24 Replies to “Judge Jones on Peer Review (courtesy of Casey Luskin)

  1. 1
    scordova says:

    I see that our very own John Davison is on the list provided by Casey. It’s good to see Davison’s work along side that of my other friends who are on that list. It unfortunate Judge Jones did not recognize these publications in a landmark Federal case. Jones may yet have an opportunity to go down in infamy.

    Salvador

  2. 2
    KevinWParker says:

    I would like to see someone rebut Judge Jones’s statements USING ONLY EVIDENCE PRESENTED AT THE TRIAL. Jones was not allowed to go out and look for his own evidence, any more than a jury member is allowed to go out and inspect the scene of the crime. I am willing to concede that there are peer-reviewed publications supporting ID, but the plaintiffs in Dover made a good case that there are none such, and the defense did a very poor job of rebutting it.

  3. 3
    olegt says:

    Judge Jones did not come up with these statements on his own. It was Michael Behe who said during cross examination: \”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\”.

  4. 4
    Tom English says:

    Salvador or Bill,

    Would you please tell me where the list of peer-reviewed ID publications appears in the Kitzmiller evidence?

  5. 5

    Some of these were listed in my expert witness report, which the judge had and read before the Thomas More Law Center removed me as an expert witness. See Appendix 3 here: http://www.designinference.com.....embski.pdf.

  6. 6
    scordova says:

    Tom,

    I heard that an amicus brief was filed, by discovery institute with the judge.

    See Amicus Brief.

    Still, imho, the issue here is the Judge made a ruling that is not consistent with the truth. Whether he was knowlegeable or not, by the courts own standards, “ignorance is not an excuse.” I guess it doesn’t apply to federal rulings. Further, he shouldn’t be making rulings for all time on the very nature of things that might change.

    Salvador

  7. 7
    Tom English says:

    Judges regularly see evidence that they exclude from consideration at trial. Bill withdrew as an expert witness, and therefore his report was not evidence. In a fair trial, the judge bases his decision only on the evidence.

    The rest of the story about Bill’s withdrawal from the trial is that the plaintiffs’ tried to keep Jeffrey Shallit, who was originally supposed to rebut Bill’s testimony, as an expert witness. Judge Jones ruled against this. So the defendants lost Bill, and the plaintiffs lost Shallit.

    It is worth mentioning that Judge Jones wrote:

    “Dembski’s fears have been borne out not only in his own career, but also in the careers of other respected academics who have made the case for intelligent design. For example, the U.S. Office of Special Counsel recently conducted an investigation revealing how Smithsonian Institution scientists retaliated against a Smithsonian research associate [Richard von Sternberg] who edited a biology journal containing an article laying out the evidence for intelligent design.

    Given his legitimate concerns, Dembski withdrew to protect his work, his career prospects, and his colleagues.”

    At the bottom of the page containing this text, Judge Jones has a long footnote sketching the mistreatment of von Sternberg.

  8. 8
    MikeFNQ says:

    Shouldn’t this thread be renamed “Casey Luskin vs Michael Behe: Why Judge Jones should have ignored Michael Behe”?

  9. 9
    Scott says:

    A list of peer-reviewed Pro-ID papers & books:

    http://www.discovery.org/scrip.....38;id=2640

  10. 10
    Strangelove says:

    Scott, peer-edited is not the same as peer-reviewed. I wonder why they don’t split those up into two groups instead of lumping them together.

  11. 11
    Scott says:

    Sounds like hair-splitting to me. And knowing how the peer review process seems to work these days, I’m just glad that there are indeed pro-ID publications which made it thru.

  12. 12
    scordova says:

    olegt wrote:

    : \”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\”.

    That’s not the same as saying there are no peer-reviewed articles on ID.

    If one said, “there are no 2006-No.1 draft picks on the Washington Redskins this year”, one wouldn’t be justified in saying “there are no number no 2006-No.1 draft picks on any team”. Olegt misinterpreted the statment BADLY!

  13. 13
    Chris Hyland says:

    It would be interesting to know how many ID papers have been rejected by miansteam journals.

