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Miscellaneous meanderings and philosophical ramblings. The title from a spiral notebook I used to jot down my thoughts on religion and other matters some years ago. I like to write, think and express my views on various issues. Robust discussion is welcome.

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Friday, June 10, 2005

Intelligent Design - New Yorker editorial - part 1

If you haven't heard, The New Yorker recently had an editorial by H. Allen Orr that criticized Intelligent Design. It seems that some might view this as an authoritative destruction of ID proponents. However, those who do not place an unfalsifiable faith in naturalism will not go away so quitely. I found this response and due to its length, I will include Dembski's reply to Orr in a follow-up post.

Refuted Before it was Written: A Guide to Allen Orr's "Devolution" Article in The New Yorker

by Casey Luskin

On May 23, 2005, evolutionary biologist H. Allen Orr published an editorial against intelligent design in the The New Yorker entitled "Devolution: Why intelligent design isn’t." The New Yorker is known as a fairly liberal magazine. I would love to see more liberals take intelligent design seriously, but apparently The New Yorker is still holding out, as the editorial was predictably critical of intelligent design. Nonetheless, Dr. Orr deserves some credit because he implies that scientists should actively engage ID proponents, and at various points makes some accurate descriptions of the scientific claims of intelligent design proponents. Yet when he becomes critical, nearly every substantive point Dr. Orr makes against intelligent design has been already refuted somewhere-or-another by ID proponents.

Below is response to Orr's lengthy article, but not in the typical fashion. This response is a simply a guide to rebutting Orr's article: it is a collection of Orr's claims and links to responses to his common, and already-refuted objections to intelligent design. Claims of Orr will be in the grey boxes, followed by brief discussions with interspersed links to further rebuttals.

Many scientists avoid discussing I.D. for strategic reasons. If a scientific claim can be loosely defined as one that scientists take seriously enough to debate, then engaging the intelligent-design movement on scientific grounds, they worry, cedes what it most desires: recognition that its claims are legitimate scientific ones.

Response: This is an interesting admission from Orr, as he appears to concede that many scientists have tried to ignore intelligent design. I think Orr deserves credit for acknowledging the fact that ID has been purposefully ignored by many scientists. This concession from an insider in the anti-ID mainstream scientific community (certainly large portions of the mainstream scientific community are not anti-ID, but there are portions of it which are anti-ID) shows that intelligent design faces intense political opposition rather than fair consideration by scientists.

It's been said that revolutions in thought pass through 3 phases:

1. People ignore the idea.
2. Then people they ridicule the idea (and some resort to lots of unjustified namecalling towards its proponents).
3. Then people accept the idea (and some pretend like they'd done so all along).

Given the recent attention given to ID in Nature, and Orr's subsequent comments, it appears that the "ignore phase" is completely over. To his credit, Orr's piece generally took a respectful tone. But one need not search far in many media fora and on various Darwinist internet blogs to find that the "ridicule" phase is finally in full swing. Additionally, I would like to note that past attempts by prominent scientific journals to rebut the scientific claims of ID while giving the appearance of ignoring it is discussed here.

In the past few years, college students across the country have formed Intelligent Design and Evolution Awareness chapters. Clearly, a policy of limited scientific engagement has failed.

Response: As an initial trivial side-note, Orr failed to completely identify our organization, under the commonly known name of "IDEA Chapters." Secondly, Orr has made an interesting point: why should "limited scientific engagement" be the policy of scientists? Shouldn't they want to seek truth and want to understand if intelligent design is a viable explanation? Again, this seems to indicate that intelligent design is not being given a fair hearing by scientists.

Orr is correct that such an "ignore it 'til you can't anymore" policy fails. Many Darwinists are now recommending that scientists actively engage ID, as is recounted here. Darwinists may think that we are fearful of such scientific engagement because we don't think our ideas will hold up. This couldn't be further from the truth, as it is clearly seen here that IDEA Clubs actively pursue interactions with Darwinists and applaud those who are willing to come to IDEA events to learn about and discuss intelligent design.

The reason why so many students are interested in intelligent design is because they aren't hearing about it in their classes, or are hearing about it in an exceedingly one-sided manner. This piques their interest because students are keen at smelling when there is information they aren't being told. This only furthers student interest in intelligent design. The best way for all scientists to "deal" with intelligent design is to confront it in an honest and open-minded manner. If this happens, then intelligent design advocates know they have nothing to fear from having the cards laid out on the table.

