September 2007 Archives

Evolvable by design

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The work by Panos Oikonomou, a graduate student at the Physics Department, University of Chicago, recently caught my eye. His website explains that he is

… interested in studying the relationship between network topology, dynamics and evolution. I explore possible evolutionary advantages of such features, like the scale-free distribution.

He recently wrote a paper “Effects of topology on network evolution”, Panos Oikonomou and Philippe Cluzel, Nature Physics, August 2006.

In the paper, the authors compare the characteristics of a random network versus a scale free network. A random network is one in which each node has on the average the same number of connections to other nodes. For scale free networks, the connectivity follows a power law distribution. They tested how the two different networks ‘responded’ to evolutionary processes

Our simulations show that populations containing these scale-free networks can easily produce a number of functional variations which allow each population to evolve rapidly and smoothly towards some target function. By contrast, equivalent random networks evolve slowly, through a succession of rare fortuitous random mutations.

Last week I spoke at an evolutionary psychology class at a local university. I had spoken there two years ago, and that had been successful enough that I was invited back to talk about various issues involved with anti-evolutionism.

There were about 45 students in the class, mostly upperclass psych majors, and they were quite attentive and engaged: we had lots of good discussion and lots of insightful questions.

Afterwards, the students were asked to reply on their class discussion board to the question, “What was the most significant issue for you” that came up during my presentation. The three most frequent issues mentioned were:

1. The fact that there are different varieties of creationists, and that while the IDists are the public face of the movement, the vast majority of creationists are young-earth creationists.

2. The political nature of the anti-evolution movement, and the fact that it is really an anti-science “worldview war” being waged to “overthrow materialism.” We carefully reviewed some key parts of the Wedge to get the big picture described in the IDists’ own words. (More on this later in this post.)

3. The subject of theistic evolutionists, and the fact that the ID movement denounces this subset of their fellow Christians as sellouts to materialism.

A couple of weeks ago, I posted two ridiculous quotes that are found in the Bob Jones textbook that’s involved in the California Creationism lawsuit. I’m still wading through these texts and Behe’s report explaining why it’s really a very good book for high school students to use to learn biology. It’s a slow process, and a painful one, but I’ve found another couple of outstanding quotes to share with you.

This time, I’m including three different types of quote. There are a couple where the authors say things have absolutely nothing to do with science of any kind (and are totally out to lunch even by the standards of a lot of religious people I know). There’s one where the book takes a brief detour into right-wingnuttery. I’ve also got one quote that I’m including as a special treat for those of you who might still want to claim that the book’s fine if you just overlook the insane religious stuff - an example of a case where the authors manage to mangle a very basic concept from genetics.

We’ll start with the insane, and move from there to the political, then conclude with the merely wrong.

Read more (at The Questionable Authority, where comments may be left):

The UK government has issued new guidelines to teachers on what to teach about creationism and intelligent design in science classes. They are pretty explicit that creationism and ID do not belong.

The Guardian, Creationism out of the classroom

You can Download the full text appropriately titled “GUIDANCE ON THE PLACE OF CREATIONISM AND INTELLIGENT DESIGN IN SCIENCE LESSONS”

Creationism and intelligent design are sometimes claimed to be scientific theories. This is not the case as they have no underpinning scientific principles, or explanations, and are not accepted by the science community as a whole. Creationism and intelligent design therefore do not form part of the science National Curriculum programmes of study.

To avoid inappropriate use of resources, the guidelines also clarify that

Any resource should be checked carefully before it is used in the classroom. If resources which mention creationism or intelligent design are used, it must be made clear that neither constitutes a scientific theory.

Dembski and Common Descent

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Finally we hear the full story about Dembski’s position on Common Descent

For the record: I personally don’t believe in common descent though I think there are lines of evidence that suggest considerable evolutionary change. At the same time, there are lines of evidence that suggest considerable discontinuity among organisms. Check out chapter 5 of my forthcoming book with Jonathan Wells titled THE DESIGN OF LIFE (publication date keeps being delayed, but I think it’ll be out in November).

Wells and Dembski together… Marvelous… I am sure the book will be a hit amongst creationists and will, once again, remain totally irrelevant to science and likely to be detrimental to religious faith. But at least now we know that Dembski does reject much of the evidence supporting common descent. I wonder if he is familiar with St Augustine?

As to “Design of Life”, isn’t this the follow-up to Pandas and People, found to be unconstitutional by the Dover court?

As a side note, does the following statement strike anyone as showing a compassion one would hope to associate with a Christian?

I can’t say I feel sorry for these atheistic scientists in agreeing to interview for EXPELLED: NO INTELLIGENCE ALLOWED. When the BBC interviewed me for their Horizon documentary on ID (Horizon = the UK version of PBS Nova), they gave the ID side no warning that the program would be titled A WAR ON SCIENCE (I wouldn’t have agreed to be interviewed had I known that was going to be its title). What goes around comes around.

Of course, in this case, the scientists were told about a title which later was changed. Nevertheless, I thank Bill for his frank statements.

Adler And Bailey on Expelled

Jonathan Adler at The Volokh Conspiracy and Ron Bailey at Reason have a couple posts on the dishonesty of Ben Stein et al. in their interviewing for Expelled.

