Book review: Debating Design (Dembski/Ruse ed.) — The Panda's Thumb (Legacy Archive)

Note from author: As with most of my reviews this is a work in progress, I will update the posting with additional chapter reviews as I finish reading them.

Debating Design : From Darwin to DNA by William Dembski (Editor), Michael Ruse (Editor)

Introduction to the book by Ruse and Dembski

My review at Amazon review: “Not much of a debate”

While the title suggests that there would be a balance in arguments the anti-Darwinian arguments totally lose out against an overwhelming team of experts. Ruse, Ayala, Sober, Pennock and Miller methodically address the flaws in the scientific and philosophical arguments presented by the ID proponents. The ID proponents such as Dembski, Behe and Meyer mostly seem to be repeating old arguments while ignoring the main criticisms against their ideas.

Despite this, the book presents some interesting contributions. As a scientist and Christian I was particularly pleased with the contributions of Haught, Polkinghorne, Ward and others in part III “Theistic evolution” showing how evolution and divine Providence need not be at odds.

23 Comments

Frank J · 18 August 2004

While many admit that God (oops, the designer) could have used Darwinian evolution, most seem to reject this based on theological grounds. In other words, rather than being a scientific movement, ID is far more a theological movement.
— PvM

My conclusion is that most of them are rejecting it on *strategic* grounds, not theological, and certainly not scientific. That is, they know darned well that their designer uses Darwinian evolution, but they also know that they can fool the public by recycling all those misrepresentations of evolution, which have nothing to do with their "evidence of design." But as long as the public can be fooled by the false dichotomy, and be oblivious to the fact that ID has no testable alternative of how and when the designer created species, IDers can indirectly promote all the mutually contradictory creationisms, all the while knowing that they all failed the tests.

Bob Maurus · 18 August 2004

And so, ID remains, as it was and always shall be, an empty and cynical exercise in negative proofs, and a stand-in for Divine Creation.

PvM, thanks for the PDF files. I've got some reading to do.

Dada · 21 August 2004

Kenneth Miller in the chapter "The Flagellum Unspun: The Collapse of "Irreducible Complexity", shows in intricate detail how the homology between type III secretory apparatus and the bacterial flagellum gives us a fascinating insight into the likely evolutionary pathways where the two share a common ancestor. In "Why intelligent design fails Young and Edis (ed)", Ian Musgrave shows in even more detail how science is unraveling much of the mystery behind the bacterial flagellum, leaving little room for an intelligent designer to hide. Miller also addresses the 'probability calculations' by Dembski in his book "No Free Lunch" to show how Dembski's model has little similarity to reality.

Unfortunately, Miller doesn't show that Dembsi's model has little similarity to reality. Dembski has shown that Miller's arguments are false: http://www.designinference.com/documents/2003.02.Miller_Response.htm Dembski has a good point: Miller doesn't like my number 10^(-1170), which is one improbability that I calculate for the flagellum. Fine. But in pointing out that a third of the proteins in the flagellum are closely related to components of the TTSS, Miller tacitly admits that two-thirds of the proteins in the flagellum are unique. In fact they are (indeed, if they weren't, Miller would be sure to point us to where the homologues could be found). Applied to those remaining two-third of flagellar proteins, my calculation yields something like 10^(-780), which also falls well below my universal probability bound. Even if TTSS had been possible evolutionary precursor of the flagellum there would still be too many proteins which can't be explained without Intelligent Designer.

Wesley R. Elsberry · 21 August 2004

Dada,

Best not to hitch yourself to Dembski's star on matters of biology. Dembski's "good point" ceases to be a good point if it turns out that most of the flagellar proteins have homologues, whether or not Ken Miller discussed every one of those homologies. I expect that this question will be resolved shortly, and not in Dembski's favor.

Richard Wein · 21 August 2004

It doesn't matter whether the result of Dembski's calculation is 10^(-1170) or 10^(-780). The calculation is irrelevant because it treats the flagellum as a "discrete combinatorial object" (to use his term), i.e. it calculates the probability of the flagellum arising spontaneously as a random combination of proteins. It utterly ignores central concepts of evolutionary theory such as genetics and natural selection! It is just the old creationist "tornado in a junkyard" strawman.

The only reason Dembski included this irrelevant calculation was because he wrote in "The Design Inference" that his method required a probability calculation to be performed. Since he cannot provide a relevant one, he has thrown in this irrelevant one, hoping that some of his readers won't spot the difference.