Living organisms are too complex to be explained by any natural—or, more precisely, by any mindless—process. Instead, the design inherent in organisms can be accounted for only by invoking a designer, and one who is very, very smart.

Response: Again, to his credit, Orr gets a many things right in his depiction of intelligent design. In fact, I would like to commend Orr for his treatment in this section. But readers might mistake that intelligent design is merely a negative argument against evolution. See our "Is ID just a negative argument against evolution?" FAQ for a response to this common objection.

These claims [of ID proponents] have been championed by a tireless group of writers, most of them associated with the Center for Science and Culture at the Discovery Institute, a Seattle-based think tank that sponsors projects in science, religion, and national defense, among other areas.

Response: These "writers" are often scientists, professors, scholars, and other academics who are qualified to speak on this subject. So labeling individuals at Discovery "writers" doesn't tell the whole story. Additionally, Orr seems to imply that Discovery is highly involved in religious activities. I just did a quick survey of the website of the Discovery Institute and it appears that of their 6 major programs, none of them are primarily focused on religion. Of their four "other programs" only two seem to deal specifically with religion. But Orr should be commended at least for mentioning that Discovery does do science.

As biologists pointed out, there are several different ways that Darwinian evolution can build irreducibly complex systems. In one, elaborate structures may evolve for one reason and then get co-opted for some entirely different, irreducibly complex function. Who says those thirty flagellar proteins weren’t present in bacteria long before bacteria sported flagella? They may have been performing other jobs in the cell and only later got drafted into flagellum-building. Indeed, there’s now strong evidence that several flagellar proteins once played roles in a type of molecular pump found in the membranes of bacterial cells

Response: This is one of Orr's counterpoints to ID which has been responded to time-and-time again by ID proponents. Orr is claiming that (1) co-optation is a viable explanation for how the parts of the flagellum came together, and that (2) the a "molecular pump" (aka the Type Three Secretory System) is one part which was co-opted into the flagellum. Even the introductory ID documentary Unlocking the Mystery of Life tackles this objection just fine. As seen here, here, and here, ID proponents have made many comments regarding the inability of co-optation to account for the flagellum. Firstly, as discussed here, many of the arguments that proteins found in the flagellum are have similar "homologues" elsewhere in the cell are quite weak. Thus, Orr's claim that "They may have been performing other jobs in the cell and only later got drafted into flagellum-building" is highly questionable. Regarding the "molecular pump," as documented here, and especially here, the Type Three Secretory System cannot be a precursor to the flagellum, and even if it could be, it would only account for less than 1/3 of the total flagellar proteins. Orr's arguments that co-optation can explain the origin of the flagellum have been extensively rebutted by ID proponents long before this article was published.

We add new parts like global-positioning systems to cars not because they’re necessary but because they’re nice. But no one would be surprised if, in fifty years, computers that rely on G.P.S. actually drove our cars. At that point, G.P.S. would no longer be an attractive option; it would be an essential piece of automotive technology. It’s important to see that this process is thoroughly Darwinian: each change might well be small and each represents an improvement

Response: The problem with Orr's argument here is that the very points made by ID proponents about the flagellum is that the parts in it aren't just "nice" they are "necessary" for function! This is discussed here and also in Darwin's Black Box by Michael Behe. As William Dembski writes "Even the simplest bacterial flagellum requires around forty proteins for its assembly and structure. All the proteins are necessary in the sense that lacking any of them a working flagellum does not result." (See Dembski's The Logical Underpinnings of Intelligent Design for details.) Experimental data seems to confirm Dembski's claim, meaning that we can't evolve a flagellum by making "nice" little additions--we have many parts which are "necessary" all at once to get any functional flagellar motor. This defies Orr's attempt at an explanation.

William Dembski once criticized Orr for failing to provide a good example of how the flagellum evolved. Dembski wrote. "Indeed, if such accounts [of the evolution of the flagellum] were available, Orr would merely need to cite them and intelligent design would be finished." Where are Orr's cites?

