August 2006 Archives

Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design. Regnery Publishing, Inc. Washington, DC.^Amazon

Read the entire series.

Jonathan Wells has recently written The Politically Incorrect Guide to Darwinism and Intelligent Design. Wells’s book is stuffed full of misrepresentations, distortions, and plain falsehoods. My Thumb colleagues are reviewing whole chapters, but my purpose here is to focus in some detail on just one of Wells’s claims to illustrate his scurrilous tactics.

The claim I focus on is from Chapter 16, “American Lysenkoism”. Mark Perakh has already documented how Wells manipulated partial quotations from Perakh’s earlier essay on Lysenkoism to create misrepresentations of what Perakh actually wrote. Here I will describe Wells’s dishonesty about a specific episode in Ohio last year.

Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design. Regnery Publishing, Inc. Washington, DC.^Amazon

Read the entire series.

Chapter 15 is entitled “Darwinism’s War on Traditional Christianity”. For much of this chapter, the reader will find Wells on his soapbox about this or that aspect of, you guessed it, “Traditional Christianity”. And, like “Darwinism” in the first chapter, Wells struggles to find a definition for his term. Wells chooses a current version of the Nicene Creed as the sort of “creedal affirmations that” traditionally unite Christians. (Apparently the litmus suggested by Jesus was inadequate.) Wells almost approaches clarity when he implies that if one doesn’t adhere to the tenets of the (current?) Nicene Creed, one cannot seriously consider him or herself as a Christian. (No word yet on the apparently non-Christians who affirmed a prior version of the Nicene Creed.)

There are two important things to say about Wells’s definition of a “Traditional Christian”. First, the commitment to the tenets of the Nicene Creed is hardly a universal litmus for determining who is and who is not a Christian. A Protestant, even one who subscribes to every tenet of the Nicene Creed, who thinks that Wells is right is encouraged to try to obtain the sacramental elements from a Catholic communion and see how far he gets. (According to Catholic tradition, Protestants cannot receive Catholic communion.)

The second important thing to note is that Jonathan Wells is styling himself as a defender of “Traditional Christianity.”

Read that again: Jonathan Wells, Traditional Christianity. Not to be impolite, but to us here at the Thumb Wells defending “Traditional Christianity” reads as queer as Ann Coulter defending “traditional values”.

This is a report on the summer institute, “Exploring the Borderlands: Science and Religion in the 21^st Century,” held by the Jefferson Center for Science and Religion. In the words of the Center, the conference featured workshops on “such ‘hot’ issues as the stem cell controversy, the evolution vs. Intelligent Design squabble, whether homosexuality is a ‘chosen lifestyle,’ … whether Buddhism speaks to neuroscience, how does a Muslim scientist look at religion and freedom, [and] is our universe simply ‘accidental’ .…”

The Jefferson Center, www.thejeffcenter.org, was founded a few years ago in Ashland, Oregon, home of the Oregon Shakespeare Festival. According to its Website, the Center is concerned with, among other things, “dogmatic and tyrannical religious groups opposed to change, freedom, and human rights.” Thus, they “seek a humanistic and naturalistic alternative to dogmatic, supernatural, and fundamentalist religious thought and the values that come with them” and promote “progressive, rational, and critical thinking, … caring for our planet and all humanity, … [and] working to end all forms of oppression and discrimination in both society and especially in religion.”

To further some or all of these ends, the Center organized its second summer institute, a 2.5-day affair held over the weekend of August 4-6 at the Unitarian Center in Ashland. For a summary by Nigel Leaves, go to their Website and click on “Current Newsletter,” or “Newsletter Archive,” as appropriate.

Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design. Regnery Publishing, Inc. Washington, DC.^Amazon

Read the entire series.

I’ll address in this article chapter sixteen, “American Lysenkoism”, in Jonathan Wells’s Politically Incorrect Guide to Darwinism and Intelligent Design. As Wells (1994) explained, he went to study biology at the behest of his spiritual “father” the Reverend Sun-Myung Moon, with an explicit goal to devote his life to “destroying Darwinism”. Since he set out to destroy “Darwinism” before having sufficiently familiarized himself with it, this immediately points to his lack of impartiality when dealing with “Darwinism.” Wells’s goal was not to evaluate “Darwinism” on its merits but to search for any arguments, regardless of their merits, which would serve his goal set in advance. This alone is a strong warning to the consumers of Wells’s literary output: take Wells’s arguments with a good dose of salt; he is not an unbiased judge of evidence, but a partisan of an anti-evolution effort whose goal is not to find the truth but to prove his viewpoint regardless of means.

In a box in the margin of chapter sixteen Wells writes: “Lysenkoism is now rearing its ugly head in the US, as Darwinists use their government positions to destroy the careers of their critics.”

Really? Thousands of biologists in the USSR at the time of Lysenko’s reign were arrested, exiled to Siberia, and many of them shot in the basements of the notorious Lubyanka prison, while intelligent design advocates in the US thrive on lavish donations from ultra-religious sources, have their own publishing outlets, lecture all over the country without any interference from genuine scientists, endlessly appear on TV and radio shows, and enjoy support from the extreme right-wing pundits and commentators?

Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design. Regnery Publishing, Inc. Washington, DC.^Amazon

Read the entire series.

