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ID theorist Mike Behe was refused a response in Microbe

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See Challenge to Uncommon Descenters from ID Facebook page: “Hundreds of labs show, it is claimed, that the bacterial flagellum is not irreducibly complex.”

Behe relies,

I responded to that paper six years ago, soon after it came out, at Uncommon Descent:

What I didn’t do then at the blog is to say that I had submitted my response as a letter to the Editor of Microbe, which he turned down. My correspondence with him is below.

In “Evolution of the Bacterial Flagellum” (July 2007) Wong et al seek to counter arguments of intelligent design proponents such as myself that the flagellum did not evolve by random mutation and natural selection. Unfortunately, their otherwise-fine review misunderstands design reasoning and so fails to engage that issue. The critical passage from Wong et al is the first paragraph:

Proponents of the intelligent design (ID) explanation for how organisms developed claim that the bacterial flagellum (BF) is irreducibly complex. They argue that this structure is so complicated that it could not have emerged through random selection but had to be designed by an intelligent entity. One part of this claim is that each flagellar component is used solely for the purpose of making a flagellum that, in turn, is used only for motility. Further, each flagellar protein is assumed to have appeared independently of the other component proteins.

Although the first two sentences are correct, the last two sentences are quite wrong. (The authors cite no references for these latter claims.) It is no part of the design argument that each component of an irreducibly complex structure must be used solely for that purpose, nor that each part must arise independently. In my 1996 book Darwin’s Black Box, which brought the concept of irreducible complexity to wide public attention, I pointed out the fact that, for example, proteins of the blood clotting cascade share sequence homology with each other and with other serine proteases, and the fact that ciliary proteins such as tubulin are involved in other tasks in the cell. Yet I explained that neither sequence homology nor multiple functions showed how integrated systems containing many parts could be put together by small random steps. Unfortunately, Wong et al spend their efforts addressing their own erroneous assertions. They fail to address the only pertinent question, the question of whether random, unintelligent processes — even when filtered by natural selection — could plausibly build a structure such as the flagellum.

To address the adequacy of random processes plus selection would require rigorous experiments or calculations showing that the intricate, functional structures are not too improbable given the evolutionary resources available. Recent work bears negatively on this difficult question. In long term laboratory evolution experiments over tens of thousands of generations (Lenski, R.E. 2004. Phenotypic and genomic evolution during a 20,000-generation experiment with the bacterium Escherichia coli. Plant Breeding Reviews 24:225-265), cultures of E. coli were repeatedly seen to lose the ability to make ribose and maltose, and to repair their DNA. Some mutations shut down expression of their flagellar genes, apparently to conserve energy. No selected mutations were observed which could plausibly be argued to be the incipient stages of some new, complex functional system. Similar kinds of results are seen in other well-studied evolutionary systems. For example, in response to strong pressure from the malarial parasite, the human genome has suffered a handful of positively-selected-yet-degradative mutations (Carter, R. and Mendis, K.N. 2002. Evolutionary and historical aspects of the burden of malaria. Clin. Microbiol. Rev. 15:564-594), including ones that render nonfunctional the genes for glucose-6-phosphate dehydrogenase, the alpha and beta chains of hemoglobin, band 3 protein, and others. Again, no selected mutations were observed which could plausibly be argued to be the incipient stages of some new, complex functional system.

To a skeptic such as myself, this does not look like the sort of process which could build complex molecular machinery. Those who would argue persuasively against intelligent design must address this basic issue. – Michael J. Behe, Department of Biological Sciences, Lehigh University

Lacey replied,

Thank you for your recent letter on Dr. Saier’s article. We are declining to publish the letter as it does not address the main points of the article. The article and Microbe’s decision to publish it were not intended to address the broad question of the validity of evolution. ASM has published its Statement on the Scientific Basis for Evolution which summarizes the views of the Society on the topic:

