On EvolutionNews, John West attempts in 2nd part of a multipart series (does anyone remember the multi-part series that was going to address the criticisms of Meyer's Hopeless Monster paper?) to argue why the Judge in the Kitzmiller case was wrong.
West still seems to misunderstand some of the relevant issues.

For an earlier article in which I discuss West's similar flaws see Activist Judge or just poor reading skills and Sandefur's Why Kitzmiller is Not An "Activist" Decision and Further Thoughts on West's Attack on Judge Jones

He focuses on four particular "facts" which the Judge got wrong. Now, as is the case with all 'facts' they are open to interpretation. As I will show, the Judge hardly got the facts wrong, he merely disagreed with the interpretation of the Discovery Institute's Amicus Brief.

Fact 1: Judge Jones wrongly claims there are NO peer-reviewed scientific articles favoring ID.

Note that the Judge actually claims

Judge Jones wrote:

A final indicator of how ID has failed to demonstrate scientific warrant is the complete absence of peer-reviewed publications supporting the theory.

The difference between favoring and supporting should be self evident.

While the Discovery Institute is quick to claim a list of so-called scientific articles favoring ID, on closer examination it becomes quickly self evident that none of these actually support such a theory, mostly because any such theory is lacking and no attempt is made to explain the data using this so-called theory of ID.

The Judge observed from the testimony by Padian and Forrest as well as by Minnich and Behe that:

Judge Jones wrote:

The evidence presented in this case demonstrates that ID is not supported by any peer-reviewed research, data or publications. Both Drs. Padian and Forrest testified that recent literature reviews of scientific and medical-electronic databases disclosed no studies supporting a biological concept of ID. (17:42-43 (Padian); 11:32-33 (Forrest)).

On cross-examination, Professor Behe admitted that: "There are no peer reviewed articles by anyone advocating for intelligent design supported by pertinent experiments or calculations which provide detailed rigorous accounts of how intelligent design of any biological system occurred." (22:22-23 (Behe)). Additionally, Professor Behe conceded that there are no peer-reviewed papers supporting his claims that complex molecular systems, like the bacterial flagellum, the blood-clotting cascade, and the immune system, were intelligently designed. (21:61-62 (complex molecular systems), 23:4-5 (immune system), and 22:124-25 (blood-clotting cascade) (Behe)). In that regard, there are no peer-reviewed articles supporting Professor Behe's argument that certain complex molecular
structures are "irreducibly complex."17 (21:62, 22:124-25 (Behe)). In addition to failing to produce papers in peer-reviewed journals, ID also features no scientific research or testing. (28:114-15 (Fuller); 18:22-23, 105-06 (Behe)).

and the following footnote

Judge Jones wrote:

The one article referenced by both Professors Behe and Minnich as supporting ID is an article written by Behe and Snoke entitled "Simulating evolution by gene duplication of protein features that require multiple amino acid residues." (P-721). A review of the article indicates that it does not mention either irreducible complexity or ID. In fact, Professor Behe admitted that the study which forms the basis for the article did not rule out many known evolutionary mechanisms and that the research actually might support evolutionary pathways if a biologically realistic population size were used. (22:41-45 (Behe); P-756).

West wrote:

A number of the peer-reviewed articles supportive of design were referenced by biologist Scott Minnich during his testimony at trial. Was Judge Jones asleep during that part of Dr. Minnich's testimony?

From Minnich's testimony:

Q. Have you authored any articles appearing in peer reviewed science journals that make intelligent design arguments?

A. Not directly.

Q. You say not directly. Are there articles that provide support for intelligent design arguments that you've published?

A. I think so. I think all of them do. I think they're, you know, dissecting intricate components of subcellular organelles that support the general contention of irreducible complexity and design.

The DI also tries to peddle its 'peer reviewed' books. Funny that Behe's book is not mentioned anymore. The fiasco with the level of "peer review" of this book show how meaningless peer review is as it comes to books.

In conclusion, while the DI may argue that many or several relevant peer-reviewed examples exist supporting both Behe's irreducible complexity as well as Intelligent Design, Behe himself seems to be unaware of such papers. And in fact, on closer scrutiny none of these papers provide any support for Intelligent Design in any scientifically relevant manner.

Fact 2: Judge Jones wrongly treats theologian/philosopher Thomas Aquinas as the ultimate source of the argument to design.

Again West seems to be having a reading comprehension problem since the judge stated and West even quotes this

Judge Jones wrote:

He traced this argument back to at least Thomas Aquinas in the 13th century, who framed the argument as a syllogism: Wherever complex design exists, there must have been a designer; nature is complex; therefore nature must have had an intelligent designer.

What part of 'at least' causes West problems?

West again finishes with an ad hominem

West wrote:

Judge Jones either didn't read the brief, which is part of the official record of the case, or he again ignored the evidence simply because it didn't fit his predetermined conclusions.

