Michael Behe’s got a new book out, and both Michael Ruse and Ken Miller were underwhelmed, to put it mildly. * In fact, one gets the impression that they not only found Behe unpersuasive, but when comparing Behe's latest with an earlier work, "Darwin’s Black Box", they were distinctly disappointed. Perhaps it’s because Behe pretty much abandons the argument for which he’s best-known ("irreducible complexity", or IC) and, instead, has essentially gone backwards, reviving bogus probability arguments after the fashion of Fred Hoyle.

Why has this happened? Perhaps it’s because Behe was embarrassed by the evidence presented in the Dover trial by folk like Dr. Miller, who memorably demonstrated how Behe's favorite alleged example of IC (the bacterial flagellum) could've evolved from different arrangements of protein with different functions. Perhaps it was because, under oath, Behe was presented with a large pile of publications that covered the general topic of molecular evolution, literature that "Darwin's Black Box" attempted to suggest did not exist.

Or, more poignantly, perhaps it is because there is something like a revolution underway in comparative genomics which is providing, as Sean Carroll has phrased it, forensic evidence for molecular evolution. Here’s a particularly good example of the kind of thing that gives Michael Behe and the rest of the folks hollering ‘irreducible complexity’ fits: a highly-detailed and through account of the putative evolutionary relationships of a particular family of proteins, the globins.

The study in question ("A phylogenomic profile of globins", by Vinograd, et. al,) appears on-line and compares 330 different prokaryote and eukaryote genomes. The massive bibliography takes up nearly eight full pages and contains 147 citations. At the end of the study, there are several graphic displays of the data relationships, including a very neat and easy-to-follow Venn diagram on page 31. The broadest conclusion of the study is that there is a clear pattern of molecular evolution within this family of proteins, which in the prokaryotic genomes are neither as widely-distributed nor share the same functions as in eukaryotes. More specifically, the results support the claim that (quoting from page 3) "since the hemoglobins in organisms other than animals are enzymes or sensors, it is likely that the evolution of an oxygen transport function accompanied the emergence of multicellular animals."

I think an objective observer would be forced to conclude that Dr. Behe’s claim that there "has never been a meeting, or a book, or a paper on details of the evolution of complex biochemical systems" (Darwin’s Black Box, pg. 179) is manifestly false, and it can be expected that even more detailed accounts of molecular evolution are probably just around the corner. The more detail provided by observations, the less inference required, to the point where the whole complexity objection becomes irrelevant.
Has 'irreducibly complexity' become irrelevant? Darwin knew nothing about the bacterial flagellum, much less molecular evolution, but he surely would've recognized the general form of Behe's argument. Darwin observed, "If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case."
And, indeed, when Dr. Behe first looked at things like molecular cascades and the flagellum he may have persuaded himself that he had discovered such cases, things which to his rather limited understanding of biology seemed complex, and irreducibly so. Suggestively, Behe's new book essentially abandons this tack, as if he no longer has confidence in the specifics of his pet examples. The irreducibility of no structure, no protein, no process seems demonstrable. With Darwin, we can find no such case.

Behe, M. Darwin's Black Box: The Biochemical Challenge to Evolution. Free Press. New York. 1996.

Behe, M. The Edge of Evolution: The Search for the Limits of Darwinism. Free Press. New York. 2007.

Carroll, S. "God As Genetic Engineer." Science, Vol. 316. no. 5830, pp. 1427 - 1428. June 8, 2007.

Carroll, S. The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution. W.W. Norton. New York. 2006.

Darwin, C. On the origin of species by means of natural selection, or, The preservation of favoured races in the struggle for life. London: John Murray, 1859.

Kitzmiller v. Dover Area School District. Trial transcript: Day 12 (October 19), PM Session, Pt. 1 URL: http://www.talkorigins.org/faqs/dover/day12pm.html

Miller, K. "The Flagellum Unspun: The Collapse of "Irreducible Complexity". 2002. URL: http://www.millerandlevine.com/km/evol/design2/article.html

Miller, K. "Falling Over The Edge." Nature 447, pg. 1055 - 1056, June 27 2007.

Ruse, M. "Design? Maybe. Intelligent? We have our doubts." The Globe and Mail. June 2, 2007.