  14. 14
    scordova says:

    Here is at least one, and a very major one:

    Haldane’s Dilemma and Peer Review

    I have little doubt it would have passed if it were reviewed by Cornell geneticist John Sanford or any number of ID-sympathetic geneticists unworried about their jobs. But at the hands of Crow and Ewens, it didn’t stand a chance. This is a very compelling story!

    Salvador

  15. 15
    Scott says:

    I’d be interested to know how many peer-review committee members would experience academic/career persecution if they accepted pro-ID papers.

  16. 16
    Chris Hyland says:

    “Here is at least one, and a very major one” I’m not sure why thats pro-ID, but in any case so far we have a ratio of over ten to one so I’d say ID doesn’t have much to complain about so far.

    “I’d be interested to know how many peer-review committee members would experience academic/career persecution if they accepted pro-ID papers.”

    As far as I’m aware the process in confidential.

  17. 17
    Casey Luskin says:

    Hi all, I’d like to weigh in on this briefly. I apologize for this long comment, but since I haven’t hardly ever posted here, perhaps one could say I’ve saved up some comment-space. I hope this comment helps to clarify this matter, however.

    Did Judge Jones have Evidence of Peer Review?

    Someone noted that Discovery Institute submitted a brief listing many peer-reviewed papers. But the evidence was also directly in the record: With regards to Tom English’s inquiry, both Scott Minnich and Michael Behe testified before the court about pro-ID peer-reviewed papers:

    Q. Are there peer reviewed articles that make arguments for aspects of intelligent design that you’re aware of?
    A. I think there are around ten of them now that are in the literature that address this, I’m not sure of an exact number, but within the last couple of years.

    (Minnich Testimony, Day 20, PM, pg. 27)

    Q. Dr. Minnich, you’re not aware of any research articles advocating intelligent design in any peer reviewed scientific journals, are you?
    A. I think yesterday there was, as I mentioned, there were around, between, I don’t know, seven and ten. I don’t have the specific ones. But Dr. Axe published one or two papers in the journal Biological Chemistry that were specifically addressing concepts within intelligent design. Mike Behe had one. Steve Meyer has had one. So, you know, I think the argument that you’re not publishing in peer reviewed literature was valid. Now there are a couple out there. How many do we have to publish before it is in the literature and being evaluated? I mean, do we have to have 25? 50? I mean, give me a number.

    (Minnich Testimony, Day 21, AM, pg. 34)

    Expert witness testimony about the alleged lack of peer-reviewed papers was enough for Judge Jones to cite to Kevin Padian’s and Barbara Forrest’s claims that ID had no peer-reviewed papers (see pg. 87-88 of the online decision). But Judge Jones apparently ignored Minnich’s expert testimony which said precisely the opposite.

    Behe also testified to this effect:

    Q. Have you authored any articles appearing in peer reviewed science journals that make intelligent design arguments?
    A. Yes, I did, one.
    Q. What article is that?
    A. It was an article that I published with a man named David Snoke, who’s in the physics department at the University of Pittsburgh, and was published in a journal called Protein Science.
    (Behe Testimony, Day 10 AM, pg. 44)

    Now obviously we all know the Protein Science paper doesn’t say the phrases “intelligent design” or “irreducible complexity,” but I think most of us on this site agree tht it bears directly on those topics. Yet as I discuss here, by Judge Jones’s standards, the lack of a phase “intelligent design” should not preclude one from arguing the paper supports “intelligent design”:

    Judge Jones wrote that “Dr. Miller refuted Pandas’ claim that evolution cannot account for new genetic information and pointed to more than three dozen peer-reviewed scientific publications showing the origin of new genetic information by evolutionary processes.” (Kitzmiller v. Dover, 400 F.Supp. 2d 707, 744 (2005)). Miller’s discussion relied entirely upon the review article “The Origin of New Genes: Glimpses From the Young and Old” (by Manyuan Long, et al., Nature Reviews Genetics (4):865-875 (Nov., 2003)) and its citations to provide the “more than three dozen” articles. Yet the body text of the article does not even contain the word “information”, much less the phrase “new genetic information.” The word “information” appears once in the entire Long et al. article–in the title of reference #103. (Peer-Review, Intelligent Design, and John Derbyshire’s New Bumper Sticker (Part II))

    Yet Judge Jones refused to count Behe & Snoke’s Protein Science Paper because it “does not mention either irreducible complexity or ID.” (pg. 88 of online decision). Plain and simple: Judge Jones applied a double-standard to ID versus evolution papers.