Biologists actually know a great deal about the evolution of biochemical systems, irreducibly complex or not. It’s significant, for instance, that the proteins that typically make up the parts of these systems are often similar to one another. (Blood clotting—another of Behe’s examples of irreducible complexity—involves at least twenty proteins, several of which are similar, and all of which are needed to make clots, to localize or remove clots, or to prevent the runaway clotting of all blood.) And biologists understand why these proteins are so similar. Each gene in an organism’s genome encodes a particular protein. Occasionally, the stretch of DNA that makes up a particular gene will get accidentally copied, yielding a genome that includes two versions of the gene. Over many generations, one version of the gene will often keep its original function while the other one slowly changes by mutation and natural selection, picking up a new, though usually related, function. This process of “gene duplication” has given rise to entire families of proteins that have similar functions; they often act in the same biochemical pathway or sit in the same cellular structure. There’s no doubt that gene duplication plays an extremely important role in the evolution of biological complexity.

Response: Michael Behe has responded extensively to claims that the blood clotting cascade is not irreducibly complex, here and here.

The most serious problem in Dembski’s account involves specified complexity. Organisms aren’t trying to match any “independently given pattern”: evolution has no goal, and the history of life isn’t trying to get anywhere. If building a sophisticated structure like an eye increases the number of children produced, evolution may well build an eye. But if destroying a sophisticated structure like the eye increases the number of children produced, evolution will just as happily destroy the eye. Species of fish and crustaceans that have moved into the total darkness of caves, where eyes are both unnecessary and costly, often have degenerate eyes, or eyes that begin to form only to be covered by skin—crazy contraptions that no intelligent agent would design. Despite all the loose talk about design and machines, organisms aren’t striving to realize some engineer’s blueprint; they’re striving (if they can be said to strive at all) only to have more offspring than the next fellow.

Response: If you leave a TV set unused on the top of a mountain for 40 years, chances it will stop working. But nobody will claim that the loss of its function is evidence that it wasn't designed in the first place. Eyeless cave-dwelling animals are a great example of loss of function. Intelligent design theory has no problem relegating loss-of-function to natural selection. Indeed, William Dembski even sees this phenomenon as a promising being part of the ID research program, which can investigate, the "Perturbation Problem--How has the original design been modified and what factors have modified it? This requires an account of both the natural and the intelligent causes that have modified the object over its causal history. " (Intelligent Design Coming Clean.) The problem ID is interested in is the acquisition of functions in the first place--How did the functional eye first arise? This is a question better put to ID than "how was an eye's function lost."

Another problem here is that Orr seems to be assuming the truth of his own argument here. If complex biological structures exist, for which there would be no function but for an exceedingly complex and unlikely arrangement of parts, then the creative process must have been goal directed! If Orr is correct that "evolution has no goal" then perhaps the correct answer is that "evolution didn't produce these structures which require a goal-directed process in order to arise!"

On the other hand, intelligent agents can think with the "end in mind" and design objects with a goal in mind. The best "goal-directed" process out to explain the origin of these structures there is intelligent design.

Another problem with Dembski’s arguments concerns the N.F.L. theorems. Recent work shows that these theorems don’t hold in the case of co-evolution, when two or more species evolve in response to one another. And most evolution is surely co-evolution. Organisms do not spend most of their time adapting to rocks; they are perpetually challenged by, and adapting to, a rapidly changing suite of viruses, parasites, predators, and prey. A theorem that doesn’t apply to these situations is a theorem whose relevance to biology is unclear. As it happens, David Wolpert, one of the authors of the N.F.L. theorems, recently denounced Dembski’s use of those theorems as “fatally informal and imprecise.” Dembski’s apparent response has been a tactical retreat. In 2002, Dembski triumphantly proclaimed, “The No Free Lunch theorems dash any hope of generating specified complexity via evolutionary algorithms.” Now he says, “I certainly never argued that the N.F.L. theorems provide a direct refutation of Darwinism.”

