June 4, 2006 - June 10, 2006 Archives

Sometimes serendipity presents you with an opportunity to educate those who are confused by the claims of Intelligent Design and somewhat unfamiliar with evolutionary theory. So let me start with the answer and then look at the question.

Genetic Programming (GP) has a proven capability to routinely evolve software that provides a solution function for the specified problem. Prior work in this area has been based upon the use of relatively small sets of pre-defined operators and terminals germane to the problem domain. This paper reports on GP experiments involving a large set of general purpose operators and terminals. Specifically, a microprocessor architecture with 660 instructions and 255 bytes of memory provides the operators and terminals for a GP environment. Using this environment, GP is applied to the beginning programmer problem of generating a desired string output, e.g., “Hello World”. Results are presented on: the feasibility of using this large operator set and architectural representation; and, the computations required to breed string outputting programs vs. the size of the string and the GP parameters employed.

Genetic Evolution of Machine Language Software Ronald L. Crepeau NCCOSC RDTE Division San Diego, CA 92152-5000 July 1995

The Results?

From Figure 5 it can be seen that this run achieved a correct output (fitness = 352) at about 150,000 spawnings (100 to 1200 generations). By about 450,000 spawnings, the agent was composed of less than 100 instructions. Ultimately, the agent size reduced to 58 instructions before the process was terminated.

Next question?

Nick in New Mexico

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We in New Mexico are honored to have PT’s own Nick Matzke as our guest this weekend.

Nick was in-studio on the NMSR Science Watch radio show today, and gave a gripping rundown of the Dover ID Trial from the inside… matzke.jpg KABQ 1350 AM Board Op Lindsey sets levels for Nick on the Science Watch radio show (Sat 10th)

AND, Nick is giving a FREE SPEECH tomorrow (Sunday, June 11th) at UNM’s Anthropology lecture hall.


It’s sponsored by CESE.

Singer and teleology

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Dembski argues, without supporting evidence, that when the natural processes of chance and regularity have been eliminated, that which remains should be called ‘Intelligent Design’. This definition presumes that ‘Intelligent Design’ is not reducible to natural processes, leading to the inevitable conclusion that Intelligent Design is about the supernatural.

In the early 20th century, Edgar Singer presented his thesis on mechanism and teleology. Krikorian read the following paper during the 1955 memorial meeting for Edgar A. Singer, Jr., at the University of Pennsylvania.

Since living beings are defined in terms of teleology, the laws that apply to them can be called teleological laws. These laws, as earlier noted, are statements of averages. It is because the laws are of this character that we may describe the behavior of living beings in terms of chance, spontaneity, and variability, and in some cases even of freedom.

Since behavioral sciences captures the behavior of intelligent, living beings in teleological laws which are expressed as a ‘law of averages’ or in other words, expected behavior, combined with chance, variability and spontaneity. Or to use Dembski’s terminology: reducible to regularity and chance. In fact, advertising, Amazon’s suggestions, all are based on predictable characteristics of intelligent life. In other words, the claim that intelligent design cannot be reduced to regularity and chance seems to go against common sense knowledge.

I wrote recently how evolution and phylogenetic analysis of HIV isolates has provided evidence that the progenitor to HIV jumped into humans in Cameroon or a nearby area. Obviously it’s a topic that’s interesting to me, but may seem a bit esoteric to some. RPM over at Evolgen has a new post showing another application of phylogenetic analysis to HIV that may be of interest to readers here, where infectious disease epidemiology meets CSI.

As I reported awhile ago, the Discovery Institute’s attempts to add “critical analysis” language to the parts of the South Carolina biology curriculum that deal with evolution have failed. The Board of Education did not add those changes, and the Educational Oversight Committee, led by creationist Sen. Mike Fair, finally conceded on that front and decided to accept the standards without the creationist language. Fair and his ally Bob Walker, who is a representative in the lower house, are apparently banking on a budget proviso requiring all textbooks adopted by the state to contain no less than 10% material be given up to 10% weighting for the promotion of “higher-order thinking skills”. In the Bizarro world inhabited by the Discovery Institute, where words mean the precise opposite of what they normally mean, this apparently implies creationism. Walker tried to get the House Education and Public Works committee to add an amendment to a bill to codify this somewhere other than in an obscure budget proviso, but that attempt failed miserably.

So that’s where things stand. But remember: The Discovery Institute exists on Planet Bizarro. In their world, things are the opposite of what they seem:

South Carolina Set to Join Four Other States Calling for Critical Analysis of Evolution.

Columbia, SC – The South Carolina Education Oversight Committee (EOC) will vote Monday, June 12, on whether to give final approval to science standards for biology that require students to summarize how scientists “investigate and critically analyze aspects of evolutionary theory.” The standards were approved unanimously by the South Carolina Board of Education on May 31. Four other states (Minnesota, Pennsylvania, Kansas, and New Mexico) already have science education standards encouraging critical analysis of evolution.

