Irreducible Complexity

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.

59 Replies to “ID theorist Mike Behe was refused a response in Microbe

  1. 1
    CentralScrutinizer says:

    Hehe

  2. 2
    Mung says:

    If ID were a valid scientific theory it would be published.

  3. 3
    Timothy Kershner says:

    Thank you, Prof. Behe — for your prompt response to our concerns. We understood that the article was a few years old, but it was found (after an extensive google search) to be the “BEST of the BEST” arguments regarding IC systems and the BF. Not only did you provide an excellent response, but it pleases us to learn that you had address this issue years ago, Unfortunately most of the world never knew it do to the suppression that is clearly taking place.

    Again, thanks.

  4. 4
    Box says:

    I don’t understand how this Dr. Lacey can live with himself.

  5. 5
    Mapou says:

    Mung:

    If ID were a valid scientific theory it would be published.

    Not quite. Rather, if ID were a Darwin butt-kissing theory, it would be published. Dr. Behe just has more gonads and honesty than some other folks, that’s all. Sorry to phrase it this way but it must be said.

  6. 6
    Mung says:

    If butt-kissing leads to increased reproductive success …

  7. 7
    bornagain77 says:

    The obstacles for Darwinian evolution to produce a Bacterial Flagellum, or any comparable molecular machine, are severe. First is the problem of getting proteins in the first place. Assuming a ribosome, a protein factory, is already in place ready to ‘randomly’ spit out proteins, the odds of funding a novel protein are astronomical,,

    The Case Against a Darwinian Origin of Protein Folds – Douglas Axe – 2010
    Excerpt Pg. 11: “Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin.”
    http://bio-complexity.org/ojs/.....O-C.2010.1

    But let’s suppose that functional proteins are already in place and we merely want to change an existing protein into a similarly sequenced protein of a new function. Does that generous concession to Darwinists help??

    Stability effects of mutations and protein evolvability. October 2009
    Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,,
    http://www.ncbi.nlm.nih.gov/pubmed/19765975

    When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe
    Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.
    http://www.biologicinstitute.o.....nt-collide

    Well, we can’t find useful proteins in the first place, and even if we did have useful proteins in place they are found to be severely constrained in their plasticity so as to ‘randomly’ evolve into new functions. But this is mot even to the level of building a molecular machine yet. Let’s suppose that proteins were trying to build a molecular machine, what are the odds that novel protein-protein binding sites, in which different proteins combine to perform a new and useful function, will be generated?

    “The immediate, most important implication is that complexes with more than two different binding sites-ones that require three or more proteins-are beyond the edge of evolution, past what is biologically reasonable to expect Darwinian evolution to have accomplished in all of life in all of the billion-year history of the world. The reasoning is straightforward. The odds of getting two independent things right are the multiple of the odds of getting each right by itself. So, other things being equal, the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the world in the last 4 billion years, so the odds are against a single event of this variety in the history of life. It is biologically unreasonable.”
    – Michael Behe – The Edge of Evolution – page 146

    Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution
    “Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell–both ones we’ve discovered so far and ones we haven’t–at best extremely limited benefit, since no such process was able to do much of anything. It’s critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing–neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered–was of much use.”
    http://www.evolutionnews.org/2.....20071.html

    Waiting Longer for Two Mutations – Michael J. Behe
    Excerpt: Citing malaria literature sources (White 2004) I had noted that the de novo appearance of chloroquine resistance in Plasmodium falciparum was an event of probability of 1 in 10^20. I then wrote that ‘for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years’ (1 quadrillion years)(Behe 2007) (because that is the extrapolated time that it would take to produce 10^20 humans). Durrett and Schmidt (2008, p. 1507) retort that my number ‘is 5 million times larger than the calculation we have just given’ using their model (which nonetheless “using their model” gives a prohibitively long waiting time of 216 million years). Their criticism compares apples to oranges. My figure of 10^20 is an empirical statistic from the literature; it is not, as their calculation is, a theoretical estimate from a population genetics model. Generally, when the results of a simple model disagree with observational data, it is an indication that the model is inadequate.
    http://www.discovery.org/a/9461

    Please note that Dr. Behe, even though the numbers from their model still supported his overall conclusion for the rarity of spontaneous binding site formation, was indignant with the weight they were giving to their ‘hypothetical’ model over what the empirical evidence actually said (good for him! He is a true scientist to the core!).