Richard Wein · 21 August 2004

A question to PvM or anyone alse who's read "Debating Design". Is there anything at all that's new in Behe's chapter? I assume he still hasn't come up with the revised definition of IC which he promised a few years ago, after he finally admitted the old one was flawed.

Pim van Meurs · 21 August 2004

Dembski has attempted to show that Miller's claims are false but Miller is correct, Dembski's strawman calculations totally miss the point. It's ironic that Dada quotes from a part in Dembski's response which is shown to be wrong by Ussery and Musgrave. That Dembski's understanding of biology is quite lacking should not come as a surprise, in fact most of the proteins have found homologues. The bacterial flagellum seems to be hardly the enigma for evolution that Dembski and Behe imagined it to be. Dembski's probability calculations, fail to accurately describe the actual mechanisms involved in the formation of the flagellum, Dembski's claims about homologies totally flawed. If it can be shown that the flagellum can evolve from a precursor TTTS, another icon of ID will fall. but worse another gap for our God has been filled. Such is the risk when exposing one's faith to scientific disproof. Ussery shows some of the problems with Dembski's flagellum argument (and there are many), Musgrave shows not only what is wrong with Dembski but provides for an in depth overview of the evidence and provides some testable pathways. What has ID done in increasing our understanding of the flagellum? Nothing... That's the real problem with an argument which is based on our ignorance. It cannot afford to reduce our ignorance. That's even worse that being wrong about the flagellum, the fact that the ID position fails to contribute in any manner to our scientific knowledge bu trather has to rely on maintaining our ignorance. Luckily science has not be restrained by such concerns and has shown how most of the proteins in the flagellum have homologues and have provided us with some fascinating insight into the likely pathways. So Dada, does it surprise you to hear that Dembski was wrong again?

But in pointing out that a third of the proteins in the flagellum are closely related to components of the TTSS, Miller tacitly admits that two-thirds of the proteins in the flagellum are unique.

See how an eliminative filter once agains fails? That explanatory filter is full of false positives :-)

Steve · 21 August 2004

Behe's broken definition, Dembski's Clogged Filter, to the extent that any claims ID has made are falsifiable, they have been falsified. Nothing special about hypotheses getting shot down by data. That in itself is ordinary. But the 'scientists' involved have a moral responsibility to not misrepresent their work as successful, or benefit from others' doing so.

Pim van Meurs · 21 August 2004

A question to PvM or anyone alse who's read "Debating Design". Is there anything at all that's new in Behe's chapter? I assume he still hasn't come up with the revised definition of IC which he promised a few years ago, after he finally admitted the old one was flawed.
— Richard Wein

Behe quotes Franklin Harold in "The way of the cell" who states that "but we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical system, only wishful specialtions" Behe then continues: As a sufficient response to such claims I will simply rely on Harold's statement quote here as well as the other reviewers who agree that there is a dearth of Darwinian explanations. After all, if prominent scientists, who are no fans of intelligent design agree that the system remains unexplained then that should settle the matter." Behe then discusses the mousetrap and the blood clotting cascade, spending a lot of time discussion a mostly non issue about a disagreement between him and Doolittle stating that Doolittle misread the article. But his point is that if opponents of ID can raise at most erroneous arguments in support of Darwinism that this should be taken as evidence that IC systems are a much more severe problem than Darwinists recognize. Behe is spending much time on trying to turn around the argument with grand display of rhetoric but as far as I can tell seems to spend little time exploring the real issues. Thus we end with Behe's beautiful rhetorical statement "THe misconceived arguments by Darwinists that I have recounted here offer strong encouragement to me that the hypothesis of Intelligent Design is on the right track. After all, if well-informed opponents of an idea attack it by citing data that, when considered objectively, actually demonstrates its force, then one is entitled to be confident that the idea is worth investigating. Why would Behe ruin this beautiful sample of rhetoric with actual presenting a revised version of IC which is not flawed? Behe seems to spend little time exploring the advances made by science in understanding the evolutionary history of the bacterial flagellum. He does mention a paper by Yonekura "the bacterial flagellar cap as the rotary promoter of flagellin self assembly" in Science 290 2148-52 (2000) as evidence of the elegancy and intricacy of the assembly process for a flagellum. No references to Nick Matzke's work or recent research that shows that most of the proteins have been found to have homologues. Of course, the introduction already sets the stage for Behe's argument which states that "Behe turns the table on these counterexamples, arguing that these examples in fact underscore the barrier that irreducible complexity poses to Darwinian explanations and, if anything, show the need for design explanations". Beautiful rhetoric but not much science or evidence that Behe is familiar with amount of knowledge gathered about the bacterial flagellum since he made his argument in 1996. This Icon of ID offered the potential for proponents of ID to show off the potential of ID as a scientifically relevant contributor to our knowledge. What we find instead is an argument deeply entrenched in rhetoric and surprisingly little science.

