Intelligent Design and Peer Review

A Response to Eugenie Scott and the NCSE
By William A. Dembski
Discovery Institute
November 1, 2003
Print ArticleOriginally published Oct. 10, 2003

Eugenie Scott’s letter of September 30, 2003 to members of the Texas State Board of Education purports to show that intelligent design research is not published in the peer-reviewed literature. But in fact, Scott has purposely failed to disclose certain key items of information which demonstrate that intelligent design research is in fact now part of the mainstream peer-reviewed scientific literature.

I can substantiate the charge that Scott has purposely failed to disclose key information in this regard. Scott and I have met at several conferences and debates, and we correspond typically a few times a year by email. Here is a paragraph from an email she sent me on December 3, 2002 (in context, Scott is disparaging my work on intelligent design because, so she claims, it has not been cited in the appropriate peer-reviewed literature):

“It would perhaps be more interesting (and something for you to take rather more pride in) if it were the case that the scientific, engineering, and mathematical applications of evolutionary algorithms, fuzzy logic and evolution, etc., referenced TDI or your other publications and criticisms. In a quick survey of a few of the more scholarly works, I didn’t see any, but perhaps you or someone else might know of them.”

The abbreviation “TDI” here refers to my book The Design Inference (more about this book in a moment because Scott disparages it also in her letter of September 30, 2003). Now the fact is that this book has been cited in precisely the literature that Scott claims has ignored it. I pointed this out to her in an email dated December 6, 2002. Here is the key bibliographic reference, along with the annotation, that I sent her:

Chiu, D.K.Y. and Lui, T.H. Integrated use of multiple interdependent patterns for biomolecular sequence analysis. International Journal of Fuzzy Systems. Vol.4, No.3, Sept. 2002, pp.766-775.

The article begins:
“Detection of complex specified information is introduced to infer unknown underlying causes for observed patterns [10]. 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 [8]. 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.”
Reference number [10] here is to The Design Inference.

Not only does this article cite my work favorably, but it makes my work in The Design Inference the basis for the entire article. When I sent Scott this information by email, she never got back to me. Interestingly, though, she has since that exchange dropped a line of criticism that she had previously adopted; namely, she had claimed that intelligent design is unscientific because intelligent design research is not cited in the peer-reviewed scientific literature. There’s no question that it is cited (and favorably at that) in the peer-reviewed scientific literature.

What about actual intelligent design research being published in the peer-reviewed scientific literature? Scott doesn’t want to allow that my book The Design Inference properly belongs to this literature. In her letter of September 30, 2003, she remarks that this book “may have undergone a degree of editorial review” but it “did not undergo peer-review in the sense in which scientific research articles are peer-reviewed.” She then adds that The Design Inference “does not present scientific research -- Dembski’s book was published as a philosophy book.”

Every one of these remarks is false. What’s more, their falsity is readily established. Editorial review refers to a book submitted to a publisher for which the editors, who are employees of the publisher and in the business of trying to acquire, produce, and market books that are profitable, decide whether or not to accept the book for publication. Editorial review may look to expert advice regarding the accuracy, merit, or originality of the book, but the decision to publish rests solely with the editors and publishers. Peer-review, on the other hand, refers to journal articles and academic monographs (these are articles that are too long to be published in a journal and which therefore appear in book form) that are submitted to referees who are experts in the topic being addressed and who must give a positive review of the article or monograph if it is to be published at all. The Design Inference went through peer-review and not merely editorial review.

