Home » Darwinism, Intelligent Design » OU Biochemist Phillip Klebba on the Bacterial Flagellum

OU Biochemist Phillip Klebba on the Bacterial Flagellum

My to-do list for some time has included addressing University of Oklahoma biochemist Phillip Klebba’s written response to my September 17, 2007 OU lecture at Meacham Auditorium. Klebba, during the Q&A, asserted that biologists know full well how the bacterial flagellum arose without the need for intelligent design. He then proceeded to describe a four-stage evolutionary process that went from a pilum to the type-three secretory system to an ATP-type motor to the full flagellum. I told him during the Q&A that he was bluffing and that his account of flagellar evolution did not provide the specificity needed to confirm its plausibility. He then lectured me on the fact that I’m not a biologist and thus was not in a position to make such a pronouncement. But the fact is that one does not have to be a biologist to assess Klebba’s claims. Rather, one needs some elementary facility with logic to see whether his claims stack up.

Fortunately, Klebba wrote up his proposal on flagellar evolution in an essay for the OU student newspaper (the essay appeared September 20, 2007 here). I urge UD readers to look at it carefully for it betrays the bankruptcy of evolutionary theorizing when it comes to explaining the emergence of molecular machines. Contrary to molecular and cell biologists such as James Shapiro and Franklin Harold, who regard current evolutionary explanations of molecular machines as spectacularly unsuccessful, Klebba proclaims that the problem is solved:

The evolutionary relationships that led to the bacterial flagellar motor — the poster of irreducible complexity for proponents of intelligent design — are now well-known among scientists studying the biochemistry of bacterial cell envelopes. In brief, the flagellar assembly, which propels bacteria through fluid environments, consists of a long, hollow polymeric filament, a basal body that holds the filament in the cell membrane system, and a molecular motor complex containing a stator and rotor that turn the filament around and around when it is energized.

I’m afraid that after all these years in the ID business, I’m still not entirely used to the brazenness of evolutionary theorists in proclaiming that its unsolved problems are solved. Klebba continues:

In reality, a number of precursors to the complete flagellar assembly are known. They provide the stepwise development of novel functions, and when juxtaposed together, lead to a selectable trait. The emergence of the flagellar motility system involves a progression from pili to type-III secretory systems, that acquires the proton-motive, force-driven rotational capability of the ATP synthase motor (a primary source of energy generation) and sensory and regulatory systems that determine the direction and the duration of cell propagation. Each individual system alone has survival benefits for the cell. When combined one-by-one, they provide a stepwise path to the development of a new advantageous trait: the ability to swim toward something desirable, e.g., high concentrations of sugars — and away from something noxious, e.g., high concentrations of acid. This adaptive evolutionary progression is simple and logical, but unfortunately, is not understood by Dembski and his colleagues.

Actually, my colleagues and I understand such explanations all too well. In fact, why stop at four evolutionary stages in explaining the flagellum? Nick Matzke some years back had six (see my reply to Matzke’s proposal here). Klebba, Matzke, and others seem not to understand that arguments from imagination in which one posits a few putative evolutionary precursors do not constitute a detailed testable model for how the flagellum arose. Take Klebba’s transition from a pilum to a type-three secretory system. Precisely which pilum and which type-three secretory system does he have in mind? How exactly did a pilum shed its hair-like filament in becoming a type-three secretory system (last I looked, type-three secretory systems are microsyringes that do not have hair-like filaments)? What new genes need to be added to form a type-three secretory system from a pilum? What old genes need to be lost to form a type-three secretory system from a pilum? In the evolution from the pilum to the type-three secretory system, how many intermediate systems whose functions were neither that of a pilum nor that of a type-three secretory system were there? Klebba and his colleagues never answer such questions.

To me it is mindboggling that evolutionary theorists continue to get away with this sort of shoddy reasoning (no, wait, I wrote an essay on “Evolutionary Logic” some years ago — I do understand!). Systems like the bacterial flagellum are engineered systems. An engineer explaining the technological evolution of such a system would have to exhibit the actual systems in its evolution and show the precise changes required to go from one system to the next. Evolutionary dreamers like Klebba, on the other hand, need merely cite some general categories of systems and then proclaim that “evolution” (used as a conjuring word like “abracadabra”) can tie them all together.