Back here on Planet Earth, the Board of Education did not add the “critical analysis” language to the curriculum standards, and the EOC cannot accept standards containing that language without the Board of Education adding them first. But when declaring victory, why let a little thing like defeat get in your way?

Edited to add: It was brought to my attention that the science curriculum does actually contain one sentence about “critical analysis” that was added a year ago, so the DI press release isn’t technically untrue. It is, however, grossly misleading in that the changes they lobbied for all throughout the first half of this year, which included adding “critical analysis” language to each and every indicator dealing with evolution, were rejected. It was these changes, not the one from last year, that created the impasse between the EOC and BOE. The EOC’s June 12th vote is noteworthy in that it will end this impasse with the Discovery Institute failing to get the changes they wanted.

While Intelligent Design remains unable to explain much of anything in science, evolution has identified another mechanism. PZ Myer already discussed this example of Genetic Accommodation and I would like to use this as another example of the scientific relevancy of evolutionary science versus the scientific vacuity of Intelligent Design.

PZ Myers Wrote:

Here’s some very cool news: scientists have directly observed the evolution of a complex, polygenic, polyphenic trait by genetic assimilation and accommodation in the laboratory. This is important, because it is simultaneously yet another demonstration of the fact of evolution, and an exploration of mechanisms of evolution—showing that evolution is more sophisticated than changes in the coding sequences of individual genes spreading through a population, but is also a consequence of the accumulation of masked variation, synergistic interactions between different alleles and the environment, and perhaps most importantly, changes in gene regulation.

The schedule for the special symposium on “Intelligent Design on Trial: Lessons from the Kitzmiller v. Dover creationism case,” on Monday, June 26, 2006 at the Society for the Study of Evolution meeting at SUNY-Stony Brook has been updated (see below).

Further update: Rob Pennock informs me that the symposium will be videotaped, with the intention of putting it on the internet after the meeting.

In other news, although some helpful suggestions have been made, I am still seeking housing for June 24-27, since I was invited only after dorm housing had closed. Like I said, I’ll pay my share and bring a sleeping pad or something. Surely there is a penniless grad student out there somewhere. Email me: matzkeATncseweb.org. (Update: found housing and received several kind offers. Thanks very much.)

Also, I just noticed that in just one day PT became the top google hit for “SSE 2006”, while the actual meeting website is ranked #6.

Tangled Bank #54


Remember the “we’re-creationists-and-proud-of-it” creationists? Well, despite the press that ID has been getting, the older sort are still around. Today, they’re discussing not the beginning of the universe, but the end. Evidently they don’t like “dark matter” and “dark energy”, explanations that astrophysicists have proposed to explain certain puzzling phenomenon like the fact that galaxies spin faster than the gravity from their observed stars seems to allow.

Now, I think it is perfectly reasonable to criticize these explanations on their merits – it is conceivable, for example, that dark matter doesn’t exist and that instead we need some new physics to describe gravity at the very coarse scale – see for example the latest on MOND (Modified Newtonian Dynamics) in New Scientist (plain text). And the answer to this question could impact our view of the eventual fate of the Universe – i.e., will we get a “Big Crunch” or not?

But I think the creationist solution to the problem leaves something to be desired:

Evolutionists accuse creationists of inventing a “God of the Gaps” to cover for their ignorance of true science. It would appear that the high priests of astrophysics have their own Gods of the Gaps, namely dark matter and dark energy. What will happen to the universe? It won’t be the Big Crunch or the Big Chill, but the Big Furnace: “But the day of the Lord will come like a thief, in which the heavens will pass away with a roar and the elements will be destroyed with intense heat, and the earth and its works will be burned up. Since all these things are to be destroyed in this way, what sort of people ought you to be in holy conduct and godliness, looking for and hastening the coming of the day of God, because of which the heavens will be destroyed by burning, and the elements will melt with intense heat! But according to His promise we are looking for new heavens and a new earth, in which righteousness dwells” (2 Peter 3:10-13).

Astrophysics, schmastrophysics!

The summer 2006 edition of Stanford Medical Magazine has devoted their issue to “The evolutionary war.” Being the alumni magazine of a medical school, of course they have an article on “Darwin in medical school.” It’s a nice overview, discussing a bit of the history of “Darwinian medicine” and the pros and cons of teaching it in an already over-scheduled medical school curriculum.

(Continued at Aetiology)

The mighty Kent Hovind has struck out.