To see this, it is enough to note that The Design Inference was published by Cambridge University Press as part of a Cambridge monograph series: Cambridge Studies in Probability, Induction, and Decision Theory. Scott doesn’t point this out in her letter of September 30, 2003 because if she had, her claim that my book being editorially reviewed but not peer-reviewed would have instantly collapsed. Academic monograph series, like the Cambridge series that published my book, have an academic review board that is structured and functions identically to the review boards of academic journals. At the time of my book’s publication, the review board for Cambridge Studies in Probability, Induction, and Decision Theory included members of the National Academy of Sciences as well as one Nobel laureate, John Harsanyi, who shared the prize in 1994 with John Nash, the protagonist in the film A Beautiful Mind. As it is, The Design Inference had to pass peer-review with three anonymous referees before Brian Skyrms, who heads the academic review board for this Cambridge series, would recommend it for publication to the Cambridge University Press editors in New York. Brian Skyrms is on the faculty of the University of California at Irvine as well as a member of the National Academic of Sciences. It is easy enough to confirm what I’m saying here by contacting him. Scott either got her facts wrong or never bothered to check them in the first place.

What about Scott’s claim that The Design Inference “does not present scientific research—Dembski’s book was published as a philosophy book.” It is true that Cambridge University Press officially lists this book as a philosophy monograph. But why should how the book is listed by its publisher be relevant to deciding whether it does or does not contain genuine scientific content? The Library of Congress Control Number (LCCN) for The Design Inference is QA279.D455. As any mathematician knows, QA refers to mathematics and the 270s refer to probability and statistics. Is Scott therefore willing to accept that The Design Inference does present scientific research after all because the Library of Congress treats it as a mathematical and statistical monograph rather than as a philosophical monograph?

How this book is listed is beside the point. I submit that the book makes a genuine contribution to the statistical literature, laying out in full technical detail a method of design detection applicable to biology. Scott can dispute this if she likes, but to do so she needs to engage the actual content of my book and not dismiss it simply because the publisher lists it one way or another. Also, it’s worth noting that up until I pointed out to her that The Design Inference is cited in the peer-reviewed mathematical and biological literature, her main line of argument against the scientific merit of my work was that it wasn’t being cited in the peer-reviewed scientific literature. As I showed above, this line of criticism is no longer tenable.

I’ve discussed at length Scott’s treatment of my own work because this is where I’m best qualified to speak to the issue of peer review in relation to intelligent design. As for the other claims in her letter of September 30, 2003, let me briefly offer three remarks:

**Discovery Institute is only the tip of the iceberg for scientists who support intelligent design. Intelligent design research is being published in precisely the places Scott claims it is not being published. What’s more, intelligent design has a developing research program. For some details, see the attached ID FAQ that I handed out on September 10, 2003 at the textbook hearings in Austin. It is also available on my website:

**Scott’s charge that critics of Darwinian evolution, like me and my colleagues at Discovery Institute, “misquote” or “quote-mine” the work of scientists has degenerated into a slogan. As a slogan, its effect is to shut down discussion before it can get started. Scientists have no special privileges over anyone else. If they say things that are false, inaccurate, or stupid, they need to be called to account. Reasoned discourse in a free society demands that people, and that includes scientists, confront the record of their words. One can dispute what the words meant in context, but it is not enough merely to assert that the words were quoted out of context.

**Finally, in her letter of September 30, 2003, Scott objects to my use of a statement she made in an interview with Salon. I am supposed to have implied that “Scott believes that textbooks should not discuss arguments about how evolution occurs.” She protests that she “was not discussing doubts about how evolution happened but rather doubts about whether evolution happened.” (Emphasis hers.) But if she really believes that there are many views of how evolution occurred, why does she and her lobbying group the NCSE support only one view on how evolution occurred, namely, the Darwinian view? Why, for instance, isn’t she demanding that the biology textbooks describe the controversy between neo-Darwinists (like John Maynard Smith) and self-organizational theorists (like Stuart Kauffman)? Neither disputes whether evolution has happened. Yet the self-organizational theorists strongly dispute that the Darwinian view adequately explains how evolution occurred. All the textbooks ignore the self-organizational challenge to Darwinism. If Scott is such a champion of pluralism concerning how evolution happened, why isn’t she pressing for the inclusion of self-organizational theory in the biology textbooks? Why do all her lobbying efforts promote neo-Darwinism as the only view of how evolution occurred that’s appropriate for the textbooks? I submit it is because, as she said in her Salon interview, to do otherwise will only “confuse kids about the soundness of evolution as a science.” In other words, to ensure that kids are not confused about whether evolution occurred, textbooks need to tell them only one story about how evolution occurred, namely, the Darwinian story. This isn’t education. It’s indoctrination.