Knowledge of the microbial world is essential to understanding the evolution of life on Earth. The characteristics of microorganisms—small size, rapid reproduction, mobility, and facility in exchanging genetic information—allow them to adapt rapidly to environmental influences. In microbiology, the validity of evolutionary principles is supported by [1] readily demonstrated mutation, recombination and selection, which are the fundamental mechanisms of evolution; [2] comparisons based on genomic data that support a common ancestry of life; and [3] observable rates of genetic change and the extent of genomic diversity which indicate that divergence has occurred over a very long scale of geologic time, and testify to the great antiquity of life on Earth. Thus, microorganisms illustrate evolution in action, and microbiologists have been able to make use of the microbes’ evolutionary capacity in the development of life-improving and life-saving innovations in medicine, agriculture, and for the environment. By contrast, proposed alternatives to evolution, such as intelligent design and other forms of creationism, are not scientific, in part because they fail to provide a framework for useful, testable predictions. The use of the supposed “irreducible complexity” of the bacterial flagellum as an argument to endow nonscientific concepts with what appears to be legitimacy, is spurious and not based on fact. Evolution is not mere conjecture, but a conclusive discovery supported by a coherent body of integrated evidence. Overwhelmingly, the scientific community, regardless of religious belief, accepts evolution as central to an understanding of life and the life sciences. A fundamental aspect of the practice of science is to separate one’s personal beliefs from the pursuit of understanding of the natural world. It is important that society and future generations recognize the legitimacy of testable, verified, fact-based learning about the origins and diversity of life. – Patrick Lacey, production Manager, Microbe (formerly ASM News)

Behe replied,

Dear Dr. Lacey,

Thanks very much for your email. However, your statement that my letter “does not address the main points of the article” is quite difficult to understand. The clearly stated purpose of the Wong et al article is to refute intelligent design reasoning. My letter shows that the authors misunderstand design reasoning, so that the supposed refutation addresses a straw man. How can that not be “address[ing] the main points”?

If you will read my letter with attention, Dr. Lacey, you will notice that I did not question “the validity of evolution”. In fact, although many people are confused on this point, the concept of intelligent design has no proper quarrel with the validity of evolution. Intelligent design is quite compatible with descent with modification. It simply argues that some facets of life resulted from intelligent planning or direction, rather than relying exclusively on random events, as Darwinian theory proposes. My discussion in the letter of the results of random mutations in experiments on E. coli, and in human/malaria evolutionary warfare underscores this point.

Dr. Lacey, most publications consider it responsible journalism to publish letters by well-known advocates of views attacked in articles. The purpose, of course, is to avoid misleading readers of the journal by unknowingly misstating or caricaturing a position. In order that your readers will not form a mistaken view of what the intelligent design argument actually states, I ask you to reconsider the decision not to publish my letter. – Best wishes, Mike Behe

Of course the letter was never published! Why ever should it be? Lacey is just another feeder at the government teat of Darwinism. He gets a salary from helping suppress growing doubt.

Just think how many tenured Darwin mediocrities batten off your taxes, knowing that, like him, they need fear no challenge from facts. They also teach at the high schools your taxes pay for.

