Book review: Debating Design (Dembski/Ruse ed.)

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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.

John Haught’s “Darwin, Design and Divine Providence”, explains the main reason why Intelligent Design proponents so strongly oppose Darwinism and why they are wrong. Surprisingly it is based on the same argument that some evolutionists use to ‘disprove’ religion. Namely the idea that “Darwinism renders the notion of a divine Providence implausible”. This is an interesting observation which may help explain the strong anti-Darwinism found in ID proponents. 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. This helps one to understand why ID was quickly to abandon the efforts of teaching of intelligent design in favor of the teachings of ‘the controversy’. While little real controversy exists, this allows for a ‘wedge’ for ID to get its message across. Haught’s contribution offers a refreshing insight into why Darwinism can be theologically acceptable. In “God after Darwin” Haught observed that

“A God whose very essence is to be the world’s open future is not a planner or a designer but an infinitely liberating source of new possibilities and new life. It seems to me that neo-Darwinian biology can live and thrive quite comfortably within the horizon of such a vision of ultimate reality.”

Haught shows convincingly how Darwinian evolution does not inevitably entail a materialistic philosophy and that the theological notion of Providence is different from the idea of Intelligent Design. Haught thus argues that evolution and divine Providence are compatible. In fact the ultimate love (God’s Providence) can only be found in the contingency of life, free of ant predestination or rigidities. Haught’s chapter is a must read for scientists and Christians.

Ayala’s argument in “Design without Designer: Darwin’s Greatest Discovery” is very similar to Ruse’s namely that teleology in nature is the expected outcome of the processes of evolution which include natural selection. Thus the appearance of teleology by itself is not sufficient to infer intelligent design. In other words, even if we can infer design, we cannot exclude “natural selection” as its designer. One of the earliest people to point out this limitation in Dembski’s argument was Wesley Elsberry.

In “DNA by Design? Stephen Meyer and the Return of the God Hypothesis” Pennock addresses many of the claims by Meyer and shows why they are without much merit. Pennock points out the ‘cut and paste’ approach of Meyer in which old arguments, even after been shown to be erroneous, end up in later publications (especially in publications that are not peer reviewed such as newspapers). Pennock not only shows that the anti-Darwinian implications of the Cambrian explosion are mostly “blown out of proportion” (pardon the pun), but also that ID proponents fail to present much of a scientific argument in favor of their own claims. Questions which remain unanswered include “what about phyla which arose after the Cambrian? Where they also ‘designed’?”, “what about the species that arose since the explosion such as us humans?”

Elliott Sober in “The Design Argument” shows what is wrong with the philosophical and logical foundations of the “intelligent design” argument as proposed by Dembski. By showing that there is no probabilistic equivalent to the “modus tollens” argument, Sober shows how the foundation of the design argument is fundamentally and irreparably flawed. Modus tollens is the argument that “if P then Q”, followed by the observation that “Q” is false, hence P is false. But when dealing with probabilistic arguments, such as found in the intelligent design approach, modus tollens does not hold anymore. In other words, if a hypothesis states that an observation is very unlikely, it does not mean that the hypothesis is unlikely. Probabilistic arguments to show “intelligent design” are quite common and all suffer from the above flaw. Because of this “Intelligent Design” has to show that the probability of a particular observation or event “E” is more probable given the intelligent design hypothesis than a naturalistic hypothesis. But this means that “intelligent design” has to be formulated in a positive rather than its usual negative (eliminative) form. Intelligent Design inferences are typically stated as not(chance and/or regularity) thus intelligent design. This argument, also known as “argument from ignorance” forms a poor logical and scientific foundation for science. Hence we have to reject the “intelligent design” claims based on such an approach. That the “intelligent design” approach is indeed unsuitable for scientific inquiry can be observed in a total absence of “intelligent design” hypotheses relevant to science. As Del Ratzsch has stated (I paraphrase), in order for intelligent design to be relevant it has to show that it can give better ‘non ad hoc’ explanations of the observations. An “intelligent designer” did it fails that requirement.

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.

