It seems that ID has chosen to rekindle the ‘how does evolution create information’ question. See for instance “Richard Dawkins on the Origin of Genetic Information” at EvolutionNews.org where spokesperson Luskin presents this question. And yet, the question has been answered many times, so why are ID activist ignoring these explanations or pretending that it has not been answered succinctly and successfully?

One of the basic claims of ID is that processes of regularity and chance cannot create complex specified information. ID relies here on an equivocation of the term ‘information’ since ID’s definition of information is merely a measure of our inability to explain it. In other words, unlike the complexity and information that science can explain, ID relies on that which science cannot explain (yet?) and calls it complexity or information.

Confused? I bet… Many ID proponents have similarly fallen victim to the bait and switch approach here.

So whenever ID states that science cannot explain complex specified information, all one has to do is point out the tautological nature of the claim. When ID then switches to the more common definition of information and complexity, it is trivial to show how evolutionary processes can indeed generate in principle information and complexity.

The real question then becomes: Where these processes indeed involved in the evolution of life on earth? While science provides a rich framework to study these questions, ID is left at the sidelines, unable to contribute anything relevant since it refuses to constrain its designer, it refuses to provide pathways and processes.

And remember, whenever science proposes a pathway, all ID can do is reject a strawman version of it, namely a pathways based on pure chance. Of course, any non trivial scientific pathway is inaccessible to the calculations needed by ID to make its case.

On “Threads from Henry’s Web”, Henry Neufeld writes more about Colling and ‘teaching the controversy’

This action shows some of the destructive potential of ignorance, but it also removes any fig-leaf of respectability from the “teach the controversy” argument. The advocates of creationism generally do not want the controversy taught. They want to win. If they were to win a court case allowing their materials into the public school classrooms, their next move would be to prevent critical examination of those ideas, and then to prevent the teaching of evolutionary theory itself. I simply don’t believe the public propaganda. I never have, but the evidence that it is pure propaganda just keeps building up.

Henry describes himself as “… an author and lecturer, owner of Energion Publications, and president of Pacesetters Bible School.” His description of the problems and risks of ID seem timely and to the point.

On Evolution News, Crowther argues that

The Privileged Planet: Such a Dangerous Idea Its Author Had To Be Stifled

Of course, most who are familiar with the facts will understand that Crowther’s assertions are without much merit.
First of all, even Hauptman, who spoke out against Gonzalez, was clear to state that it was the scientific vacuity of ID which affected his vote about Gonzalez.

“[But] intelligent design is not even a theory. It has not made its first prediction, nor suffered its first test by measurement. Its proponents can call it anything they like, but it is not science,” added Hauptman. “It is purely a question of what is science and what is not, and a physics department is not obligated to support notions that do not even begin to meet scientific standards.

Although some have called systems biology a ‘friend of Intelligent Design’, reality is that systems biology is all but a friend of what is best known as ‘ignorance’.

In a recent article in BioSystems 88 (2007) 163–172, titled “Alternative routes and mutational robustness in complex regulatory networks”, Andreas Wagner and Jeremiah White describe how

Alternative pathways through a gene regulation network connect a regulatory molecule to its (indirect) regulatory target via different intermediate regulators. We here show for two large transcriptional regulation networks, and for 15 different signal transduction networks, that multiple alternative pathways between regulator and target pairs are the rule rather than the exception. We find that in the yeast transcriptional regulation network intermediate regulators that are part of many alternative pathways between a regulator and target pair evolve at faster rates. This variation is not solely explicable by higher expression levels of such regulators, nor is it solely explicable by their variable usage in different physiological or environmental conditions, as indicated by their variable expression. This suggests that such pathways can continue to function despite amino acid changes that may impair one intermediate regulator. Our results underscore the importance of systems biology approaches to understand functional and evolutionary constraints on genes and proteins.

So while ID proponents are arguing for an ‘edge’ to evolution, real science is uncovering a remarkable richness for evolution.

So let me ask the following question: Who has contributed to scientific knowledge here?

At Darwin or Design Jason Rennie talks to Dr Ryan Nichols. Dr Nichols wrote an interesting paper called Scientific content, testability, and the vacuity of Intelligent Design.

There are Hours of additional content

I appreciate Rennie’s link to Scientific content, testability, and the vacuity of Intelligent Design where I discuss Nichols’ paper and the vacuity of ID.

The actual paper by Nichols does not seem to be available online: Ryan Nichols, Scientific content, testability, and the vacuity of Intelligent Design theory The American Catholic Philosophical Quarterly, 2003 ,vol. 77 ,no 4 ,pp. 591 - 611.