    Behe and Peer-Review

    Did Behe really say there were no peer-reviewed papers? Michael Behe never said upon cross-examination “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.” Those were the words of Eric Rothschild, plaintiffs’ attorney, who, as much as he misrepresents intelligent design, is clearly a skilled cross-examiner. Here’s what actually happened–it’s a little complicated, but please try to follow me:

    Mr. Rothschild started off by leading Behe down a line of questioning where he was asking Behe if there are papers talking about the evolution of biological systems. Behe said that he needed to qualify his answers in order to say “no.” Behe explained that while some papers purport to talk about the evolution, the pro-evolution publications are lacking “[A.] … detailed rigorous accounts for complex molecular machines, not just either hypothetical accounts or sequence comparisons or such things.”

    (Behe Testimony [Behe speaking], Day 12 AM, pg. 22)

    Mr. Rothschild saw this as an opportunity to get Behe concede that ID didn’t meet that standard either. He then immediately asked Behe if equivalent accounts exist in the peer-reviewed literature about how such molecular machines were intelligently designed:

    Q. And, in fact, 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, is that correct?
    A. That is correct, yes.

    (Behe Testimony, Day 12 AM, pg. 22-23…note: Rothschild’s question here is where the statement Judge Jones attributes to Behe comes from)

    So what was going on here? Behe at this point had in his mind extremely detailed, rigorous explanations for how things originated via evolution. Behe was never asked “are there any peer-reviewed papers supporting ID?” He was thinking about highly detailed rigorous explanations with calculations, etc.

    Mr. Rothschild did a good job here as an attorney: he got Behe to have his mind fixated upon a high, but reasonable standard of rigor which Behe knew evolution failed. Then he asked Behe if ID met that level of rigor. Behe said “no,” but not because ID lacked peer-reviewed papers, but because as is seen directly below, the question asked “how intelligent design of any biological system occurred,” and Behe recognizes that intelligent design is less concerned with the “how designed” than with the “if designed”:

    Q. And again, intelligent design doesn’t describe how it happened?
    A. That’s correct, only to say that intelligence was involved somewhere in the process.
    (Behe testimony, Day 12, AM, pg. 67)

    So Mr. Rothschild’s question set up a false standard for Behe, because Mr. Rothschild’s question asked about the “how,” but Behe makes it clear that in terms of high level of detail, intelligent design is less about the “how designed” question and more about the “if designed” question. But Behe never said there was no direct support for intelligent design in the peer-reviewed literature. Yet Judge Jones cited Behe’s statements here to justify his claims “In addition to failing to produce papers in peer-reviewed journals,” “complete absence of peer-reviewed publications supporting the theory,” and “ID is not supported by any peer-reviewed research, data or publications.” (pgs. 88-88 of online decision).

    This summarizes almost all of Judge Jones’s analysis on peer-review. Was it fair? I don’t think so. And I think Judge Jones cited Behe’s agreement with Rothschild’s question to claim something much bigger, and much different, than what Behe was actually saying.

  18. 18
    Michaels7 says:

    “Judge Jones did not come up with these statements on his own. It was Michael Behe who said during cross examination: \”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\”.”

    By the quotes above I immediately assumed Behe said those exact words when in fact, he did not. This is misleading had it been left unchallenged by Casey.

    Thanks Casey for the long explanation of the transcripts.

    Its disgusting how one field of science must enforce its beliefs without criticism by judicial tyranny over the public. Being outgunned by lawyers does not insure truth wins, it only insures that young minds remain closed – in the past.

    That was easy up until a decade ago even, with one book and one teacher, but it will not last with the information revolution taking place.

  19. 19
    Tom English says:

    Casey,

    While I acknowledge that ID has peer-reviewed publications, the fact is that Judge Jones had to weigh conflicting expert testimony. Padian and Forrest said there were no peer-reviewed ID publications, and Minnich said “there were around, between, I don’t know, seven and ten. I don’t have the specific ones.”

    Judge Jones had to decide whom to believe, if anyone. Clearly he believed Padian and Forrest. His error, then, is that he failed to explain in the decision why he believed Padian and Forrest and disbelieved Minnich.

