January 2007 Archives

The Dover Books Cometh


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There’s an interesting op-ed on teaching evolution in today’s edition of the International Herald Tribune. The opinion piece is written by Michael Balter, and suggests that, “The best way to teach the theory of evolution is to teach this contentious history.” To support this position, Balter points to a 2005 study by Steven Verhey that was published in the November, 2005 issue of BioScience, that suggested that creationist students were more likely to change their views if the curriculum directly addressed creationist objections to evolution.

Balter has been advocating this position for a while now, and his views have been discussed at The Panda’s Thumb before now. Still, the position appears to be at least superficially reasonable, so it’s probably worth another quick look.

Read more (at The Questionable Authority):

Jones, Luskin, and Text


A literary genre, “stream of unconsciousness”, flows from the pen of Casey Luskin. A recent instance of this concerned responses to me, Ed Brayton, and Tim Sandefur concerning Luskin’s claims that legal principles would cause higher courts to “disapprove of” the Kitzmiller decision because of the amount of text Jones copied from the plaintiffs’s proposed findings of fact. I take a look at Luskin’s response and point out some problems in Luskin’s accuracy of recount, structure of argument, premises, and show that Luskin’s asserted “errors” on Jones’s part are either nothing of the sort or don’t signify anything that a higher court would find to be reversible error.

Check it out on the Austringer.

Tangled Bank #72

The Tangled Bank

The latest Tangled Bank is online at Ouroboros, and it's a big one. I noticed what seemed to be an awful lot of entries whizzing through my mailbox on the way, so I had a suspicion that we were giving Chris a workout with this edition.

I suppose everyone has someone who they consider an embarrassment to their alma mater. I can probably think of a dozen just off the top of my head regarding my undergraduate institution (including a number of politicians who shall remain nameless). However, one who really sticks in my craw is the infamous Jonathan Wells of the Discovery Institute, who also happens to be a Yale alum (Divinity school—small comfort that it wasn’t Yale College, at least).

So, Wells has been back polluting Yale lately, via the Opinion pages of the student newspaper, the Yale Daily News. Predictably, Wells mischaracterizes evolution, but he also uses his “authority” as a theologian to rail against the upcoming Evolution Sunday sermons, following a previous editorial by Jonathan Dudley describing Evolution Sunday as “not entirely benign.” Dudley is a student at the Divinity school where Wells received his degree, and according to the YDN, is also a molecular oncology researcher at the Yale School of Medicine–so he dislikes the perceived conflict between science and religion. As such, he’s in favor of events like Evolution Sunday that seek to counter this idea, but he’s worried that one argument from authority is being traded for another:

(Continued at Aetiology)

More on the “costs” of evolution

Walter ReMine (an anti-evolutionist who ardently believes that “Haldane’s Dilemma” is a real problem for evolution) recently updated the entry for “Haldane’s Dilemma” at the CreationWiki. The update does not directly refer to my recent posts on the topic, but does address the points that I made. Actually, “address” is probably the wrong word - he provides a hand-waving dismissal without actually responding to any of the specific points I raised. Ordinarily, a hand-waving response isn’t worth the effort needed to write a reply, but in this case the errors that ReMine makes are worth discussing simply because they provide a convenient jumping-off point for a discussion of the way evolution actually works.

Read More (at The Questionable Authority):

flock%20of%20dodos.jpg Bill Dembski ‘discusses’ a new book, to be released soon, titled Flock of Dodos: Behind Modern Creationism & Intelligent Design Cambridge House Press, Inc. (release date 02.28.07) By Barrett Brown, Jon P. Alston

The book description may explain why the book is almost outselling some of Dembski’s own books, before it has been released…

The Deceitful Critics of Intelligent Design


Kazmer Ujvarosy (chief scientist of the Frontline Science Institute, one of the most prestigious research organizations dedicated to Intelligent Design) explains the theory of Intelligent Design in a very clear manner

First of all, they allege that ID theorists failed to name the designer.


If ID critics want me to be even more specific, Christ identified himself as that intelligence which created the universe to make reproductions of himself in the form of human beings. In other words we find design in nature because Christ constitutes the seed of the universe, or the cosmic system’s input and output. As he disclosed it in Revelation 22:13, “I am the Alpha and the Omega, the First and the Last, the Beginning and the End.”

It only gets better

Hello Panda’s Thumbers. I haven’t posted for quite a few months, although there is news from Kansas that I’ll have to share in just a few days.

But here’s the quick way to put up a post - offer something written by someone else.

A few months ago Pulitzer Price winning author Edward Humes (www.edwardhumes.com) contacted Liz Craig and me at Kansas Citizens for Science, offering us an advance copy of his new book, “Monkey Girl,” about the Dover trial. I had been interviewed by Ed back during the Kansas 2005 “science hearings,” and material about Kansas is in “Monkey Girl” as background material.

We passed the book over to fellow KCFS board member Pat Hayes, whose blog Red State Rabble is a popular daily read for many. Pat loved the book, and wrote an excellent post about it. I’d like to pass Pat’s post on in its entirety, although you can go here and read in its home location if you wish, particularly if you want to follow the links to online book stores or to the audio excerpts. There’s a lot about Kansas here, but this is timely given that the Kansas Board of Education will be voting in just two weeks to throw out the creationist science standards and to adopt the high-quality standards written by the duly-appointed science standards writing committee.