Direct link to podcast

It’s another day, and Casey “The Energizer Bunny” Luskin is at it again, claiming that ID successfully predicted that “junk DNA” would be found to have a function. He has yet to explain how and why he believes that “Darwinism” somehow stifled research into those areas of the genome, and ignores the fact that scientists routinely use our understanding of evolution, common descent, and natural selection to identify areas of the genome to identify non-coding regions that are likely to have function. He does, however, provide us with an explanation for why he thinks that Intelligent Design somehow “predicts” function for all of the so-called “junk” DNA:

Intelligent design begins by studying the types of complexity produced by intelligent agents. We observe that intelligent agents produce things for a purpose, that is, to fulfill some function. This leads ID proponents to an expectation—yes, a prediction—that DNA will not tend to contain meaningless junk but will contain structures that have (or once had) a function for the organism. ID does not lead us to the expectation that our cells’ DNA will be largely non-functional garbate. The hypothesis—that “junk”-DNA will have function—is obviously experimentally testable. In fact, I know pro-ID biologists studying the function of junk-DNA who were inspired to do such research due to intelligent design. One biologist in particular is not yet tenured, and so I will not disclose his/her name. Suffice it to say, for this biologist, finding function for non-coding DNA was directly inspired by intelligent design.

If that explanation looks familiar to you, it should. It’s pretty much the same one he gave last month. This leads me to my two challenges - one that’s addressed to most of you, and one just for Casey:

Read more (at The Questionable Authority, where comments may be left):

Barbara Forrest and Paul Gross have a paper titled Biochemistry by design published in TRENDS in Biochemical Sciences Vol.32 No.7 , 2007. (10 pages including 1.75 pages of references) I am not surprised why the defense in the Kitzmiller trial tried to get Forrest removed as an expert witness.

Creationists are attempting to use biochemistry to win acceptance for their doctrine in the public mind and especially in state-funded schools. Biochemist Michael Behe is a major figure in this effort. His contention that certain cellular structures and biochemical processes – bacterial flagella, the blood-clotting cascade and the vertebrate immune system – cannot be the products of evolution has generated vigorous opposition from fellow scientists, many of whom have refuted Behe’s claims. Yet, despite these refutations and a decisive defeat in a US federal court case, Behe and his associates at the Discovery Institute continue to cultivate American supporters. They are also stepping up their efforts abroad and, worryingly, have achieved some success. Should biochemists (and other scientists) be concerned? We think they should be.

I apologize to James Hall for using his phrase in describing what Robert Crowther, and other Intelligent Design proponents, seem to be involved in when they are objecting to the simple fact that Intelligent Design is a straightforward argument from ignorance.

The problem is that ID proponents have used equivocating language which has led to much confusion amongst its followers. I cannot blame Crowther for taking serious the claims of his DI fellows, but merely claiming that ID is not an argument from ignorance is merely begging the question.

While it is relatively straightforward to reach the conclusion that ID is an argument from ignorance, it does require some careful analysis of how various terminologies are being used by ID proponents.

I have always found it fascinating how ID proponents try to avoid dealing with the real issues and instead focus on strawmen. For instance, Calvert and now Luskin are obsessed with the idea that:

Darwinian logic often contends that because a given proportion of ID proponents are creationists, ID must therefore be creationism. It’s a twist on the genetic fallacy, one I like to call the Darwinist “Genesis Genetic Argument.” As noted, it implies that each any and every argument made by a creationist must be equivalent to arguing for full-blooded creationism.

Much is wrong with this claim. If it were only so simple.

Dembski, quoting Moorad Alexanian:

Dembski wrote:

One can similarly say of Darwinian Theory of evolution, “I see evolutionary theory as not a theory–only a set of curious conjectures in search of a theory. True, it has great explanatory power, but a viable theory must have more than that. It must make predictions which can be falsified or confirmed.”

I am glad that at least Dembski is accepting the explanatory power of evolutionary theory, so now the question is merely, does evolutionary theory make predictions which can be falsified or confirmed.

However, a more urgent issue has been raised, namely, ID not only lacks explanatory power but also fails to make any non-trivial predictions.

We all remember Dembski’s admission that

As for your example, I’m not going to take the bait. You’re asking me to play a game: “Provide as much detail in terms of possible causal mechanisms for your ID position as I do for my Darwinian position.” ID is not a mechanistic theory, and it’s not ID’s task to match your pathetic level of detail in telling mechanistic stories. If ID is correct and an intelligence is responsible and indispensable for certain structures, then it makes no sense to try to ape your method of connecting the dots. True, there may be dots to be connected. But there may also be fundamental discontinuities, and with IC systems that is what ID is discovering.”