    I think everyone should see Judge Jones’ FULL explanation of why he did not count the article by Behe and Snoke as a peer-reviewed ID publication.

    “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).”

    So the problem goes much deeper than a failure to mention ID or IC. The research was not clearly tied to ID or IC. In contrast, the notion that “The Origin of New Genes” addresses “the origin of new genetic information” is hardly a stretch. I think you are wrong in saying that Judge Jones applied a double standard.

  20. 20
    olegt says:

    Michael7, Casey,

    I myself assumed that Behe said those words (I looked up the Wikipedia entry on [url=http://en.wikipedia.org/wiki/Michael_Behe#Dover_testimony]Michael Behe[/url]). He, in fact, did not. Those were words by plaintiff attorney Rothschild. Nonetheless, Behe agreed to that statement. Whether you like it or not, the exchange accurately reflects the status of ID in scientific literature.

  21. 21
    Casey Luskin says:

    Tom and Olegt,

    I appreciate your comments.

    Tom, you are right, the Judge has to decide who to believe–in fact that’s what Judges do. Two questions now arise: (1) Did Padian and Forrest give misleading testimony and (2) Did the Judge believe the party whose witnesses were accurately representing the state of ID-published support? I think the answer to both questions is “no.” And I agree with you that it would have been helpful if Judge Jones had explained why he disbelieved Minnich (and Behe) and believed Forrest & Padian.

    But in fact there are many examples where Judge Jones simply accepted what the plaintiffs said and ignored what the defense said. Judge Jones repeatedly believed the plaintiffs’ misrepresentations of ID when they said things like (1) ID appeals to the supernatural; (2) ID is just a negative argument against evolution; (3) ID has published no peer-reviewed literature; and (4) ID hasn’t been the subject of testing and research. In each case the Judge accepted the plaintiffs’ misconstrual of ID, even though it was patently false. I’m not going to get into all of this here right now, but a lot of this is addressed in Traipsing Into Evolution or if you don’t want to read a book, a lot of the arguments are summarized here. I’ll briefly deal with Jones’s claim that ID hasn’t undergone testing or research:

    Judge Jones continually believed the wrong people. He even made some claims that were plainly contradicted by courtroom testimony: Judge Jones wrote, ID has not “the subject of testing and research.” Yet I physically observed Scott Minnith testify and show numerous slides of his own laboratory experiments which did genetic knockout experiments on the bacterial flagellum and show that it is irreducibly complex (see Minnich’s Day 20 pm testimony, pg. 103-112). How can Judge Jones then say that ID hasn’t undergone “testing and research”? Judge Jones didn’t even mention Minnich’s slides in his ruling; he just ignored it as if it never happened. This is a consistent pattern we see in the ruling.

    In response to Olegt, I appreciate your comments and honesty, but I will just say that if you are right about Behe being right, it is for reasons that really don’t mean much. As I explain in my post above, Judge Jones took the exchange to claim much more than what Behe conceded, and Behe didn’t concede that ID lacks published support:

    So Mr. Rothschild’s question set up a false standard for Behe, because Mr. Rothschild’s question asked about the “how,” but Behe makes it clear that in terms of high level of detail, intelligent design is less about the “how designed” question and more about the “if designed” question. But Behe never said there was no direct support for intelligent design in the peer-reviewed literature. Yet Judge Jones cited Behe’s statements here to justify his claims “In addition to failing to produce papers in peer-reviewed journals,” “complete absence of peer-reviewed publications supporting the theory,” and “ID is not supported by any peer-reviewed research, data or publications.” (pgs. 88-88 of online decision).

    I will say this much though: I appreciate Olegt being here and I hope that he will stay, whether or not he is an ID-critic. And I hope that people at UncommonDescent will continue to treat ID-skeptics with the utmost respect. Thanks all, it’s been fun.

    Sincerely,

    Casey

    p.s. I may post some of these comments at EvolutionNews over the weekend.

  22. 22
    Charlie says:

    Hi Casey,
    Did you get the answer to your first question wrong?