Response: Orr provides no citation or context for his "tactical retreat" of Dembski. However, it seems odd to claim that Dembski is in a "tactical retreat" with regards to N.F.L. theorems because as late as March, 2005 (i.e. 2 months ago), Dembski wrote "The No Free Lunch regress, by demonstrating the incompleteness of stochastic mechanisms to explain assisted searches, fundamentally challenges the materialist dogma that reduces all intelligence to chance and necessity." (William Dembski, Searching Large Spaces: Displacement and the No Free Lunch Regress) Perhaps Dembski's "retreat" was not a recantation but rather clarification of his views. From this quote given here in Dembski's March, 2005 article, it seems clear that Dembski has not softened in his views whatsoever. Orr's depiction of Dembski could also be taken to show that Dembski is strengthening or updating his arguments in response to criticisms. Why, then is Orr critical? Shouldn't Dembski he should be lauded for being open to correction or is Orr not willing to grant such commendations for his own tactical reasons

But it’s striking that Dembski’s views on the history of life contradict Behe’s. Dembski believes that Darwinism is incapable of building anything interesting; Behe seems to believe that, given a cell, Darwinism might well have built you and me. Although proponents of I.D. routinely inflate the significance of minor squabbles among evolutionary biologists (did the peppered moth evolve dark color as a defense against birds or for other reasons?), they seldom acknowledge their own, often major differences of opinion. In the end, it’s hard to view intelligent design as a coherent movement in any but a political sense.

Response: Orr claims that Dembski believes that Darwinism can't build "anything interesting" but that Behe believes that, given a cell, Darwinism could have built you and me. According to Orr, because Dembski has stronger doubts about Darwin's mechanism than Behe, they all must have political motivations for making their claims. This is not a logical argument on the part of Orr. Furthermore, if Orr's questionable mode of argumentation were correct, it could equally be applied to evolution, where Orr concedes there are differences in opinion. In reality, there is diversity of views in the ID movement but again, Orr should be lauding this as a strength of the potential of the movement, not a weakness. Despite any perceived differences in the views of Dembski and Behe, they agree on some core tenets of ID: that Darwin's mechanism can't produce some things and ID is the best explanation. This is why Dembski writes the following showing how they both agree that Darwin's mechanism is impotent in some key respects:

"Behe, by contrast, requires a much more demanding form of possibility in assessing the ability of the Darwinian mechanism to produce irreducible complexity. For Behe, it's a probabilistic form in which highly improbable, functionally specified structures cannot happen by chance. This weds Behe's work on irreducible complexity to mine on specified complexity. Both Behe and I understand chance here very broadly, and thus include the Darwinian mechanism of natural selection and random variation. The logical force of our argument purports to be the same as "You can't walk into a Las Vegas casino and get a hundred double zeros in a row playing roulette." There's a sheer possibility that this could happen by chance, but not a real possibility." (Dembski, Sheer vs. Real Possibilities: A Response to Allen Orr)

It is clear that both Behe and Dembski agree that Darwin's mechanism is impotent and that design is the best explanation. If they disagree on some other details, this does not negate the force of the overall argument.

Finally, it's not even clear that Orr's characterization of Dembski's views is correct. Orr claims that Dembski thinks that Darwinism has done nothing, but yet Dembski has written, "It is, for instance, a logical possibility that the design in the bacterial flagellum was front-loaded into the universe at the Big Bang and subsequently expressed itself in the course of natural history as a miniature outboard motor on the back of E. Coli. Whether this is what actually happened is another question (more on this later), but it is certainly a live possibility..." (Intelligent Design Coming Clean) This quote alone refutes Orr's claim that Dembski and Behe are necessarily in conflict over their views about the history of life.

Even if Orr's criticisms of ID were valid, he seems to fail to recognize that these sorts of criticisms equally apply to his own theory. In any case, Dembski has recounted a a number of core tenets that ID proponents agree upon.

It’s also hard to view it as a real research program. Though people often picture science as a collection of clever theories, scientists are generally staunch pragmatists: to scientists, a good theory is one that inspires new experiments and provides unexpected insights into familiar phenomena. ... In the nearly ten years since the publication of Behe’s book, by contrast, I.D. has inspired no nontrivial experiments and has provided no surprising insights into biology. As the years pass, intelligent design looks less and less like the science it claimed to be and more and more like an extended exercise in polemics.
Response: What is missing here is perhaps more interesting than what is present. Darwinists used to say that ID proponents had produced no peer-reviewed publications. In fact, they have, and here are 3 of them:

  1. “The origin of biological information and the higher taxonomic categories” by Stephen C. Meyer, Proceedings of the Biological Society of Washington 117(2):213-239 (2004) (explicitly advocating that intelligent design is the best explanation for the origin of biological information in the Cambrian explosion)
  2. Michael Behe and David W. Snoke, “Simulating evolution by gene duplication of protein features that require multiple amino acid residues,” Protein Science, 13 (2004). (testing for irreducible complexity among protein-protein binding sites)
  3. Jonathan Wells, “Do Centrioles Generate a Polar Ejection Force?,” Rivista di Biologia / Biology Forum, 98:71-96 (2005). (using explicitly ID assumptions to elucidate the behavior of centrioles—with potential applications to cancer research)