Nuff said

Robert Crowther wrote:

Critics of intelligent design theory often throw this question out thinking to highlight a weakness in ID. Richards shows that the theory’s inability to identify the designer is not a weakness, but a strength. ID does not identify the designer is because ID limits its claims to those which can be established by empirical evidence.

This is yet another example of why ID is scientifically vacuous. Indeed, if the designer could be established by empirical evidence, it would immediately eliminate the ‘Intelligent Designer’ as proposed by ID, namely a supernatural designer called ‘God’. In fact, in order to establish a ‘designer’ and in fact ‘design’ science inevitably uses such concepts as means, motives, opportunity, capability and so on. In addition, science uses eye witness accounts, physical evidence and more to support its thesis.

So how does ID infer design? Simple by arguing that a particular system or event cannot be explained by natural processes and thus should be seen as evidence for design. While ID also requires a specification, such specification is trivial, all that is required is some imagination about function.

ID faces a real problem: Either it insists that it cannot determine much of anything about the Designer which makes the ID inference inherently unreliable and thus useless (Dembski) or it attempts to become scientifically relevant but then it can at best conclude ‘we don’t know’.

So why do ID proponents still insist on such a flawed premise? Kitzmiller and Judge Jones explain.

The UK government has followed in the footsteps of the Dover ruling by confirming that “intelligent design”, aka “neo-creationism” will not be taught in schools as part of the National Curriculum, reports VNU Net.

“The government is clear that creationism and intelligent design are not part of the science National Curriculum programmes of study and should not be taught as science.”

Recently the Council or Europe released a report addressing their concerns with “Intelligent Design”.

After lamenting the honorary degree bestowed on Judge Jones, Dembski has set his sights on the Council of Europe who recently released a working document

The theory of evolution is being attacked by religious fundamentalists who call for creationist theories to be taught in European schools alongside or even in place of it. From a scientific view point there is absolutely no doubt that evolution is a central theory for our understanding of the Universe and of life on Earth.

Creationism in any of its forms, such as “intelligent design”, is not based on facts, does not use any scientific reasoning and its contents are pathetically inadequate for science classes.

The Assembly calls on education authorities in member States to promote scientific knowledge and the teaching of evolution and to oppose firmly any attempts at teaching creationism as a scientific discipline.

Dembski was not amused:

Dembski wrote:

The Council of Europe may justly be renamed as “The European Council for the Advancement of Atheism.” To believe in a God who acts in the world (aka theism) henceforward constitutes “religious extremism.” It will be interesting to see at what point advocacy of ID is regarded in Europe as a “hate crime” against … science? … society? … humanity?

This just after the Discovery Institute were touting the ‘expansion’ of ID into Europe. What has gone wrong?

As a side note, the term religious terrorism was used in the statement but in a rather different context. And neither does the proposal mention that the advocacy of ID is seen as a hate crime as the document is about the dangers of creationism (which includes ID) in education.

Given all of the recent ignorant yammering about “junk DNA” on the Discovery Institute’s blog and other ID blogs – unfortunately partially derived from a fair bit of ignorant yammering in the science media on the same topic – I think it is worth it to post a very simple and insightful post from April 2007 by T. Ryan Gregory entitled “The Onion Test.” Gregory is a professor at the University of Guelph and runs genomesize.org, an online database of animal genome sizes. He has recently become one heck of science blogger (at Genomicron) and has been doing a yeoman’s job of attempting to explain patiently and calmly to the world what the real scientific issues are with genome size, the “junk DNA” concept, and the problems with the ubiquitous-but-bogus storyline about junk DNA. Said ubiquitous-but-bogus storyline goes something like this: “Scientists have found that junk DNA is functional! Weren’t scientists (er, other scientists) stupid to think it was junk! What morons! Three cheers for our pet idea, which is that junk DNA does X.” ID advocates, who don’t even have an “X”, repeat the story but instead just riff off the vague idea that someone somewhere has explained what the function of “junk DNA” is, have played this storyline for all it’s worth, adding a completely vapid “We told you so!” on top of it.

For a dose of reality, I recommend that everyone read Gregory’s Onion Test. I quote it below for your convenience.

On Uncommon Descent Luskin asks Ayala the following question:

How would dual coding genes, which are nearly impossible to arise by chance, evolve via Darwinian processes?