    It is also important to note that Dr. Behe’s research agrees with the extreme difficulty that was found for scientists trying to ‘purposely design’ a single protein-protein binding site:

    Viral-Binding Protein Design Makes the Case for Intelligent Design Sick! (as in cool) – Fazale Rana – June 2011
    Excerpt: When considering this study, it is remarkable to note how much effort it took to design a protein that binds to a specific location on the hemagglutinin molecule. As biochemists Bryan Der and Brian Kuhlman point out while commenting on this work, the design of these proteins required:
    “…cutting-edge software developed by ~20 groups worldwide and 100,000 hours of highly parallel computing time. It also involved using a technique known as yeast display to screen candidate proteins and select those with high binding affinities, as well as x-ray crystallography to validate designs.2?
    If it takes this much work and intellectual input to create a single protein from scratch, is it really reasonable to think that undirected evolutionary processes could accomplish this task routinely?
    In other words, the researchers from the University of Washington and The Scripps Institute have unwittingly provided empirical evidence that the high-precision interactions required for PPIs requires intelligent agency to arise.
    http://www.reasons.org/article.....as-in-cool

    Computer-designed proteins programmed to disarm variety of flu viruses – June 1, 2012
    Excerpt: The research efforts, akin to docking a space station but on a molecular level, are made possible by computers that can describe the landscapes of forces involved on the submicroscopic scale.,, These maps were used to reprogram the design to achieve a more precise interaction between the inhibitor protein and the virus molecule. It also enabled the scientists, they said, “to leapfrog over bottlenecks” to improve the activity of the binder.
    http://phys.org/news/2012-06-c.....ruses.html

    So the Darwinian argument, since they have no real empirical evidence to appeal to to support their claims, appears to be:

    Darwinism Not Proved Impossible Therefore It must be True – Plantinga
    http://www.metacafe.com/watch/10285716/

    Music:

    Overcome – Jeremy Camp
    http://myktis.com/songs/overcome/

  8. 8

    Well, at least there’s no conspiracy, right?

  9. 9
    tjguy says:

    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!

    It is not an honest exchange of ideas that is valued, but only propaganda that supports the reigning paradigm. Ideas that challenge the paradigm can be discussed only in a negative way. But rebuttals are not allowed.

  10. 10
    Jerad says:

    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.

    No attempt to poison the well of civilised discourse here. Just some clearly objective reporting.

  11. 11
    Brent says:

    Jerad @10,

    I was a little sympathetic to your position against KF (though I didn’t follow it in detail), but it is quite difficult to continue that sympathy after your post above.

    It seems like the poison was clearly in the well to begin with. If you have evidence that we put it there that is one thing, but from the quoted text from Behe and Lacey, it appears that your quote mine above is really just revealing a previously existing fact, the poison already in the well.

  12. 12

    For the record, I agree that Lacey’s response was disingenous. I also note that the article gives no reference to any source for their contention that

    Proponents of the intelligent design (ID) explanation for how organisms developed claim that the bacterial flagellum (BF) is irreducibly complex.

    which is the first sentence of their review, and they continue to give unsourced assertions regarding the assumptions of ID proponents. In other words, they attribute views to people unnamed, and claim to show that those views are false.

    They should have cited the claims they consider false directly, and if they misrepresented them, those cited should have had right of reply.

  13. 13
    gpuccio says:

    I have never doubted the strength and value of Behe’s IC argument, since I first read his “Darwin’s black box”. There is only one way to summarize things: he is simply right.

    Darwinists’ attempts to “answer” Behe’s arguments have always appeared to me for what they are: bad thinking, false answers to wrong questions. Moreover, Behe has kindly taken the time to explain repeatedly why they are not an argument against his argument. I can only be happy that the issue has been given space here, again.

    Lacey’s behaviour can only be considered, charitably, as a shame and as depressing news about human nature (for those few who still retain some illusions about that issue).

    Behe is a great thinker and a great man. He deserves our full appreciation and support.

  14. 14

    I agree that Behe is the best of the ID scientists.

    I disagree that he is “simply right”. He is, I would argue, simply wrong in many key aspects of his argument.

  15. 15
    gpuccio says:

    Elizabeth:

    Thank you for your appreciation of Behe. I did not expect you to agree on the real issues, obviously. I know your position.