Comments
tjguy, no problemmoCentralScrutinizer
September 26, 2013
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The most absurd thing is that the article by Wong et al was written to denounce the ID position, yet Behe wasn't allowed to counter the arguments because ID isn't a scientific viewpoint. Anyone else catch the overwhelming hypocrisy?OldArmy94
September 24, 2013
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Elizabeth Liddle: Behe presented a scientific case that merited consideration. Why shouldn’t scientists consider it? Indeed. And why doesn't he publish? No one is standing in his way.Mung
September 24, 2013
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Behe's mousetrap example is ingenious. It's a fairly simple apparatus that functions only when all its components are assembled. Each component on its own—platform, spring, holding bar, trap hammer, catch—is not a mousetrap and cannot function as such. All the parts are needed simultaneously and have to be assembled for there to be a working trap. Likewise, a cell can function as such only when all its components are assembled. He uses this illustration to explain what he terms “irreducible complexity.” Makes sense to me. On the other hand, we also have Robert Naeye, a writer for Astronomy magazine and an evolutionist, wrote that life on earth is the result of “a long sequence of improbable events [that] transpired in just the right way to bring forth our existence, as if we had won a million-dollar lottery a million times in a row.” [“OK, Where Are They?” Astronomy, July 1996, p.36] If you won the lottery even three times in a row, you'd be under suspicion (if not arrested) for rigging the results.Barb
September 24, 2013
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More Irreducible Complexity Is Found in Flagellar Assembly - September 24, 2013 Concluding Statement: Eleven years is a lot of time to refute the claims about flagellar assembly made in Unlocking the Mystery of Life, if they were vulnerable to falsification. Instead, higher resolution studies confirm them. Not only that, research into the precision assembly of flagella is provoking more investigation of the assembly of other molecular machines. It's a measure of the robustness of a scientific theory when increasing data strengthen its tenets over time and motivate further research. Irreducible complexity lives! - http://www.evolutionnews.org/2013/09/more_irreducibl077051.htmlbornagain77
September 24, 2013
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Did Michael Behe State Exaptation has been "Shown" to Produce Irreducible Complexity? - August 2012 http://www.evolutionnews.org/2012/08/did_michael_beh063271.htmlbornagain77
September 24, 2013
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JDH
You stated that you believe the editor’s statement is disingenuous ( a polite way of saying he is just lying ). My question is, do you think the disingenuous response is an exception to the usual way ID arguments are handled or standard operating procedure for the anit-ID community. Of course, I believe it is the latter, but I have strong confirmation bias working in favor of this conclusion.
I don't know the answer to that, JDH. I think it is likely that there is a bias against ID arguments, borne partly from experience of poor ones, borne partly of a sense that ID is not itself an unbiased project (contrary to the beliefs of many here, evolutionary science doesn't have an atheist agenda, while ID clearly has a theist one), and partly of simple gut bias. However, the important issue is not whether an ID person has right of reply to a paper such as the one referred to, but whether that paper should have got into print without an editor pulling them up on the lack of reference to the ID arguments cited. Had they referenced the claim properly, then the Behe's right of reply would have been clear, if it was misrepresented (which it was, but you can't necessarily tell, because it was not referenced, so round we go), and Lacey wouldn't have had a leg to stand on. And these things do happen. The system should ensure it doesn't, but peer-review isn't perfect and editorial review isn't perfect. To me, that is where the problem began here, and cascaded down. So, poor show on the part of Microbe. And I don't think that is common. There is a reason why academics are normally so anal about referencing. My own view is that ID academics have mistaken genuine problems with their research for bias against their research. Both are possible factors, but at least part of the bias, I would say, arises from the history of problems. I honestly think that the biggest problem with ID is this lack of insight into the real flaws in the science. And because of that lack of insight, rejections by mainstream science is interpreted as bias. Yes, there's bias, but it's not, I suggest, against the philosophical ID stance, but simply against authors who repeatedly produce arguments that don't stand up to rigorous analysis. The papers from the Ithaca conference are a case in point. One or two would probably make it through individual peer=review, but the rest are nowhere close. Getting published is hard, and all scientists have the regular experience of having papers rejected, over and over. But you read the reviews, and you address the issues, and you rewrite, and you resubmit, and eventually you get the thing through. It doesn't mean the resulting paper is perfectly, and bad papers still get through, but it does mean that constant revision in the light of rigorous criticism is endemic to the entire project. Obviously IDists will disagree with this analysis, but as someone with probably less bias than most against the ID project, that is the way I see it.Elizabeth B Liddle
September 24, 2013
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Central, Deepest apologies! Obviously I misread the tone of the post.tjguy
September 24, 2013
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Excuse the typos ^ My summary is basically that "Co-option" may very well be a part of the equation here, but all it really shows me at this point is that the BF was "Intelligently engineered" through a process of "Co-option and scaffolding" and of course the final product would be selected for. I see no "logical or physical" evidence that would lead me to believe that this complex process happens with very little rhyme or reason.Timothy Kershner
September 24, 2013