Chapter 9 in Wells’s Politically Incorrect Guide to Evolution and Intelligent Design, “The Secret of Life”, is like previous chapters, a rehash of well-known creationist arguments. This time the topics are DNA, the genetic code, and the origin of biological information. In addition, Wells uses up a third of the chapter with some excuse-making for the lack of peer-reviewed papers supporting “intelligent design”, and with a completely misleading account of the purported “persecution” of an ID-friendly scientist by the “Darwinist orthodoxy”.

As far as the scientific arguments go, after giving an overview of DNA structure and function, Wells presents three main objections to the current scientific understanding of evolution at the DNA level, which in a nutshell go like this:

According to Red State Rabble, Father Coyne is undergoing chemotherapy for colon cancer. This would seem to shed light on the reasons for his recent resignation.

Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design. Regnery Publishing, Inc. Washington, DC.^Amazon

Read the entire series.

Jonathan Wells is a titular developmental biologist, so you’d expect he’d at least get something right in his chapter on development and evolution in The Politically Incorrect Guide to Darwinism and Intelligent Design, but no: he instead uses his nominal knowledge of a complex field to muddle up the research and misuse the data to generate a spurious impression of a science that is unaware of basic issues. He ping-pongs back and forth in a remarkably incoherent fashion, but that incoherence is central to his argument: he wants to leave the reader so baffled about the facts of embryology that they’ll throw up their hands and decide development is all wrong.

Do not be misled. The state of Jonathan Wells’s brain is in no way the state of the modern fields of molecular genetics, developmental biology, and evo-devo.

Here’s my shorter version of Wells’s chapter 3, titled “Why you didn’t ‘evolve’ in your mother’s womb.” It may sound familiar to many of you.

The strongest evidence for Darwin’s theory was embryology, but Karl Ernst von Baer, who laid out the laws of development, did not think they supported evolution, and Ernst Haeckel twisted and distorted von Baer’s laws and faked his data to support Darwinism. He was wrong, and the earliest stages of vertebrate embryos do not resemble one another at all, so Darwinism was built on a false foundation, and they’re still using Haeckel’s faked data in our textbooks. Oh, and mutant fruit flies are still just flies.

That’s right, it’s a rather boring rewrite of a premise of his book, Icons of Evolution, which I hammered on over three years ago. He hasn’t learned a thing since, and he’s making exactly the same arguments. I’ll take a different tack this time and expose the sleight of hand he’s pulling.

A reflection on the ID movement

So where is the ID movement going now in this post-Dover, post-Kansas world?

Well, it seems to me that they are giving up on trying to seriously sell ID as science. Instead, they are forging full-steam ahead with their cultural “war of the worldviews” agenda, pitting materialism and atheism (as represented by science) against religious belief (as represented by their particular flavor of fundamentalist Christianity.)

Let’s take a quick look at what they are up to:

If you’re interested in biology and not reading Sandra Porter’s Discovering Biology in a Digital World, you should be. As she notes in her profile, her passion is “developing instructional materials for 21^st century biology,” and it shows–she provides all kinds of little online experiments you can run yourself, even with minimal knowledge of molecular biology (she shows you how, step by step, and even discusses the results). She’s recently finished a 4-part series on HIV. The experiment in a nutshell, as she notes:

We are going to compare a protein sequence from a wild type, drug-sensitive, HIV virus with protein sequences from HIV samples that were isolated from patients who were taking an anti-viral drug (actually a protease inhibitor) called “Atazanavir.”

Part I. Today, I’ll introduce the experiment and give a link to a short flash movie on HIV. Part II. Instructions for the experiment. Part III. Look at the sequence results. Part IV. Look at protein structures and see if we can explain why the experiment worked the way it did.

You can do this all yourself by just checking out her website–or, even better, use it to show others how evolution works, and how it can be examined at the molecular level. She has tons of other resources on there as well, so be sure to browse around beyond just the HIV posts.

Coturnix over at Blog Around the Clock needs help. His friend Kevin is doing a survey of herps in China and can’t identify a frog. (Snakes are his speciality.) Can anyone here identify it? Pictures of the unidentified species, along with some known ones, can be found here.

Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design. Regnery Publishing, Inc. Washington, DC.^Amazon

Read the entire series.

By titling his first chapter “Wars and Rumors”, Jonathan Wells invokes a snippet of scripture in which Jesus describes the end times

And ye shall hear of wars and rumours of wars: see that ye be not troubled: for all [these things] must come to pass, but the end is not yet.

(Matt 24:6)

Wells uses such dramatic quotations and general martial language because the struggle between “intelligent design” and science is very much a culture war, at least to him and other creationists. In order to advance his thesis, Wells has to convey the idea that “Darwinism” pits itself against traditional Christianity: to allow pupils to learn it is to give them up to atheism, decadence, liberalism and to lose the culture war.

Note that Wells does not wage war against evolution. In fact, he is at pains to make it (somewhat) clear that he wages war against “Darwinism”, which in context might sound like the sort of thing any sensible Christian would want to guard against. Unfortunately, Wells isn’t exactly clear what he means by Darwinism as opposed to evolution. In this chapter and chapter fifteen, “Darwinism’s War on Traditional Christianity”, we find many references to “Darwinism”. Assuming that even creationist words have meaning, let us set those invocations in series while adjusting the language only to merge them syntactically. Presumably there is consistency of meaning, and this will hopefully help us gain a greater understanding of what this nasty Darwinism thing is.