Tangled Bank #89

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The Tangled Bank

Read all about the latest science-related blogging in the latest edition at Aardvarchaeology.

In the Light of Evolution I: Adaptation and Complex Design PNAS May 15, 2007; 104 (Suppl. 1)

With many contributions about information, complexity and evolutionary theory from some of the world foremost experts.

Introduction John C. Avise and Francisco J. Ayala From the Academy: Colloquium Perspective: In the light of evolution I: Adaptation and complex design

Darwin’s elucidation of natural selection as a creative evolutionary force was one of the monumental intellectual achievements in the history of science, not only revolutionizing thought across the biological sciences but also fundamentally impacting much discourse in the social sciences, philosophy, and religion. No longer were explanations for the origin and marvelous adaptations of organisms necessarily to be sought solely in the context of supernatural causation. Instead, biological outcomes could now be interpreted within the critical scientific framework of natural processes governed by natural processes and laws.

and the concluding remarks

Overall, the collection of ideas and data in this Colloquium is highly eclectic but nonetheless broadly illustrative of modern scientific attempts to understand the evolution of complex adaptations. These scientific endeavors are coming at a time of resurgent societal interest in supernatural explanations for biological complexity. Especially in the United States, proponents of intelligent design (ID)—the latest reincarnation of religious creationism—argue that biotic complexity can only be the product of a supreme intelligence (i.e., God). In the closing article of this Colloquium, Eugenie Scott and Nicholas Matzke (23) examine the history of the ID movement, and they conclude that although without scientific merit, the crusade itself is of consequence to broader society because it represents a serious assault on the integrity of science education.

Perhaps there is a middle ground for scientific and theological interpretations of complex biological design. In his 1973 commentary titled “Nothing in Biology Makes Sense Except in the Light of Evolution” (24), Theodosius Dobzhansky famously proclaimed “I am a creationist and an evolutionist. Evolution is God’s, or Nature’s method of creation.” Regardless of what our personal philosophical persuasion may be, let us rejoice in biotic complexity and in the scientific efforts to understand its geneses.

With the publication in 1859 of On the Origin of Species by Means of Natural Selection, Charles Darwin established evolution by common descent as the dominant scientific explanation for nature s diversity. This was to be his gift to science and society at last, we had an explanation for how life came to be on Earth.

Scientists agree that the evolutionary origin of animals and plants is a scientific conclusion beyond reasonable doubt. They place it beside such established concepts as the roundness of the earth, its revolution around the sun, and the molecular composition of matter. That evolution has occurred, in other words, is a fact.

Yet as we approach the bicentennial celebration of Darwin s birth, the world finds itself divided over the truth of evolutionary theory. Consistently endorsed as good science by experts and overwhelmingly accepted as fact by the scientific community, it is not always accepted by the public and our schools continue to be battlegrounds for this conflict. From the Tennessee trial of a biology teacher who dared to teach Darwin s theory to his students in 1925 to Tammy Kitzmiller s 2005 battle to keep intelligent design out of the Dover district schools in Pennsylvania, it s clear that we need to cut through the propaganda to quell the cacophony of raging debate.

With the publication of Darwin s Gift, a voice at once fresh and familiar brings a rational, measured perspective to the science of evolution. An acclaimed evolutionary biologist with a background in theology, Francisco Ayala offers clear explanations of the science, reviews the history that led us to ratify Darwin s theories, and ultimately provides a clear path for a confused and conflicted public.

Order your copy at The National Academies Press (PDF available!!)

According to various press reports and news releases, there is a major new paper out in PNAS proposing that the pleistocene megafauna of North America (mammoths and the like) was killed off by an impact event (or atmospheric detonation of a comet). There was a brief report on this awhile ago when a paper was presented at the American Geophysical Union meeting this summer. This is a cool idea. However, despite the press announcements I can’t find the paper on the PNAS website. Anyone have any luck?

In the last few days we have witnessed a virtual epidemic of ill informed claims from our ID friends, so this time I will address a claim by Bornagain77 at UcD who argues:

I would also like to point out that since ENCODE found “an extensive overlapping network” for the human genome, this recently discovered fact clearly indicates that scientists are completely misinterpreting the genetic data from their preconceived evolutionary perspective, since the Evolution hypothesis requires that the genome be a “multiple independent collection of selectable genes”. Thus I predict all similarity based evidence culled from different genomes in support of the evolution hypothesis will have to be reinterpreted, from the proper engineering perspective, since it is now clearly impossible for the evolutionary scenario to overcome the the demonstrated poly-constrained nature of a poly-functional genome (Sanford Gentic Entropy; 2005)!!!