Luskin “argues” that

Leading evolutionary biologist Francisco Ayala recently wrote in Proceedings for the National Academy of Sciences (PNAS) that “Chance is an integral part of the evolutionary process.” Ayala then explained why he thinks Darwinian evolution is right and ID is wrong: “Biological evolution differs from a painting or an artifact in that it is not the outcome of preconceived design. The design of organisms is not intelligent but imperfect and, at times, outright dysfunctional.” (“Darwin’s greatest discovery: Design without designer,” PNAS, 104:8567–8573 (May 15, 2007), emphasis added.) This questionable standard and conclusion is Ayala’s punchline against ID.

Ignoring for a moment the empty rhetoric of Luskin, let’s explore how Ayala may answer the question. Oh wait…

So-called “junk DNA” has been much the buzz lately. A recent (and outstandingly lousy) Wired magazine article on the topic uncritically printed assertions by the Discovery Institute’s lead hack Stephen Meyer that the discovery that some regions of DNA once thought to be functionless do have functions is, “a confirmation of a natural empirical prediction or expectation of the theory of intelligent design, and it disconfirms the neo-Darwinian hypothesis,” The author of the Wired article does not provide us with any explanation of how ID “theory” made that prediction, but a more recent article at the Discovery Institute’s Media Complaints Division does.

The basis for this astounding prediction (yes, I am using “astounding” sarcastically) is actually pretty simple, as Casey Luskin explains. “[D]esign theorists,” he tells us, “recognize that ‘Intelligent agents typically create functional things.’” That’s right. We can predict that noncoding DNA has some sort of function for the animal because we know that designers usually design functional things. If you have paid any sort of attention to what Intelligent Design proponents have said over the years, I should probably apologize to your next of kin, because there’s a pretty good chance that your head just exploded.

For the survivors, here’s why the sheer chutzpah of Casey’s assertion is enough to cause neurological overload.

In The Perimeter of Ignorance, Neil deGrasse Tyson, explains in no uncertain terms why Intelligent Design is scientifically vacuous.

Another practice that isn’t science is embracing ignorance. Yet it’s fundamental to the philosophy of intelligent design: I don’t know what this is. I don’t know how it works. It’s too complicated for me to figure out. It’s too complicated for any human being to figure out. So it must be the product of a higher intelligence.

Most notable quote

And what comedian designer configured the region between our legs-an entertainment complex built around a sewage system?

Neil deGrasse Tyson is the Frederick P. Rose Director of the Hayden Planetarium at the American Museum of Natural History and holds a PhD in Astrophysics and has an impressive CV

What is remarkable is how scientists come to realize more and more how ID is scientifically vacuous, as evidenced fully by its proven inability to contribute in a non-begging manner to our scientific knowledge beyond ‘poof’ and asking for more will quickly be dismissed as ‘pathetic’. Such is the life of an ID proponent…

Hat tip: Red State Rabble (watch the video)

On Higgaion, a Religion Scholar and Christian named Christopher Heard (Associate Professor of Religion) has responded to the attacks by the Discovery Institute on Hector Avalos.

Have I mentioned that I disagree with Hector on a number of points? He’s an atheist and I’m a believer; that alone will tell you that we don’t see eye to eye. But I am outraged by the DI’s attempts to slander a reputable and ethical scholar just because they’re upset that he got tenure when their pal didn’t.

Once again we learn how desperate the Discovery Institute has become now that most of the news media have failed to respond to their virtual onslaught of ‘press releases’. Probably because the media was quick to appreciate the level of inflationary ‘logic’ so common in Discovery Institute ‘press releases’.

What is ironic to me is that while objecting to what they believe to be religious discrimination, viewpoint discrimination and attacks on academic freedom (of speech), the DI is quick to abandon such concepts when it comes to Hector Avalos.

On Uncommon Descent Denyse comments on a paper which found how flies have ‘free will’. While ID proponents are quick to argue that (Darwinian) evolutionary pathways cannot explain ‘free will’, I will show, in a future posting, that this is a fallacious argument based on the common appeal to ignorance found amongst ID claims. In this specific case, I will present how science explains the evolution of Levy flight patterns.

In the mean time I would like to invite any ID proponent to step forward with ID’s best explanation for the existence of ‘Levy flight patterns’ as found in these fruit flies.