Despite no longer working as legal counsel for the Discovery Institute, Seth Cooper has still been quite busy writing articles on their behalf slamming Judge Jones’ ruling in Kitzmiller. Not content with the whopper he told a few months ago in an article he wrote with Joe Manzari of the American Enterprise Institute, he’s now back with this article on the DI website. Wesley Elsberry has already handled the main charge that Cooper makes regarding the question of whether Judge Jones should have allowed the plaintiffs to subpeona draft versions of the next edition of Pandas; I’m going to deal with some of the other arguments he makes.

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

PT reader TW points to Sam Kean’s CHE update. In brief, Evolutionary Biology is a valid major.

There has also been a press release from the Dept. of Education:

Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design. Regnery Publishing, Inc. Washington, DC.^Amazon

Read the entire series.

Jonathan Wells is one of the most notorious activists of the political ad campaign known as “intelligent design”. He is most well known for his attacks on modern biology, specifically his 2000 book, Icons of Evolution, which was panned by the scientific community for its fraudulent presentation of modern biology.

Does Jonathan Wells, aiming once again at the popular market, restore his scientific and academic reputation with his latest book, The Politically Incorrect Guide to Darwinism and Intelligent Design, or is it just old trash in a new bag? To find out, you will need to read our multi-part review, which begins tomorrow.

One thing is for sure, Jonathan Wells is too modest. His recently published, The Politically Incorrect Guide to Darwinism and Intelligent Design, is not only politically incorrect but incorrect in most other ways as well: scientifically, logically, historically, legally, academically, and morally.

With all the flap about D. James Kennedy and his “no Darwin, no Hitler” pseudo-documentary (see Pharyngula and Dispatches from the Culture Wars for the sordid details), I was reminded of some incidents that took place three years ago in New Mexico involving D. James Kennedy and the NM chapter of the Intelligent Design Network.

In 2003, when New Mexico was in the process of developing new science standards, Kennedy deployed his Center for Reclaiming America’s 1500 New Mexican “E-army” members to bombard the NM State Board of Education with letters opposing teaching “evolution only” in the schools.

This article fondly mentions the help of IDnet-NM’s leader Joe Renick in this effort.

The purpose of this post is to show that D. James Kennedy and Joe Renick are integrity-challenged “Birds of a Feather.” Since D. J. Kennedy is getting a lot of negative press this week, I’ll focus here on Joe Renick, who hired the Zogby Polling Firm for some extremely dubious research that purported to show New Mexican scientists were in favor of teaching ID in schools. A rather large flap ensued, and even the heads of Sandia and Los Alamos Labs entered the fray. When the dust settled, Renick promised to stop using the poll.

That was over three years ago. However, as of August 22^nd, 2006, Renick’s group is still using those bogus Zogby polling results.

Three years of broken IDnet promises. I’m shocked - shocked!

So, you may or may not be aware of the latest “challenge” to evolutionary theory–DI Fellow Jonathan Wells’ new book, “The Politically Incorrect Guide to Darwinism and Intelligent Design.” Following in the footsteps of Tom Bethell’s “Politically Incorrect Guide to Science” (whose terrible chapter on AIDS I reviewed here), the book is just all shades of terrible. (As has been pointed out by many others who’ve read books in the “Politically Incorrect” series, they should just drop the pretense of “Politically”–simply “Incorrect” sums them up much better). I’ll have a more comprehensive review of one of Wells’ chapters (discussing, essentially, how evolution plays no role in medicine, antibiotic resistance, etc.) next week some time, and you’ll be seeing others pop up as well (see this post for the collected links), but for today I want to focus on a small part of the final chapter (titled “Scientific Revolution”. Yeah, go ahead and snicker).

You probably remember Forest Mims III. He was the other party in the “Eric Pianka advocates genocide” saga. (See also here and here to remind yourself of the absurdity of the whole situation). Mims is a creationist and another Discovery Institute Fellow, and an amateur scientist. According to Wells, he’s made a bizarre claim: that the fact that influenza viruses haven’t evolved resistance to UV light is evidence for design. I thought that Casey Luskin’s piece on intelligent design and flu was as bad as it gets, but I think this is a toss-up; you just can’t make this stuff up.

(Continued at Aetiology)

There are many new developments in the controversy surrounding D. James Kennedy’s propaganda piece claiming that Darwin led directly to Hitler. The Anti-Defamation League has condemned the program, Kennedy has responded and there is much more to discuss. I’ve written up a long entry on the matter, including reviews from academic historians who reveal the shoddy reasoning behind the program’s primary source of information and a load of historical facts that prove the program’s central thesis to be utter nonsense.

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

Over at Red State Rabble, Pat Hayes, has an interesting commentary on the Discovery Institute’s reaction to the apparent retirement of “intelligent design” creationism critic, Jesuit Father George V. Coyne, from the directorship of the Vatican Observatory.

If Discovery, as the main think tank championing intelligent design, doesn’t address metaphysical and religious questions then we have to ask: On what basis are they weighing in on theological questions such as Rev. Coyne’s alleged support for “Process Theology?”

If intelligent design, as its proponents claim, can tell us nothing about the nature of God, then why is Bruce Chapman – in his official capacity as Director and using Discovery’s Evolution News and Views blog to deliver the message – even addressing the question of whether or not “God is still learning and could not have known what his world was becoming.”

And finally, if intelligent design is truly a scientific theory as claimed, what is the scientific proof that provides the evidentiary basis for making a determination about the truth or falsity of what God knows and what he doesn’t.

Go read Pat Hayes’s Theological Deviations.

