July 2, 2006 - July 8, 2006 Archives

Here follows the guts of my new C++ program for solving Steiner Tree problems with a Genetic Algorithm.

I have eliminated much of the Microsoft Foundation Class support code, focusing mainly on the number-crunching routines. I will be happy to share the complete code with interested parties.

The original FORTRAN version from five years ago is still online at NMSR.

You’ll see that I’ve cleaned up and organized everything quite a bit, and completely re-done the snippet which checks for properly connected solutions.

Dave August 21st, 2006

A couple weeks ago, William Dembski posted an anonymous “edited report” of a talk Ken Miller gave at Texas Tech in March. The “edited report” suggests that Miller should be considered an ID supporter. The only problem is that the “edited report” completely fabricates the question and answer it uses to make its point. Ken Miller has posted a response on his website.

Read Texas Tech – The Real Answer.

Did you ever wonder what was behind that weird amicus brief that a Hindu group filed (with ID advocate Edward Sisson’s help) in support of the evolution warning label sticker in Selman v. Cobb County? You remember, the one that ended by citing a Supreme Court decision, only the Supreme Court in question was the Supreme Court of India? Well, you’re in luck, because I just came across an article by Meera Nanda on Vedic creationists and the alliance they’ve formed with the more traditional conservative evangelical creationists here the U.S. I’d pay good money to see these two groups in the same room with Harun Yahya…

Those of you who have followed creationism/intelligent design literature over the years have probably felt as if you’re living in an alternate universe sometimes. In that literature, many times it seems as if “up” means “down” and “highly supported by the evidence” means “a theory in crisis.”

You may not have been following the comments to this post on AIDS denial (and lord, I can’t blame you), but if you have been, you’ve seen a similar phenomenon, where it’s suggested that mutations found in RNA viruses are just due to sloppy lab work, essentially blowing off an entire field of research.

This, of course, has implications far beyond HIV. Phylogenetic analyses based on genetic mutations are used to determine relationships for all kinds of organisms–including humans. In infectious disease epidemiology, they can be used to pinpoint the origin of a virus, or to track and predict its spread, as I’ve written about previously. A new paper in Nature uses similar methodology to examine the introduction of influenza H5N1 into Nigeria.

(Continued at Aetiology).

Folks may find these online videos or recordings interesting:

The DI’s David DeWolf in April, complaining about the Kitzmiller decision and ignoring all of the substantive points made by Judge Jones.

Joel Cracraft, Nick Matzke, Barbara Forrest, and a creationist guy in February at Columbia University in February. See especially my talk, where I give the 20-minute version of the “how I helped out in Kitzmiller” lecture I have given various places.

The American Enterprise Institute Forum that took place last October during the Kitzmiller case, and where TMLC attorney Richard Thompson took the DI to task for changing their tune. These videos were temporarily online at CSPAN but the AEI has a permanent archive and supplemental materials.

An April meeting of the San Francisco Commonwealth Club with a matchup of Casey Luskin and Cornelius Hunter vs. Eugenie Scott and Eric Rothschild, with two other guys providing constant distractions. Listen especially for Luskin’s admission that ID lost big in Kitzmiller, and Eric Rothschild’s dissection of various vague nonanswers by Cornelius Hunter.

An online “webinar” put up by Pepper-Hamilton, the law firm that contributed major pro bono support for the Kitzmiller case. Participants include Eric Rothschild, Steve Harvey, and Kenneth Miller.

Ohio: Here We Go Again

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Regular readers of the Thumb will recall that in February, the Ohio State Board of Education removed the “critical analysis of evolution” standard, benchmark, and lesson plan from the state’s science standards. The matter was referred to the Achievement Committee of the Board, with instructions to consider whether a replacement should be inserted, and if so, what it should be. That was a hammer blow to the creationists on the board and to the Disco Institute.

Now, consistent with the creationist tradition of repackaging old trash, we learn that the creationists on the Achievement Committee of the Ohio State BOE are pushing yet another load of of the same odoriferous garbage, this time extending it to include global warming as well as evolution. This is the Disco Institute’s replacement for its failed “teach the controversy about evolution” tactic, broadening it to include still more pseudoscience.

More below the fold.

One of the twenty-year goals of the Discovery Institute's Wedge was to see the influence of "design theory" in the fine arts. I've often wondered what that could possible mean. And now, thanks to Access Research Network's "ID Arts Initiative" I now know.

Read more at Stranger Fruit.

Nature, one of the top journals for scientific research, published an article today about the most popular science blogs. The Panda’s Thumb came out number two, and Jack Krebs was quoted about our success:

Being a group blog is key, says contributor Jack Krebs, president of Kansas Citizens for Science. “We have some of the most well-informed observers and critics of the ‘intelligent design’ and creationist movements.” The nature of the topic helps too, he adds. “There is an interest, a hunger even, for thoughtful analysis of the issues related to evolution and creationism.”

In addition, PT contributor, PZ Myers, found his personal blog, Pharyngula as the most popular science blog.

Over all, six of the top fifty science blogs were personal blogs of PT contributors.

1Paul MyersPharyngula
2Group BlogThe Panda’s Thumb
7Tara SmithAetiology
18John LynchStranger Fruit
21Jason RosenhouseEvolutionBlog
26Mike DunfordThe Questionable Authority
30John WilkinsEvolving Thoughts

This entry provides a link (at the bottom of the entry) to the full text of my chapter (chapter 11) in the anthology Why Intelligent Design Fails: The Scientific Critique of the New Creationism (WIDF, edited by Matt Young and Taner Edis, © Rutgers Univ. Press, 2004) posted on Talk Reason website. The publisher has granted permission to post this material online with the proviso that the posted text would not be either printed or otherwise downloaded without permission from Rutgers Univ. Press. The full title of the chapter is “There Is a Free Lunch After All: William Dembski’s Wrong Answers to Irrelevant Questions.”