The Discovery Institute’s Casey Luskin is all atwitter about a new web article from German creationist Wolf-Ekkehard Lönnig [1] about how the giraffe is some kind of massive problem for evolution. Major planks [2] include the alleged lack of transitional fossils between the different fossil giraffe genera (never mind that creationists elsewhere typically accept that the differences between mammalian genera are small, and put the “created kind” or “basic type” at a higher taxonomic level), some confusion about whether one of the giraffe vertebrae is cervical or thoracic or something in between (note to creationists: read about homeotic shifts), and the allegation that there is no evidence for a feeding advantage for tall giraffes, relying on the fact that male giraffes are taller than female giraffes and a 1996 paper in American Naturalist (Simmons & Scheepers 1996, “Winning by a Neck: Sexual Selection in the Evolution of Giraffe”) that attempted to buck conventional wisdom and suggest that sexual selection was the cause of long necks in giraffes.

Sadly, the last plank is particularly bogus, since it completely ignores and displays no knowledge of a massively relevant and quite brilliant paper, published just back in January 2007 in American Naturalist, that constitutes an experimental demonstration of the relative feeding advantage of giraffe height:

John Wise, a biology professor at SMU has written an opinion on Intelligent Design

John Wise wrote:

Quoting Johnson’s own words, “The objective is to convince people that Darwinism is inherently atheistic, thus shifting the debate from creationism vs. evolution to the existence of God vs. the non-existence of God.” In other words, don’t allow this to be about creationism-ID versus science. Make people think this is all about a choice they have to make between God and science. This is deceptive at best.

ending with a brilliant reminder

The foundations of Intelligent Design are in politics and religion, not science. The nature of what we have learned about our physical world does not have to conflict with our faith and understanding of the spiritual domain. Don’t let your faith become dependent on the politics of flawed pseudoscience.

Although many have read the transcripts of the Kitzmiller v. Dover trial (HTML version | PDF version) and found them interesting, reading the transcripts does not give the full sense of what it was like to be in the Kitzmiller courtroom. In real life, in addition to the witness answering questions, the lawyers and witnesses were constantly referring to exhibits that were digitally projected onto a large screen on the right wall of the courtroom. Usually the exhibits were just documents, but when the science witnesses testified, their powerpoint presentations contain fossils, flagella, and everything else in between. I think it is safe to say that the testimony is much easier to understand when read with the demonstrative exhibits available (the exhibit lists and a few exhibits are available online).

However, it takes a lot of work to convert the slides to web format, add captions, embed them in HTML, etc. But as a first step, I and others at NCSE have done this for Kevin Padian’s testimony (testimony+slides | just slides).

I have just read the latest post of young-earth creationist/Discovery Institute fellow/Biola professor/blogger John Mark Reynolds. I think I am just going to have to occasionally serve the role of his guilty conscience in matters scientific. He has apparently thrown his own scientific conscience down a well somewhere, or he wouldn’t be able to say the wildly hypocritical things he does.

On UcD, Salvador Cordova, makes the common and fallacious argument that ID somehow predicted function in ‘junk DNA’. In fact, there is no logical foundation for this claim as ID lacks predictive power beyond ‘Darwinism does not explain X’. At most Sal can claim that people who are also proponents of ID have ‘predicted’ function for Junk DNA. But as such they are not much different from scientists who have predicted function for Junk DNA as well. Where they differ is in what motivated them to reach such a conclusion.

Cordova wrote:

ID theory has provided positive inspiration toward scientific inquiry and participating in the reversal of “the greatest mistake in the history molecular biology”, a mistake inspired by Darwinist dogma.

ID has contributed little either in predicting or establishing function in ‘Junk DNA’ but it also seems to be basing its claims on further ignorance about the origin and evolution of the term Junk DNA (which originated from the ideas of proponents of neutral evolution and was originally limited to refer to pseudogenes). While it should not come as a surprise that ID attempts to ride on the coat tails of real science, such an attempt can be quickly countered.

Nevertheless, even in his enthusiasm, Sal seems to have downgraded ID’s contribution to ‘positive inspiration’. Even ID proponents seem to shy away from making claims that ID is scientifically fertile and are willing to settle for ‘inspirational’.

Already in 1998 Should Scientists Scrap the Notion of Junk DNA? Bob Kuska describes how science had come to realize the many treasures in ‘junk DNA”.

(Journal of the National Cancer Institute, Volume 90, Number 14 Pp. 1032-1033)

and Bring in Da Noise, Bring in Da Junk–the Semantics of Junk DNA

A detailed eyewitness report on the Discovery Institute’s conference revival at Southern Methodist University last weekend has been published. This bit (p. 3) is particularly good:

At this point, we were fed up with the sheer lack of science being discussed. (Remember, ID theorists claim to support a science, not a religion.) So we held up our signs. They bore questions such as, “Why do we have wisdom teeth if they do not fit our jaws?” and “Why did it take 20 species of elephant to go extinct to get two species that survived?” and “Why do the ribosomes (protein synthesizing machinery) in our mitochondria match those of bacteria?” to name a few.