Toward the close of his essay, Klebba remarks: “As a researcher who understands the biochemistry that was the main subject of the lecture, I was surprised to find the discussion much less substantive than I anticipated.” The lack of substance is entirely on Klebba’s part. Indeed, simply citing his own credentials and then offering a handwaving account of how the flagellum arose does not resolve an outstanding open problem confronting evolutionary theory, namely, how Darwinian processes can actually clear the brick wall that they constantly seem to run into when trying to account for molecular machines such as the flagellum.

I ran Klebba’s essay by a molecular biologist colleague who works professionally on the flagellum (not Behe). Here’s what s/he wrote back:

I imagine Phil is citing the Matzke/Pallen article or Milt Saier’s recent article. What I find interesting is that both admit we have no evolutionary scheme to account for the flagella; instead they merely offer a “plausible” account. That being in print, it is now taken for gospel. Both Pallen and Saier have changed they position radically in recent publications. In 2005, Pallen wrote a bioinformatics paper asking how good is the E. coli/Salmonella flagella paradigm across the phylogenetic tree. Amazingly, it holds up well by their blast comparisons. In 2006, the situation has changed where they state now that to use E.coli/Salmonella for a paradigm, as used by ID proponents, doesn’t make sense — there is no true flagellum. Saier likewise argued in 2005 that based on bioinformatics, the flagellum must have arisen before the Type 3 system. Now he conveniently asserts that both are the product of some hypothetical ancestral protein secretion system. . . . [O]ne might ask where did Phil Klebba get his information (or more precisely his “revelation”) that the evolution of the flagellum has been worked out??? When no one knows. From Matzke? Someone with a Master’s degree in Geography? Reminds me of the old adage applied to fundamentalist preachers — “Argument weak, shout here!”

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51 Responses to OU Biochemist Phillip Klebba on the Bacterial Flagellum

  1. If there is anything in Dr. Klebba’s pontification it is that the IC nature of the bacterial flagellum is scientifically falsifiable. The day that the biological community can demonstrate a mutation-event by mutation-event path from a pre-flagellum to a flagellum where each event produces a bacterium that within some realistic environment has an advantage over its predicessor, I will contend that the inevolvability of the bacterial flagellum will have been falsified.

    I say to the scientif commmunity, quit claiming that IC is non-falsifiable. Falsify it! Put up, or shut up!

  2. They just don’t get it. Or perhaps they actually do and instinctively understand that it will be death to the Darwinian paradigm to acknowledge any aspect of the now-too-obvious information-based intelligent design at the very core of biological life.

    The “arguments from imagination” (exactly right!) that the Darwinists rely on in their contorted attempts to shake off the ID onslaught are full of holes in logic, fact and premise.

    Take the notion of co-option, for example, imagining that a pilum somehow became a type-three secretory system and was thereafter available for “co-option” into a flagellum.
    This PZ Meyer-type reasoning fails to grasp the most basic tenet of Intelligent Design theory, namely that even a pilum, or molecular syringe, are themselves irreducibly complex units. The pilum is manufactured and specified for a particular function; as is a molecular syringe; as is the flagellum. As is a mousetrap. PZ-type reasoning is akin to imagining a VW Beetle “evolving” into a submarine – in effect, postulating a mongrel contraption of no practical use (a topic adequately addressed in a previous post.)

    Likewise, to remove part of the mousetrap and use the remaining component as a tie-pin actually proves design by an external intelligent agent, and disproves Darwinism. (The “intelligence” of one so doing remains questionable, nonetheless.) Co-opting a mousetrap as a tie-pin proves design and disproves Darwinism because the external agent applies knowledge and information that he or she has about how things work, and simultaneously disproves supposed Darwinian upward-and-better progression because the resulting “tie-pin” is neither elegant, efficient or functional.

    It seems blindingly obvious that intelligence is behind the information-rich genomic operating systems and program codes that govern process, function and form in every aspect of biological organisms.

  3. I critiqued Matzke’s explanation for the flagellum here:

    http://telicthoughts.com/combi.....endencies/

    based on the issue of combinatorial dependencies in machine design and the “you can’t get there from here” problem of stepwise unintelligent design. Interestingly enough, although he regularly comments on Telic Thought’s posts he total abstained from responding to my criticisms.