Vinograd, et al. "A phylogenomic profile of globins", in BMC Evolutionary Biology, Vol. 6, No. 31, April 7, 2007. URL: http://www.biomedcentral.com/1471-2148/6/31/abstract

(* = regrettably, as Ruse and Miller's reviews are up-to-the-minute, they aren't free. A quick gloss of Ruse's review is available here, however, along with similar reviews from Sean Carroll and Jerry Coyne. Miller's review is summarized here. )



OK, I admit it, I'm a fan boy for all things Potter. I live in the Potterverse, and I'm excited. For those of you who share my enthusiams, here's the drill:aMuggleNet reports that a German site has a very large number of clips of the upcoming Harry Potter movie available to view here. Devoted fans who have already read the books should decide for themselves whether or not viewing these clips (in German) will spoil the film. Myself, I left the sound off and drooled over the visuals, often wondering exactly what I was seeing. You've been warned. Don't look, if you don't want to know anything in advance!



As mentioned before, here's a fair question or two for any skeptics/atheists who will be in the Fresno area in the month of July (when, would you believe, it gets kinda hot)....

  1. How can you go to hell when you're already there?
  2. Have you considered attending a Meetup of the 'Fresno Atheists'?

Yes, Virginia---while there may not be a Santa Claus (heretics!), there is, in fact, such a group. And you know what? I've been known to pop in and get my two cents in. I like the group regulars and they do a fine job of making me feel welcome. And we get to drink BEER. And eat PIZZA. I know some of y'all don't believe in the hereafter, but really, doesn't this sound like a slice of heaven? Here's the details:

When? Thursday, July 5, 2007, 7:00 PM
Where? Round Table Pizza*

*(5763 N. First Street Fresno, CA 93710 (559) 449-7676)

For more details, check out this page. There's a map, and a link to Mark, the Meetup organizer.


Quick! Who is the closest thing to a celebrity produced by my alma mater, Desert High School ("The Fighting Scorpions")?
If you attended the school between 1977-1982 you are likely to know the answer to this question. If you don't know the answer, then pay attention: I'd like to introduce you to Cynthia Ettinger.

She's prolific, as her IMDB entry shows. Her most recent major splash was a regular character on HBO's spooky 'Carnivale' series. Less well-known is the critical acclaim she has received for her work on the stage as a member of the legendary 'Actor's Gang' troupe founded in 1981 by a then-unknown Tim Robbins and colleagues from the UCLA Theatre Department. She won rave reviews for her performance as serial killer Jolene Palmer in the Carson Kreitzer play 'Self Defense'. I could go on and on, really.

Yet, for all that, the greatest number of links you'll find to Cyndy's work on the Internet is the fact that she played the role of Martha Kent on the pilot for "Smallville", only to be replaced at the last moment by a name actress, Annette O'Toole. Such is the power, I suppose, of geekdom and sci-fi conventions. Here's hoping that at some point someone will realize that my old high school sparring partner (we battled our way through various theatrical productions) will be recognized for what she is: a singularly gifted artist of the first rank.


What to do if you're a skeptic by temperament, but the popular culture prefers 'conversion narratives' that move from skepticism to belief, rather than the other way around? PZ has a good discussion of that here. Bronze Dog chimes in with a novel scenario here. The initial thread was inspired by an observation by science journalist Chris Mooney. Me? I think it has to do with a real clash between the expectations of narrative structure held in the popular culture and the nature of skepticism.

The problem with a skeptical/debunking sort of outcome in a drama is one of sympathy. People have to care about the characters in order to become emotionally invested in a drama, and contemporary audiences are unlikely to care about people that they perceive as foolish or tragic, Shakespeare be damned. There is a marked preference for characters who may be human, may be fallible, but predictably have some degree of growth, some triumph over their circumstances and their weaknesses.

Now, if you have a protagonist who believes 'X', and belief in 'X' is the substance of the drama, then the failure of 'X' to be sustained could only make the protagonist a foolish or tragic figure. If, on the other hand, the antagonist is the one promoting 'X', then the protagonist can be heroic at the expense of the antagonist (and hence, toward the debunking of 'X'). But once you switch the promotion/debunking of 'X' from protagonist to antagonist the moral question of conversion, of what to believe, no longer becomes the central point of the drama. The audience just knows, somehow, that the protagonist will end up being right, despite the evidence, and the drama lies not in whether they will be vindicated, but in how vindication will be achieved.

An exception to this was the Ridley Scott film "Matchstick Men". In this film, Nicholas Cage's character is a con man with an obsessive-compulsive disorder who ends up being conned himself on a grand scale. He does, indeed, end up not believing in 'X' when we were led to believe 'X' is true. Despite the considerable charm shown by Cage, he 's not that sympathetic a character. Much is made of the fact that his typical 'mark' is unpleasant and driven by greed, as if this makes him somehow more sympathetic. In the end, the 'hero' achieves his vindication by adopting a conventional (and honest) life. The film ends not with Cage's character out-conning those who conned him (which would've been more of a crowd-pleaser) but by rejecting the life of illusion and his mastery thereof.