Salvador Cordova (Young Earth Creationist)

Darwinian TE (Theistic Evolution) just doesn’t cut it scientifically.

What a riot, as opposed to the scientifically defensible Young Earth variant or the scientifically vacuous Intelligent Design variant?

Today, we have part 3 of John Mark Reynold’s four six-part exercise in rationalizing institutionalized ignorance of geology, aka young-earth creationism. See previous discussion of part 1 and part 2. The really fascinating thing about Reynolds is how he can contradict his own professed high principles within seconds of stating them. For example:

The question is: “What is true?”, not what fits my preconceived philosophy of science or theology.

Way to go, great sentiment. Clearly, then, we should look at the physical evidence and conclude that the earth is not young and the global flood of Noah did not happen – oh, wait:

An olden goldie from Sarkar, Director and Professor at the Biodiversity and Biocultural Conservation Laboratory, of the University of Texas-Austin, who had the good fortune (sic) to debate Paul Nelson.

“It wasn’t much of a debate, with Nelson conceding that intelligent design was far from being a scientific theory, that it had no legitimacy as part of a high school curriculum, and that it had to develop a laboratory research record before it can be taken seriously.”

Wow, was that all?

On UcD, Dembski posts a ‘response’ to Steve Reuland and others pointing out that the paper which Dembski called pro-ID wasn’t.

Dembski wrote:

I posted a reference the other day to a peer-reviewed paper by two Finnish ID-supporters that I claimed supported ID. The paper highlighted that evolutionary methods work to the degree that they are directed. As is typical with our detractors, whenever a pro-ID paper by pro-ID scientists comes out in a peer-reviewed biology journal, they try their best to show that it doesn’t actually support ID. An example is the following post at PT by Steve Reuland:

The response seems to be that it was a paper by two ID supporters (interestingly enough Dembski may have out-ed the second author).

What is Dembski’s ‘devastating argument’? Now stop snickering and pay attention

So let me spell it out: DIRECTED EVOLUTION IS NON-DARWINIAN. DARWINIAN EVOLUTION IS NON-DIRECTED.

Egnor wrote:

Dr. Cartwright is mistaken. Darwin asserted that all natural biological complexity arose by random undesigned variation and natural selection.

Anyone familiar with Darwin would understand that this is incorrect. In fact, Darwin is clear that he considers natural selection one of various mechanisms, although he considered it the most relevant one.
Also, Egnor may want to familiarize himself with the concept of randomness as used by Darwin.
In fact, Darwin used an analogy to artificial selection to formulate his thesis of natural selection, in other words, one may argue that in this sense, Darwin identified the designer.

Charles Darwin wrote:

Furthermore, I am convinced that Natural Selection has been the main but not exclusive means of modification.

Source: Origin of Species, Introduction, page 6

John Mark Reynolds has put up the second part of an essay he is writing on the topic of how young-earth creationists like himself can rationalize sacrificing their scientific honesty on the altar of Biblical inerrancy. Here was my post on part 1.

Here’s a really stunning bit:

Christianity has a general view of the world that accounts for why science works … it allows the cosmos to be a cosmos (ordered) in a deep sense. Secularism lacks the same strength.

On UcD, Dembski shows such a level of despair about the lack of fertility of the ID thesis that he is willing to claim anything which mentions the word Darwin(ism) and problem(atic) as ID friendly. While Dembski provides, as usual, little more than a snippet introduction and fails to formulate much of anything similar to what could be considered an argument, I argue that his claim that the paper is pro-ID is lacking in logic, supporting evidence and relevance.

It is helpful to remind ourselves of what Intelligent Design is, free from its rhetoric and equivocation: “The set theoretic complement of chance and regularity”. In other words, that which cannot be explained by chance and regularity is given the label ‘intelligent design’. In this case we notice that the authors are talking about science exploring a better understanding of proteins (in other words regularities) as well as Darwinian approaches to design proteins (regularity and chance).

Here’s a pro-ID article without the usual disclaimers (e.g., a ritualistic suck-up to Darwin, an obligatory sneer at ID). Perhaps this is a sign of things to come.

Protein engineering: opportunities and challenges
Matti Leisola and Ossi Turunen

Journal Applied Microbiology and Biotechnology
SOURCE: http://www.springerlink.com/content/d51477251558…

|Abstract: The extraordinary properties of natural proteins demonstrate that life-like protein engineering is both achievable and valuable. Rapid progress and impressive results have been made towards this goal using rational design and random techniques or a combination of both. However, we still do not have a general theory on how to specify a structure that is suited to a target function nor can we specify a sequence that folds to a target structure. There is also overreliance on the Darwinian blind search to obtain practical results. In the long run, random methods cannot replace insight in constructing life-like proteins. For the near future, however, in enzyme development, we need to rely on a combination of both.