On June 5th 2006, Hovind pled nolo contendere as charged to three counts: constructing a building without a permit, refusing to sign a citation and violating the county building code. Hovind was ordered to pay $225.00 per count. The plea brings to an end a 5-year battle over a $50.00 building permit. Hovind estimates he spent $40,000 in legal expenses on this case. Meanwhile, the property taxes for Dinosaur Adventure Land are in arrears in an amount of $10,338.36 ($4,955.23 for 2005 and 5,383.13 for 2003 and 2004).

In both criminal and civil trials in the United States, a plea of "nolo contendere" means that the defendant neither admits nor disputes the charge or no contest. It literally means "I do not wish to contend." Spiro Agnew famously approximated it as "I didn't do it, but I'll never do it again." This plea is only recognised in the U.S. No formal plea is required in civil matters where paper pleadings are used.

We’ve got a sudden rash of ID activity here in Michigan. The MCFS board got word yesterday that the House Education Committee in Michigan was going to hold a hearing this morning on HB 5251, a bill that would require the teaching of all the major ID arguments in public school science classes. We had thought this bill was dead in light of HB 5606, which was signed into law in April. But the pro-ID language had been taken out of that bill, so the sponsors of 5251 have revived it.

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

In Is Intelligent Design Testable: A response to Eugenie Scott Dembski tries to defend ID against the observation that ID does not present any testable hypotheses. Eugenie Scott responded to Dembski in The Big Tent and the Camel’s Nose

Eugenie Scott Wrote:

In my talk, I wasn’t deploring the untestability of ID per se but the fact that its proponents don’t present testable models. I was referring to the fact that ID proponents don’t present a model at allin the sense of saying what happened when. At least YEC presents a view of “what happens”: the universe appeared within thousands of years ago, at one time, in its present form, living things are descended from specially created “kinds” from which they have not varied except in trivial ways, there was a universal flood that produced the modern geological features, and humans are specially created apart from all other forms. So what happened in the ID model?

If ID is interested in ‘teaching the controversy’ and informing students about good science, then why is it that ID activists have so far refused to take much of any stance on the ‘scientific’ claims by the young earth creationists?

Eugenie ends with the following observation and question

SSE 2006 meeting

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Update: just see the newer post for the revised schedule. (Update: I have added the info on the keynote speakers for June 26, and we are going to try and get the event recorded.) Alrighty, who is coming to the 2006 meeting of the Society for the Study of Evolution (SSE), the Society of Systematic Biologists (SSB), and the American Society of Naturalists (ASN), aka SSE 2006, aka Evolution 2006 at SUNY Stony Brook?

Well, it looks like I am going (Note: I may need to bring a sleeping bag and crash on someone’s floor, housing looks fully booked – see my note and contact info) – because someone or other recently realized I ought to be there for this:

Monday, 26 June – Sessions. Symposium title: Intelligent Design on Trial: Lessons from the Kitzmiller v. Dover creationism case. Organizers: Robert T. Pennock, Michigan State University and Brian Alters, McGill University List of Speakers

* Robert T. Pennock , Michigan State University, “The Ground Rules of Science” * Barbara Forrest, Southeastern Louisiana University, “On Being a ‘Hybrid Expert’: Detailing the Intelligent Design ‘Wedge Strategy’ in Federal Court” * John F. Haught, Georgetown University, ŸEvolution and Faith: “What is at Stake?” * Brian Alters, McGill University, “But is it Good Pedagogy?” * Brian Rehm, Kitzmiller Plaintiff & Current Dover School Board member, “From parent and teacher to plaintiff and director” * Kenneth R. Miller, Brown University, “Fossils, Genes, and Mousetraps - The 21st Century Case for Evolution” * Lauri Lebo, Lauri Lebo, Lead Local Reporter in Dover, “Beyond ‘He said, she said:’ How to be fair when the debate isn’t balanced.”

Format: Morning Session: 60 minute slots (45 minute talks / 15 min Q&A). Afternoon Session: (30 min, 60 min, 30 min talks, then 30 min joint Q&A). This will be a full day event.

Monday, June 26, 7:00-8:30 pm – SSE Education Committee Public Outreach Lecture

Speakers: Eric Rothschild & Steve Harvey, Pepper Hamilton LLP. Title: “In Defense of the First Amendment: An Up-Close Look at the Landmark ‘Intelligent Design’ Case of Kitzmiller v. Dover Area School District”

In other words, we’re getting the band back together!

Yesterday (June 5, 2006) Kansas Citizens for Science sent an open letter to the superintendents of Kansas public schools explaining why the current 2005 KBOE standards are seriously flawed, and suggesting that districts adopt the Recommended Standards developed by the science standards writing committee instead. We have asked that each superintendent distribute the letter to the district’s Board members also. I have included the whole letter below: see Recommended Standards on the KCFS News site for related information.

Read more of the story here.

