peer reviewed ID publications?

Dear Discovery Institute,

Today we will be considering the validity of your claim that there is a strong base of peer-reviewed articles and books on Intelligent Design. The articles in question will be taken directly from your website ( http://www.discovery.org/a/2640 ). The following question will be raised: do these publications truly qualify as peer-reviewed works in a valid sense (ie. a peer review system that doesn't include ID merely because it is ID, but rather on it's scientific merits?)/

The first questionable articles are those published in "Darwinism, Design, & Public Education, edited by John Angus Campbell and Stephen C. Meyer" (from your site). The fact that Meyer is both an editor of the book and also a major player in the internal politics of the Discovery Institute, it is apparent that there would, of course, be papers supportive of Intelligent Design included in this book. Therefore, it is not possible to consider this work an independent scientific publication due to the fact that ID is essentially guaranteed inclusion in the text with little or no regards to the validity of ID as a "science". Other ID-based or ID/evolution debate-based conference and journal publications are also removed with this group.

Removal of those sources strongly cuts down the base of "peer-reviewed" journal articles listed on your site. We will continue by removing "peer-reviewed" books, especially those that are either edited by strong ID proponents or attempting to cover both ID and evolution. While books may have valid information in them, the fact is that they are not required to be scientifically accurate, and thus are not admissible for consideration as scientific publication under our qualifications in this blog. This once again severly cuts down the list of so-called "peer-reviewed" publications.

Now we can begin to look at the scientific papers left. The first step in this process is to remove the journal articles that have been listed multiple times on your database (ie. multiple listings for single articles...almost seems like you're trying to make it look like you have more articles than you do...). Then we can begin looking at these papers (quotes taken from listed site unless stated otherwise:

"M.J. Behe and D.W. Snoke, “Simulating Evolution by Gene Duplication of Protein Features That Require Multiple Amino Acid Residues,” Protein Science, 13 (2004): 2651-2664.
In this article, Behe and Snoke show how difficult it is for unguided evolutionary processes to take existing protein structures and add novel proteins whose interface compatibility is such that they could combine functionally with the original proteins. By demonstrating inherent limitations to unguided evolutionary processes, this work gives indirect scientific support to intelligent design and bolsters Behe’s case for intelligent design in answer to some of his critics. "

"Indirect scientific support" does not qualify as a scientific article on Intelligent Design. Nice try, but the ID movement needs to do more than this if they hope to gain scientific validity. We will now remove all articles providing only "indirect scientific support" for ID from our list.

The following article is introduced as if it provides a compelling peer-reviewed article supportive of ID, implying that ID has actually gotten through the peer-review process:

"D. A. Axe, “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds,” Journal of Molecular Biology, Vol. 341 (2004): 1295–1315.
This experimental study found that functional protein folds are extremely rare, finding that, “roughly one in 1064 signature-consistent sequences forms a working domain” and that the “overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 1077.” Axe concludes that “functional folds require highly extraordinary sequences.” Since Darwinian evolution only preserves biological structures which confer a functional advantage, this indicates it would be very difficult for such a blind mechanism to produce functional protein folds. This research also shows that there are high levels of specified complexity in enzymes, a hallmark indicator of intelligent design. Axe himself has confirmed that this study adds to the evidence for intelligent design: "In the 2004 paper I reported experimental data used to put a number on the rarity of sequences expected to form working enzymes. The reported figure is less than one in a trillion trillion trillion trillion trillion trillion. Again, yes, this finding does seem to call into question the adequacy of chance, and that certainly adds to the case for intelligent design." See Scientist Says His Peer-Reviewed Research in the Journal of Molecular Biology "Adds to the Case for Intelligent Design".

However, here it looks as if the author himself is stating that the article does not provide direct support for ID:

" concluded in the 2000 JMB paper that enzymatic catalysis entails "severe sequence constraints". The more severe these constraints are, the less likely it is that they can be met by chance. So, yes, that finding is very relevant to the question of the adequacy of chance, which is very relevant to the case for design. In the 2004 paper I reported experimental data used to put a number on the rarity of sequences expected to form working enzymes. The reported figure is less than one in a trillion trillion trillion trillion trillion trillion. Again, yes, this finding does seem to call into question the adequacy of chance, and that certainly adds to the case for intelligent design. " ( http://www.evolutionnews.org/2007/01/journal_of_molecular_biology_a.html )

Here's another indirect article. Although the ID term "complex specified information" is used in description, this paper is still not a pure ID-supportive paper that has made it through peer-review:

"D.K.Y. Chiu & T.H. Lui, “Integrated Use of Multiple Interdependent Patterns for Biomolecular Sequence Analysis,” International Journal of Fuzzy Systems, 4(3) (September 2002): 766-775.
The opening paragraph of this article reads: Detection of complex specified information is introduced to infer unknown underlying causes for observed patterns. By complex information, it refers to information obtained from observed pattern or patterns that are highly improbable by random chance alone. We evaluate here the complex pattern corresponding to multiple observations of statistical interdependency such that they all deviate significantly from the prior or null hypothesis. Such multiple interdependent patterns when consistently observed can be a powerful indication of common underlying causes. That is, detection of significant multiple interdependent patterns in a consistent way can lead to the discovery of possible new or hidden knowledge.” "

Lets keep looking! Here's a math-based publication:

"
Ø. A. Voie, "Biological function and the genetic code are interdependent," Chaos, Solitons and Fractals, Vol 28(4) (2006): 1000-1004.
In this article, Norwegian scientist Øyvind Albert Voie examines an implication of Gödel’s incompleteness theorem for theories about the origin of life. Gödel’s first incompleteness theorem states that certain true statements within a formal system are unprovable from the axioms of the formal system. Voie then argues that the information processing system in the cell constitutes a kind of formal system because it “expresses both function and sign systems.” As such, by Gödel’s theorem it possesses many properties that are not deducible from the axioms which underlie the formal system, in this case, the laws of nature. He cites Michael Polanyi’s seminal essay, Life’s Irreducible Structure, in support of this claim. As Polanyi put it, “the structure of life is a set of boundary conditions that harness the laws of physics and chemistry their (the boundary condition's) structure cannot be defined in terms of the laws that they harness.” As he further explained, “As the arrangement of a printed page is extraneous to the chemistry of the printed page, so is the base sequence in a DNA molecule extraneous to the chemical forces at work in the DNA molecule.” Like Polanyi, Voie argues that the information and function of DNA and the cellular replication machinery must originate from a source that transcends physics and chemistry. In particular, since as Voie argues, “chance and necessity cannot explain sign systems, meaning, purpose, and goals,” and since “mind possesses other properties that do not have these limitations,” it is “therefore very natural that many scientists believe that life is rather a subsystem of some Mind greater than humans.”"

Looks promising at first glance. However, once the paper is looked at, it doesn't seem to argue in favor of ID. Here's the abstract and conclusion for the paper:

"Life never ceases to astonish scientists as its secrets are more and more revealed. In particular the origin of life remains a mystery. One wonders how the scientific community could unravel a one-time past-tense event with such low probability. This paper shows that there are logical reasons for this problem. Life expresses both function and sign systems. This parallels the logically necessary symbolic self-referring structure in self-reproducing systems. Due to the abstract realm of function and sign systems, life is not a subsystem of natural laws. This suggests that our reason is limited in respect to solve the problem of the origin of life and that we are left taking life as an axiom...

Subsystems of the mind as functional objects or formal systems are unique in respect to other phenomena that follows the laws of nature and are subsystems of the universe. Life express both function and sign systems, which indicates that it is not a subsystem of the universe, since chance and necessity cannot explain sign systems, meaning, purpose, and goals [26]. Quite contrary, the human mind possesses other properties that do not have these limitations, the property of creativity with ability to create through choice with intent. This choice doesn’t violate any laws. It merely uses dynamically inert configurable switches to record into physicality the nonphysical choices of mind. It is therefore very natural that many scientists believe that life is rather a subsystem of some Mind greater than humans or symbolic number cruncher referred to by [25]. At least as observers we are left taking life as an axiom as Nils Bohr suggested in a lecture published in Nature [27] “life is consistent with, but undecidable from physics and chemistry” [19]."
http://home.online.no/~albvoie/index.cfm

While this article appears, at first, to support ID, a close read of the article shows that it, in fact, does not. Hypothetical mathematical arguments are employed to give an idea of complexity to the origin of life. However, science has shown us time and time again that mathematical probability arguments are often misguided. The following site also shows us more rebuttals of ID peer-review claims: http://www.talkorigins.org/indexcc/CI/CI001_4.html

The only articles left are either exceedingly difficult to access or continue to employ the same type of logic discussed above. If ID was a valid scientific entity, however, one would expect common, easily accessible, staunchly pro-ID papers published in mainstream journals such as Science or Nature rather than a few papers supposedly in support of ID that yet never seem to imply that ID is the cause behind these papers in obscure journals (for the most part). Publications in books put together by ID advocates or authors attempting to cover the ID movement and evolutionary theory do not count as independent peer-reviewed articles due to the fact that at least some pro-ID papers are guaranteed publication in these works by default. Somehow, the fact that the Discovery Institute repeats the listing of multiple articles multiple times on this list, as well as the fact that most of these publications are published specifically in bodies that are meant by nature to include ID theory publications, leads me to wonder about the validity of the Discovery Institute's claims. What is especially telling is the fact that many of the papers that the ID movement use for support don't even involve ID within the pagese of the papers involved. It seems like Discovery Institute is fishing for any possible citation in an attempt to buy credibility for their pet theory.