Despite Bornagain’s blind reliance on the work by Sanford, scientists have done some real science and shown actually quite the contrary. I will show that an interdependent network of is not only an inevitable outcome of evolutionary processes but that the nature of these networks, contrary to ‘intuition’ facilitate evolution rather than prohibit it. See for instance the work by Barabasi on scale free networks, the work by Stadler, Schuster, Toussaint and others on neutrality, RNA networks and many more:

Just a quick example:

The Emergence of Overlapping Scale-free Genetic Architecture in Digital Organisms by Gerlee

We have studied the evolution of genetic architecture in digital organisms and found that the gene overlap follows a scale-free distribution, which is commonly found in metabolic networks of many organisms. Our results show that the slope of the scale-free distribution depends on the mutation rate and that the gene development is driven by expansion of already existing genes, which is in direct correspondence to the preferential growth algorithm that gives rise to scale-free networks. To further validate our results we have constructed a simple model of gene development, which recapitulates the results from the evolutionary process and shows that the mutation rate affects the tendency of genes to cluster. In addition we could relate the slope of the scale-free distribution to the genetic complexity of the organisms and show that a high mutation rate gives rise to a more complex genetic architecture.

It somewhat surprises me that Sanford and IDers are unfamiliar with the extensive research on Scale Free networks, especially since I have discussed them in depth on Pandas Thumb. Contrary to intuition, overlapping scale free networks are not only common in the genome but their origins and evolution can be quite well explained using evolutionary theory.

I thank BornAgain for his contribution which allowed me to put to rest yet another creationist myth.

Poor St Augustine.

So, after all the kvetching the Discovery Institute did over the Guillermo Gonzalez tenure denial case, why aren’t they rushing to the defense of one Steve Bitterman, a community college professor at Southwest Community College here in Iowa. The case is still developing, but what is known is that Bitterman was fired last week–apparently for teaching that Genesis isn’t literal. More over at Aetiology

Most of the readers of this blog are intelligent, interested, scientifically literate individuals, but I’m guessing that at least a few of you aren’t familiar with one of the nouns in the title. Those of you who do know what a conodont is are probably wondering what it has to do with the others. If you bear with me for a little bit, the connection will be clear shortly. It has to do with fossils, fossilization, and the latest spectacular misunderstanding of those two things at Uncommon Descent.

Conodonts are (or, rather, were) an interesting group of animals. They were around from late in the Cambrian period until the end of the Triassic, and were quite common during most of the period. They’re not well known to most people outside of geology because the vast bulk of the evidence we have for them consists of very tiny tooth-like fossils. Most are only a millimeter or two in size, and are very hard to see without a microscope. They’ve received a lot of attention from paleontologists over the years because they’re very useful little critters, particularly for geologists who work in the oil and gas industry. The thing is, for a long time nobody knew just what sort of critters they actually were.

Read more (at The Questionable Authority, where comments may be left):

Continued Uncommon Junk Talk

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On Uncommon Descent, defender of ID against creationist nonsense, Davescot makes the following comment about a posting by Paul Nelson about the fascinating complexity of the genome:

DaveScot Wrote:

I still fail to see how ID predicts no junk DNA. Random mutation definitely happens and if it’s good at *anything* it’s good at producing unorganized, non-functional crappola. It can produce crap out of nothing and it’s even better at making crap out of stuff that wasn’t crap to begin with.

Of course, Davescot has failed to follow the ID game play which includes the fallacious argument that ID predicted Junk DNA to have function. A poster name BFast is quick to remind DaveScot of his technical foul.

Bfast Wrote:

Bottom line, significant IDers have said for a long time “there’s value in that junk” and the darwinists have said the opposite, that “there cannot be value in that junk because there would be too many mutations per generation to be managed by RM+NS.”

The IDers said it, it proved to be true, it’s a confirmed prediction.

BFast is Right, Wrong and Wrong. Not too shabby for an ID defender.

I was going to comment on the posting by Casey Luskin about “Scientific Journals Promoting Evolution alongside Materialism”, but Jim Ridlon beat me to it and has performed a nice “fiskin’ of Luskin” As I had guessed, the articles indicate a far more moderate view than one may get from Luskin’s posting.

Eventually, Luskin explains his real motive

[…], it seems that they are nonetheless working hard to disprove Judge Jones’s Kitzmiller ruling that held it is “utterly false” to believe that “evolutionary theory is antithetical to a belief in the existence of a supreme being.”

Which of course is still correct. Evolutionary theory is non antithetical to a belief in the existence of a supreme being. It’s when religion pretends to be scientific that it encroaches onto science and the fact that science disproves its claims, merely suggests the vacuity of such attempts.

Sure, evolutionary theory can be used to argue for or against religion, and neither argument is more privileged than the other, unless religion abuses evolutionary theory. Such examples include Young Earth Creationism and Intelligent Design Creationism which attempt to make scientific claims in favor of their religious faith. When science clearly and decisively exposes the scientific vacuity of their arguments, creationists may whine that evolution is anti-religion. But it is the attempts by creationists which has caused their claims to do damage to science and faith alike.

Luskin’s Latest Lie

If you love predictability, you’ve got to love the Discovery Institute. Whenever someone publishes a paper about human evolution, it’s a pretty safe bet that someone there will soon take the time to explain how having learned something new means that we somehow know less than we did before. You can set your watch by it, almost.

The latest example comes from Casey Luskin. He “discusses” a paper that came out in Nature this week that reported on some fossils from Dmanisi, Georgia. Several skulls have been described from this site already, and the current paper focuses on post-cranial (less technically, non-skull) remains.