Thus, we see that ID is being applied to explain the origin of biological complexity in the Cambrian Explosion (Meyer, 2004), to help explain how cells work (Wells, 2005), contributing to cancer research, and also inspiring theoretical research into the evolvability of various protein-protein bonds (Behe and Snoke, 2004). Behe and Snoke (2004)'s article directly refutes Orr's claim that ID inspires no new research: their article is directly derived from Behe's claims about irreducible complexity at the biochemical level, and is an attempt to test those claims. (See this link for more information on publications of ID proponents.) Given that about 85% of the budget of the Discovery Institute's Center for Science and Culture goes to scientific research (see this blog posting for details), it seems that ID is interested in science, and not just politics. ID proponents have published dozens of scholarly books from reputable publishers with scientific emphases, as well as a growing number of publications in mainstream scientific journals. Orr just isn't willing to concede these points!

In 1999, a document from the Discovery Institute was posted, anonymously, on the Internet. This Wedge Document, as it came to be called, described not only the institute’s long-term goals but its strategies for accomplishing them. The document begins by labelling the idea that human beings are created in the image of God “one of the bedrock principles on which Western civilization was built.” It goes on to decry the catastrophic legacy of Darwin, Marx, and Freud—the alleged fathers of a “materialistic conception of reality” that eventually “infected virtually every area of our culture.” The mission of the Discovery Institute’s scientific wing is then spelled out: “nothing less than the overthrow of materialism and its cultural legacies.” It seems fair to conclude that the Discovery Institute has set its sights a bit higher than, say, reconstructing the origins of the bacterial flagellum.

Response: For a detailed response from Discovery regarding the Wedge Document, see this article by John West.

Pope John Paul II himself acknowledged, in a 1996 address to the Pontifical Academy of Sciences, that new research “leads to the recognition of the theory of evolution as more than a hypothesis.” Whatever larger conclusions one thinks should follow from Darwinism, the historical fact is that evolution and religion have often coexisted. As the philosopher Michael Ruse observes, “It is simply not the case that people take up evolution in the morning, and become atheists as an encore in the afternoon.”

Response: I agree with Orr that it is at least possible to believe in God and neo-Darwinism. For some examples, a good volume by theistic evolutionists is "Perspectives on an Evolving Creation" (edited by Keith B. Miller). It should be noted, however, that the current Pope is very skeptical of Darwinism's compatibility with Christianity (see for details). But neo-Darwinism, if it is the correct account, has mandatory implications for a theist's views about how God has operated in the world. See this link for an extensive discussion. But that's beside the point, because the point is whether or not neo-Darwinism is a viable hypothesis to explain the diversity of life on earth, and the evidence points to "not."

On this point, out of genuine curiosity, I would like to publicly ask Dr. Orr to share with us his personal religious beliefs. Perhaps some personal testimony from himself about what he believes about God and religion, and why, would be helpful. I publicly invite Allen Orr to explain to us how his Darwinian view of life interfaces with his personal religious beliefs. Public disclosure of Orr's personal views would go much further towards reassuring people that it is possible to believe in God and evolution than would his mere citation to a statement by a pope who said that God and evolution are compatible. My e-mail address is

Orr devotes much space to critique but never provides any viable evolutionary explanations for the origin of the flagellum or the blood clotting cascade. Orr's article focuses a lot on issues which have nothing to do with the science of intelligent design theory. To keep this focus where it should be --- on the science --- I will reiterate a challenge Dembski posed long ago to Allen Orr: "Indeed, if such accounts [of the evolution of the flagellum] were available, Orr would merely need to cite them and intelligent design would be finished." (Evolution's Logic of Credulity: An Unfettered Response to Allen Orr.) Orr has been given a chance in this latest article to explain how the flagellum evolved, but he has offered nothing more than weak arguments about homology and molecular pumps which have been refuted over-and-over again by ID proponents. Where is the viable citation to how the flagellum evolved? Unless Orr can meet Dembski's challenge, his case is not looking good.
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