Textbook Hearing, Austin, Texas, September 10, 2003
(available at after September 10, 2003>
by William A. Dembski

What is intelligent design?
Intelligent design is the science that studies how to detect intelligence. Recall astronomer Carl Sagan’s novel Contact about the search for extraterrestrial intelligence (or SETI). Sagan based the SETI researchers’ methods of design detection on scientific practice. Real-life SETI researchers have thus far failed to detect designed signals from distant space. But if they encountered such a signal, as the astronomers in Sagan’s novel did, they too would infer design. Intelligent design research currently focuses on developing reliable methods of design detection and then applying these methods, especially to biological systems.

Does research supporting intelligent design appear in the peer-reviewed literature?
Here are a few recent peer-reviewed publications supporting intelligent design in biology. There is also a widely recognized peer-reviewed literature in physics and cosmology supporting intelligent design (see, for instance, the work of Paul Davies, Frank Tipler, Fred Hoyle, and Guillermo Gonzalez).

• W.A. Dembski, The Design Inference: Eliminating Chance through Small Probabilities (Cambridge: Cambridge University Pres, 1998). This book was published by Cambridge University Press and peer-reviewed as part of a distinguished monograph series, Cambridge Studies in Probability, Induction, and Decision Theory. The editorial board of that series includes members of the National Academy of Sciences as well as one Nobel laureate, John Harsanyi, who shared the prize in 1994 with John Nash, the protagonist in the film A Beautiful Mind. Commenting on the ideas in this book, Paul Davies remarks: “Dembski’s attempt to quantify design, or provide mathematical criteria for design, is extremely useful. I’m concerned that the suspicion of a hidden agenda is going to prevent that sort of work from receiving the recognition it deserves. Strictly speaking, you see, science should be judged purely on the science and not on the scientist.” Quoted in L. Witham, By Design (San Francisco: Encounter Books, 2003), p. 149. • D.D. Axe, “Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors,” Journal of Molecular Biology, 301 (2000): 585–595. This work shows that certain enzymes are extremely sensitive to perturbation. Perturbation in this case does not simply diminish existing function or alter function, but removes all possibility of function. This implies that neo-Darwinian theory has no purchase on these systems. Moreover, the probabilities implicit in such extreme-functional-sensitivity analyses are precisely those needed for a design inference. • W.-E. Loennig & H. Saedler, “Chromosome Rearrangements and Transposable Elements,” Annual Review of Genetics, 36 (2002): 389–410. This article examines the role of transposons in the abrupt origin of new species and the possibility of an partly predetermined generation of biodiversity and new species. The authors’ approach in non-Darwinian, and they cite favorably on the work of Michael Behe and William Dembski.

• 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 [10]. 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 [8]. 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.” Reference number [10] here is to William Dembski’s The Design Inference.

• M.J. Denton & J.C. Marshall, “The Laws of Form Revisited,” Nature, 410 (22 March 2001): 417; M.J. Denton, J.C. Marshall & M. Legge, (2002) “The Protein Folds as Platonic Forms: New Support for the pre-Darwinian Conception of Evolution by Natural Law,” Journal of Theoretical Biology 219 (2002): 325–342. This research is thoroughly non-Darwinian and looks to laws of form embedded in nature to bring about biological structures. The intelligent design research program is broad, and design like this that’s programmed into nature falls within its ambit.

What research topics does a design-theoretic research program explore?
  • Methods of Design Detection. Methods of design detection are widely employed in various special sciences (e.g., archeology, cryptography, and the Search for Extraterrestrial Intelligence or SETI). Design theorists investigate the scope and validity of such methods.

  • Biological Information. What is the nature of biological information? How do function and fitness relate to it? What are the obstacles that face material mechanisms in attempting to generate biological information? What are the theoretical and empirical grounds for thinking that intelligence is indispensable to the origin of biological information?