  4. I think this statement of Phillip Klebba’s is very telling:

    No biologist or biochemist argues we understand all the mechanisms of nature.

    Clearly we don’t.

    However, we need not look to intelligent design for the explanation of these puzzles, but rather await the stepwise progress of human technology and knowledge.

    It’s no these leaps of human understanding win Nobel prizes — the peak of intellectual recognition.

    Thus, one one hand he is, at least, honest enough to admit gaps exist in our knowledge.

    Then he makes a serious error in logic:

    “However, we need not look to intelligent design for the explanation of these puzzles”

    So I ask, How in the world does he know the answer will not be found in the ID line of inquiry prior to investigation.

    To presume a purely materialistic answer prior to investigation is just plain wrong. As well I point out that the prior presumptions of materialism have been blatantly wrong on every major discovery in science this last century.

    1. Materialism did not predict the big bang. Yet Theism always said the universe was created.

    2. Materialism did not predict a sub-atomic (quantum) world that blatantly defies our concepts of time and space. Yet Theism always said the universe is the craftsmanship of God who is not limited by time or space.

    3. Materialism did not predict the fact that time, as we understand it, comes to a complete stop at the speed of light, as revealed by Einstein’s special theory of relativity. Yet Theism always said that God exists in a timeless eternity.

    4. Materialism did not predict the stunning precision for the underlying universal constants for the universe, found in the Anthropic Principle, which allows life as we know it to be possible. Yet Theism always said God laid the foundation of the universe, so the stunning, unchanging, clockwork precision found for the various universal constants is not at all unexpected for Theism.

    5. Materialism predicted that complex life in this universe should be fairly common. Yet statistical analysis of the many required parameters that enable complex life to be possible on earth reveals that the earth is extremely unique in its ability to support complex life in this universe. Theism would have expected the earth to be extremely unique in this universe in its ability to support complex life.

    6. Materialism did not predict the fact that the DNA code is, according to Bill Gates, far, far more advanced than any computer code ever written by man. Yet Theism would have naturally expected this level of complexity in the DNA code.

    7. Materialism presumed a extremely beneficial and flexible mutation rate for DNA, which is not the case at all. Yet Theism would have naturally presumed such a high if not, what most likely is, complete negative mutation rate to an organism’s DNA.

    8. Materialism presumed a very simple first life form. Yet the simplest life ever found on Earth is, according to Geneticist Michael Denton PhD., far more complex than any machine man has made through concerted effort. Yet Theism would have naturally expected this level of complexity for the “simplest” life on earth.

    9. Materialism predicted that it took a very long time for life to develop on earth. Yet we find evidence for “complex” photo-synthetic life in the oldest sedimentary rocks ever found on earth (Minik T. Rosing and Robert Frei, “U-Rich Archaean Sea-Floor Sediments from Greenland—Indications of >3700 Ma Oxygenic Photosynthesis”, Earth and Planetary Science Letters 6907 (2003): 1-8) Theism would have naturally expected this sudden appearance of life on earth.

    Just what gives Phillip Klebba, or any scientist for that matter, the audacity to say what we are and what we are not allowed to discover in science? What If God actually did create life on earth? Would not Phillip Klebba’s preconceived philosophical (materialistic) bias prior to investigation prevent us from finding it, or at least delay its discovery by the scientific method?

    As well I point out that breakthroughs in Quantum mechanics, specifically quantum non-locality, offer promising lines of inquiry for ID by manipulating the complex specified information (CSI) of “large” biological molecules.

    From a quick search I found these following papers backing up my assertion:

    Robust quantum entanglement can involve millions of atoms or molecules.

    http://listserv.arizona.edu/cg.....&P=59

    Nonlocal Effects of Chemical Substances on the Brain
    Produced through Quantum Entanglement

    http://www.ptep-online.com/ind.....-06-04.PDF

    [QA01.04] Quantum Control of Molecules
    Kent R. Wilson (University of California, San Diego)

    please note this fact:

    “non-local control of large molecules in solution (including proteins)”

    Not this is what I call a VERY promising line of research!