So be sure to read to the end to read Pat’s strong endorsement of “Monkey Girl,” and put it on your reading list when it comes out in just a few days.

Wells vs Mutant Mice


Discovery Institute Fellow Jonathan Wells has for some time insisted that genes actually don’t do much, and that mutations in genes cannot play a significant role in evolution. One aspect of this is his claim that mutations in genes play little role in cancer. If he can throw doubt on the ability of genetic mutation to produce cancer, then by implication genetic mutation is not a force in evolutionary biology, and cannot be sculpted by natural selection. I have written about genes, cancer and Jonathan Wells before showing that he is greatly mistaken. However, recently published work has provided yet more evidence for a central role of genetic mutation in cancer, and further demolishes (if that is possible) Wells’s thesis[1,2,3,4].

No fewer than four Intelligent Design Creationism measures have been introduced in the current 60-day 2007 session of the State Legislature of New Mexico. There are two pairs of measures, with corresponding actions before the Senate and the House.

The Senate sponsor is State Sen. Steve Komadina, who has introduced both Senate Bill 371, “SCHOOL SCIENCE CONTENT STANDARDS,” and Senate Joint Memorial 9, “OBJECTIVE TEACHING OF BIOLOGICAL ORIGINS.”

The House sponsor is State Rep. W. C. “Dub” Williams, who has introduced identical resolutions House Bill 506 and House Joint Memorial 14

While the House and Senate Bills explicity avoid the E-word (evolution), the Joint Memorials attack evolution four times each.

On Monday, January 29th, House Joint Memorial 14 was considered by the House Judiciary committee, and was tabled after a lengthy discussion.

Basic Concepts: Measuring Fitness


Over at scienceblogs.com, there is an ongoing series of posts covering basic concepts in science. John Wilkins (who was the one who had the idea for the series in the first place) is maintaining a list of posts in the series. If you are interested in evolution, you will probably appreciate all of the posts in the biology section of the list. The following post is my first contribution to this series. I’m crossposting it here because the concept - fitness - has come up in the comments in both of my two most recent posts here.

In 1862, the British philosopher Herbert Spencer used the phrase “survival of the fittest” to describe Darwin’s concept of natural selection. It’s not a bad phrase, really, and it doesn’t do a bad job of describing natural selection - the individuals in any population that are “fittest” - best suited to reproduce - are the ones most likely to reproduce successfully. If this is correct (and it is), we can expect that “fitness” would be a very important concept in evolutionary biology. It is, of course, and John Wilkins has already provided a good explanation of the concept in general. I’m going to look at something a little more specific - how can we measure fitness.

Continue reading (at The Questionable Authority):

Fisking Turner

Jeffrey Shallit has already replied to this deeply silly opinion piece from biologist J. Scott Turner. But there is so much inanity in Turner's piece that I couldn't resist taking a shot at it myself. A subscription is required to read the essay online, but I think I've quoted enough of it to give you a pretty good idea. Comments can be left over at EvolutinBlog. Enjoy!

Yesterday’s post on evolutionary speed limits and Haldane’s Dilemma has sparked some interesting discussion, and some of the comments have already started to move beyond the very simple scenario that I outlined. Next week, I’ll post a couple of more complex examples, and look at the effect of things like a lower frequency of mutants in the starting population, what can happen with two mutations being selected at the same time, and whether mutations need to be fixed to be evolutionarily meaningful. I’ll also go over a couple of basic concepts that might help in understanding those scenarios.

Today, I’m just going to respond to part of one of the comments that was left on the last post. This is mostly because it’s an interesting question that deserves a thorough response, partly because the question involves some basic concepts that should be explained before I dive into more detail, and partly because it’s Friday and I really don’t want to spend the time plugging numbers in to work up another example.

Caligula, fairly early on in the comments, raises a point that involves a concept that is very basic to evolutionary biology: fitness:

Read more (at The Questionable Authority):

How fast can evolution work?


There’s been a bit of talk about “Evolutionary Speed Limits” over at the Intelligent Design weblog Uncommon Descent. Most of the discussion involves “Haldane’s Dilemma.” This concept is rooted in an article written by the noted evolutionary geneticist J. B. S Haldane in 1957. There’s a lot of math involved, and you can see it over at the Wikipedia page I linked above. The bottom line, for those not interested in the math, is this: according to Haldane’s calculations, a species cannot reasonably fix beneficial mutations (a particular mutation becomes “fixed” when it is present in all of the population) at a rate any faster than 1 mutation per 300 generations.

A number of anti-evolutionists have taken this as evidence against evolution. If, they argue, genetic changes can only be fixed at a rate of 1 per 300 generations, how can evolution possibly explain the differences between species like humans and chimps, where not nearly enough generations have passed to account for the number of differences that we observe. There are a number of problems with using Haldane’s calculations in this way, and in this post I’m going to look at one of those - the one that I think is the most important. For clarity, I should probably make sure that I am very explicit about what, exactly, the problem is before I start, so here it is:

Using Haldane’s 1 substitution per 300 generations as a speed limit for all evolution is wrong because Haldane’s calculations and concerns only apply under certain very specific circumstances.