Today’s Chronicle of Higher Education has a news article by Sam Kean that describes more creationist shenanigans in the Federal Government. Kean reports that a new “SMART Grant” makes funds available to science, engineering and foreign language students – with the exception of students majoring in evolutionary biology.

The Education Department has a system of codes for undergraduate majors–the “CIP codes”– which includes evolutionary biology (code 26.1303). The list of majors eligible for the SMART grant omits only this code among all the biological disciplines.

Hi All,

Wesley and I are working on fixing the server issues that this website has been having. We switched to a new connection a month or so ago and PT’s popularity is overwealming it. We’re working to optimize the server for short term solutions and looking at solutions for the long haul.

On his Evolution List blog, Allen MacNeill discusses a paper written by one of his students of the Cornell ‘Evolution and Design’ seminar. The paper, written by Elena Broaddus, discusses the topic of our ““innate” tendency to infer purpose in nature”.

The posting starts with some interesting pictures of ‘faces’ found in nature. We are all very familiar with detecting ‘design’ in clouds and there are countless instances where people see faces or other attributes in natural objects. Elena addresses this ‘innate tendency’ that leads us to infer purpose in nature.

This morning I am doing a live online discussion/debate with Mustafa Akyol (of Kansas hearings fame) at Islamonline.net. It is starting in a few minutes.

They came for a contest that might someday be viewed as a pivotal moment in the eternal conflict between Darwin and Design.

On one side were the Intelligent Designers. They came from California and Alabama, New Mexico and England, Finland and the Netherlands, and from all around the world. They came from academia, and from industry, and from the armed services. They came armed with computer spreadsheets, home-made programs, graph paper and calculators. They applied trigonometry and calculus, intuition and insight, knowledge of minimal soap films and surface tension, database optimizing algorithms and random searches, and other techniques available only to Intelligent Designers. And they strived to answer the tricky question “What is the Steiner Tree (smallest possible network of straight line segments connecting six given points) for the network shown in “Take the Design Challenge!”

On the other side were Evolutionary (or Genetic) Algorithms, in which herds of digital organisms were bred over many generations. Each organism was a string of numbers and letters, which were “transcribed” by fixed rules as representing some of the billions upon billions of possible candidate networks for the given problem. Those organisms whose lengths were smaller gained a slightly better chance at being a parent of one of the organisms of the next generation, and mutations of the strings were allowed to happen occasionally. In this process, no trigonometry or calculus was required. No information about characteristics of Steiner Trees was necessary. But, as the strings competed with each other, marvelous and unexpected designs began to appear.

Although most of the Intelligent Designers were not members of the “Intelligent Design” movement, which had been officially invited to respond, the ID community did indeed weigh in, via the efforts of Salvador Cordova, one of the IDers running the show at William Dembski’s blog Uncommon Descent.

So, what is the Answer? Did Salvador do better than Darwin? Did our team of Intelligent Designers find the True Steiner, or did they, like the evolutionary algorithm, find “MacGyver” (not-quite-perfect-but-extremely-functional) solutions also?

Readers, let’s enter the Design Room and meet our Winners!

In the evolution/creationism controversy, there is a sub-debate about public debates: should scientists and science fans engage in oral public debates with creationists? Sometimes it is said that the answer is always “no” – debates are sport, not serious discussion, and creationists can employ the “Gish Gallop” to rattle off hundreds of bogus claims, each of which would take minutes or hours to debunk in the fashion done on talk.origins. But the real answer is “it depends”, because there are circumstances when it is appropriate – neutral forums, a setup that allows individual topics to be discussed in depth, you are an expert debater like Kenneth Miller, etc. On the other hand, if you are being invited to a debate set up by creationists for the purpose of promoting creationism, with their rules, press, etc., and their audience bussed in from fundamentalist churches, and when they are planning to record, broadcast, and sell recordings of the event to promote creationism/ID – then you should think twice about whether or not you are being “set up,” and whether or not your participation is helping or hurting the cause of science education.

Here is another situation in which you should think twice. On the web, I just stumbled on this announcement of a series of upcoming ID events in Florida, called “Darwin of Design?” See the line I bolded:

Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design. Regnery Publishing, Inc. Washington, DC.^Amazon

Synopsis: One thing is for sure, Jonathan Wells is too modest. His recently published, The Politically Incorrect Guide to Darwinism and Intelligent Design, is not only politically incorrect but incorrect in most other ways as well: scientifically, logically, historically, legally, academically, and morally.

Introduction — Chapter 1 — Chapter 2 — Chapter 3 — Chapter 4 — Chapter 5 — Chapter 6 — Chapter 7 — Chapter 8 — Chapter 9 — Chapter 10 — Chapter 11 — Chapter 12 — Chapter 13 — Chapter 14 — Chapter 15 — Chapter 16 — Chapter 17 — Ohio — Legal

Chronological Listing

Reviews will be posted as they become available.

Reviews are written by members of the Thumb, and the series is edited by Reed A. Cartwright.

Back in 1999, I started a draft of an article about objections to evolutionary computation. It looks like now would be a good time to remind people that these arguments against evolutionary computation have long been addressed.

Okay, cubs, it’s time to play everyone’s favorite game, “Who Said Something Stupid?” Rules are simple: in your comment to this post, identify the dim bulb who uttered each of the following outrageous statements. Creativity in your guess will be rewarded, but points will be deducted for snorts and guffaws that lead to spewing coffee on your keyboard.