    When I say that Behe is simply right, I am just briefly summarizing a conclusion from a very detailed analysis of the question. We could spend days here debating the matter, but I really don’t feel like doing that now, and probably neither do you.

  16. 16
    Jerad says:

    I agree that Behe is the best of the ID scientists.

    I agree, he is not afraid to state his case and stand up for what he believes.

  17. 17
    Jerad says:

    I was a little sympathetic to your position against KF (though I didn’t follow it in detail), but it is quite difficult to continue that sympathy after your post above.

    It seems like the poison was clearly in the well to begin with. If you have evidence that we put it there that is one thing, but from the quoted text from Behe and Lacey, it appears that your quote mine above is really just revealing a previously existing fact, the poison already in the well

    I just thought News’ statements were a bit over the top and didn’t help the situation. I don’t think I quotemined really; I just reproduced that last statements in the original post. But I’ll leave it.

  18. 18

    No, probably not, gpuccio 🙂

    I think we will have to agree to differ on that point. But good to see you!

  19. 19
  20. 20
    JGuy says:

    Mung @ 3

    If ID were a valid scientific theory it would be published.

    Why would they take the time to publish some official rebuttals against non-scientific theories (ID claims)? Doesn’t that give ID some modicum of respect, i.e. it somehow merited a supposed scientific response?

  21. 21
    gpuccio says:

    JGuy:

    Why would they take the time to publish some official rebuttals against non-scientific theories (ID claims)? Doesn’t that give ID some modicum of respect, i.e. it somehow merited a supposed scientific response?

    Maybe I am a cynic, but I can’t see anything good in the supposed “scientific responses” to Behe’s “Darwin’s black box”.

    The facts are simple. A scientist, a biochemist, had published a book aimed to the general public which introduced a new, very strong argument against the neo darwinian dogma, and in favor of ID. They simply could not tolerate that.

    The series of papers, interventions, false new concepts (cooption, scaffolding, you name it…), that ensued was only aimed to discredit Behe and his concepts. After all, the general public is usually scientifically gullible, and we know all too well where the real power is…

  22. 22
    Box says:

    Quote from an interesting article about philosopher William Lane Craig at The Chronicle Review:

    N.Scheider:
    When, during a conversation in a swank hotel lobby in Manhattan, I mentioned to Richard Dawkins that I was working on a story about William Lane Craig, the muscles in his face clenched.
    “Why are you publicizing him?” Dawkins demanded, twice. The best-selling “New Atheist” professor went on to assure me that I shouldn’t bother, that he’d met Craig in Mexico—they opposed each other in a prime-time, three-on-three debate staged in a boxing ring—and found him “very unimpressive.”
    “I mean, whose side are you on?” Dawkins said. “Are you religious?”

  23. 23

    “Co-option” and “scaffolding” are not “false new concepts”.

  24. 24

    JGuy:

    Why would they take the time to publish some official rebuttals against non-scientific theories (ID claims)? Doesn’t that give ID some modicum of respect, i.e. it somehow merited a supposed scientific response?

    Behe presented a scientific case that merited consideration.

    Why shouldn’t scientists consider it?

  25. 25
    Brent says:

    Jerad @17,

    It looks like we have a little different idea of what a quote mine is. Anyway, I understand your thinking, but it’s hard to come to another conclusion when the evidence of blatant bias is in front of our faces.

  26. 26
    kairosfocus says:

    Brent: Thanks for being open enough to recognise the point. I have decided that it is necessary to take time to plainly state some unpleasant and unwelcome facts on what is going on. Remember, I learned about most of these things dealing with communist subversives — probably when you were a child or even earlier. Maybe I will tell you of the time when, at a protest rally, one of these tried to set an angry crowd on me. By the grace of God, unbeknownst to me, standing next to me was a young man who was much bigger than either the agitator or myself. He growled to him: watch yourself, bwoy, and the agitator, visibly startled, vanished. I left the crowd as with snakes like that anything can happen. Later there was a confrontation with riot police that could easily have ended badly indeed. 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. But, we need to identify what is going on, make necessary connexions, expose and counter. Slander, censorship, career busting and more are simply unacceptable. And, today marks a full year of obvious inability to provide observationally backed warrant for the capability of blind watchmaker mechanisms to account for OOL or of body plans. It remains the case that the only observationally known and analytically plausible explanation for the required FSCO/I is design. KF

  27. 27
    Axel says:

    Nor ’emergentism’, Elizabeth….. Cough. Cough.