Read the rest (at The Questionable Authority):

Yesterday, I pointed out that Jonathan Wells was grossly ignorant of basic ideas in evo-devo. This isn't too surprising; he's a creationist, he has an agenda to destroy evolutionary biology, and he's going to rail against evolution…same ol', same ol'. That's nothing, though. Wells and his fellows at the Discovery Institute have an even more radical goal of fighting natural, material explanations of many other phenomena, and his latest screed at the DI house organ is against natural explanations of development. Not evolution, not evo-devo, just plain basic developmental biology—apparently, he wants to imply that the development of the embryo requires the intervention of a Designer, or as he refers to that busy being in this essay, a postmaster.

Continue reading "Jonathan Wells knows nothing about development, part II" (on Pharyngula)

PZ reports on Wells: Jonathan Wells knows nothing about development, part I

If one were asked who the very worst advocate for Intelligent Design creationism was, it would be a difficult decision—there are so many choices! Should we go back to first principles and pick PJ Johnson, the cunning lawyer who has the goal of undermining all of science? Smarmy and obtuse Sal Cordova? Pompous and vacuous William Dembski? I’m afraid my personal most loathed ID creationist has got to be Jonathan Wells.

The reason? The man claims to be a developmental biologist, my favorite field of science, and actually has some credentials in the discipline…but every time he speaks out on the subject, he stuns me with his ignorance. Here he is, trying to explain the Cambrian explosion.

Read the rest of the story at Pharyngula

Note that this is part I, apparently Jonathan Wells has written an even more outrageous claim.

Honesty in Advertising


The NCSE reports on an Antievolution bill in Mississippi

Mississippi’s House Bill 625, introduced by Representative Mike Lott (R-District 104) on January 9, 2007, and referred to the House Committee on Education, would provide, if enacted, “The school board of a school district may allow the teaching of creationism or intelligent design in the schools within the district. However, if the theory of evolution is required to be taught as part of the school district’s science curriculum, in order to provide students with a comprehensive education in science, the school board also must include the teaching of creationism or intelligent design in the science curriculum.” A similar provision was part of 2005’s House Bill 953, of which Lott was the chief sponsor; HB 953 died in committee on January 31, 2006.

Comment: Seems that the faithful have not gotten the Discovery Institute’s memo. However, the link between ID and creationism seems undeniable once again.

Update on Kenya


The East African Standard has a new (well, a week and a half old, but new to me) article concerning the attempts by evangelicals to suppress the hominid fossils currently on display in Kenya’s National Museum. You may remember when this ruckus first began several months ago. We now learn that churches are planning on holding “major demonstrations to the museum to press for the removal of the bones.”

Confusion by design about design


On UncommonDescent, GilDodgen quotes from Denyse’s comments

GilDodgen Wrote:
Denyse Wrote:

Bear with a simple lay hack here a moment: Why must we know a designer’s intentions in order to detect design?

If the fire marshall’s office suspects arson, do the investigators worry much about WHY?

Surely they investigate, confirm their finding, and turn the information over to other authorities and interested parties, without having the least idea why someone torched the joint.

ALL they need to be sure of is that the joint did not torch itself, via natural causes.

The observation Denyse makes is so obvious that one would need a Ph.D. in obfuscation not to see it. Common sense is not so common, at least among those with a foundational commitment to materialism.

Gil is right, Denyse’s observation is so obvious and wrong. Of course, in order for this to understand, it requires one to shed the veil of ignorance and determine how design is detected in real life and furthermore how intelligent design wants to detect “Design”. Note that I am distinguishing between design and Design to avoid the equivocation so commonly found in ID literature, leading to much confusion amongst its followers.

On Pandasthumb, our dear friend Salvador Cordova (YEC) presents us with the following “argument”

Pellionisz FractoGene has demonstrated at least one layer of linguistic architecture for the junk DNA. A linguistic structure suggest function even if the structure is not fully understood (like seeing an undecoded communication, the communication has function, but it is not understood). Furthermore, Fracis Collins called it hubris to say any part of the genome is junk.

Salvador may perhaps not be familiar with the term ‘non-coding DNA’ which describes much better the scientific thinking on the somewhat unfortunate term “junk DNA”, especially since the term seems to be used for cherry picking rhetoric. In this posting I will explore the term junk DNA, address some of the findings in research that DNA and junk DNA show “linguistic features” and show why ID remains fully vacuous since it cannot predict let alone explain “junk DNA”.

Intelligent Design Creationism lacks explanatory power

Author and Professor of Philosophy of Science / Logic at Calvin College, Del Ratzsch, explains how the approach chosen by Dembski to infer ‘design’ is far from the robust agency driven conception of design that most people would imagine. In other words, the concept of design as used by Dembski has little similarity to what most people imagine design to involve.

Del Ratzsch Wrote:

“I do not wish to play down or denigrate what Dembski has done. There is much of value in the Design Inference. But I think that some aspects of even the limited task Dembski set for himself still remains to be tamed.” “That Dembski is not employing the robust, standard, agency-derived conception of design that most of his supporters and many of his critics have assumed seems clear.”

Source: Del Ratzsch in “Nature, Design, and Science:The Status of Design in Natural Science”, SUNY Press, 2001.

Not only does Intelligent Design use a watered down concept of design, this concept also leads to the admission that design does not necessarily leads to agency (a designer).

Ryan Nichols Wrote:

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 (Explanatory Filter) 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”

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

At Darwin or Design Jason Rennie talks to Dr Ryan Nichols.