After finding the author of the quote, place your vote for the stupidest statement of the month. Winners will be decided by me at an arbitrary point in time, and will be notified telepathically. The prize for correctly identifying all of the authors will be a sincere pat on the back (i.e., with claws retracted) and a virtual pint of virtual Pilsener at the virtual Pub.

The prize for the author of the winningest statement will be the negative attention of a small number of people for a fairly short period of time. And the perpetual linking of his or her name with his or her stupid comment on web archives everywhere.

Ready? Let’s play!

In July, I described a Genetic Algorithm that, unlike Dawkins’ “Weasel” experiment, specifies no fixed “Target” for the simulation, but instead rewards those members of the current population which use fewer or shorter segments to connect a fixed set of points. As the algorithm progresses, it finds a multitude of answers for the math problem called “Minimization of Steiner Trees,” i.e. the shortest possible straight-line networks connecting the fixed points.

Last Monday, I posted Take the Design Challenge, wherein I called for solutions to a tricky little 6-point network. Next Monday, I will announce the winners (there are 20 entries already, several with true Steiner Solutions, and others with almost-as-good “MacGyver” solutions).

Imagine my surprise, then, when I found Salvador Cordova at Uncommon Descent spewing blatant falsehoods about this work. I was shocked - shocked, I say - to catch the UD Software Engineers in a lie. And quite a lie it is - with the help of mathematicians like Carl Gauss, I’m going to lift the veil from the obfuscations of IDers, and prove it’s a Lie, much as you would prove a mathematical theorem.

On August 24, the International Astronomical Union is going to vote on a proposal (here is the official resolution) to define the term “planet” such that Pluto stays in, and three bodies get added. This would require the re-writing of textbooks and make millions of first-graders learn 12 planets instead of nine. The planet status of Pluto has long provoked heated and fairly pointless and silly debate, much of it by people who are only vaguely familiar with astronomy but feel strongly about the definition of planet, a tradition which I fully intend to continue here.

Get your Charles Darwin Bobblehead now! (In support of SIU’s Darwin Day 2007.)

(Note: In the previous version of this post the Darwin Bobbleheads were about three feet tall as displayed on the monitor and so didn’t even fit on the screen. The poster responsible has been sacked.)

Lawrence Krauss tells us in an article in today’s New York Times. Step one: Have people who think that the Earth is only 6500 years old running your school board:

The chairman of the school board, Dr. Steve Abrams, a veterinarian, is not merely a strict creationist. He has openly stated that he believes that God created the universe 6,500 years ago, although he was quoted in The New York Times this month as saying that his personal faith “doesn’t have anything to do with science.”

“I can separate them,” he continued, adding, “My personal views of Scripture have no room in the science classroom.”

A key concern should not be whether Dr. Abrams’s religious views have a place in the classroom, but rather how someone whose religious views require a denial of essentially all modern scientific knowledge can be chairman of a state school board.

As they say, read the whole thing.

Since posting my essay on Genetic Algorithms, I’ve since developed a brand-new C++ version of my Steiner Networks genetic algorithm, a vast improvement over the old Fortran number-clunker I developed five years ago.

And already, the new code is leading to some very interesting results.

In light of William Dembski’s remarks in No Free Lunch, basically arguing that in all Genetic Algorithms,

… the fitness function … is well-defined and readily supplies the complex specified information that an optimal crooked wire genetic antenna [or any other problem solved with Genetic Algorithms] seems to acquire for free,

I’m giving Intelligent Design proponents (and everyone else!) a chance to actually Design something!

As you recall, my algorithm involves finding Steiner Trees, the shortest networks of straight-line segments connecting a given collection of fixed points. These networks may include additional variable “Steiner Points” where segments may meet.

The Challenge Here is a collection of six fixed points. Designers, send your candidates for the Steiner Solution for this particular 6-point system to me at nmsrdaveATswcp.com (replace the AT with an @ if you please).

I will announce the winners (if any) in a week’s time, and also will present the answer that Evolution came up with. I’m interested in proposed solutions from any and all (you don’t have to be in the ID camp), but am especially interested in solutions by ID advocates, since y’all are saying that the solution is already implicitly defined in the statement of the problem (finding shortest connected networks). Here’s a Hint:

Someone didn’t get the DI memo in Arkansas:

One of the assembly’s officers, former state lawmaker Gunner DeLay of Fort Smith, is the Republican candidate for attorney general.

DeLay said he wrote a paper in law school on what he says is a teacher’s “right to academic freedom” under the First Amendment to the U. S. Constitution to teach subjects that are “scientifically valid.”

He said that could include intelligent design.

“The basis of my paper was that although legislative mandated efforts to teach creation science or intelligent design have been struck down, the courts have left open teaching those theories under an instructor’s First Amendment right to academic freedom,” DeLay said.

Such protected speech would have to have a “scientific basis,” DeLay said, adding that a science teacher “could not come in and say we’re all born under a cabbage leaf.”

“The old creation science is the new intelligent design. And yes, I think it’s scientifically valid,” DeLay said.

Hat Tip: Eric Meikle.