  28. 28
    Andre says:

    Here is another photo of the insect gears system

    http://cdn.physorg.com/newman/.....oningm.jpg

    Here is what will happen if you only have 1 gear.

    http://www.millerplastics.com/.....ars4-l.jpg

    So what is irreducible complexity really? It’s not about the parts but about the SUM OF THE PARTS performing a very specific function, Mindless processes cannot build or create IC because IC is deliberate planning of how parts together perform that very specific function.

    http://www.youtube.com/watch?v=vOo3TLgL0kM

    Why is this so difficult to understand?

  29. 29
    kairosfocus says:

    F/N: EL neatly side steps the many challenges faced by her talking points, as usual. Let’s clip Menuge, using the ID founds UD post no 3 from coming on three years ago, on IC:

    ____________

    >> IC is a barrier to the usual suggested counter-argument, co-option or exaptation based on a conveniently available cluster of existing or duplicated parts. For instance, Angus Menuge has noted that:

    For a working [bacterial] flagellum to be built by exaptation, the five following conditions would all have to be met:

    C1: Availability. Among the parts available for recruitment to form the flagellum, there would need to be ones capable of performing the highly specialized tasks of paddle, rotor, and motor, even though all of these items serve some other function or no function.

    C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.

    C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.

    C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a flagellum are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.

    C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if a paddle, rotor, and motor are put together in the right order, they also need to interface correctly.

    ( Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004). HT: ENV.)

    In short, the co-ordinated and functional organisation of a complex system is itself a factor that needs credible explanation.

    However, as Luskin notes for the iconic flagellum, “Those who purport to explain flagellar evolution almost always only address C1 and ignore C2-C5.” [ENV.]

    And yet, unless all five factors are properly addressed, the matter has plainly not been adequately explained. Worse, the classic attempted rebuttal, the Type Three Secretory System [T3SS] is not only based on a subset of the genes for the flagellum [as part of the self-assembly the flagellum must push components out of the cell], but functionally, it works to help certain bacteria prey on eukaryote organisms. Thus, if anything the T3SS is not only a component part that has to be integrated under C1 – 5, but it is credibly derivative of the flagellum and an adaptation that is subsequent to the origin of Eukaryotes. Also, it is just one of several components, and is arguably itself an IC system. (Cf Dembski here.) >>
    ____________

    And the darwinist talking points drum on and on as though nothing is wrong.

    KF

  30. 30
    kairosfocus says:

    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.

  31. 31
    Axel says:

    ‘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!

  32. 32
    Jerad says:

    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.

  33. 33
    Brent says:

    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.)

  34. 34
    Brent says:

    Cross-posted just now Jerad, dude! Sorry!

    But be careful because KF may take the gloves off now 😉

  35. 35
    Loghin says:

    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).

  36. 36
    Jerad says:

    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.

  37. 37
    Loghin says:

    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.

  38. 38
    CentralScrutinizer says:

    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.

  39. 39
    Collin says:

    Taht was his point. He was rebutting Mung who said it was not a scientific theory.

  40. 40
    Collin says:

    So I messed up the last post. I was responding to Dr. Liddle at 24.

  41. 41
    Brent says:

    Jerad,

    I was just kidding.

  42. 42

    Thanks, Collin. I wasn’t quite sure what JGuy meant.

  43. 43
    JDH says:

    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.

  44. 44
    JGuy says:

    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.

  45. 45
    vikingmom says:

    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!

  46. 46
    Phinehas says:

    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.

  47. 47
    Querius says:

    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.

  48. 48
    Timothy Kershner says:

    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.

  49. 49

    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.

    Th

  50. 50
    Timothy Kershner says:

    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.

  51. 51
    Timothy Kershner says:

    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.

  52. 52
    tjguy says:

    Central,

    Deepest apologies!

    Obviously I misread the tone of the post.

  53. 53

    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.

  54. 54
    bornagain77 says:

    Did Michael Behe State Exaptation has been “Shown” to Produce Irreducible Complexity? – August 2012
    http://www.evolutionnews.org/2.....63271.html

  55. 55
    bornagain77 says:

    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/2.....77051.html

  56. 56
    Barb says:

    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.

  57. 57
    Mung says:

    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.

  58. 58
    OldArmy94 says:

    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?

  59. 59
    CentralScrutinizer says:

    tjguy, no problemmo

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