Steve Reuland already defused much of the ‘claims’ made in a posting on PT called The Pro-ID Paper That Wasn’t. I intent to focus instead on the scientific irrelevance that is better known as “Intelligent Design”

Few things are more ironic than young-earth creationist John Mark Reynolds (theologian at Biola, Discovery Institute fellow, leader in the ID movement) lecturing scientists about truth, stubborn facts, and having an “open philosophy of science.” If there’s an earthquake in LA today, it won’t be the tectonic plates shifting, it will be the simultaneous detonation of thousands of irony meters. How does the man get up in morning, when young-earth creationism is as hopelessly false on the empirical facts as anything ever has been in the whole history of science, and when the fundamentalist movement’s promotion of young-earth creationism is perhaps the biggest example of systematic fraud ever perpetrated on the American public? If you ever need an example of an ID advocate blathering lip service about “truth”, while shamelessly disregarding it in practice at the exact same time, here you go.

Via John Wilkins, a law student’s dissection of his professor’s insistence that the universe displays evidence of design. It’s an excellent analysis of the emptiness of the intelligent design movement’s argument for detecting design in the world. An extract:

I said that in order to infer intelligence from something, you would need an analytical framework. For example, “These particular factors, present in a given phenomenon, are indicative of intelligence for these reasons. Etc. Those factors are present in this phenomenon, therefore we can conclude that this phenomenon is the result of intelligence.” It seems like a simple framework; no more than instructions on how to recognize something, a sort of “Field Guide to Discerning Intelligence in the World.”

Some people, whose intellectual honesty is as questionable as my professor’s, have actually tried to posit “particular factors” that should be indicative of intelligence. Popular methods include Michael Behe’s “irreducible complexity” and William Dembski’s “specified complexity.” Neither is satisfactory. Behe’s idea has been shown wrong by experiment and Dembski’s idea assumes that we can know the probability of the occurrence of any phenomena. (“Specified complexity” is supposed to be anything that is both highly complex and highly unlikely. Except how do you know if it is unlikely? What is the probability of trees? Impossible to say.)

Nobody has yet come up with a convincing “Field Guide to Discerning Intelligence in the World,” but that did not stop my professor from insisting that I have no basis for failing to see intelligence in “natural” phenomena. Apparently it did not occur to him that since he (via Cicero, or vice versa) was making the proposition that “Intelligence is evident in natural phenomena,” it was up to him to explain why exactly that proposition should be accepted, not up to me to demonstrate why it is incorrect.

Just so. ID creationists endlessly assert that they have a methodology for detecting design in biological things, but when push comes to shove, they never ever actually apply it. Has anyone ever seen systematically gathered validation or reliability data on any of their design detection methods? I haven’t. So why is the methodology so difficult to apply? Because it rests firmly (and solely) on the claim “I know it when I see it”. And who is doing the “seeing” is the main variable, not the “it”. It’s an entirely subjective notion.

RBH

The Dallas News reports that at the Southern Methodist University, several science professors have objected to a planned presentation on “Intelligent Design”. Acutely familiar with the history of Intelligent Design, the science professors state that:

“These are conferences of and for believers and their sympathetic recruits,” said the letter sent to administrators by the department. “They have no place on an academic campus with their polemics hidden behind a deceptive mask.”

The SMU quickly clarified its position

“Although SMU makes its facilities available as a community service, and in support of the free marketplace of ideas, providing facilities for those programs does not imply SMU’s endorsement of the presenters’ views,” the statement said.

The concern is real namely that

Many SMU science professors say they are worried that merely allowing “Darwin vs. Design” on campus could give the public impression that Intelligent Design has support from scientists at the school.

Which led the departments of Anthropology, Biological Sciences and Geological Sciences to respond as follows:

“In this case, the Departments of Anthropology, Biological Sciences, and Geological Sciences in SMU’s Dedman College of Humanities and Sciences wish to reaffirm their commitment to applying rigorous scientific principles to teaching and research on the subject of evolution.”