The control and eventual eradication of the smallpox virus from the wild is one of the most heralded success stories in all of public health. Indeed, smallpox has played a central role in the history of vaccination. Even prior to Edward Jenner’s use of the related cowpox virus to protect against smallpox disease, it was known that inoculation with materials from an infectious smallpox pustule or scab (dubbed “variolation”) could protect an individual from death due to smallpox, generally resulting instead in a mild form of the illness. Jenner’s observation that milkmaids seemed to be protected from the disease–and his use of material from cowpox pustules instead of smallpox–resulted in the development of the science of vaccination. World-wide use of the smallpox vaccine, along with a mass vaccination campaign led by the World Health Orgainzation, resulted in the end of naturally-occurring smallpox on the planet, with the exception of stores of the virus held in the United States and Russia.

This feat is being attempted currently with measles and polio viruses, but it’s been much more difficult, and eradication of these viruses may never be attainable. Below, I discuss some aspects that are critical to a campaign that seeks to eradicate a disease, and a new paper on the evolution of smallpox viruses.

(Continued at Aetiology)

…Tricks like a dog cancer cell becoming an independent pathogen and spreading through the dog population. Drop everything and go read Carl Zimmer’s post about the recent discovery of a dog cancer cell lineage that has left behind its multicellular ancestry. Rather like HeLa cells, except in the wild without human help. If I thought that “phylum” and “phylum-level bodyplan” were inviolable, unchanging character complexes (which I don’t), this example of a super-phyletic macroevolutionary change, on microevolutionary timescales, would rock my world.

One of the contributors on the “Uncommon Descent” weblog, “BarryA”, has joined the ranks of intelligent design advocates who want in on Monday-morning quarterbacking the Kitzmiller v. DASD case. “BarryA” wrote that Judge Jones was incompetent in permitting Eric Rothschild to present defense expert Michael Behe with a stack of papers and textbooks about the evolution of the immune system, one of those systems that Behe calls “irreducibly complex”. Behe had said this about it, ““We can look high or we can look low in books or in journals, but the result is the same. The scientific literature has no answers to the question of the origin of the immune system.” Rothschild wanted to go into how many papers and how much work was out in the literature. ID advocates have become fond of calling the practice of showing up their essential cluelessness by reference to the scientific literature as “literature bluffing”. The only bluff around that point in the KvD trial, though, was Behe’s.

My response is over at the Austringer.

Science magazine has just published the results of international polls assessing public acceptance of evolution around the world: Jon D. Miller, Eugenie C. Scott, and Shinji Okamoto (2006) “.” Science Aug 11 2006: 765-766 (Supporting Online Material)

The results are at left. Only one country beats the U.S. in the race to the bottom: Turkey, probably the only country in the list with more severe fundamentalism vs. modernism issues than the U.S. But the people in the U.K. can take heart – a BBC poll this spring (which was widely cited by creationists to support the idea that U.S. antievolutionism is not weird), said that less than half of Britons went for evolution. That result is strongly contradicted by this survey, where the U.K. ranks near the top in accepting evolution (as well they should, Darwin is on the money there).

Today appears to be Hovind-Fest at Dispatches from the Culture Wars. I have two posts there that might be of interest to creationist watchers here at the Panda’s Thumb. The first post is a guest post from Skip Evans that recalls his long history of interaction with the world’s looniest creationist, along with some reminiscing from me as well. The second post contains information on a court ruling in Washington that doesn’t bode well for Hovind’s arguments in court in Florida. A fellow whacko from the Embassy of Heaven church, represented by Glen Stoll, the same attorney that has represented Hovind before, tried to make the same claims Hovind does - the court has no jurisdiction, he’s employed by God, he has no income, etc - as a way of getting out of paying child support. The court smacked down that argument hard.

Comments may be left at Dispatches from the Culture Wars.

The Seattle Times published an editorial Tuesday that was reprinted in the Lawrence, Kansas, Journal World today: Seattle applauds Kansas vote

The basic take-home point: Intelligent Design is dead as an attempt to disguise creationism as science.

Oh yes, it is alive and well as a cultural and religious force among anti-evolutionists - that problem still exists. But all this talk about there being anything to ID as science has been rejected by the courts, rejected by the voters, and rejected and ignored due to lack of any substance or relevance by the world of science.

The Seattle-based Discovery Institute has hitched their wagon to a sinking ship (pardon the mixed metaphor.) The only places they have made any temporary progress is when they has tried to use political bodies that were so far out of the mainstream that their successes, such as they have been, were bound to be short-lived.

Here are some excerpts from the editorial:

Over at Uncommon Descent, Wm. Dembski has a blog titled “Paley updated and videoized” :

August 9, 2006 Paley updated and videoized

Kids growing up watching this video are going to find it harder later in life to swallow Darwinian evolution:

http://www.kids4truth.com/watchmaker/watch.html Filed under: Intelligent Design — William Dembski @ 10:49 am

After watching the video, I clicked the “Learn more about The Watchmaker” button, and found a surprisingly clear statement of what “Intelligent Design” (ID) is, in a nutshell:

We believe the [Intelligent Design] movement is helpful to the Biblical Creationism movement because it causes people to see the lunacy of the Theory of Evolution.

By George - I think they got it! (And from the way Dembski is pumping the video on his blog, one must assume he approves…)

It’s not that Creationism led to Scientific Creation, which led to Intelligent Design, which led to “Evidence Against Evolution” - it’s that Creationism IS “Evidence Against Evolution.”

The ID proponents are still smarting from last years resounding defeat in the Kitzmiller case, where ID was publicly shown not to be science. Once again, the ID folks have posted their list of supposedly “peer-reviewed” articles that allegedly support ID. Unfortunately for them, this list is bogus, the articles are either not peer-reviewed by any standard working scientists would recognize, or if peer-reviewed have nothing to do with ID. The infamous Behe & Snoke paper, for example, shows that in the absence of natural selection, neutral drift alone can efficiently produce protein binding sites in realistically-sized populations in times consistent with the fossil record. This finding is hardly ID friendly.