And finally, William Dembski himself, when asked to describe how Intelligent Design explains something responds that:

William 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.

Source: William A. Dembski Organisms using GAs vs. Organisms being built by GAs thread at ISCID 18. September 2002

While ID proponents are quick to claim that ID does lead to predictions, logic dictates that these claims are without merrit. In order to make a prediction, one has to know the motives, means and opportunities of the designer, one has to be able to constrain the designer.

A major disanalogy between the ID hypothesis and other scientific hypotheses is that the ID hypothesis fails to be scientifically tractable, at least insofar as the appeal to a trancendent intelligent agent as the designer: that is, an agent that transcends the confines of this universe. (As defined above, an hypothesis is scientifically tractable if and only if through scientific and empirical means we can develop and test models of its internal dynamics, often through applying the scientific results we have obtained in other domains.) Suppose, for instance, one claims that the designer is the monotheist’s God. Almost all monotheists would agree that one cannot significantly develop and test models of God’s internal dynamics through scientific means, since we cannot use science to significantly probe and test God’s psychology. On the other hand, suppose one adopts Michael Behe’s proposal (and that of many leading advocates of ID) to leave unspecified the nature of the designer. If we take this approach, then it is difficult to see how the intelligent design hypothesis could even be minimally scientifically tractable, since we would be unable to say much of anything about the internal dynamics of the designer.


Moreover, notice that, just as in the big bang theory, no additional scientific work is done if we add to the above hypotheses the claim that God, or some other transcendent intelligence, created or designed life on earth. In the big bang theory, for instance, neither the claim that God created the big bang, nor that it occurred uncaused, gives the hypothesis any significant additional explanatory or predictive power. Theists, for example, might find it philosophically necessary to hypothesize a creator to account for the big bang, but it is best not to consider such an hypothesis part of science since it is not scientifically tractable, and adds nothing of interest scientifically. Similarly, the hypothesis that some designer created the basic kinds will not give hypothesis (ii) above–that is, the hypothesis that the basic kinds simply appeared fully formed at various points in earth’s history–any additional explanatory or predictive power. And the reason for this is that the designer’s psychology is not scientifically tractable: we cannot form models of the designer’s internal dynamics. Of course, in analogy to the big bang, one might nonetheless feel philosophically compelled to hypothesize a creator to explain the origination of life.


It is often stated by anti-evolution forces that evolution is not a fact; a rhetorically powerful but ultimately meaningless statement. As should be obvious from the discussions in this paper, evolution is a model. A model, by its very nature, never becomes a “fact” that is it never becomes certain but always remains tentative. Trying to classify evolution or any empirical model as fact or not-fact is a failure of categories and indicates a profound ignorance of the nature of empirical knowledge. Evolution is a model, hence tentative, but a model with extraordinary predictive power. That is high praise, the highest science can give. Similar arguments are also made against other models: science has not proven X . For example X might be global warming due to green-house gases. Of course science has not proven X . Proofs are the domain of mathematics, not the empirical sciences. When people use the X is not a fact or Y is not proven gambits it is a tacit admission they have lost the science argument and they are just trying to downplay the significance of that failing.

Source: B.K. Jennings On the Nature of Science

Intelligent Design Creationism does not provide any alternative theory

Bruce Gordon Wrote:

Design theory has had considerable difficulty gaining a hearing in academic contexts, as evidenced most recently by the the Polanyi Center affair at Baylor University. One of the principle reasons for this resistance and controversy is not far to seek: design-theoretic research has been hijacked as part of a larger cultural and political movement. In particular, the theory has been prematurely drawn into discussions of public science education where it has no business making an appearance without broad recognition from the scientific community that it is making a worthwhile contribution to our understanding of the natural world.

Source: Bruce Gordon Intelligent Design Movement Struggles with Identity Crisis Research News & Opportunities in Science and Theology. January 2001, p. 9

Philip 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.

Source: Philip Johnson In the matter of Berkeley v. Berkeley by Michelangelo D’Agostino 10, 2006 p31 Berkeley Science Review See also Panda’s Thumb posting

Paul Nelson Wrote:

Easily the biggest challenge facing the ID community is to develop a full-fledged theory of biological design. We don’t have such a theory right now, and that’s a problem. Without a theory, it’s very hard to know where to direct your research focus. Right now, we’ve got a bag of powerful intuitions, and a handful of notions such as ‘irreducible complexity’ and ‘specified complexity’-but, as yet, no general theory of biological design.

Source: Paul Nelson, The Measure of DesignTouchstone Magazine 7/8 (2004): pp 64 – 65.

Science Daily reports Evolutionary Scrap-heap Challenge: Antifreeze Fish Make Sense Out Of Junk DNA

Scientists at the University of Illinois have discovered an antifreeze-protein gene in cod that has evolved from non-coding or ‘junk’ DNA. Since the creation of these antifreeze proteins is directly driven by polar glaciation, by studying their evolutionary history the scientists hope to pinpoint the time of onset of freezing conditions in the polar and subpolar seas. Professor Cheng will present her latest results at the Annual Main Meeting of the Society for Experimental Biology in Canterbury on Tuesday the 4th April

Hattip Pete Dunkelberg

Dr. Dino gets 10 years


Convicted felon Kent Hovind’s sentencing was today, and again the Pensacola News-Journal has the story:

Pensacola evangelist Kent Hovind was sentenced Friday afternoon to 10 years in prison on charges of tax fraud.