I’m not going to bother with a detailed, point-by-point rebuttal of Casey’s claims. (See this post by Afarensis for that.) Instead, I’m just going to look at one of the more glaringly dishonest tactics that Casey used this time.

Read more (at The Questionable Authority, where comments may be left):

Steven Pinker, The Stuff of Thought: Language as a Window into Human Nature, New York: Viking, 2007, p. 280.

The abundance of Steves in turn-of-the-century science has led to the most formidable weapon in the fight against neo-creationism today: Project Steve. A brainchild of the National Center for Science Education, the initiative is a parody of the creationist tradition of publishing lists of several dozen “scientists who dissent from Darwinism.” The NCSE replies: “Oh, yeah? Well, we have a list of several hundred scientists who affirm evolution—just named Steve!” (And Stephanie, Steffi, Stefan, and Esteban.) Part satire, part memorial to Stephen Jay Gould, the project maintains a Steve-O-Meter (now pointing past 800) and has spun off a T-shirt, a song, a mascot (Professor Steve Steve, a panda puppet), and a paper in the respected scientific journal Annals of Improbable Research called “The Morphology of Steve” (based on the T-shirt sizes ordered by the signatories).

Hat tip Glenn Branch.

Antievolutionists have long sought to subvert and infiltrate the public school science classrooms, looking to turn all those lecterns into pulpits to deliver their narrow sectarian doctrines. We’ve seen takeovers of classrooms, of school boards, and the promulgation of legislation to set things up the way they’d like it. Now, we have another untoward development: not content with turning science class into Sectarian Sunday School, they want taxpayers to chip in money to serve the cause. That’s right, instead of passing a collection plate where one gets a choice of contributing or not, they do want to pick your pockets.

The Times-Picayune has the story.

Sen. David Vitter, R-La., earmarked $100,000 in a spending bill for a Louisiana Christian group that has challenged the teaching of Darwinian evolution in the public school system and to which he has political ties.

The money is included in the labor, health and education financing bill for fiscal 2008 and specifies payment to the Louisiana Family Forum “to develop a plan to promote better science education.”

More on the Austringer.

On ERV’s blog we find an article titled Irreducible Complexity Reflects Human Ignorance about Phillip Klebba, Professor of Chemistry and Biochemistry at the University of Oklahoma. It was Klebba’s relentless questions during the Q&A of Dembski’s talk at the Trinity Baptist Church Oklahoma University in Norman Oklahoma which forced Dembski to admit to the level of ignorance that is required for ID.

The Baptist Trinity Church had invited Dembski “to penetrate the university campus with the gospel” (source). After all, what better way to introduce the students to the gospel than through the ideas of William Dembski? Dembski presented a talk titled “Why Atheism is no Longer Intellectually Fulfilling: The Challenge of Intelligent Design to Unintelligent Evolution”. During the Q&A, Dembski found out that the students were not impressed by his arguments. While Dembski may have contributed to the successes of Atheism on the University, he also managed to show to the audience present why ID is scientifically vacuous.

The Committee on Culture, Science and Education has revised its working document after an earlier submission had been delayed. The Committee has done an excellent job at distinguishing between the scientifically vacuous concepts of creationism and Intelligent Design while still ensuring that freedom of religion is not affected

Not surprisingly the reaction from ID has been predictable. Davescot calls it “A Socialist Manifesto on Evolution.”, ignoring the varied makeup of the committee. Why the ad hominem response? Because the Committee has reached some accurate conclusions about Intelligent Design.

The intelligent design movement would seem to be anti-science for several reasons. Firstly, the nature of the science is distorted. Secondly, the objectives of the science are distorted. The writings of the leaders of this movement show that their motivations and objectives are not scientific but religious.

The intelligent design ideas annihilate any research process. It identifies difficulties and immediately jumps to the conclusion that the only way to resolve them is to resort to an intelligent cause without looking for other explanations. It is thus unacceptable to want to teach it in science courses. It is not enough to present it as an alternative theory in order to have it included in the science syllabus. In order to claim to be scientific, it is only necessary to refer to natural causes in one’s explanations. The intelligent design ideas, however, only refers to supernatural causes.

Does this mean that there is no place for ID? Of course not.

Woops!

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Due to a database corruption (stupid search and replace), we just lost a day’s worth of comments.

I hope nobody had said anything cool.

Remember that Dembski and others have admitted that processes of variation and selection (chance and regularity) can in fact increase the information content of the genome. As such, it seems that whether or not Dawkins can explain the origin of information, seem irrelevant. However, as Ridlon shows, Dawkins indeed attempted to explain the origin of information in the genome. I invite Casey Luskin, or other ID proponents, to explain why they believe Dawkins’ explanation is flawed. In addition, I invite them to either admit or deny that Dembski and others have dropped the flawed argument that processes of regularity and chance cannot create information in the genome?

JM Ridlon Wrote:

If you will notice, Casey Luskin’s article “Richard Dawkins on the Origin of Genetic Information” has been updated. I emailed Casey yesterday and mentioned that the EvolutionNews blog statement of purpose is as such:

“The misreporting of the evolution issue is one key reason for this site. Unfortunately, much of the news coverage has been sloppy, inaccurate, and in some cases, overtly biased. Evolution News & Views presents analysis of that coverage, as well as original reporting that accurately delivers information about the current state of the debate over Darwinian evolution.”