Dembski in “The Logical Underpinnings of Intelligent Design” continues to argue his fallacious claim that his explanatory filter has no ‘false positives’ despite the fact that such false positives are unavoidable. Failing to address the criticisms by his opponents and even fellow ID proponents such as Del Ratzsch, Dembski still argues the logically impossible namely that his filter does not suffer from false positives. In fact Dembski more recently has accepted false positives as an inevitable risk of doing science but he also maintains that false positives would render the explanatory filter useless. Seems to me that the only logical conclusion thus is that the explanatory filter (which is used to infer intelligent design) is useless. A conclusion already reached by intelligent design proponents such as Del Ratzsch who stated

“So typically, patterns that are likely candidates for design are first identified as such by some unspecified (“mysterious”) means, then with the pattern in hand S picks out side information identified (by unspecified means) as relevant to the particular pattern, then sees whether the pattern in question is among the various patterns that could have been constructed from that side information. What this means, of course, is that Dembski’s design inference will not be particularly useful either in initial recognition or identification of design.”

From page 159 of Del Ratzsch’s “Nature design and science: The Status of Design in Natural Science”, Suny Series in Philosophy and Biology, State University of New York Press (April 1, 2001) which is an excellent book by an intelligent design proponent who often takes an unpopular stance within the ID movement.

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.


Update August 21

Behe’s argument is that :

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.

In other words, a beautiful rhetorical argument in the form of reversed form of “appeal to authority”.

Behe ends with

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.

The rhetoric and the lack of much scientifically relevant data suggests to me that ID is indeed on the right track. A track to scientific obscurity. As the ultimate Icon of ID, one would expect design proponents to extend the argument by adding positive knowledge about the flagellum showing how indeed the system is not only irreducibly complex but that Darwinian pathways are less and less likely the more knowledge we acquire. Of course the problem seems to be that with increased knowledge the gap narrows significantly.



Update August 19

Behe’s arguments are also self defeating. First of all he argues that Irreducible Complexity seems to be difficult to fit into a Darwinian perspective but as has been shown in “Thornhill, R.H., Ussery, D.W. 2000. “A classification of possible routes of Darwinian evolution.” J. Theor. Bio. 203: 111-116.”, such a notion is untenable. In chapter 15 Michael Roberts shows the great use Behe makes of rhetoric. “Having led the reader through many explainable and unexplainable (unexplained? PvM) functions and having used the rhetorical appeal of his mousetrap, he (Behe) uses an inductive rhetorical argument and argues that the absence of an explanation, as in the case of blood clotting, indicates the direct activity of a Designer. He rapidly moves from possibility to probability to moral certainty, but that certainty is only certain until an explanation is found. … and his conclusion of a Designer is only a ‘restatement of fact’ based on his original argument” (page 286). In other words, the conclusion of intelligent design not only suffers from being a ‘God of the Gaps’ or ‘appeal to ignorance’ argument but additionally depends strongly on the presumption that intelligent design is correct. This becomes even more evident when we hear Behe make the following statement

A second point that is often overlooked but should be emphasized is that Intelligent Design can happily coexist with even a large degree of natural selection. Antibiotics and pesticide resistance, antifreeze proteins in tish and plants, and more may indeed be explained by a Darwinian mechanism. The critical claim of ID is not that natural selection doesn’t explain anything, but that it doesn’t explain everything.

Michael Behe p. 356

In other words, ID is scientifically meaningless as it explains everything and anything. If we find a natural pathway to a biologically complex (or even irreducibly complex) system, it is compatible with ID, and if we remain ignorant it is (even more) compatible with ID.

So what explanations does ID have to offer one may wonder? Behe is quickly to point out the ‘just so stories’ of Darwinism but seems to fail to realize in his rhetoric that the same problem exists in an even more insurmountable format for ID. Namely not just the existance of ‘just so stories’ but the complete lack of any story beyond ignorance. After engaging in more rhetorical arguments about the blood clotting cascade and the moustrap, while ignoring examples in which science has progressed in its understanding of for instance the bacterial flagellum, Behe concludes “the misconceived arguments by Darwinist 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”.