David Wilson · 21 August 2004

A question to PvM or anyone alse who's read "Debating Design". Is there anything at all that's new in Behe's chapter? I assume he still hasn't come up with the revised definition of IC which he promised a few years ago, after he finally admitted the old one was flawed.
— Richard Wein

I'm not sure if this qualifies, but in this article Behe admits that "irreducible complexity could be better formulated in evolutionary terms by focusing on a proposed pathway, and on whether each step that would be necessary to build a certain system using that pathway was selected or unselected." He doesn't exactly abandon his original definition, since he says openly that he still thinks it's a "reasonable definition of IC", but he does admit that "it has some drawbacks". However he does propose a new definition in the article:

An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway.

I have very little idea of the extent to which he has subsequently made use of this new definition. Here is the only other article of his where I have seen him use it. For critics of Behe's arguments, his use of the new definition has the advantage of highlighting one of the fundamental blunders on which they have always been based. Here is the key passage from the above-cited article.

If the improbability of the pathway exceeds the available probabilistic resources (roughly the number of organisms over the relevant time in the relevant phylogenetic branch) then Darwinism is deemed an unlikely explanation and intelligent design a likely one.

This is nothing other than the standard statistical blunder of which so many creationists seem to be so enamoured---namely, the mistaken belief that if a proposed explanation for some observed event entails a minuscule a priori probability that the event would have occurred, then that by itself constitutes sufficient justification for rejecting the proposed explanation.

Pim van Meurs · 21 August 2004

the definition of unselected steps seems to indeed make a theory depending on selection less likely but lets not forget that there are many ways for a particular step to be unselected and still become fixated. I believe the terms are hitch hicking (the change is linked to other beneficial changes). In this case the step is unselected in the sense used by Behe but in historical context it would be Darwinian nevertheless since the overall fitness increased. Another example would be 'selective sweep'. Or there is neutral evolution which seems to be more and more a key element in issues relating to evolvability, and reliability. Darwin was in fact quite clear that he considered selection but one of the mechanisms of evolution.

Let's define an IC system is one in which one can unambiguously define one or more steps which required the actions of an intelligent designer. Let's see how well IC does in biology under such a definition.

Eliminative arguments, appeal to ignorance, God of the gaps, what has ID to offer scientifically? So far the evidence suggests "not much". And in my personal opinion, that's not likely going to change. Partially that can be explained by the lack of enthusiasm among ID proponents to pursue ID hypotheses in any meaningful manner, partially because gap arguments have never been very succesful in the past and partially because ID is fundamentally flawed at the theoretic level.

Pim van Meurs · 21 August 2004

See also the EvoWiki which outlines the various definitions. ID evolving, imagine that...

Fascinating how even among themselves ID proponents seem to be unclear as to the definition of these terms.

Steve · 22 August 2004

So Behe thinks he will be proven correct as soon as people establish that in certain biological systems, there exist several components which could never have been selected at any time in the past, under any circumstances, in combination with any other components, and/or as parts in any other cellular system?

Dembski never answered my question about how will we know ID is finally worth giving attention. But this is an acceptable one. As soon as somebody proves the above, let me know. I'll drop everything to study it.

Steve · 22 August 2004

But first I'll study the proof, because I have much to learn from people who can do this impossible thing.

RBH · 22 August 2004

This is mildly off-topic, but for some time I've been amused by the fact that as of today at least (8/22/04), the ISCID "Encyclopedia of Science and Philosophy" has an entry for "complexity" that doesn't include Dembski's improbability definition. :)

RBH

Richard Wein · 22 August 2004

Thanks, David, but that was only a "tentative" new definition, and Behe has never mentioned it again. He probably realizes that switching to that definition would do him no good, since he would then be unable to demonstrate that any structure is IC.

Richard Wein · 22 August 2004

Here is the only other article of his where I have seen him use it.
— David

Such a system is irreducibly complex, requiring several steps to be taken independently of each other before having selective value.
— Behe (from the article cited by David)

That's a good example of Behe equivocating over the meaning of IC. Here he is implicitly using his tentative new definition of IC, though he doesn't mention that new definition anywhere in the article.

Dada · 22 August 2004

PvM

It's ironic that Dada quotes from a part in Dembski's response which is shown to be wrong by Ussery and Musgrave.