  23. 23
    Tom English says:

    Casey,

    Thanks for your civility. As I wrote above, I wish Judge Jones had discussed Minnich’s claims explicitly. But I think we can make good sense of his statements about peer-reviewed publications by taking context into account and by reading carefully. Prior to addressing peer-reviewed publications, Judge Jones writes that evidence of irreducible complexity discredits Darwinism but does not support intelligent design. He states that the notion that evidence against Darwinism is evidence for ID depends on a false dichotomy of Darwinism and ID. When he later addresses peer-reviewed publications, he focuses on publications that support ID. One would expect him not to count publications that merely support irreducible complexity as support for ID.

    Before getting into details, note in your post above that Minnich was questioned only about peer-reviewed articles, not publications. Also, a reading of pp. 87-88 of the decision reveals that Judge Jones uses “peer-reviewed publication” synonymously with “peer-reviewed journal article.” While this is not the usage of scientists, it is clear in the plain-language text what Judge Jones means.

    Regarding the false dichotomy of Darwinism and ID, Judge Jones writes,

    “ID is at bottom premised upon a false dichotomy, namely, that to the extent evolutionary theory is discredited, ID is confirmed.” (p. 71)

    “ID proponents primarily argue for design through negative arguments against evolution, as illustrated by Professor Behe’s argument that “irreducibly complex” systems cannot be produced through Darwinian, or any natural, mechanisms. (5:38-41 (Pennock); 1:39, 2:15, 2:35-37, 3:96 (Miller); 16:72-73 (Padian); 10:148 (Forrest)). However, we believe that arguments against evolution are not arguments for design.” (pp. 71-72)

    Now for Judge Jones’ comments on peer-reviewed publications (journal articles):

    “As we will discuss in more detail below, it is additionally important to note that ID has failed to gain acceptance in the scientific community, it has not generated peer-reviewed publications, nor has it been the subject of testing and research.” (p. 64)

    This is just an introductory statement, not to be parsed closely. The actual discussion of peer-reviewed publications begins 23 pages later.

    “Accordingly, the one textbook to which the Dover ID Policy directs students contains outdated concepts and badly flawed science, as recognized by even the defense experts in this case.

    A final indicator of how ID has failed to demonstrate scientific warrant is the complete absence of peer-reviewed publications supporting the theory.” (pp. 86-87)

    The last sentence is merely transitional. It begins a paragraph that discusses the importance of peer review. Support for the claim comes in the next paragraph, which begins:

    “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.'” (pp. 87-88)

    Every sentence in this passage has a form of the word “support.” Note that in discussing Behe’s work, the judge distinguishes support for intelligent design from support for irreducible complexity.

    Returning now to the Minnich testimony you cited above,

    “Q. Dr. Minnich, you’re not aware of any research articles advocating intelligent design in any peer reviewed scientific journals, are you?
    A. I think yesterday there was, as I mentioned, there were around, between, I don’t know, seven and ten. I don’t have the specific ones. But Dr. Axe published one or two papers in the journal Biological Chemistry that were specifically addressing concepts within intelligent design. Mike Behe had one. Steve Meyer has had one.”

    Note that the question is about articles, not publications. Minnich is able to allude to only four articles. The two articles by Axe address specified complexity. The article by Behe (and Snoke) was claimed to address specified complexity, but Judge Jones ruled that it did not (see post 19). The review article by Meyer truly does advocate intelligent design, but “supports” ID by discrediting Darwinism. Given his decision that “Darwinism or ID” is a false dichotomy, should Judge Jones have counted this one?

    Interestingly, I see only four articles advocating ID (or irreducible complexity) in BIll Dembski’s annotated list of peer-reviewed publications, and they are the ones that Minnich mentioned.

  24. 24
    Casey Luskin says:

    Hi again all, I’m not sure if anyone is still following this thread but I appreciate the comments because it is good to explore these issues fully. Thanks all for their civility as well.

    Charlie asked if I was wrong to state “Did Padian and Forrest give misleading testimony”? Regarding the state of ID and peer review, I think they did give misleading testimony because anyone who suggests that ID has not published peer-reviewed papers and doesn’t talk about the papers which support ID and / or IC or CSI is not telling the whole story. I’m not saying they committed perjury, only that there’s a lot of relevant information they left off.