  • Evolvability. Evolutionary biology’s preferred research strategy consists in taking distinct biological systems and finding similarities that might be the result of a common evolutionary ancestor. Intelligent design, by contrast, focuses on a different strategy, namely, taking individual biological systems and perturbing them (both intelligently and randomly) to see how much the systems can evolve. Within this latter research strategy, limitations on evolvability by material mechanisms constitute indirect confirmation of design.

  • Evolutionary Computation. Organisms employ evolutionary computation to solve many of the tasks of living (cf. the immune system in vertebrates). But does this show that organisms originate through some form of evolutionary computation (as through a Darwinian evolutionary process)? Are GPGAs (General Purpose Genetic Algorithms) like the immune system designed or the result of evolutionary computation? Need these be mutually exclusive? Evolutionary computation occurs in the behavioral repertoire of organisms but is also used to account for the origination of certain features of organisms. Design theorists explore the relationship between these two types of evolutionary computation as well as any design intrinsic to them. One aspect of this research is writing and running computer simulations that investigate the scope and limits of evolutionary computation. One such simulation is the MESA program (Monotonic Evolutionary Simulation Algorithm) due to Micah Sparacio, John Bracht, and William Dembski. It is available online at

  • Technological Evolution (TRIZ). The only well-documented example we have of the evolution of complex multipart integrated functional systems (as we see in biology) is the technological evolution of human inventions. In the second half of the twentieth century, Russian scientists and engineers studied hundreds of thousands of patents to determine how technologies evolve. They codified their findings in a theory to which they gave the acronym TRIZ, which in English translates to Theory of Inventive Problem Solving (see Semyon 3 Savransky, Engineering of Creativity: Introduction to TRIZ Methodology of Inventive Problem Solving, CRC Publishers, 2000). The picture of technological evolution that emerges out of TRIZ parallels remarkably the history of life as we see it in the fossil record and includes the following: (1) New technologies (cf. major groups like phyla and classes) emerge suddenly as solutions to inventive problems. Such solutions require major conceptual leaps (i.e., design). As soon as a useful new technology is developed, it is applied immediately and as widely as possible (cf. convergent evolution). (2) Existing technologies (cf. species and genera) can, by contrast, be modified by trial-anderror tinkering (cf. Darwinian evolution), which amounts to solving routine problems rather than inventive problems. (The distinction between routine and inventive problems is central to TRIZ. In biology, irreducible complexity suggests one way of making the analytic cut between these types of problems. Are there other ways?) (3) Technologies approach ideality (cf. local optimization by means of natural selection) and thereafter tend not change (cf. stasis). (4) New technologies, by supplanting old technologies, can upset the ideality and stasis of the old technologies, thus forcing them to evolve in new directions (requiring the solution of new inventive problems, as in an arms race) or by driving them to extinction. Mapping TRIZ onto biological evolution provides a especially promising avenue of designtheoretic research.

  • Strong Irreducible Complexity of Molecular Machines and Metabolic Pathways. For certain enzymes (which are themselves highly complicated molecular structures) and metabolic pathways (i.e., systems of enzymes where one enzyme passes off its product to the next, as in a production line), simplification leads not to different functions but to the complete absence of all function. Systems with this feature exhibit a strengthened form of irreducible complexity. Strong irreducible complexity, as it may be called, entails that no Darwinian account can in principle be given for the emergence of such systems. Theodosius Dobzhansky, one of the founders of the neo-Darwinian synthesis, once remarked that to talk about prebiotic natural selection is a contradiction in terms—the idea being that selection could only select for things that are already functional. Research on strong irreducible complexity finds and analyzes biological systems that cannot in principle be grist for natural selection’s mill. For this research, which is only now beginning, to be completely successful would imply the unraveling of molecular Darwinism.

  • Natural and Artificial Biological Design (Bioterrorist Genetic Engineering). We are on the cusp of a bioengineering revolution whose fallout is likely to include bioterrorism. Thus we can expect to see bioterror forensics emerge as a practical scientific discipline. How will such forensic experts distinguish the terrorists’ biological designs from naturally occurring biological designs?