But what is interesting is what is missing from this list, a paper from ID luminary Jonathan Wells. Why is this paper missing? It was in previous versions of the list. Could it be that Wells made a testable hypothesis, and it was shown to be wrong?

Over at ID the Future, Paul Nelson has a brief post regarding the doping scandal that will likely deprive cyclist Floyd Landis of his recent Tour de France victory. For those who do not follow cycling, several tests performed after the race showed that Landis had an unusual ratio of testosterone-like hormones in his blood, and that the hormones found contained amounts of specific carbon isotopes not compatible with endogenous origin (for a thorough discussion of the tests and the reasons for Landis’s failure, see this post at Jake Young’s Pure Pedantry blog, as well as links and follow-ups therein). The conclusion from the anti-doping agency was that Landis had (voluntarily or not) taken artificial steroids, and therefore ought to be disqualified.

Nelson extracts his own moral from the story, which is that we can scientifically detect the result of intelligent action without having to exclude every possible natural source of the hormonal imbalance, and, implicitly, that therefore ID is a viable scientific program and - ta-dah! – those evil Darwinists who claim otherwise are just selling smoke. However, Nelson’s attempt at ‘roiding up ID is just as easy to spot as Landis’s.

The Society for the Study of Evolution has published the anti-Wedge Document

The document is titled “Countering the Wedge: A multi-pronged, multi-year strategy to oppose creationism and intelligent design in the science curriculum of public schools” and is authored by Massimo Pigliucci, David Baum and Mark McPeek

Anti-Wedge Document Wrote:

The existence of a massive and well-funded network of anti-evolutionary groups has contributed to the persistence of creationism, but at the same time scientists could have been more effective in outreach and education (Pigliucci 2002, 2005). Thus, while scientists certainly cannot hope by themselves to overcome the problem, it seems increasingly clear that inaction is no longer an option. The public already perceives academics as aloof and isolated, lost in a pampered world of irrelevancies, unwilling or unable to come out of the ivory tower even for brief periods to explain why their research is worthwhile (Sagan 1995). We think that professional societies ought to take the lead and generate an internal cultural change within academia, to help scientists rethink their priorities and make outreach and public involvement a matter of normal practice, rather than a suspect activity carried out only by a few individuals.

A paper that just came out in Advance Online Publication section of Nature, Murphy et al. 2006, reports the first in situ structure of a flagellar motor in a spirochete, Treponema primitia. Such things have been done before, for the bacterial lab rat Salmonella, but spirochetes are a whole different bacterial phylum, and they have weird flagella. First, instead of the flagella sticking outside of the cell and doing what any self-respecting flagellum would do, the flagella of spirochetes rotate entirely within the periplasm (the space between the inner and outer membrane, which includes the cell wall). You might think that there would be no room for the flagellum to rotate in such a restricted space, or that it would tear apart the membranes – but intuitions are very unreliable at the sub-microscopic scale. The intracellular rotation of the flagella evidently cause the whole cell to gyrate, moving it through liquid in a corkscrew-like fashion.

The success of the recent election in Kansas, in which pro-science moderates took back control of the State Board of Education, depended in part on the willingness of citizens to get out and work on behalf of pro-science candidates, and in part on having strong pro-science candidates on the ballot. Kansas isn’t the only state that will be electing members of its State Board of Education this fall. Ohio will, too, and people and organizations in Ohio are seeking strong pro-science candidates to oppose the ID creationist members of the Ohio Board.

One such organization is HOPE – Help Ohio Public Education. HOPE is actively talking with potential candidates. For example, HOPE is in discussions with a potential pro-science candidate to run in District 7, in northeastern Ohio. That seat is currrently held by one of the two ID creationist thought leaders on the Oho State BOE, the member who made the original “two modesl” motion to the Ohio Board in 2000, first foreshadowed adding global warming to the list of topics to be “critically analyzed” by Ohio school children, and continues to push trash science.

HOPE has been impressed with how much the potential candidate could contribute to solving problems of school funding, state BOE and DOE governance, and curriculum, specifically including science education. He comes with a strong background on education issues and would be an outstanding member of the state board.

Regardless of whether you’re in or out of Ohio you can help. Contact Ohio newspapers, and in particular write a letter to the editor of the Akron Beacon Journal explaining why we need good candidates for the State BOE. Help HOPE improve Ohio education and do it today. If HOPE can persuade good candidates to run we have a good chance of taking out Ohio’s answer to Connie Morris. Help HOPE get a strong candidate on the ballot this fall. Thanks!

From here. Almost as good as this one from December 23, 2005:

I imagine that reading scientific journals is mostly a drag for ID advocates: all those papers highlighting evolutionary mechanisms, identifying transitional fossils, veryfing phylogenetic-based predictions must be really irritating. There are, however, few and far between papers that set the ID advocates’ hearts all aflutter, so when one appears, they make sure to milk it for all its P.R. worth. One of the recent examples was a 2003 paper by Hirotsune and colleagues in Nature, which reported that alteration of the pattern of expression of a purported mouse pseudogene (i.e. an apparently inactivated, non-functional gene, part of the so-called “junk DNA”) results unexpectedly in the modification of the activity of its functional counterpart, leading to a series of dramatic developmental defects.