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Elizabeth -- allow me to state (for the record) that i am not directly opposed to the Anti-ID (for lack of a better term) proposition that parts were somehow co-opted or that scaffolding may come into play. I support Behe in many of his concepts (they appear to be grounded in good logic), and I'm willing to concede to any conceptual ideals (and more specifically) observed laboratory data. So, at I'll just address your first point: "If something functions as something else with parts missing, then being IC won’t be a bar to adaptive evolution because the whole point of the IC concept is that it can’t be achieved by step-wise beneficial changes (cooption)" I believe this was actually addressed in "Black Box" and the 'parts have other functions' issue doesn't particular carrying a lot of weight, unless of course we can show these precursors and that parts were just "Randomly" co-opted without rhyme and reason and then eventually an "Out-board" motor just happened to fall together in the right place at the right time and because it was a good thing got selected for. I don't find "co-option" to be a huge blow at this juncture to the IC hypothesis.Timothy Kershner
September 24, 2013
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Well, there are two issues: Firstly: If something functions as something else with parts missing, then being IC won't be a bar to adaptive evolution because the whole point of the IC concept is that it can't be achieved by step-wise beneficial changes (cooption) And if something works with more parts, and the more-parts version can be achieved stepwise ("scaffolding") as with an arch (designed or natural), then again, there may be a path with step-wise beneficial changes. So those two concepts mean that simply being IC (ceasing perform the same function if any part is removed) is not, in principle, a bar to evolution. Secondly, is the issue of whether there is actual evidence, in a particular case, for such pathways. And the Pallen and Matzke paper showed, practically, a possible cooption pathway. There is actually a third issue, which is drift. Lenski et all, in their AVIDA paper, showed that, again in principle, IC features can evolve by pathways that include many non-beneficial, and even deleterious steps. And so even in principle, being IC is not necessarily a bar to evolving by stepwise changes. Those changes, it turns out, don't have to be beneficial, and can even be deleterious. That said, I think Behe deserves credit for making an important point: that it is possible that some things simply cannot evolve by stepwise means. However, demonstrating that this is true for any one feature is not as simple as Behe seems to think, and it is certainly not obvious simply by demonstrating that a feature ceases to perform a function if any part is removed. In any case, knowing whether a feature is advantageous to an organism requires knowing something about the environment it was in when it was in its putative pre-"functional" form. That is often unknowable. ThElizabeth B Liddle
September 24, 2013
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Elizabeth - "“Co-option” and “scaffolding” are not “false new concepts”. I agree 100% with you. but, I'm presuming here that the original poster meant to convey that these "actions" which are typically utilized by intelligent agents "Co-opting parts" and "Erecting Scaffolding" are really just laid out in a fancy way that makes it appears as if the Anti-ID folk actually explained anything, and more importantly, that they actually explained anything utilizing "Observed facts in a lab setting". "Co-opting" may have occurred, but even that itself is a speculation. Even if it occurred, there is no real model as to how "RM" co-opts. stockpiles, reshapes, and re-organizes parts into a brand new system that fails to function with out all of it's core parts.Timothy Kershner
September 24, 2013
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Darwinism has encroached in an area that it has no scientific right to be, and enforced its position with political bullying. The fact remains that materialism/naturalism has limits at the origins. Simply put - The laws of physics cannot possibly create the laws of physics ("Oh, but there are special laws of physics that pertain only to the early universe." "Yes, and did those laws create themselves? How did that happen?" "Easy, the laws of physics evolved after billions of years--all scientific--you're not opposed to Science are you?") - Life and DNA cannot evolve itself out of non-living things. ("Oh, but don't you know about coacervates? After a billion years, DNA must have evolved in them by natural selection, which is obvious, because only those coacervates that had DNA could survive, which later became slime molds, which later developed light-sensitive patches, better DNA, motors, gears, feathers, and jet engines--all highly scientific--you're not opposed to Science are you?"). Think about it. The most highly evolved organisms on the planet are bacteria, followed by viruses. If anything, *they* were directly responsible in evolving larger creatures, such as ourselves, as bacterial mass transportation, community centers, and food sources rolled into one. Otherwise, in a competition between bacterial and, let's say, human evolution, humans most certainly would have lost out long ago! We simply don't reproduce fast enough, we're way too complex, and our evolutionary needs are way too specialized and demanding compared to what bacteria need.Querius
September 23, 2013
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JGuy: Don't you know? ID isn't scientific, but all the arguments against it are. By default. Because Darwinism is scientific, not ideological. So anything that questions it is ideological and not scientific. See? It all makes perfect sense.Phinehas
September 23, 2013
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Reading thru these comments and dialogues... Interesting! My nonscientific gut reaction to the "cut and paste official statemet" response to Dr. Behe was that it was like someone posting their creed or purpose statement. (This...Our Position on Evolution Contains... Statements That Must Not Be Questioned!). Sounds like a semi religious creed to me!vikingmom
September 23, 2013
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gpuccio @ 21 I won't disagree with you. I'm simply making the point that if ID wasn't scientific, why would a science journal waste time allowing a paper be published to respond to it - as if it was doing so in a scientific manner? Seems to me that it's effectively showing that it is attempting to test (i.e. Poppering) a claim in ID theory.JGuy
September 23, 2013