I admire films that try to do something different, but in the ending really is something of a whimper, rather than a bang. Even if I rolled it around in my mind and pronounced it somehow satisfying, I think one would have to admit this kind of resolution is rare. I also suspect that, in this case, it would help if one is a Scientologist....SH


I'm still something of a newbie to this blogging thing, but one of the most fascinating (and irascible) characters I've come across is this fellow Caledonian: terse, tart and contrarian, he has a positive gift for bon mots, often mixed with invective.

( The link on his name gives you a taste, starting around post #11. )

He often says things that are stark and unsparing not just of other's feelings,but against any and all sentimentality or accomodation to what is fashionable or commonly-accepted. That strikes me as valuable and useful. Problem: rather than explaining his views in full, he often acts as if his (minority) views are self-evident, and that the (majority) which can't seem to realize it are idiots. That's not a helpful stance, even if it's true! I recently sent him the following message over at Pharyngula:

"You invite misunderstanding by choosing name-calling and insult over explication. I'm going to make you the same offer I made you before, which is that I would love to read a synopsis of your views. Where, for example, do you think (Ayn) Rand got it right? Where did she get it wrong? I'd love to hear it. I have no agenda, other than an honest desire to understand your point of view.

So, tell you what, I'm going to create a thread on my blog just for that purpose. It'll be your show, old Scot. This is a friendly challenge to put up or shut up. Some people confuse my measured tone with insincerity or lack of resolve. You should be sufficiently perceptive to realize otherwise at this point! Hoping to hear from you!"

So, here it is, as promised. I'm hoping that he will grace me with his presence here....in a substantial way. If otherwise, then those of you who haven't had the pleasure will get an inkling of what I've been talking about!



(This is the first in a series of net-based resources that I intend to make available to my students, fellow travelers and other members of the general public, summarizing my views on evolutionary biology.)

Slightly more than two hundred years ago, there was general agreement among both theologians and philosophers that the best explanation for the diversity and complexity of life was the direct action of a Creator. To put it another way, the existence of Design in Nature was accepted as evidence for the action, and therefore the existence, of a Designer. Echoes of this line of reasoning can be found in scripture, as when the Psalmist remarks, "I am fearfully and wonderfully made." (Ps. 139:14)

The classic expression of this argument was given by William Paley, who observed that if he tripped upon a stone while hiking through the countryside, he would not be all that concerned about how the stone got there: for all he knew, he might have been there forever. But then Paley adds: "...suppose I had found a watch upon the ground, and it should be inquired how the watch happened to be in that place; I should hardly think of the answer I had before given, that for anything I knew, the watch might have always been there." (Paley, 1802)

Paley goes on to explain that the watch, with all of its myriad parts working together to keep time, is evidence of a Watchmaker. Since living things are arguably even more complex than watches, Paley concludes, they must have had a Maker of their own: God.

Interestingly enough, Paley’s works were required reading at Cambridge during the 1830's for those who, like Darwin, were studying for the priesthood. Charles Darwin would’ve not only known Paley’s argument very well, but if his letters are any judge, he almost certainly accepted them as a young man. (Darwin, 1996). How ironic, then, that the course of Darwin’s thought would lead most scholars today to place far less confidence in, or to even reject, the argument from Design. (Dawkins, 1996)

ID: The Design Argument Revived

Since the early 1990's, proponents of ‘intelligent design’, or ID, have revived a version of Paley’s old argument as part of an attempt to mount a critique of evolutionary biology that was not openly religious in origin or intent. The ‘ID movement’ was inspired by the writings of a law professor (Philip Johnson) who argued that science as practiced today was unfairly biased against design arguments, and that much of evolutionary biology was not so much science as it was a metaphysical system that he preferred to label ‘Darwinism’. (Johnson, 1991)

Johnson’s reasoning persuaded a number of scholars, mostly evangelical Christians, to form a Seattle-based ‘think tank’ known as the Discovery Institute (DI) whose goal was not merely to reform scientific practice, but to transform society by affirming "the reality of God by challenging the domination of materialism and naturalism in the world of the mind." (Johnson, 1997) In short, another version of the ‘culture war’. Johnson’s strategy, and a specific agenda to achieve those goals, were privately circulated in a 1998 document known as ‘The Wedge" (Discovery Institute, 1998). This document, which revealed the sectarian origins of its founders, would come back to haunt the DI once its particulars became generally known.