Now, one of the recurrent claims of Intelligent Design is that most if not all of the features of any organism, including its entire genome, should somehow be useful. Thus, ID advocates enthusiastically latched on Hirotsune’s publication as supporting their claim that “junk DNA” is, in fact, not junk at all (indeed, if you Google for “Hirotsune” and “Intelligent design”, you will find over 100 hits). Alas for them, a brand new paper by Todd Gray and colleagues in the Proceedings of the National Academy of Sciences appears to completely refute the original findings.

I found this bit of Discovery Institute fact-mangling to be even more blatant and preposterous than usual.

It seems the good folk at DI are complaining that Paul Nelson May Now be Forever Misquoted, saying

Today there is another urban myth building up a head of steam, and being helped along by Darwinists, about Discovery Fellow Paul Nelson. Gaurdian [sic]reporter Karen Armstrong reports: ‘Great shakings and darkness are descending on Planet Earth,’ says the ID philosopher Paul Nelson, ‘but they will be overshadowed by even more amazing displays of God’s power and light.’ And yet this is pure rubbish because Nelson never said anything like this, and it turns out that Armstrong never even interviewed him. Nelson points this out in his letter to the Guardian demanding a correction. (Note to Paul: don’t hold your breath)

The trouble is, when you visit Nelson’s aforementioned letter, you quickly learn that Paul Nelson is actually thanking

…the indefatigable Nick Matzke for catching a wild misattribution in Karen Armstrong’s Guardian opinion piece of 31 July 2006. I just sent the following letter to the newspaper:

To the editors, In her opinion piece of 31 July, Karen Armstrong attributed remarks to me (as a direct quote) which I did not make: http://www.guardian.co.uk/commentis[…]3810,00.html The erroneous attribution can be found near my name, Paul Nelson. This was first brought to my attention by the widely-read science blog, The Panda’s Thumb: www.pandasthumb.org

…

And there we have it. As discussed days ago on the Thumb, a Guardian reporter egregiously misquoted IDer Paul Nelson; the error was posted, corrected and discussed by Nick Matzke here on the Thumb; Paul Nelson complained to the Guardian, citing Nick’s PT blog as his source; … and so, Robert Crowther concludes

Today there is another urban myth building up a head of steam, and being helped along by Darwinists, about Discovery Fellow Paul Nelson.

We’re not making this stuff up! The Moral of the story is that it’s best to put the old brain in gear before engaging the mouth. But when you see evil “Darwinists” around every corner, I guess old habits are hard to break!

Now that the voters of Kansas have replaced the pro-ignorance majority on the state school board with a pro-science one, I highlight a comment made today that demonstrates why good standards are important for teachers who come under political pressure.

About a month ago I wrote “Georgia Education on My Mind”, in which I mentioned the struggle of one veteran science teacher, Pat New, to give her students the education they deserved. Eventually, her administrators backed off when they discovered that what she wanted to teach, evolution, was actually part of the state standards. Today she left the following comment:

I was that teacher in Mike Winerip’s New York Times article. I can’t thank the Georgia Citizens for Integrity in Science Education enough for, first of all, their fight to make sure evolution was in the Georgia science standards and, second of all, for their support when I was in the middle of fighting my administrators and parents over my teaching those standards. Having those standards in place was the reason I decided to take the stand in the first place. I knew that, finally, I could teach evolution the way it was supposed to be taught, as the backbone of life science. Thank you, all of you who fought that fight.

Pat New

(Comment 116381)

Let’s keep it up. The teachers need us.

Since U.S. District Judge Casey Rodgers refused to lift a travel ban on Kent Hovind, I’ve been wondering when the itinerary on his web site would change to list “The Hoosegow” for up-coming events. However, ol’ Doc Dino must still be floating in the ether, because he still lists an appearance in my neck of the woods, Coeur d’ Alene, Idaho, for October 21.

In addition to watching the news on Kansas, we have been meaning to post these to PT but haven’t quite gotten to it, so here is a collection of recent commentary on ID/creationism, Kitzmiller, etc. Much of this has already been noted on the NCSE News page.

Coultergeist – Jerry Coyne reviews Ann Coulter’s book Godless in The New Republic, with about as much respect as she deserves (pass-through link, free registration required). I can’t claim responsibility for the science in Coyne’s essay like Dembski did for Coulter, but I did get to comment on a draft, and Coyne (who is personally targetted repeated by Coulter) did tell me that TNR wanted the review of Coulter’s book to be in the same style that Coulter herself wrote. So that explains the invective (although it appears to me that Coyne wasn’t able to turn his scientific side off completely, there are some low-invective zones). If you want to give the ol’ irony meter a spin, check out this post from an ID blogger who is defending Coulter from Coyne:

I think Coyne might have over-reacted just a tad to the part about Ann Coutler “attacking” him. But again, fact-distorting and insult-hurling have always been favorites for Coyne and the evolution community.

If current results hold, it looks like the creationists on the 10-member Kansas Board of Education have lost two seats in the Republican primary. The likelihood is therefore that the new Board of Education will switch from being a 6-4 pro-creationism majority to at least a 6-4 pro-science majority (depending on the November general election). This probably means the pro-ID/creationism science standards are history.

So let’s sum up the last 9 months:

The results of the primary in Kansas election are beginning to come in. The unofficial results are being posted every 10 minutes here on the website of the Kansas Secretary of State.