    Regarding Tom’s comments, Tom noted that “[o]ne would expect him not to count publications that merely support irreducible complexity as support for ID.” Of course Judge Jones took the “IC never supports ID” line from the plaintiffs, and ignored Behe’s testimony otherwise. This could justify his rejection of Behe & Snoke’s paper, except Judge Jones said it didn’t even say “irreducible complexity.” But what about Meyer’s paper? It explicitly advocates for ID–and it does so in a positive argument.

    Tom also says, “[w]hile this is not the usage of scientists, it is clear in the plain-language text what Judge Jones means.” That’s an interesting argument. If you’re right, then “publication” is not being used in its ordinary sense of the word. Anything can be a publication–and I don’t know why Judge Jones would consider a book to not be a “publication”–it would be a most strange usage of the word. But if this is the case, then when Minnich testified about “articles” then that should have meant publications in the eyes of Judge Jones.

    Finally Tom, I hate to say it, but I’m not sure if you accurately read Meyer’s article. You asked : “The review article by Meyer truly does advocate intelligent design, but “supports” ID by discrediting Darwinism. Given his decision that “Darwinism or ID” is a false dichotomy, should Judge Jones have counted this one?.” Judge Jones’s false dichomotomy theory of ID was an invention on the part of the plaintiffs, which he perpetuated. And Meyer’s article does make a positive case for ID. The article does NOT support ID by discrediting Darwinism. Rather, Meyer makes a strong positive case for ID:

    “Yet we know, based on our present experience of cause and effect relationships, that design engineers–possessing purposive intelligence and rationality–have the ability to produce information-rich hierarchies in which both individual modules and the arrangements of those modules exhibit complexity and specificity–information so defined. Individual transistors, resistors, and capacitors exhibit considerable complexity and specificity of design; at a higher level of organization, their specific arrangement within an integrated circuit represents additional information and reflects further design. Conscious and rational agents have, as part of their powers of purposive intelligence, the capacity to design information-rich parts and to organize those parts into functional information-rich systems and hierarchies.”

    “What natural selection lacks, intelligent selection–purposive or goal-directed design–provides. Rational agents can arrange both matter and symbols with distant goals in mind. In using language, the human mind routinely “finds” or generates highly improbable linguistic sequences to convey an intended or preconceived idea. In the process of thought, functional objectives precede and constrain the selection of words, sounds and symbols to generate functional (and indeed meaningful) sequences from among a vast ensemble of meaningless alternative combinations of sound or symbol (Denton 1986:309-311). Similarly, the construction of complex technological objects and products, such as bridges, circuit boards, engines and software, result from the application of goal-directed constraints (Polanyi 1967, 1968). Indeed, in all functionally integrated complex systems where the cause is known by experience or observation, design engineers or other intelligent agents applied boundary constraints to limit possibilities in order to produce improbable forms, sequences or structures. Rational agents have repeatedly demonstrated the capacity to constrain the possible to actualize improbable but initially unrealized future functions. Repeated experience affirms that intelligent agents (minds) uniquely possess such causal powers. Analysis of the problem of the origin of biological information, therefore, exposes a deficiency in the causal powers of natural selection that corresponds precisely to powers that agents are uniquely known to possess. Intelligent agents have foresight. Such agents can select functional goals before they exist. They can devise or select material means to accomplish those ends from among an array of possibilities and then actualize those goals in accord with a preconceived design plan or set of functional requirements. Rational agents can constrain combinatorial space with distant outcomes in mind. The causal powers that natural selection lacks–almost by definition–are associated with the attributes of consciousness and rationality–with purposive intelligence. Thus, by invoking design to explain the origin of new biological information, contemporary design theorists are not positing an arbitrary explanatory element unmotivated by a consideration of the evidence. Instead, they are positing an entity possessing precisely the attributes and causal powers that the phenomenon in question requires as a condition of its production and explanation.”

    Intelligent Design: The Origin of Biological Information and the Higher Taxonomic Categories

    The bottom line is that even under Judge Jones logic, there were articles that his criteria, and he was told about them by experts, whom he ignored. Judge Jones should not have made such strong statements to the opposite effect. Moreover, the other paper Jones disregarded were only logical conclusions of a train of logic which had wholly false presuppositions. Why should anyone defend this?

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