The first stage of Johnson’s ‘Wedge strategy’ involved raising consciousness in the public as to what he and others regarded as the defects of ‘Darwinism’. Toward that end, those associated with the DI have produced a large number of publications. Some developed propaganda aimed at undermining public confidence in high school science curriculum through allegations of bias and impropriety (Wells, 2000). Others claimed to have inferred previously-ignored evidence for design in biological structures (Behe, 1998) or attempted to repackage probability arguments (Dembski, 1999) as evidence that such structures could not have been produced without a Designer. Much of these publications were not peer-reviewed and of those that were, none produced any original scientific research bearing on their claims.

In recent years, the ‘ID movement’ has seen much of its momentum halted when it was on the losing side of a heavily-publicized Pennsylvania court case (Kitzmiller vs. Dover) in which the plaintiffs were able to show that an attempt by a local school board to require ID in the high school curriculum amounted to pushing creationism, which previous court rulings had held constituted an attempt to privilege sectarian religious views. The judge in the case, a conservative Republican appointed by President Bush, was highly critical of the deceitful conduct of the board members, two of which obviously lied under oath in an attempt to counter past misconduct. (Jones, 2005)

Why Are Evolutionary Biologists Unpersuaded By This New Version of the 'Design Argument' ?

Simply put, the Design Argument can not be tested. God’s creative power does not appear to manifest itself in a predictable way that can detected on a lab bench, a field survey or a computer analysis. Whereas, specific predictions based upon evolutionary mechanisms are routinely tested and often found to provide an extremely good fit to the data. Evolution is a fact, natural selection is a fact, and the inference that evolution by natural selection is sufficient to explain a wide variety of features in a number of different fields of study. As Pope John Paul II has written: "The convergence, neither sought nor fabricated, of the results of work that was conducted independently is in itself a significant argument in favor of this theory." (Wojtyla, 1996)

Behe, M. Darwin’s Black Box: The Biochemical Challenge to Evolution. Free Press. New York, 1998.

Darwin, C. Charles Darwin’s Letters: A Selection, 1825-1859. Ed. F. Burkhardt. Cambridge University Press, Cambridge 1996.

Dawkins, R. The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe Without Design. W.W. Norton. New York, 1996.

Dembski, W. Intelligent Design: The Bridge Between Science and Theology. Intervarsity Press. Nashville, 1999.

Discovery Institute "The Wedge Document" 1998.

Johnson, P. Darwin On Trial. Intervarsity Press. Nashville, 1991.

Johnson, P. Defeating Darwinism by Opening Minds. Intervarsity Press. Nashville, 1997.

Jones, J. Kitzmiller, et. al. vs. Dover School District, et. al. Memorandum Opinion: Dec. 20th, 2005.

Paley, W. Natural Theology (Oxford World’s Classics) Reprint of 1802 edition, ed. M. Eddy and D. Knight. Oxford University Press, 2006.

Wells, J. Icons of Evolution: Science or Myth? Why Much of What We Teach About Evolution is Wrong.
Regnery Publishing. New York, 2000.

Wojtyla, K. Truth Can Not Contradict Truth. October 22, 1996 Address of Pope John Paul II to the Pontifical Academy of Sciences, October 22, 1996. URL: http://www.fjac.org/truth.pdf


Truth is stranger than fiction. More than two months ago, I was approached by strangers who wanted to know what I thought about Santiago Wood, the former Fresno Unified superintendent. Seems that one of them was doing some fact-checking for a school board in Florida considering employing Wood as a super, while another was a representative of the teacher's union there.

"Long on style, short on substance," I told them, or words to that effect. "He's a demagogue, rhetorically-skilled, who will promise the moon in terms of achievement but will spend most of his time hard-balling teachers on the contract in an attempt to break the will of the union. Under his leadership, the financial records of the districts will be selectively presented to the media to make it look as if the district is facing financial ruin. Calls for an independent audit and a full disclosure of the district's finances will be ignored. Demands will be made, and if the union doesn't cave to his demands immediately, administration will hold treasured programs like athletics and music hostage even while the district allegedly sits on millions of dollars well above the statutory-required reserves. Don't trust him, he failed here."

Despite my candid assessment, as of this writing, Dr. Wood is still a candidate with that school district. Weird!