After a lengthy sentencing hearing that last 5 1/2 hours, U.S. District Judge Casey Rodgers ordered Hovind also:

– Pay $640,000 in restitution to the Internal Revenue Service.

– Pay the prosecution’s court costs of $7,078.

– Serve three years parole once he is released from prison.

Not knowing anything about sentencing, I had figured Hovind would get time already served plus probation or something. I guess not. Probably with good behavior this will become 5 years or less of actual prison time. The moral of the story: living in your own personal alternate reality works for only so long. That, and don’t tick off the IRS.

Reed and I went to a flock party that was held at the North Carolina Museum of Natural Science last night. We had a great time and got to talk with Dr. Randy Olson, who is the filmmaker behind Flock of Dodos, a documentary about intelligent design’s culture war with evolution.

Reed has posted a more detailed report on his blog. I just want to mention the film’s two important points:

  • that the intelligent design movement consists of nothing but lies invented for a public relations campaign and seeks nothing less than the overthrow of the cultural legacies of the enlightenment, and
  • that scientists are utterly unable to communicate their profession to normal people, which only helps the crusade of anti-intellectualism.

Likewise, I want to suggest that y’all visit Reed’s blog and respond to his challenge about coming up with some sound bytes that frame the issue in our favor. Comments will be disabled here to encourage our readers to leave them at DRN. Don’t forget to try out the “quote comment” feature while you’re there.

Read the full report at De Rerum Natura.

Science Blogging Conference

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This weekend is the big conference. Prof. Steve Steve and I will be there. If you will be attending, please come say ‘hi’ to us. I’ll take Prof. Steve Steve’s picture with anyone who asks.

Dog + Cat = Lion + Calf


Over at the “ID is nothing but science, we really mean it” Uncommon Dissent blog, there’s an interesting little biblical discussion going on right now. In this case, DaveScot’s remarkable response to a comment on the After the Bar Closes discussion board does an amazing job at evoking that Ghostbusters kind of feel.

Read More (at The Questionable Authority):

The second chapter of my dissertation has now been published. It is freely available from the BMC Bioinformatics website. In this post I hope to provide you will a short overview of the research. The reference is

Cartwright RA (2006) Logarithmic gap costs decrease alignment accuracy. BMC Bioinformatics 7:527.

Our genomes evolve not only via point mutations (where one base changes into another base) but also via insertions and deletions. That is the addition or removal of bases. Collectively insertions and deletions are known as “indels”. Now several studies over the last fifteen years have found that the size of insertions and deletions follows a power law, i.e. a log-log plot of size versus frequency is linear. However, this observation has had little impact on bioinformatics for various reasons. Now why is this observation important? For starters, several scientists have proposed that sequences should be aligned using logarithmic gap costs (wk=a + b k + c ln k) instead of the standard affine gap costs (wk=a + b k).

Because in my first chapter I created a sequence simulation program, Dawg, that could simulate evolution using a power law of indel sizes, I felt that it was important to test this suggestion out. Specifically, whether the slowness of algorithms using logarithmic gap costs are offset by their improved accuracy. So that is exactly what I did for my second chapter, and the results were surprising.

Finish reading on De Rerum Natura » (Comments may be left there.)

Tangled Bank #71

The Tangled Bank

The latest edition, Tangled Bank #71, is set in 1771, so if you want your biology with an Enlightenment flavor, you know where to go.

It’s been awhile since we’ve had a “silliest thing” post, but I’ve got a good one. I was perusing the 2002 book The Case for Angels. The book is written by philosopher/apologist Peter S. Williams, and Dembski wrote a foreword strongly endorsing the book. In fact, Dembski concluded his foreword with the following:

There exists an invisible world that is more real and weighty than our secular imaginations can fathom. I commend this book as a way of retraining our imaginations about that reality. (Dembski foreword, p. xii)

No, he’s not talking about dark matter, although technically that fits the description perfectly. He’s not even talking about the existence of God, which of course is a famous debate. No, Dembski and Williams are talking about angels…and demons, which, if it wasn’t obvious, are the bad angels. For some reason, demonology is a topic that regularly trips up fundamentalist evangelicals. I posted one example from a modern ID advocate; another well-known example is Norman Geisler’s testimony for the creationists in the 1981 McLean v. Arkansas case. See below for Peter Williams’s take.

Jason Rennie interviews


Jason Rennie of The Sci Phi Show, who interviewed me awhile back, has put his interviews of Michael Shermer (anti-ID), Salvador Cordova (YEC/ID), Michael Behe (ID), and yours truly (guess) into a podiobook, which is I guess is what kids are doing these days. Rennie is evidently sympathetic to ID, but he does let his guests talk, which is nice in this case because at least the guests cover more than the standard talking points.

Flock Party: Raleigh


A while back I was trying to organize a Flock Party for the Triangle area; however, I have yet to get my hands on a copy of the DVD. (I guess it is taking a while for NCSU to buy its copy.) Regardless, I am excited to announce that the Museum of Natural Sciences is going to be throwing a Flock Party this Thursday, January 18th.

The film will be shown at 7:00 pm in the Museum Auditorium and is free to the public. Dr. Randy Olson, the filmmaker, will give a presentation and answer questions after the screening.