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Lizzie @12 You stated that you believe the editor's statement is disingenuous ( a polite way of saying he is just lying ). My question is, do you think the disingenuous response is an exception to the usual way ID arguments are handled or standard operating procedure for the anit-ID community. Of course, I believe it is the latter, but I have strong confirmation bias working in favor of this conclusion.JDH
September 23, 2013
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Thanks, Collin. I wasn't quite sure what JGuy meant.Elizabeth B Liddle
September 23, 2013
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Jerad, I was just kidding.Brent
September 23, 2013
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So I messed up the last post. I was responding to Dr. Liddle at 24.Collin
September 23, 2013
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Taht was his point. He was rebutting Mung who said it was not a scientific theory.
Collin
September 23, 2013
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tjguy: Why is it that none of or at least very few of the Darwinites are concerned about this kind of censorship? Central Scrutinizer just laughs and says “Hehe”. Very telling!
Say WHAT?! You got me all wrong, fella. I'm not a Darwinite. I'm laughing at blatant disregard for facts and honest exchange of ideas exhibited by Lacey. Par for the course of the Darbot establishment.CentralScrutinizer
September 23, 2013
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Pardon me, but how can I post a news item like this one on the forum? I would like to create a new topic for discussion.Loghin
September 23, 2013
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Cross-posted just now Jerad, dude! Sorry! But be careful because KF may take the gloves off now ;)
Why would my gender affect things? I don't get that. Anyway, I don't mind people disagreeing with me. If I did I'd have left long ago. I can take personal criticisms. But I'm not associated with any political, philosophical or ideological group. I'm just me. No agenda. So please don't take my statements as being anything other than my own.Jerad
September 23, 2013
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Regarding my point from the other thread. Any claim pertaining to biology must be empirical and thus technologically valid. The ID challenge is to demonstrate an internal mechanism for development (Like an automatic update mechanism). If mutations are part random, part directed than the challenge for IDers is to separate the noise from the function and use that non-linear solution for predictions (like the citrate). The Evo challenge is to demonstrate a stochastic process capable of coordinating both genetic and epigenetic processes and project a N-dimensional fitness landscape useful for predictions (current fitness landscapes are 3D and thus remarkably primitive).Loghin
September 23, 2013
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Cross-posted just now Jerad, dude! Sorry! But be careful because KF may take the gloves off now ;)Brent
September 23, 2013
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KF, I may sound contradictory here, but I'm human and get that indulgence every now and then, don't I? ;) I said I was somewhat sympathetic to Jerad (who is a "her"? I didn't realize that), but I knew there must be something to what you were saying, to her, specifically, though again, I didn't follow too closely. Moreover, though, I know exactly what you are getting at in this overarching "war" we are in. As a believer I cannot help but to have a severe awareness of the gravity of the situation; the ultimateness, the finalitiness. And, yes, there are going to have to start being lines drawn in the sand; stand here, or there. Is it any surprise that reason doesn't work with people committed to a system that undermines reason itself? (I'm not throwing stones here either, anyone: Just stating a fact that reason itself is, clearly, on trial in the naturalistic view.)Brent
September 23, 2013
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Jerad and many others like her will not realise until long after the hysteria has faded (if ever), what they have become caught up in.
Not sure who 'her' is. Not me. Check Genesis. My first name is normally spelled 'Jared'. And Jared begat Enoch.Jerad
September 23, 2013
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'Blind watchmaker'!!! Love that expression. It so perfectly epitomizes Dawkins' derangement. The presumption beggars belief. It's not a paradox, matey. It's an oxymoron. Paradoxes are surely the most striking feature of QM, but they don't occur under the mechanistic paradigm, as personified by a watchmaker, however visually challenged. What a shallow thinker!Axel
September 23, 2013
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And . . . _______ >> in the well known Dover 2005 trial, and citing ENV, ID lab researcher Scott Minnich has testified to a direct confirmation of the IC status of the flagellum:
Scott Minnich has properly tested for irreducible complexity through genetic knock-out experiments he performed in his own laboratory at the University of Idaho. He presented this evidence during the Dover trial, which showed that the bacterial flagellum is irreducibly complex with respect to its complement of thirty-five genes. As Minnich testified: “One mutation, one part knock out, it can’t swim. Put that single gene back in we restore motility. Same thing over here. We put, knock out one part, put a good copy of the gene back in, and they can swim. By definition the system is irreducibly complex. We’ve done that with all 35 components of the flagellum, and we get the same effect.” [Dover Trial, Day 20 PM Testimony, pp. 107-108. Unfortunately, Judge Jones simply ignored this fact reported by the researcher who did the work, in the open court room.]
That is, using “knockout” techniques, the 35 relevant flagellar proteins in a target bacterium were knocked out then restored one by one. The pattern for each DNA-sequence: OUT — no function, BACK IN — function restored. Thus, the flagellum is credibly empirically confirmed as irreducibly complex. >> _________ But of course Minnich supports ID. No true scientist supports ID. He is a party to what that notorious TSZ thread allowed to stand: fraud. He must be a right wing theocrat fundy would be Christofascist Nazi as well as an IDiot. No need to listen to him. And the talking points drum on . . . KF PS: I have toned down the line of talking points we are dealing with. Null is right, the real filth would choke UD's filters and would give moderators fits.kairosfocus
September 23, 2013
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