Science versus ID: Message in the sky

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A while ago I discussed the relevance of motive in determining whether or not something may have been designed. A good example of how this can be turned into a scientific concept is given in a paper submitted to Arxiv called “Message in the Sky“:

“It’s a crazy assumption that there’s a supreme being that wants to send us a message,” said Steve Hsu, an associate professor at the University of Oregon, admitting that believing in a message involves a leap of faith. “But, if you could create a universe in your laboratory, wouldn’t you want to leave a message inside?”

(Seed Magazine article)

Remarkably (or perhaps not) this ‘tongue in cheek’ paper has attracted Dembski’s attention. Remember that Dembski is still struggling with how an Intelligent Designer could inject information into our universe with zero energy:

Won for All


Last night, I had to read this book RPM mentioned. It's not very long—about 100 pages, counting a preface, an epilogue, and an afterward, and it has lots of pictures—but be warned: it's very inside baseball.

The book is Won for All: How the Drosophila Genome Was Sequenced(amzn/b&n/abe/pwll) by Michael Ashburner, and its subject is the rush to sequence the Drosophila genome in 1998-1999. It's a rather strange twist on what I expected, though. While the subtitle says "How the Drosophila Genome Was Sequenced," there is almost no science at all in the body of the book; instead, it's all about the people and the politics, with Ashburner flitting about from place to place, yelling at people and eating sushi. It's phenomenally entertaining.

Continue reading "Won for All" (on Pharyngula)

Zachary Moore, who describes himself as “ just an average Scientist-At-Large, specializing in molecular biology” and who “… dabble[s] in many interests, including religion, jeet kune do, the outdoors, cinema, tolkien, sasquatch, and homebrewing beer. “ has an interesting website called Evolution 101 with many excellent podcasts which can be downloaded from freethoughtmedia.com. Check also the transcripts of the shows as Zach’s blogsite

Creationists have considered the ‘mystery’ of the chirality of life a problem inaccessible to scientific explanation. Of course, science as usual takes little notice of claims to ignorance and has provided yet another explanation for the chirality of life.

Point in case, a recent paper in Nature shows that:

Chirality, the molecular version of right- and left-handedness, has intrigued chemists ever since Pasteur found mirror-image tartaric acid crystals. The synthesis of molecules in a single chiral form is usually achieved by using a chiral entity from the outset. But in some reactions the formation of a chiral product seems to be further amplified. Most current explanations implicate autocatalysis as the source of this asymmetry. An alternative mechanism is demonstrated this week. This new approach generates a strong bias towards one chiral form from a small initial imbalance, based on the equilibrium solid–liquid phase behaviour of amino acids. As this takes place in aqueous solution, the process might explain how a prebiotic world, with left- and right-handed molecules present in equal numbers, could turn into a living world where biomolecules favour one chiral form.

Editor’s Summary ‘Chemistry mirrors life’

The paper in question is:

Martin Klussmann, Hiroshi Iwamura, Suju P. Mathew, David H. Wells, Jr Urvish Pandya, Alan Armstrong and Donna G. Blackmond Thermodynamic control of asymmetric amplification in amino acid catalysis Nature 441, 621-623 (1 June 2006)

Based on the work by Dembski, this ‘researcher’ concludes that

So we are left to conclude that homochirality came about by some directed, non-stochastic mechanism

So let’s look at the ‘design inference’ in more detail

The Anti-Defamation League has put up the transcript of a fantastic speech given by Judge Jones back in February. Jones gives his perspective on what it was like to be the judge in the Kitzmiller case, and then uses it as a platform to talk about the larger issues of judicial independence, legal precendent, and separation of powers. It’s quite a read – I don’t think the creationists have yet realized how much they marginalize themselves with kneejerk attacks on a class act like Jones.

It’s always risky business to divine what the founding fathers might think about current developments, but I’m certain, I’m entirely certain, that by deciding the Dover case the way that I did, I performed my duties as a district judge in exactly the way that the founding fathers had in mind when they created the Federal Judiciary in Article III of the Constitution.

In fact, I will submit to you that had I decided the Dover matter in a different way, I would have then engaged in just the kind of judicial activism which critics decry. That is, to have ruled in favor of the School Board in this case based on the facts that I had before me at the conclusion of the trial, I would have had to have overlooked precedents entirely and thus impressed upon the facts of the case my sense or the sense of the public concerning what the law should be, and not what it is.

This is ad hoc justice based upon either my preferences or biases or the perceived will of the majority. Taken to its extreme, it is anarchy at any level that to rule in such a fashion represents the true work of an activist judge. And so the real criticism of my decision, and this is one which I will readily accept, is that I did not render an activist decision.

See also the NCSE news story summarizing other recent news coverage on Jones.

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