The full announcement is below the fold.

Bora of A Blog Around The Clock has edited an anthology of the best fifty posts from science and medical blogs in 2006: The Open Laboratory: The Best Writing on Science Blogs 2006. The Panda’s Thumb is represented by Ian Musgrave’s post, Denton vs Squid; the eye as suboptimal design. Several other Pandites represent their personal blogs in the anthology as well.

You can order yourself a copy of the anthology from Lulu.

Congrats to all the winners.

The nature of ID


On UcD, Bill Dembski provides a somewhat confusing commentary on the following picture from My Confined Space


WAD Wrote:

If the challenge below were met, would it be evidence for ID or for teleportation?

I guess teleportation is a purely natural process and God is of course equivalent with ID. Thank you Bill for a good laugh.

On Uncommon Descent, our friend Davescot shows once again why Intelligent Design has to hide in the shades of our ignorance. Richard B Hoppe has dealt with most of what he called Dissent Out of Bounds on Uncommon Dissent (Oops, make that “Descent”) and this posting is meant to archive the excellent comments by Febble which caused so much concern at UcD.

While UcD is well known for its aggressive moderation policies, deleting much of anything critical of ID and quickly banning those who expose ID’s scientific and religious vacuities, Uncommon Dissent seems to also favor squashing unfavorable reviews of its theses. In a thread titled ID in the UK ID activist Bill Dembski invited comments from people in the United Kingdom to comment on the recent ‘activities’ of ID in this country.

A poster, named Febble complied with the invitation and politely expressed her feelings. Soon thereafter Davescot banned Febble from participating on UcD. Why? Read on

Mystery in The Air


Capped Column snow crystal

After this storm cloud, there came another, which produced only little roses or wheels with six rounded semicircular teeth … which were quite transparent and quite flat … and formed as perfectly and symmetrically as one could possibly imagine. There followed, after this, a further quantity of such wheels joined two by two by an axle, or rather, since at the beginning these axles were quite thick, one could as well have described them as little crystal columns, decorated at each end with a six-petalled rose a little larger than their base. But after that there fell more delicate ones, and often the roses or stars at their ends were unequal. But then there fell shorter and progressively shorter ones until finally these stars completely joined, and fell as joined stars with twelve points or rays, rather long and perfectly symmetrical, in some all equal, in others alternately unequal. (1)

The beauty, symmetry and diversity of snow crystals have long fascinated scientists. Snow crystals come in endless variety of six-fold symmetric shapes, sometimes thinner than a sheet of paper and up to 3 millimeters across. How can they grow in a three dimensional bath and yet be thin? What natural processes could lead to great diversity of shapes that are complex yet symmetric? What keeps opposite sides of the growing crystal in step even as a unique shape is forming? And with slightly different temperature or humidity produces sensible hexagonal columns instead? Is there any rational explanation for the generation of these crystals out of thin air? Can you formulate a hypothesis that even has a chance?

J. Scott Turner Misses the Mark


J. Scott Turner, a professor at the SUNY College of Environmental Science & Forestry in Syracuse, New York, has a this dumb opinion piece in the January 19 2007 issue of the Chronicle of Higher Education. Since a subscription is required to read this (your university probably has a subscription), I’ll excerpt a couple of the dumber remarks:

Also amusing is the spectacle of independent-minded scientists’ running to college administrators or the courts for help in defining what is science and what is permissible discourse in their classroom.

Faced with all that hue and cry, I almost want to say: “Friends, intelligent design is just an idea.”

The strain’s very persistence invites the obvious question: If Darwin settled the issue once and for all, why does it keep coming back? Perhaps the fault lies with Darwin’s supporters. Rather than debate the strain on its merits, we scramble to the courts or the political ramparts to expel it from our classrooms and our students’ minds.

Read more at Recursivity.

Douglas Axe recently (well, sort of) published an article in the Journal of Molecular Biology entitled “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds” (Axe, J Mol Biol 341, 1295-1315, 2004). In his discussion of the experimental observations, Dr. Axe mentions some numbers that are likely to generate much discussion amongst Intelligent Design advocates and critics. For example, Stephen Meyer (2004) cites Axe at a key point in the argument in his recent article advocating Intelligent Design, “The Origin of Biological Information and the Higher Taxonomic Categories,” much discussed in previous Panda’s Thumb threads (here).

“Axe (2004) has performed site directed mutagenesis experiments on a 150-residue protein-folding domain within a B-lactamase enzyme. His experimental method improves upon earlier mutagenesis techniques and corrects for several sources of possible estimation error inherent in them. On the basis of these experiments, Axe has estimated the ratio of (a) proteins of typical size (150 residues) that perform a specified function via any folded structure to (b) the whole set of possible amino acids sequences of that size. Based on his experiments, Axe has estimated his ratio to be 1 to 10^77. Thus, the probability of finding a functional protein among the possible amino acid sequences corresponding to a 150-residue protein is similarly 1 in 10^77.”

More recently, Dembski cited Axe in his Expert Witness Report for the Dover trial (see this).

“Recent research by Douglas Axe (see Appendix 3) provides such evidence in the form of a rigorous experimental assessment of the rarity of function-bearing protein sequences. By addressing this problem at the level of single protein molecules, this work provides an empirical basis for deeming functional proteins and systems of functional proteins to be unequivocally beyond Darwinian explanation.”