May I get reference to Ussery and Musgrave's response?

That Dembski's understanding of biology is quite lacking should not come as a surprise, in fact most of the proteins have found homologues.

Evidence, please. So well over half of the proteins are found homologues and thus the Dembski's claim that 2/3 of the proteins are unique is false? Even if all proteins are found homologues there still would be huge difficulties in explaining evolution of flagellum via neo-Darwinian theory: As John Bracht (2003) points out: "The problem is that the proteins which are to become the flagellum are coming from systems that are distinctly non-flagellar in nature (after all, we are discussing the origin of that very system) and being co-modified from their original molecular interactions into an entirely new set of molecular interactions. Old interfaces and binding sites must be removed and new ones must be created. But given the sheer number of flagellar proteins that must co-evolve, [thereby] co-generating all the proteins required for flagellar function (again, this is true at some point in the flagellum's evolutionary past even if there were earlier steps that were not so tightly constrained), the Darwinian explanation is really no different from appealing to a miracle."

Dembski's probability calculations, fail to accurately describe the actual mechanisms involved in the formation of the flagellum, Dembski's claims about homologies totally flawed.

The evidence points out that flagellum didn't evolve from TTSS, TTSS "evolved" from flagellum(ref. Nguyen L. et al. Phylogenetic analyses of the constituents of Type III protein secretion systems. J. Mol. Microbiol. Biotechnl. 2(2):125-44.) I would say that your claims are totally flawed.

Pim van Meurs · 22 August 2004

for Dada: Why intelligent design fails Young and Edis (ed) Chapter 4: Darwin's transparent box: The biochemical evidence for evolution Dave Ussery Chapter 6: Evolution of the bacterial flagellum Ian Musgrave Between 80 and 88% of the proteins have so far found to have honologues. Dembski's claim shows how sensitive the explanatory filter is to side information and how ID is a gap theory. Bracht also misses the point. Many of the flagellar proteins find homologues in the secretory system. To suggest that binding sites cannot evolved under Darwinian mechanisms or that all these proteins coevolved to 'pop into' place shows an interesting strawman but like Dembski's probability calculations, little relationship to reality As far as your claim that the flagellum did not evolve from the TTTS, I said a precursor TTTS. In other words TTTS and the flagellum share a common ancestor. You quote Nguyen et al, a paper also referenced by Matzke although Nguyen's conclusion has been challenged by Gophna

Nguyen et al.'s (2000) conclusion has recently been challenged by Gophna et al. (2003), who demonstrated with phylogenetic trees of FlhA, FliI, FliP, and FliO homologs that type III virulence system sequences do not nest within flagellar sequences. This supports the view that the two systems diverged from a common ancestor, which could plausibly have been a type III export system functioning in a nonflagellar, nonpathogenic context. However, Gophna et al. (2003) are not able to exclude the possibility that virulence systems evolve more rapidly, or that the frequent lateral transfer of type III virulence system genes (Nguyen et al., 2000; Gophna et al., 2003) might have increased the rate of sequence divergence. Gophna et al. also cite for support the progressionist notion that evolution disfavors events such as the simplification of complex systems like the flagellum, a dubious proposition in modern evolutionary theory, especially considering the common evolutionary trend of simplification in pathogens and parasites. As long as known nonflagellar type III secretion systems are phylogenetically restricted and only function as specialized systems for eukaryote penetration, the suspicion will remain that they are derived from flagella. For the purposes of the current discussion it will be assumed that type III virulence systems are derived, although they still give valuable insights about the possible traits of a hypothetical ancestral type III secretion system.