Yet he failed to mention that Dawkins rebutted the video and very nicely answered the challenge: http://www.skeptics.com.au/articles/dawkins.htm. This is a prime example of “sloppy, inaccurate, and in some cases, overtly biased”. A quick google search of “Dawkins and Information” would have been enough research to have discovered Dawkins response.

Therefore, while I commend Luskin for posting the rebuttal, he still is not excused from poor research. He also doesn’t admit that Dawkins answered the question (Luskin says: Read Dawkins’ response at http://www.skeptics.com.au/articles/dawkins.htm and see if he still has yet to satisfactorily answer the question!).

Now that Luskin admits that Dawkins answers the “Information Challenge”, I think someone on Panda’s Thumb should challenge Luskin, who says, “Read Dawkins’ response … and see if he still has yet to satisfactorily answer the question!”, to show where Dawkins is wrong. Don’t let him off the hook here.

Upgrade Starts Today

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I will begin to upgrade this site today. Recent comments may be lost, so I am disabling comments until I have finished the change over.

On Design

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Well, since Michael Egnor has sort of answered my questions, it’s time for me to try to answer his. I’ll try to be less evasive than he was.

One thing I’d like to point out is that Egnor seems to be under the misapprehension that the information theory that mathematicians and computer scientists actually study has something to do with inferring design. This is simply not the case. Open up, for example, the book on Kolmogorov complexity by my colleague Ming Li, and you won’t find a word about inferring design. (It’s ID advocate Bill Dembski, of course, who is largely responsible for this confusion.) So, contrary to what Egnor thinks, as a mathematician and computer scientist I have no particular expertise on the general topic of “inferring design”. It’s just not something we do; maybe he should ask a SETI researcher, or a forensic investigator. But then again, Egnor has nor particular expertise on the topic, either.

First, some general remarks about “design”. I’ll start by saying that I don’t know exactly what he means by “designed”. One of the favorite games of ID advocates is equivocation, so it’s important to pin them down on a precise meaning. ID advocates rarely say plainly what they mean by “design”. Do they mean simply that something has a pattern to it (as in “the design of a snowflake”), or do they mean something that has a “function”, or must there necessarily be some teleology involved? I think it’s incumbent on ID advocates to make clear what they mean. But I’ll look at all three possibilities.

Read more at Recursivity

The Hox code

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The Hox genes are a set of transcription factors that exhibit an unusual property: they provide a glimpse of one way that gene expression is translated into metazoan morphology. For the most part, the genome seems to be a welter of various genes scattered about almost randomly, with no order present in their arrangement on a chromosome — the order only becomes apparent in their expression through the process of development. The Hox genes, on the other hand, seem like an island of comprehensible structure. These are all genes that specify segment identity — whether a segment of the embryo should form part of the head, thorax, or abdomen, for instance — and they're all clustered together in one (usually) tidy spot.

How do these genes work together to regulate axial patterning in chordates?

Continue reading "The Hox code" (on Pharyngula)

Have a few minutes to spare?

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[EDITED TO ADD: thanks! We reached 1000 survey responses in just about 10 hours’ time, so the survey is now closed…we really appreciate your participation!]

If so, we’d love to have your input at a quick survey looking more closely at science blog readers (and writers!):

This survey attempts to access the opinions of bloggers, blog-readers, and non-blog folk in regards to the impact of blogs on the outside world. The authors of the survey are completing an academic manuscript on the impact of science blogging and this survey will provide invaluable data to answer the following questions:

Who reads or writes blogs? What are the perceptions of blogging, and what are the views of those who read blogs? How do academics and others perceive science blogging? What, if any, influence does science blogging have on science in general?

Please consider participating in the survey as an act of ‘internet solidarity’! It will likely take 10 minutes, and a bit more if you are a blogger yourself. We thank you in advance.

I’ve been continuing to put some time into criticizing Michael Behe’s expert report on the creationist texts involved in the California Creationism Case. This is a slow process, partly because I’m also working on other projects and partly because it’s difficult to read the Bob Jones “Biology for Christian Schools” text without encountering a range of unpleasant side effects. I’ve been fighting the increased blood pressure and the nausea, and soldiering on. Along the way, I’ve encountered some real gems that I thought I’d share with you.

Today, I’m going to give you two quotes: one on Darwin, and one on sexually transmitted diseases. The two are connected only by the surreal nature of what’s being said. As you read them, please remember that this is material that’s being taught to high school students, and that the folks who are teaching this stuff are suing the University of California, because for some strange reason UC doesn’t think that people who have been taught this stuff have adequately completed an actual college preparatory class in biology. All quotes are taken from the most recent (3rd) edition of the text. I’m transcribing by hand, so unless indicated otherwise, all typos are mine.

Read more (at The Questionable Authority, where comments can be left):

It seems that ID has chosen to rekindle the ‘how does evolution create information’ question. See for instance “Richard Dawkins on the Origin of Genetic Information” at EvolutionNews.org where spokesperson Luskin presents this question. And yet, the question has been answered many times, so why are ID activist ignoring these explanations or pretending that it has not been answered succinctly and successfully?