Even weirder, however, is The Strange Saga of the former Commissioner of Education for the great state of Minnesota, Dr. Cheryl Yecke. Yecker rather disgracefully attempted to implement 'equal time' rules for the teaching of ID (a form of creationism) in Minnesota public schools a few years back over the recommendation of teachers and scientists. Not only was this proposal publicly shot down, she was removed from her post by the Minnesota State Senate. Yecke then briefly flirted with a run for Congress before accepting a job in Florida at the behest of Governor Jed Bush.

Apparently not satisfied with native Floridians, the Sunshine State is now intrigued by the potential of Dr. Yecke to serve as their state's Commissioner of Education. Dr. Yecke is apparently so keen to obtain this hallowed post that she has engaged a legal firm to harass prominent critics on the Internet with threats of legal action.

Hmmphf. Substituing rhetoric and blind faith for evidence, style for substance, a failed carpetbagger from another state for a Florida educator. Sounds eerily familar.


The Fresno Bee has seen fit to print my letter of protest regarding the subtext of the testimony of the Lindy Vivas trial which I posted about earlier. Good for them, and good (I hope) for the community.

Now, the next question is: what do you think the 'under/over' should be on the likelihood of any backlash, either in the Bee or in these gentle pages? I invite oddsmakers to leave comments!



PZ has a nice brief on R. Albert Mohler (President of the Southern Baptist Convention), who has decided to issue an alarm about the possibility that a mouse might come up to one of us and ask us for a cookie.

Please, no Cartoon Network jokes. That's way too easy.

Think about it: the head of the SBC (the largest Protestant denomination in North America) pretty much acknowledges the possibility that scientific tinkering could blur the distinction between, say, a man and a mouse.

Now, that is light years from the comfortable assumption, after Plato, that the Biblical 'kinds' (baramin) represent fixed, inviolable categories of being. Mayr has memorably described this misplaced conception as 'essentialism' and claimed that one of Darwin's most brilliant moves was to think in terms of populations of organisms, rather than 'kinds' or essential categories of organisms.

Dr. Mohler declines to engage on those terms, but instead seems to be fighting a delaying action, and I fully expect someone with Ken Ham's convictions to eventually figure out that Mohler is giving away the farm, and criticize him for it.

This is highly reminescent of Mohler's preemptive strike on the possible biological basis of homosexuality. Mohler essentially concedes that scientific research has undermined the claim that either homosexuality or non-human (but human-like) sapience is 'unnatural' or 'impossible', then flails about for some other argument, not yet contravened by evidence, that would still lead to the same conduct, the same outcomes, for the sheep in his flock. Never mind that there's no straw, you still have to make the same amount of bricks, slaves. I would be very interested to learn what John Wilkins thinks about all this!


Who wants a milquetoast managing their fantasy baseball team? Not this GM. So, without further adieu, I'd like to introduce the fiery, outspoken and decidedly godless manager of my club, the Darwin Finches, my BARB franchise.
I'd give him a lifetime contract with the organization if I wasn't worried about his eternal soul, being associated with me and all. Besides, PZ may not play so well in Peorioa. He's a bit on the irascible side: just imagine how hard it was for me to get this deceptively-cherubic expression under a baseball cap. I'm afraid the Devil Rays were as close as I could get to a cephalopod, too.



Here's a fair question or two for any skeptics/atheists who will be in the Fresno area in the month of July (when, would you believe, it gets kinda hot)....

  1. How can you go to hell when you're already there?
  2. Have you considered attending a Meetup of the 'Fresno Atheists'?

Yes, Virginia---while there may not be a Santa Claus (heretics!), there is, in fact, such a group. And you know what? I've been known to pop in and get my two cents in. I like the group regulars and they do a fine job of making me feel welcome. And we get to drink BEER. And eat PIZZA. I know some of y'all don't believe in the hereafter, but really, doesn't this sound like a slice of heaven? Here's the details:

Thursday, Jul 5, 2007, 7:00 PM

Round Table Pizza
5763 N. First Street
Fresno, CA 93710
(559) 449-7676

For more details, check out this page. There's a map, and a link to Mark, the Meetup organizer.


An earlier post took an anonymous Fresno-area pastor (highly influential) to task for undermining science education. In the comments section, a rather more distinguished colleague of mine suggested that perhaps I should've identified the fellow. I responded that I was felt conflicted on that point---but perhaps I am mistaken.

I would love to hear what others think on this matter. Since I am likely to go on future commando missions into the pews, I'm likely to encounter a similar situation. When should the errant believer be publicly 'outed' for anti-science rhetoric, and when (if ever) should they be privately counseled? How to judge when they are ignorant, as opposed to deliberately deceptive. Finally, as a believer, should I give fellow believers the 'benefit of the doubt' at any point----and if so, when?