  • Design of the Environment and Ecological Fine-Tuning. The idea that ecosystems are fine-tuned to support a harmonious balance of plant and animal life is old. How does this balance come about. Is it the result of blind Darwinian forces competing with one another and leading to a stable equilibrium? Or is there design built into such ecosystems? Can such ecosystems be improved through conscious design or is “monkeying” with such systems invariably counterproductive? Design-theoretic research promises to become a significant factor in scientific debates over the environment.

  • Steganographic Layering of Biological Information. Steganography belongs to the field of digital data embedding technologies (DDET), which also include information hiding, steganalysis, watermarking, embedded data extraction, and digital data forensics. 4 Steganography seeks efficient (high data rate) and robust (insensitive to common distortions) algorithms that can embed a high volume of hidden message bits within a cover message (typically imagery, video, or audio) without their presence being detected. Conversely, steganalysis seeks statistical tests that will detect the presence of steganography in a cover message. Key research question: To what degree do biological systems incorporate steganography, and if so, is biosteganography demonstrably designed?

  • Cosmological Fine-Tuning and Anthropic Coincidences. Although this is a well worn area of study, there are some new developments here. Guillermo Gonzalez, assistant professor of physics and astronomy at Iowa State University, and Jay Richards, a senior fellow with Seattle’s Discovery Institute, have a forthcoming book titled The Privileged Planet (along with a video based on the book) in which they make a case for planet earth as intelligently designed not only for life but also for scientific discovery. In other words, they argue that our world is designed to facilitate the scientific discovery of its own design. Aspects of Gonzalez’s work in this area have been featured on the cover story of the October 2001 Scientific American.

  • Astrobiology, SETI, and the Search for a General Biology. What might life on other planets look like? Is it realistic to think that there is life, and even conscious life, on other planets? What are the defining features that any material system must possess to be alive? How simple can a material system be and still be alive (John von Neumann posed this question over half a century ago in the context of cellular automata)? Insofar as such systems display intelligent behavior, must that intelligence be derived entirely from its material constitution or can it transcend yet nevertheless guide its behavior (cf. the mechanism vs. vitalism debate)? Is there a testable way to decide this last question? How, if at all, does quantum mechanics challenge a purely mechanistic conception of life? Design theorists are starting to investigate these questions.

  • Consciousness, Free Will, and Mind-Brain Studies. Is conscious will an illusion—we think that we have acted freely and deliberately toward some end, but in fact our brain acted on its own and then deceived us into thinking that we acted deliberately. This is the majority position in the cognitive neuroscience community, and a recent book makes just that claim in its title: The Illusion of Conscious Will by Harvard psychologist Daniel Wegner. But there is now growing evidence that consciousness is not reducible to material processes of the brain and that free will is in fact real. Jeffrey Schwartz at UCLA along with quantum physicist Henry Stapp at the Lawrence Berkeley National Laboratory are two of the key researchers presently providing experimental and theoretical support for the irreducibility of mind to brain (see Schwartz’s book The Mind and the Brain: Neuroplasticity and the Power of Mental Force).

  • Autonomy vs. Guidance. Many scientists worry that intelligent design attempts to usurp nature’s autonomy. But that is not the case. Intelligent design is attempting to restore a proper balance between nature’s autonomy and teleologic guidance. Prior to the rise of modern science all the emphasis was on teleologic guidance (typically in the form of divine design). Now the pendulum has swung to the opposite extreme, and all the emphasis is on nature’s autonomy (an absolute autonomy that excludes design). Where is the point of balance that properly respects both, and in which design becomes empirically evident? The search for that balance-point underlies all design-theoretic research. It’s not all design or all nature but a synergy of the two. Unpacking that synergy is the intelligent design research program in a nutshell.

      Please visit our Texas Textbooks Information for more information on this and other issues related to the Texas State Board of Education's coming decision on biology textbooks.