One of the basic claims of ID is that processes of regularity and chance cannot create complex specified information. ID relies here on an equivocation of the term ‘information’ since ID’s definition of information is merely a measure of our inability to explain it. In other words, unlike the complexity and information that science can explain, ID relies on that which science cannot explain (yet?) and calls it complexity or information.

Confused? I bet… Many ID proponents have similarly fallen victim to the bait and switch approach here.

So whenever ID states that science cannot explain complex specified information, all one has to do is point out the tautological nature of the claim. When ID then switches to the more common definition of information and complexity, it is trivial to show how evolutionary processes can indeed generate in principle information and complexity.

The real question then becomes: Where these processes indeed involved in the evolution of life on earth? While science provides a rich framework to study these questions, ID is left at the sidelines, unable to contribute anything relevant since it refuses to constrain its designer, it refuses to provide pathways and processes.

And remember, whenever science proposes a pathway, all ID can do is reject a strawman version of it, namely a pathways based on pure chance. Of course, any non trivial scientific pathway is inaccessible to the calculations needed by ID to make its case.

Changes are a-commin’

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Sometime early this week, we will be upgrading the server software, transitioning to PostgreSQL, and deploying a new site design. Service may get spotty, but enjoy a sample of our new look:

sample.jpg

William Saletan at Slate takes a more skeptical look at some of the research referred to in PvM’s post below.

Recent Photo Shoots

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Where Teaching the Controversy is Prohibited

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On “Threads from Henry’s Web”, Henry Neufeld writes more about Colling and ‘teaching the controversy’

This action shows some of the destructive potential of ignorance, but it also removes any fig-leaf of respectability from the “teach the controversy” argument. The advocates of creationism generally do not want the controversy taught. They want to win. If they were to win a court case allowing their materials into the public school classrooms, their next move would be to prevent critical examination of those ideas, and then to prevent the teaching of evolutionary theory itself. I simply don’t believe the public propaganda. I never have, but the evidence that it is pure propaganda just keeps building up.

Henry describes himself as “… an author and lecturer, owner of Energion Publications, and president of Pacesetters Bible School.” His description of the problems and risks of ID seem timely and to the point.

Farewell to Alex

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An acquaintance of mine died last week, and I just found out about it. Alex, Irene Pepperberg’s African grey parrot, is dead at the age of 31. There’s no particular cause that has been identified for his death, and he was pretty much just approaching middle age for an African grey. Alex is best known for being the primary subject in Pepperberg’s research on animal cognition, and especially non-human cognitive psychology, explored through Alex’s ability to communicate through spoken English.

More on the Austringer.

Nelson vs. Ruse “undebate”

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Is it just me, or is there something particularly ludicrous and pitiful about Ruse (or anyone) discussing with Paul Nelson what evidence would make Paul Nelson change his mind about ID, when Nelson isn’t even man enough to lift his head up out of the sand the tiny bit required to admit that the earth is old, that this is a hard evidentiary fact, that denying it is as perverse as denying that the Earth is round, and that the promotion of the young-earth view in evangelical churches is one of the greatest frauds in American history?

Of course, Ruse is too much of a softy to ask these kinds of questions,* which is exactly why the IDers keep inviting him (and paying him) to do these debates.

(* To be clear: Ruse is useful and a pro-science warrior on many things, but one thing he doesn’t do much of is challenge the creationists scientifically and force them to deal with the hard evidence that challenges their beliefs. Doing this takes a lot more work of course and only a few people are good at it.)

From reports that we are getting, starting yesterday a user account on YouTube, called cseministry, began fraudulently claiming that any video which criticized the felon, cheat, liar, fraud, huckster, etc. Kent Hovind violated the copyrights of the Creation Science Evangelism.

Under the draconian DMCA, CSE can use such false claims to silence their critics, with little legal risk to themselves. Once a claim has been filed, YouTube is required by US Law to remove the content immediately and without any review. The real copyright holders then have to jump through hoops to get their content back on YouTube, that is assuming that they haven’t already been falsely banned.

Hovind’s critics have a strong case against CSE’s DMCA claims because CSE’s own website waived copyright: “None of the materials produced by Creation Science Evangelism are copyrighted, so feel free to copy those and distribute them freely.” That waiver appeared in the About Creation Science Evangelism page as recently as yesterday. It looks like they’ve scrubbed their site today, after this waiver was pointed out to them. Apparently, CSE is trying to retroactively remove their productions from the public domain. (They can’t legally do this, but has the Hovind Bunch ever acted within the law?)

But more infuriating to me is that several users have reported that CSE is claiming copyright to homegrown videos that contain no CSE content, and in many cases no content by anyone other than the YouTube user. They are issuing clearly fraudulent DMCA complaints to remove videos critical of their organization and the liar that ran (runs?) it. This type of behavior should land the rest of the Hovind Bunch in jail except that fraudulent infringement notices are not illegal under the DMCA.