Given that this subject is often raised by ID proponents (such as this), and that the Biologic Institute (where Axe works) has made some news accounts, it seems appropriate to review Axe’s work. The purpose of this PT blog entry is to try and lay out the study cited above (Axe DD, J Mol Biol 341, 1295-1315, 2004) in a form that is accessible to most interested parties, and to discuss a larger context into which this work might be placed. Needless to say, the grand pronouncements being made by the ID camp are not warranted.

Science magazine has just published a graph of data taken from a general social survey of Americans that quantifies what most of us assume: a well-educated liberal who is not a fundamentalist is much more likely to accept evolution than a conservative fundamentalist with only a high school education. You can see the trend fairly clearly: here we see the percent believing in evolution vs. fundamentalism, amount of education, and self-reported political views.

(click for larger image)

The percentage of respondents believing in human evolution is plotted simultaneously against political view (conservative, moderate, liberal), education (high school or less, some college, graduate school), and respondent's religious denomination (fundamentalist or not). Belief in evolution rises along with political liberalism, independently of control variables.

Continue reading "American political conservatism impedes the understanding of science" (on Pharyngula)

More DI Distortions About Axe’s Research

I have used the analogy before comparing the ID movement to the movie Weekend at Bernie’s, where two guys drag a dead body around pretending it’s alive to keep the party going a little longer. But nowhere is that analogy more accurate than in the IDers constant flogging of the protein research of Douglas Axe, now with the Biologic Institute that the DI is funding. This work has been shredded time and and time again and shown conclusively not to support ID in the slightest, yet they keep dragging it out and propping it up with a drink in its hand, hoping no one notices the embalming fluid. and the eyes sewn shut.

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

The weblog of William Dembski is called “Uncommon Dissent Descent” (UD). It has a reputation for banning unwanted commenters (read: “evolution defenders”), but generally on the grounds that they’re obstreperous and disruptive. However, it’s becoming clear that it’s not just disruptive behavior that gets one banned: It’s also merely disagreeing, calmly and lucidly, with DaveScot.

Recently Dembski posted some remarks about ID in the United Kingdom and invited comment from UK residents. One UK resident, “Febble”, accepted the invitation. Febble remarked that she had no objection to intelligent design being taught in the UK, since under Dembski’s definition of “intelligent”, Darwinian natural selection is intelligent. She wrote

I am happy to accept “Intelligent Design” as a scientific hypothesis to account for the development of life, as proposed by yourself, Dr Dembski, as long as you stand by this definition of intelligence:

‘ by intelligence I mean the power and facility to choose between options–this coincides with the Latin etymology of “intelligence,” namely, “to choose between” ‘

From Intellligent Design Coming Clean

However, such a hypothesis need not (and should not) be presented as an “alternative to evolution” as it is described in the Truth In Science materials. Far from rejecting an agent “with the power and facility to choose between options”, this is exactly what the Theory of Evolution postulates as the agent of evolutionary change - a process of_selection_ (aka “choice”) between options.

That did not go over well. DaveScot, Dembski’s bouncer, first responded with sarcasm:

Survival of the survivors. Brilliant!

I guess we can all go home now. Case closed.

and then within minutes moved on to the core ID argument: ‘Computers are really complex and they’re designed, and cells are really really complex so they must be designed too’.

Over at Uncommon Descent, Gil Dodgen asks the question of why so many engineers reject evolution. Dave Scot then asks a similar question about doctors. Not surprisingly, their answers to these questions are self-serving and backed up only by wishful thinking. Dodgen quotes Stephen Meyer as saying that because engineers know all about “design”, they are therefore in a unique position to know about biology. (As a corollary, I suppose biologists must have special insight when it comes to designing bridges.) Even more amusing is Dave Scot’s explanation for why doctors supposedly reject evolution. They are risk adverse. I’ll let others ponder the logic of that one. But all of this begs the question: How many doctors (or engineers) reject evolution, and why do they do so? I think the question is worth looking at, even if just for fun. So let’s do something that the denizens of UD would consider totally alien – let’s look at some data.

Back in November I was interviewed and photographed by the San Francisco Chronicle for the “Facetime” section of their Sunday newsmagazine. A month or two went by without anything coming out, so I figured I’d been dropped as an uninteresting nerd or some such. Well, I figured wrong, the article is out and my soul is laid bare, including my two cents on religion if anyone’s interested, and the influence of my dear beloved grandmother, college roommates (but see below), and this very group of Panda’s Thumb bloggers on my somewhat strange life. The reporter, Sam Whiting, conducts the “Facetime” interview by asking rapid-fire questions for 20 minutes, and then they excerpt the juiciest bits, resulting in a short piece that really cuts to the chase. Mission accomplished, I’d say.

Interesting choice of headline. Prof. Steve Steve is pleased:

Baby pandas! Baby pandas! Baby pandas! POSTED: 10:07 a.m. EST, January 3, 2007

BEIJING, China (AP) – A mini-baby boom last year has pushed up the number of pandas bred in captivity in China to 217, state media said Wednesday.

Some 34 pandas were born by artificial insemination in 2006 and 30 survived – both record numbers for the endangered species, Cao Qingyao, a spokesman for the State Forestry Administration, was quoted as saying by the Xinhua News Agency.

The previous record was the 21 baby pandas born in China’s zoos and breeding centers in 2005.