The reason for posting this chapter right now becomes clear if we notice that many points discussed in that chapter have recently been revisited by several writers, in particular on the Panda’s Thumb (PT) weblog (for example, see this and this ). The points in question include

* distinction between “targeted” and “targetless” search algorithms,

* the merits and shortcomings of Dawkins’s evolutionary algorithms,

* Dembski’s misuse of the No Free Lunch theorems,

* his contrived “displacement problem,” etc.

Many points discussed in this chapter have also been briefly addressed in my article published in the Skeptic magazine (vol. 11, No 4, 2005). The text of that article is available online ( see here ). Moreover, the NFL theorems and their application to evolutionary algorithms have been briefly discussed online as well ( see this ).

It has to be pointed out that the discussion of Dembski’s “displacement problem” in this chapter as well as in the article in the Skeptic only covers the initial version of that “problem” as it was rendered by Dembski in his No Free Lunch book. More recently, Dembski had modified the “displacement problem,” and this newer rendition naturally was not yet discussed either in chapter 11 of WIDF or in the article in the Skeptic. The new version of that “problem” has been though briefly addressed here .

Read There Is a Free Lunch After All on Talk Reason .

Genetic Algorithms are simplified simulations of evolution that often produce surprising and useful answers in their own right. Creationists and Intelligent Design proponents often criticize such algorithms for not generating true novelty, and claim that these mathematical recipes always sneak the “answer” into the program via the algorithm’s fitness testing functions.


There’s a little problem with this claim, however. While some Genetic Algorithms, such as Richard Dawkin’s “Weasel” simulation, or the “Hello World” genetic algorithm discussed a few days ago on the Thumb, indeed include a precise description of the intended “Target” during “fitness testing” on of the numerical organisms being bred by the programmer, such precise specifications are normally only used for tutorial demonstrations rather than generation of true novelty.

In this post, I will present my research on a Genetic Algorithm I developed a few years ago, for the specific purpose of addressing the question Can Genetic Algorithms Succeed Without Precise “Targets”? For this investigation, I picked a math problem for which there is a single, specific answer, yet one for which several interesting “quasi-answers” - multiple “targets” - also exist.

PT readers, you are about to enter the Strange and Curious world of “The MacGyvers.” Buckle up your seat belts, folks - our ride through Fitness Landscapes could get a little bumpy.

Tangled Bank #57

The Tangled Bank

There is a new edition of the Tangled Bank at e3 Information Overload.

Discovery Institute co-founder and investment strategist George Gilder has written an article appearing in the new issue of the prominent conservative magazine National Review. The DI has the article available here, which is convenient for those of you who don’t have 5 subscriptions to the National Review like I do.

Would you believe that the article is terrible? In looking at reactions to Gilder’s previous articles, the most consistent criticism is that his writing is abstruse, incoherent, and filled with terminology that he either doesn’t understand or intentionally misuses (or worse, invents on his own). This piece continues that time-honored tradition.

First of all, very little of it has anything to do with evolution, whether by Darwinian means or any other. (He even spends several paragraphs plugging his own books, which have no clear relevance, but I guess the guy needs all the royalties he can get.) Staying true to the Discovery Institute’s tactics, he associates things with evolutionary biology that have little or no association at all, and in every case these just happen to be things that are disliked by right-wing ideologues such as George Gilder. People like him apparently need an all-purpose boogyman to make sense of the world, but it’s a poor substitute for genuine understanding. And in this case it has resulted in an article that consists mostly of disjointed ramblings with no coherent thesis. Secondly, Gilder has an bad habit of throwing in random quotes from noteworthy scientists, most of whom would probably have a very low opinion of George Gilder. In virtually no case do these quotes have any real relevance to whatever point, if there is one, that Gilder is trying to make. They appear to serve as the literary equivalent of name-dropping, lending a façade of authority to an otherwise nonsensical piece. And then there is Gilder’s favorite tactic, which is to wax profound about one scientific advance or another (with no indication that he knows what he’s talking about), and pretend as if this alone somehow constitutes an argument. There is just painfully little that rises up to the level of coherence.

Below the fold I will try to address the few claims that are on-topic and comprehensible enough to address. That’s not many, but it’s worth clearing a few things up.

This is a guest appearance of Mark Frank. It is his first appearance on the Panda’s Thumb. Mark Frank offers his take on the concepts of specification and design inference. In certain aspects Frank’s ideas seem to jibe with the appoach adopted by Elliott Sober, but also seem to add some substantive nuances.

The Intelligent Design (ID) movement proposes that it is possible to detect whether something has been designed by inspecting it, assessing whether it might have been produced by either necessity or chance alone, and, if the answer is negative, concluding it must have been designed. This means there is no need to make any commitments about the nature of the designer.

This approach relies heavily on the concept of specification. The proponents of ID have made various attempts to define specification. A recent attempt is in a paper written by William Dembski in 2005 which is clearly intended to supersede previous attempts. This essay examines this revised definition of specification and highlights some issues in Dembski’s paper. It also proposes that our intuitive understanding of when an outcome is implausible is much better explained by a comparison of the likelihoods of different hypotheses. Finally the essay considers some of Dembski’s objections to the comparison of likelihoods and Bayesian approaches in general.

Continue reading Detecting Design: Specification versus Likelihood on Talk Reason

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