Source Matzke (above) and Musgrave (2004) show that there are deep links between the structures found in the bacterial flagellum and secretory systems. Musgrave presents a proposed evolutionary pathway. 1. A secretory system areose first based around the SMC rod and pore forming complex which is both ancestral to the flagellum and the type-III secretory system 2. Association with an ion pump (later to become the motor protein) improved secreation. As Musgrave shows the motor proteins can freely associate and dissociate with the flagellar structure. Such loose coupling is an important find. 3. Next the protoflagellar filament arose and gliding-twitching motility arose which was then refiend into swimming motility 4. Regulation and switching can be added later Wvidence of a variety of intermediates that function well include 1. Simple secretory systems powered by proton motors 2. Gliding secretory systems powered by proton motors homologous to those of 1, guided by chemical sensing systems 3. Rotating swimming secretory systems powered by proton motors homologoous to those of 1. guided by chemical sensing systems homologous to those of gliding secretory systems And finally there is the type-II secretion, type-IV gliding motility and the archaebacterial flagellar motility swtimming to support this model. So contrary to Dembski's argument that researchers have nothing more than a type-III topoint to, reality is that research in these 6 years have found many more homologies between flagellar proteins and other systems, including the motor proteins, researchers have realized that the archaebacterial and eubacterial flagellua are entirely diffrernt, researchers have uncovered deep links between secretion and mobility. Compare that with what ID has contributed namely: "I could not imagine that the flagellum could evolve via Darwinian pathways". Unaware of this scientific knowledge, Dembski's claims show once again clearly how sensitive the explanatory filter is to side information (background knowledge) and thus false positives. Nick Matzke and Ian Musgrave have shown how scientific inquiry and knowledge leads to potential pathways for flagellar evolution. Compare this with the strawman probability calculations of Dembski or Dembski's familiarity with the research in this area. Matzke showed how the function of the hypothetically evolving system (figure 7) would go from export, to secretion to adhesion to dispersal to taxis (table 6), showing how original function is a meaningless concept in understanding how IC systems may evolve. By redefining IC to 'original function' ID is unable to model likely evolutionary pathways and should thus be rejected as scientifically relevant. Another Icon of ID seems to be ready to expose the lack of scientific relevance of ID.

Pim van Meurs · 22 August 2004

Gophna "Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events", Gene 312 (2003) 151--163

Abstract Type III secretion systems (TTSS) are unique bacterial mechanisms that mediate elaborate interactions with their hosts. The fact that several of the TTSS proteins are closely related to flagellar export proteins has led to the suggestion that TTSS had evolved from flagella. Here we reconstruct the evolutionary history of four conserved type III secretion proteins and their phylogenetic relationships with flagellar paralogs. Our analysis indicates that the TTSS and the flagellar export mechanism share a common ancestor, but have evolved independently from one another. The suggestion that TTSS genes have evolved from genes encoding flagellar proteins is effectively refuted. A comparison of the species tree, as deduced from 16S rDNA sequences, to the protein phylogenetic trees has led to the identification of several major lateral transfer events involving clusters of TTSS genes. It is hypothesized that horizontal gene transfer has occurred much earlier and more frequently than previously inferred for TTSS genes and is, consequently, a major force shaping the evolution of species that harbor type III secretion systems.

Ariel Blocker, Kaoru Komoriya and Shin-Ichi Aizawa "Type III secretion systems and bacterial flagella: Insights into their function from structural similarities." PNAS (2003) vol. 100 no. 6 3027-3030 See their figure 1.

Donald M · 22 September 2004

Behe, in "Irreducible Complexity: Obstacle to Darwinian Evolution ", focuses on the concept of irreducible complexity as a reliable indicator of intelligent design but irreducible complexity has been shown to be able to arise under fully natural processes thus it is not a very reliable indicator of design. In fact the argument from IC (irreducible complexity) mostly centers around our ignorance of the actual details. While the bacterial flagellum may have appeared to be IC, more and more research provides us with fascinating insights as to how it may have evolved (Musgrave, Matzke). See also Kenneth Miller in this volume.
— Pim van Meurs

Pim, Could you kindly provide citations for Musgrave and Matzke's research? I can't find them, but I might not be searching in the right place. Thanks much. Donald M

Nick (Matzke) · 22 September 2004

Donald M., I think Pim is out of town, but he is referring to:

Musgrave, Ian (2004). "Evolution of the Bacterial Flagellum", in: Young, M., and Edis, T. (Eds.), Why Intelligent Design Fails: A Scientific Critique of the Neocreationism, Rutgers University Press, Piscataway, N.J.

"Evolution in (Brownian) space: a model for the origin of the bacterial flagellum" by Nick Matzke. Read the background page first. This essay is the most detailed examination of the issue around, but although less than a year old is already out of date.

You should also read (and probably start with):

"Answering the biochemical argument from design", by Kenneth Miller (2003), in: Manson, N. (Ed.), God and design: the teleological argument and modern science, Routledge, London, pp. 292-307. Amazon link

Miller, Kenneth (2004)"The Flagellum Unspun", in: Dembski, W., and Ruse, M. (Eds.), Debating Design: from Darwin to DNA, Cambridge University Press, New York, pp. 81-97. Amazon link

tyler · 14 October 2004

Hey:

I have not read "Debating Design" yet. However I was very interested in the sections authored by Paul Davies and Walter Bradley. Will anyone give me a brief review of the arguments from both of these people?