Just when you believe that ID activists could not shoot themselves in the foot any further, Casey Luskin comes to the rescue, and Dembski decides to add some fuel to the smoldering fire. So what is going on this time that ticked of our friends at the Ministry of Media Complaints at the Discovery Institute’s Center for the Renewal of Science and Religion? At Red State Rabble, Pat Hayes and at the Austringer Wesley Elsberry explain Casey Luskin’s misplaced ‘outrage’ and show how once again, poor reading and listening skills (see also my previous posting about Dembski mangling Darwin) allow ID activists to create yet another strawman.

While ID is busy with their theological arguments, science is still waiting patiently for ID to present a scientific case ever since ID was found and ruled to be scientifically vacuous.

Enjoy.

On Red State Rabble, Pat Hayes shows the vacuity of Dembski’s ‘arguments’. Dembski had blogged on his Uncommon Descent website a quote from Darwin’s Descent of Man. What follows is Pat Hayes fisking Dembski’s comments.

Dembski wrote:

Darwin wrote:

The reckless, degraded, and often vicious members of society, tend to increase at a quicker rate than the provident and generally virtuous members. Or as Mr. Greg puts the case: “The careless, squalid, unaspiring Irishman multiplies like rabbits: the frugal, foreseeing, self-respecting, ambitious Scot, stern in his morality, spiritual in his faith, sagacious and disciplined in his intelligence, passes his best years in struggle and in celibacy, marries late, and leaves few behind him. Given a land originally peopled by a thousand Saxons and a thousand Celts—and in a dozen generations five-sixths of the population would be Celts, but five-sixths of the property, of the power, of the intellect, would belong to the one-sixth of Saxons that remained. In the eternal ‘struggle for existence,’ it would be the inferior and less favoured race that had prevailed—and prevailed by virtue not of its good qualities but of its faults.”

Sounds pretty damning, doesn’t it? But is it?

On Uncommon Descent, JohnnyB states that

I’m currently working through Robustness and Evolvability in Living Systems, and came across the following information which seems to be right in line with Denton’s evolution by natural law ideas:

A final, especially counterintuitive feature of RNA sequence space is that all frequent structures are near each other in sequence space. Consider a randomly chosen sequence that folds into a frequent structure and ask how far one has to step away from the original sequence to find a sequence that folds into this second structure…For instance, for RNAs of length n = 100 nucleotides, a sphere of r = 15 mutational steps contains with probability one a sequence for any common structure. This implies that one has to search a vanishingly small fraction of sequence space…to find all common structures.

Yes, laws of nature have indeed led to RNA space being extremely suitable for ‘evolution’ due to its scale free nature. Of course, scale free networks have been shown to be able to arise from the simple process of duplication and preferential attachment. And that’s exactly what we observe in for instance gene duplication. In other words, johnnyb has once again observed how the designer is quite natural, reducing even further ID’s standing and underlining ID’s scientific vacuity as it provides NO explanations as to why, how etc. Unlike science.

I have discussed these fascinating properties of RNA space and the topic of evolvability in many postings at PandasThumb. It’s good to come to realize that some IDers are actually reading scientific research, even though accepting scientific explanations completely undermines ID’s attempt to hide in ignorance.
JohnnyB also gives me some hope that IDers, properly exposed to real science, will quickly reject Intelligent Design as scientifically vacuous.

Briant Trent, professional essayist, screenwriter and novelist, reports in the American Chronicle on a question he asked Intelligent Design proponent Jonathan Wells during the Cato Insitute sponsored debate between Shermer and Wells.

His simple question, and Wells’ answer shows the scientific vacuity of Intelligent Design. So what was the question? Brian asked Wells what his alternative to the evidence for natural selection was

“I don’t think I’m obligated to propose an alternate theory,” Wells publicly stated. “I don’t pretend to have an alternate theory that explains the history of life.”

On Uncommon Descent Bill Dembski shows some confusion as to how to interpret the research by Oliver Rando and Kevin Verstrepen. While it may be that Dembski could not spare the time from his supposedly busy research (sic) schedule, a simple reading of the actual article would have resolved much of the confusion.

Remember to use the secret handshake whenever you need to get an ID paper past the Darwinian goalies: “Although these observations do not undermine Darwin’s theory, …”

ABSTRACT: According to classical evolutionary theory, phenotypic variation originates from random mutations that are independent of selective pressure. However, recent findings suggest that organisms have evolved mechanisms to influence the timing or genomic location of heritable variability. Hypervariable contingency loci and epigenetic switches increase the variability of specific phenotypes; error-prone DNA replicases produce bursts of variability in times of stress. Interestingly, these mechanisms seem to tune the variability of a given phenotype to match the variability of the acting selective pressure. Although these observations do not undermine Darwin’s theory, they suggest that selection and variability are less independent than once thought.

Rando O