Update: And Now a Video

Tangled Bank #88

The Tangled Bank

It's time for a brand new Tangled Bank at the Behavioral Ecology blog. It's got man-boobs, screwworms, and kumatos, so you don't want to miss it.

Politics on your mind?

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The Seattle Times has an interesting article on the link between political views and the brain

In a study likely to raise the hackles of some conservatives, scientists at New York University and the University of California, Los Angeles, found that a specific region of the brain’s cortex is more sensitive in people who consider themselves liberals than in self-declared conservatives.

Based on the findings we can make some predictions

Based on the results, Sulloway said, liberals could be expected to more readily accept new social, scientific or religious ideas.

Or alternatively, conservatives will be less ready to accept new scientific ideas.

Imagine that

Well now we understand

Analyzing the data, Sulloway said liberals were 4.9 times more likely than conservatives to show activity in the brain circuits that deal with conflicts and were 2.2 times more likely to score in the top half of the distribution for accuracy.

ID proponents are quick to argue ‘viewpoint discrimination’ whenever their attempts to introduce their scientifically vacuous ideas fail. If ID were really interested in protecting people from viewpoint discrimination then surely they will be outraged by the following article Can God Love Darwin, Too?

Remember RIchard Colling, a biologist and professor at Olivet Nazarene University in Illinois. In 2004, Colling wrote a book called “Random Designer”.

… as he said in a letter to students and colleagues this year—“I want you to know the truth that God is bigger, far more profound and vastly more creative than you may have known.” Moreover, he said, God “cares enough about creation to harness even the forces of [Darwinian] randomness.”

Caldwell Loses Suit Against Roseville

The endlessly litigious Larry Caldwell has lost his lawsuit against the Roseville school district in California. Caldwell’s suit claimed that the school board violated his constitutional rights by giving due consideration to his proposals to put anti-evolution material into science classes. The court granted summary judgment in favor of the school district, which is pretty much a thorough smackdown.

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

Library Collection Policies

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readingrainbow.jpg I learned today via an email sent to EvolDir, that some graduate students at Portland State University have put together a petition for Darwin Day. They plan to present this petition on February 12, 2009 to the Library of Congress, libraries, and bookstores, formally asking that that the anti-science works of creationists and intelligent design activists no longer be classified as “science” in libraries and bookstores.

Their hearts are in the right place, but I believe that they have misunderstood the issues facing our libraries and bookstores.

Aww. Michael Egnor Notices Me

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Well, I see that physician and Discovery Institute shill Michael Egnor has noticed me.

Egnor, a man whose arrogance and ignorance has already led to the coining of a new word, is unhappy about my critique of Tom Bethell. So unhappy, in fact, that he has to resort to forging fake quotes from my article.

Egnor claims that I called Bethell “a liar” - he uses those two words, and puts them in quotes. Any reasonable person would come to the conclusion that they appear in my article. Only problem is, the word “liar” doesn’t appear anywhere in my piece, as a text search will easily confirm. Gee, a Discovery Institute spokesman misleading the public - what is the world coming to?

Read more of the silly saga at Recursivity

Whoa

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From Cassini Raw Images, specifically here.

Another definition of ID

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According to the Waco Tribune‘s story on the Baylor controversy:

Intelligent design asserts that certain things in the universe can result only from an intelligent cause or God.

HT: Andrea Bottaro

Iapetus flyby today!

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What with graduate school and all, I almost forgot about the thing I have been anticipating for months – the Cassini spacecraft‘s superclose flyby of Iapetus. It’s happening right now apparently. So finally we might find out whether or not that crazy equatorial ring really is a spaceship runway like the UFOologists say. I mean, obviously a perfectly straight line of mountains on the equator can’t be explained by natural regularities or random chance, so it’s got to be ID, right? And of course the creos will say that whatever they find is evidence for a young universe.

Bethell the Buffoon

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Check out the final exchange about intelligent design between John Derbyshire and Tom Bethell, where Bethell insists that creationism and intelligent design are as different as chalk and cheese. (Part 1 here; Part 2 here.)

In it, Bethell demonstrates once again why he is a blathering buffoon. Bethell tells us that “Structures or signals of specified complexity permit an inference to design without any necessary recourse to the supernatural” without bothering to mention that “specified complexity” is junk mathematics and doesn’t permit an inference to anything at all, except that Bethell is rather gullible to accept William Dembski’s assurances as gospel.

Read more at Recursivity.

One of the most puzzling aspects of the recent Dembski - Baylor spat over the web site for Robert Marks’s “Evolutionary Informatics Lab” was the basis for Dembski’s part time appointment at Baylor as “Senior Research Scientist” (a post-doctoral position). Dembski has stated that Marks had “procured a small grant from the LifeWorks Foundation” specifically for him to work on the project. The impression given is that an indepedent agency found Dembski and his ideas scientifically worthwhile enough to put some dough into them. The strange thing was, a Google search for “Liferworks Foundation” only seemed to yield a Tennessee-based charity with a focus on the arts, and little apparent interest in science, whether of the mainstream or pseudo- varieties.

I’m with the Banned

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With great pleasure I hooked up via teh internet with those crazy cats at the AtBC (After the Bar Closes) disscussion forum last month, to visit the Darwin Exhibition at the Field Museum in Chicago! (I love people who diss creationism.)

