Prusinkiewicz et al.titled Evolution and Development of Inflorescence Architectures, published in Science 8 June 2007:

In this paper, the authors not only show how, despite a multitude of possible forms, severe constraints are placed on biological diversity, but also show how the existence of ‘worm holes’ in fitness space link the various architectures. A beautiful story about scientific inquiry.

By Dr. Hans Roskam, Institute of Biology Leiden (IBL), University of Leiden and Dr. Gerdien de Jong, Evolutionary Population Biology, University of Utrecht.

Dutch biologists are in great turmoil due to the censorship of BBC nature documentaries by the Dutch Evangelische Omroep (Evangelical Broadcasting, EO), a fundamentalist Christian public broadcasting company. As a fundamentalist Christian organisation inspired by the word of God as revealed in the literal text of the Bible, the EO denies all science that falsifies this literal text.

Consequently, all references to evolution, speciation, descent and millions of years are removed from BBC documentaries as broadcasted by the EO. BBC documentaries are  ‘neutralized’, that is, non-offending to creationist views by replacing spoken English text by an intentionally falsely translated spoken Dutch text, or by cutting whole scenes. Nevertheless, the documentaries are presented to the Dutch public as BBC documentaries. For instance, the EO DVD “Het Leven van Zoogdieren”, their censored version of Sir David Attenborough’s “The Life of Mammals” is explicitly presented as “written and presented by David Attenborough”, despite its many deviations and sins of omission.