Beautiful rhetoric which shows once again the scientific emptiness of the intelligent design hypothesis. It’s force is not to be found in actual scientific arguments or evidence but rather in our ignorance. If Behe really believed the idea was worth investigating one would have expected that since the publication of his book he would have embarked on ID relevant research. The opposite seems to be true however, ID relevant research is painfully lacking other than in the unsupported claims by Dembski that ID friendly research exists in the form of the ISCID bibliography. I have seen the ISCID bibliography and it does not present any relevant ID research. Unless one confuses anti-Darwinian with pro-ID. But that is just rhetoric not science.


Finally, Meyer, in “The Cambrian Information Explosion: Evidence for Intelligent Design” raises the old canard (can we say Icon of Intelligent Design) of the Cambrian explosion much of the arguments seem to be contrary to (again) recent scientific findings making the Cambrian explosion as an argument for design one based on our ignorance more than on a positive contribution to our scientific understanding. Contrary to what ID proponents seem to suggest, the Cambrian explosion was not the origin of complex life although it was a period of rapid divergence. Multicellular life can be traced back to the pre-Cambrian and bacteria to more than 3.5 billion years ago. Beautiful transitional fossil evidence and evidence of phyla level evolution can be found. The Cambrian explosion is hardly the enigma Meyer seems to want it to be. In other words, the Cambrian explosion, as described by Meyer mostly is a strawman argument, or in simpler terms an argument at odds with both the evidence and the scientific understanding of this event. But even ignoring these shortcomings, Meyer does not present any scientific evidence why the Cambrian explosion should be seen as ‘evidence of intelligent design’. Kenneth Miller raised a good question: If all these organisms were designed by an intelligent design during the Cambrian why did most of them go extinct?


TABLE OF CONTENTS

INTRODUCTION
1. General Introduction p. 3
William A. Dembski
2. The Argument from Design: A Brief History p. 13
Michael Ruse
3. Who's Afraid of ID? A Survey of the Intelligent Design Movement p. 32
Angus Menuge
PART I: DARWINISM
4. Design without Designer: Darwin's Greatest Discovery p. 55
Francisco J. Ayala
5. The Flagellum Unspun: The Collapse of "Irreducible Complexity" p. 81
Kenneth R. Miller
6. The Design Argument p. 98
Elliott Sober
7. DNA by Design? Stephen Meyer and the Return of the God Hypothesis p. 130
Robert T. Pennock
PART II: COMPLEX SELF-ORGANIZATION
8. Prolegomenon to a General Biology p. 151
Stuart Kauffman
9. Darwinism, Design, and Complex Systems Dynamics p. 173
Bruce H. Weber and David J. Depew
10. Emergent Complexity, Teleology, and the Arrow of Time p. 191
Paul Davies
11. The Emergence of Biological Value p. 210
James Barham
PART III: THEISTIC EVOLUTION
12. Darwin, Design, and Divine Providence p. 229
John F. Haught
13. The Inbuilt Potentiality of Creation p. 246
John Polkinghorne
14. Theistic Evolution p. 261
Keith Ward
15. Intelligent Design: Some Geological, Historical, and Theological Questions p. 275
Michael Roberts
16. The Argument from Laws of Nature Reassessed p. 294
Richard Swinburne
PART IV: INTELLIGENT DESIGN
17. The Logical Underpinnings of Intelligent Design p. 311
William A. Dembski
18. Information, Entropy, and the Origin of Life p. 331
Walter L. Bradley
19. Irreducible Complexity: Obstacle to Darwinian Evolution p. 352
Michael J. Behe
20. The Cambrian Information Explosion: Evidence for Intelligent Design p. 371
Stephen C. Meyer

Change History

Aug 18: spell checked Aug 19: Added additional comments on Behe’s rhetoric Aug 21: Added examples of Behe’s beautiful rhetoric

23 Comments

PvM Wrote:

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.

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.

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.

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/docu[…]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.

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.

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.

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.

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 :-)

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.

Richard Wein Wrote:

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.

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.

Richard Wein Wrote:

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.

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.

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.

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.

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.

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

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

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.

David Wrote:

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

Behe (from the article cited by David) Wrote:

Such a system is irreducibly complex, requiring several steps to be taken independently of each other before having selective value.

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.

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.

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.

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.

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Donald M.,

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

You should also read (and probably start with):

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?

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This page contains a single entry by PvM published on August 17, 2004 5:52 PM.

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