Before I describe our adventure, I want to remind you that you can join my Facebook group, or friend me on MySpace. The Facebook group also serves as the fan group for PT. I also have a gallery of pictures from my adventures that you can look through. I working on collecting all my pictures there.

Also don’t forget to submit your best science blogging posts to the 2007 Science Blogging Anthology and join us at the 2008 Science Blogging Conference.

Behe and the California Creationism Case

Last week, I reposted four old articles that I wrote back in 2005, when a group representing a number of Christian schools in California filed a lawsuit against the University of California claiming that UC’s rejection of several of their courses was illegal “viewpoint discrimination.” In a more recent post, I mentioned that there’s a hearing on motions for summary judgement scheduled for later this month. I also mentioned that the Christian schools claim that all they are doing is “adding a religious viewpoint” to “standard course material.” It doesn’t take a genius to see that the “viewpoint” presented in some of the textbooks used in the rejected courses is explicitly opposed to the actual science of biology. It certainly represents something very far from the “standard” course material for high school biology. (Or, for that matter, biology anywhere in the reality-based universe.) Nevertheless, the Christian schools seem to be determined to argue that they really do teach the “standard” scientific material.

And they’ve got help - an expert witness. That’s right, the Christian schools have found themselves someone who is willing to stand up and argue that a textbook that “puts the Word of God first and science second” really does teach standard science. Who, you might wonder, is the scientist brave enough to stand up to the harsh wind of reality and claim that teaching that, “man is a special creation that is completely separate from the physical universe and the animal kingdom,” is just an addition to “standard” science? Professor Michael Joseph Behe of Lehigh University, that’s who.

Read more (at The Questionable Authority, where comments can be left):

The aptly named Progressive Conservative leader John Tory, in his push to fund religious schools in Ontario, says it would be just fine with him if Christian schools teach creationism as a legitimate alternative to evolution.

Read more at Recursivity.

Intelligently designed confusion

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On Evolution News, Crowther argues that

The Privileged Planet: Such a Dangerous Idea Its Author Had To Be Stifled

Of course, most who are familiar with the facts will understand that Crowther’s assertions are without much merit. First of all, even Hauptman, who spoke out against Gonzalez, was clear to state that it was the scientific vacuity of ID which affected his vote about Gonzalez.

“[But] intelligent design is not even a theory. It has not made its first prediction, nor suffered its first test by measurement. Its proponents can call it anything they like, but it is not science,” added Hauptman. “It is purely a question of what is science and what is not, and a physics department is not obligated to support notions that do not even begin to meet scientific standards.

Over the last few days, I reposted a series of four articles that I wrote two years ago. Those articles discuss a California lawsuit filed by a group of Christian schools against the University of California. They are suing in an attempt to force UC to recognize some of their classes as meeting the requirements that UC sets for high school students who are applying for admission to the system. Several subjects are involved in the suit, but as a biologist I’m mostly interested in the biology courses that are involved.

At the moment, the next scheduled event in the case comes on September 24th, when the judge will hear arguments on motions for summary judgement. I’m not a legal expert, and I don’t spend as much time following Constitutional Law for fun as Ed does, but I’ve got a feeling that the motion for summary judgement filed by the Christian schools will fail, and the case will go to trial. A motion for summary judgement can only be granted if there are no significant disputes about material facts in the case. In this particular case, at least as far as the science books are concerned, there is a significant dispute about the facts.

The plaintiffs (the Christian schools) claim that their courses, “add to standard content a banned book, a religious viewpoint that God created man and woman, or the viewpoint of creation or Intelligent Design,” and that this constitutes “viewpoint discrimination.” (Brief for Summary Judgement p. 20). Someone from the Association of Christian Schools International, one of the plaintiffs in the case, left a comment on a couple of the old articles that elaborated a bit on that - the case, he claimed, is not about creationism, it’s about “illegal viewpoint discrimination.

Read more (at The Questionable Authority, where comments can be left):

Last night, a strange post appeared at Uncommon Descent, under the byline “Botnik”, claiming to report on a letter by Baylor University President John Lilley about the University’s disavowal of the Orwellianly named “Evolutionary Informatics Laboratory” that had been created a few months ago by engineering professor Robert Marks in collaboration with Dembski. The alleged letter had a decidely non-“presidential” tone, and caused many UD commenters to immediately attack Lilley as a puppet of the ACLU, a member of the vast NCSE-led atheist conspiracy, etc. As tempers flared, the letter was identified as a “P-A-R-O-D-Y” a few hours after the original posting.

What the intended goal of the “parody” was, other than to risk getting the Baylor Administration more upset about ID-related shenanigans, is unclear. Wes discusses the matter further at The Austringer.

SEE UPDATE BELOW FOLD

Last week I told y’all about how AiG had corrupted Kentucky’s government. Well according to an email that I received today, the tax-funded Northern Kentucky Convention & Visitors Bureau will change its inflammatory and specious description of the creation anti-museum. The Sunday’s Kentucky Enquirer is going to have a story on it. Someone should post the link in comments when it come available.

Sounds like our public pressure worked. Good job everyone.

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