National Geographic a photo of them all lined up a few months back…

Titan Has Liquid Lakes, Scientists Report in Nature Jan. 3, 2007 (Source: JPL)

Liquid Lakes on Titan The existence of oceans or lakes of liquid methane on Saturn’s moon Titan was predicted more than 20 years ago. But with a dense haze preventing a closer look it has not been possible to confirm their presence. Until the Cassini flyby of July 22, 2006, that is.

Scientists report definitive evidence of the presence of lakes filled with liquid methane on Saturn’s moon Titan in this week’s journal Nature cover story.

Radar imaging data from a July 22, 2006, flyby provide convincing evidence for large bodies of liquid on Titan today. A new false-color radar view gives a taste of what Cassini saw. Some highlights of the article follow below.

Here's some happy news for all you warriors against creationism: Mark Isaak's Counter-Creationism Handbook(amzn/b&n/abe/pwll), that wonderfully indispensable and entirely portable version of the Index to Creationist Claims, can now be purchased in paperback for less than $15. It was previously only available in a rather pricey but but extremely well bound edition. Next time you attend a talk by Ken Ham or Duane Gish or any of the common-as-dirt wandering creationists (or Kent Hovind, once they let him out of jail*), you'll want a copy of this with you—teach them to fear the power of well-referenced and clear answers to their crazy objections.

*Say, do you think we ought to take up a collection and buy a copy for the prison library?

Tangled Bank #70


Russian Scopes Trial


Today, the Baltimore Sun has the first detailed news article on Russia’s 21st-century Scopes Monkey Trial. It comes complete with monkeys:

The Shraibers announced their plans for the lawsuit at a March news conference that featured free bananas. In July, when they mailed the paperwork to court, they were accompanied by an actor in a monkey suit - a stunt since dubbed “stupid” by Romanov, who asked that the monkey not come near him.

It’s a new year, and it will be a busy one here in Iowa when it comes to evolutionary biology. I want to highlight two upcoming events: Iowa City’s first annual Darwin Day celebration featuring a lecture by Massimo Pigliucci, and an upcoming symposium on evolution and intelligent design, featuring John Haught and Wesley Elsberry. These events will be held in February and March, respectively; more information on both of them can be found over at Aetiology. Hope to see some readers there!

In 1988, Purvis et al proposed an interesting hypothesis about silent mutations:

Purvis IJ, Bettany AJ, Santiago TC, Coggins JR, Duncan K, Eason R, Brown AJ. The efficiency of folding of some proteins is increased by controlled rates of translation in vivo. A hypothesis. J Mol Biol. 1987 Jan 20;193(2):413-7.

We propose that the way in which some proteins fold is affected by the rates at which regions of their polypeptide chains are translated in vivo. Furthermore, we suggest that their gene sequences have evolved to control the rate of translational elongation such that the synthesis of defined portions of their polypeptide chains is separated temporally. We stress that many proteins are capable of folding efficiently into their native conformations without the help of differential translation rates. For these proteins the amino acid sequence does indeed contain all the information needed for the polypeptide chain to fold correctly (even in vitro, after denaturation). However, other proteins clearly do not fold efficiently into their native conformation in vitro. We argue that the efficiency of folding of these problematic proteins in vivo may be improved by controlled synthesis of the nascent polypeptide.

The Sternberg saga continues, spurred by this podcast by the DI’s Rob Crowther. They’re still flogging this silly claim that the NCSE was “spying on” Sternberg; in fact, all they were doing was trying to find out whether he was in league with Meyer and the DI to surreptitiously get Meyer’s substandard and inappropriate article published (and of course, the evidence clearly suggests exactly that). I love the way they’re spinning this - it’s “spying” to do the same sorts of google searches that, I’m sure, DI employees do every single day. They use that word “spying” quite intentionally, of course; it evokes just the right sinister image of men lurking in the shadows and planting bugs in your house.

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

Richard Dawkins gave an excellent lecture at the Kansas University's Hall Center for the Humanities on October 1 2006, discussing "The God Delusion". The full video can be watched at this link/ Since Dawkins is such an excellent communicator, I intend to provide some highlights of his talk on PandasThumb. Dawkins explains how creationists seem to be fond on gaps and take any opportunity to point to scientists admitting to such gaps. However, as Dawkins explained elsewhere as well, creationists seem to be fond of quote mining as well, even if it requires removing much of the argument.
I once introduced a chapter on the so-called Cambrian Explosion with the words: "It is as though the fossils were planted there without any evolutionary history." Again, this was a rhetorical overture, intended to whet the reader's appetite for the explanation. Inevitably, my remark was gleefully quoted out of context. Creationists adore "gaps" in the fossil record.

The declining scientific content expressed by the National Park Service has been an issue for years; the latest complaints (that I wrote about, and that Wesley Elsberry has now brought up) are just recent flareups of awareness. The National Park Service seems determined to strip out anything intellectually challenging from the experiences in their parks — the ideal seems to be Chevy Chase's reaction from the movie Vacation (if you don't know what I mean, here's a short homage). Pete Dunkelberg has brought a letter in Science from 28 October 2005 to my attention — it accuses the Park Service of dumbing down the interpretive material and turning it into a purely aesthetic experience.

Continue reading "Science and the National Park Service: a festering problem" (on Pharyngula)

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