Fact 3: Judge Jones wrongly claims that intelligent design "requires supernatural creation." (p. 30, emphasis added)

West complains that since ID proponents at times have stated that ID does not rely on the supernatural, that therefor the Judge must be wrong. However, simple logic shows that ID is all about the supernatural. West seems for instance to be rejecting the work by Dembski in this area. While ID's claims have evolved, its foundation on the supernatural cannot be denied.

As the Judge points out

Judge Jones wrote:

Prominent ID proponents have made abundantly clear that the designer is supernatural.

So while the DI may have submitted examples of ID proponents arguing now that ID is not about the supernatural, it's hard to put the 'genie back into the bottle'.

Again, the people who actually testified disagreed with West's interpretation, and remarkably this includes the defense witnesses as well. These include Behe, Minnich and Fuller

Judge Jones wrote:

Defendants' expert witness ID proponents confirmed that the existence of a supernatural designer is a hallmark of ID. First, Professor Behe has written that by ID he means "not designed by the laws of nature," and that it is "implausible that the designer is a natural entity." (P-647 at 193; P-718 at 696, 700).

Minnich is quoted:

Judge Jones wrote:

Professor Minnich testified that for ID to be considered science, the ground rules of science have to be broadened so that supernatural forces can be considered. (38:97 (Minnich)).

And defense witness Fuller

Judge Jones wrote:

Third, Professor Steven William Fuller testified that it is ID's project to change the ground rules of science to include the supernatural. (Trial Tr. vol. 28, Fuller Test., 20-24, Oct. 24, 2005).

It's hard to argue with defense witnesses now is it... But perhaps West considers their testimony to be a misrepresentation?

But the Judge did not stop with the defense witnesses, he also looked at public statements made by ID proponents

Johnson: Turning from defense expert witnesses to leading ID proponents, Johnson has concluded that science must be redefined to
include the supernatural if religious challenges to evolution are to get a hearing. (11:8-15 (Forrest); P-429).

Dembski: Additionally, Dembski agrees that science is ruled by
methodological naturalism and argues that this rule must be overturned if ID is to prosper. (Trial Tr. vol. 5, Pennock Test., 32-34, Sept. 28, 2005).

The Judge also observes that

Judge Jones wrote:

Although contrary to Fuller, defense experts Professors Behe and Minnich testified that ID is not creationism, their testimony was primarily by way of bare assertion and it failed to directly rebut the creationist history of Pandas or other evidence presented by Plaintiffs showing the commonality between creationism and ID.

Seems the Judge considered the evidence to be more convincing than the 'just so stories'.

Well, that's enough so far. It should be no surprise that the Judge's findings based on the actual evidence presented disagrees with how ID is presently 'sold' to the unaware public. However there is sufficient testimony and evidence to lay to rest most of the claims made by West.

Okay just for fun some quotes of ID proponents showing how the supernatural is required for ID:

Dembski:

The view that science must be restricted solely to purposeless, naturalistic, material processes also has a name. It's called methodological naturalism. "So long as methodological naturalism sets the ground rules for how the game of science is to be played, (intelligent design) has no chance (in) Hades."

Original Quote Here

Or see the article I wrote Ayn Rand Institute: The Bait and Switch of "Intelligent Design"

ID and Dembski have attempted to conflate the issue of the supernatural. Since they claim that science, because of its adherence to methodological naturalism, cannot address design, they must thus hold that criminology and archaeology for instance, are unable to address design. Thus, the conclusion that design must be supernatural becomes self evident. Although at other times ID proponents argue that science succesfully applies design detection. Such a confused argument. Depending on the circumstances ID argues either that design cannot be detected by science and on other occasions that science can in fact detect design.
Now it is self evident that Dembski's portrayal of methodological naturalism is flawed but at the same time his arguments reveal a deeper issue namely the inability of science to deal with an unembodied designer who resides outside nature.

Another great example

Ah, but we have experience with radio transmitters. At least with extraterrestrial intelligences we can guess what might have happened. But we don't have any experience with unembodied designers, and that's clearly what we're dealing with when it comes to design in biology. Actually, if an unembodied designer is responsible for biological complexity, then we do have quite a bit of experience with such a designer through the designed objects (not least ourselves) that confront us all the time. On the other hand, it is true that we possess very little insight at this time into how such a designer acted to bring about the complex biological systems that have emerged over the course of natural history.

Link

As Answers.com informs us

Un·em·bod·ied
a.

1. Free from a corporeal body; disembodied; as, unembodied spirits. Byron.

2. Not embodied; not collected into a body; not yet organized; as, unembodied militia.

And

The reason that attributing specified complexity to intelligence for biological systems is regarded as problematic is because such an intelligence would in all likelihood have to be unembodied (though strictly speaking this is not required of intelligent design—the designer could in principle be an embodied intelligence, as with the panspermia theories).

http://www.leaderu.com/offices/dembski/docs/bd-meta098.html

Strictly speaking ID is not about the supernatural but practically speaking we are not interested in natural designers. After all, science already deals with such designers quite adequately. As Wilkins and Elsberry show in The advantages of theft over toil: the design inference and arguing from ignorance ID is concerned with rarefied design.

Originally posted on the Panda's Thumb weblog.