    Would Phillip Klebba even investigate the possibility of manipulating useful information non-locally as a ID proponent would?

    I think not, for I believe he would not even consider it possible in the first place for it definitely is not a line of inquiry a materialist would use to investigate.

    So yes, science will go on and wonderful breakthroughs will occur, in spite of materialistic impediments, and the breakthroughs will be no thanks to the materialism Phillip Klebba so blindly places his trust and faith in.

  5. [...] OU Biochemist Phillip Klebba on the Bacterial Flagellum Klebba wrote up his proposal on flagellar evolution in an essay for the OU student newspaper (the essay appeared September 20, 2007 here). I urge UD readers to look at it carefully for it betrays the bankruptcy of evolutionary theorizing when it comes to explaining the emergence of molecular machines. Contrary to molecular and cell biologists such as James Shapiro and Franklin Harold, who regard current evolutionary explanations of molecular machines as spectacularly unsuccessful, Klebba proclaims that the problem is solved: [...]

  6. Explanations of the sort Klebba puts forth remind me of the Hawaiian Island analogy, in which the existance of the Hawaiian chain is offered as evidence for a land bridge between L.A. and Tokyo! (There are 137 islands and atolls in the Hawaiian chain)

  7. Man, I love posts like this…thank you Bill!

    Amazing that the evolutionists always claim that we are the ones who never ask questions and just state that “goddit”.

    Yet, here are the questions being asked by IDists…

    “Take Klebba’s transition from a pilum to a type-three secretory system. Precisely which pilum and which type-three secretory system does he have in mind? How exactly did a pilum shed its hair-like filament in becoming a type-three secretory system (last I looked, type-three secretory systems are microsyringes that do not have hair-like filaments)? What new genes need to be added to form a type-three secretory system from a pilum? What old genes need to be lost to form a type-three secretory system from a pilum? In the evolution from the pilum to the type-three secretory system, how many intermediate systems whose functions were neither that of a pilum nor that of a type-three secretory system were there? Klebba and his colleagues never answer such questions.”

    …and Klebba claims that science has already solved the mystery of the evolution of the flagellum!

    Mind boggling, the logic these folks possess.

  8. Is he as Klebba as he thinks he is?

  9. When combined one-by-one, they provide a stepwise path to the development of a new advantageous trait.

    Yeah, but how exactly are the pre-cursors combined, and what force is joining them together? And why should these separate items coalesce at all?

    Is this supposed to be the way a true responsible scientist does science? Here we have someone blaming others for shoddy thinking and giving us an excellent of demonstration of it at the same time. Probably the only good thing about the article.

    Hi all. New to this site. Glad to be here.

  10. Well, he teaches at OU, and that explains a lot. I grew up in Texas, and long ago we learned not to expect too much from our friends from north of the Red River. I remember when I was a teenager, my sister (who is very petite) was flirting with an Okie boy. He was teasing her about being so small, and she was trying to prove she was 16. Finally, she pulled our her drivers license and was about to show it to him when my father pushed her hand down and said, “Honey, haven’t I ever told you never to embarrass an Okie by asking him to read!”

  11. BarryA,

    Michael Strauss teaches at OU.

  12. In any case he is apparently not clever enough to realize that he has falsified natural selection. The steps he describes are impossible without a definite end in view. A tuning pin cannot come into being except in the context of a piano. Natural selection knows nothing and cannot conceive of such concepts as “swim toward” or “swim away.” And what are we to make of the use of the word “desirable”?

  13. 13
    Benjamin L. Harville

    bornagain77: “To presume a purely materialistic answer prior to investigation is just plain wrong.”

    I disagree. For centuries, naturalism has worked very well in explaining the natural world. There’s no reason to think it will stop working now.

  14. I wonder if you all remember that rather clever animated video “showing” how a normal looking ‘mouse-trap’ can be built starting out with only a length of wire just by re-shaping the wire, all the while leaving behind ‘intermediates’ that were ‘functional’ mouse-traps. I bet its still somewhere on the internet.

    I once considered this video problematic since it seemed to some to provide an explanation of how irreducibly complex features could come about in a ‘step-by-step’ fashion. I no longer consider it an “explanation”, but rather an “illustration”. An illustration of what? Of a “just-so story”. Indeed, that is all it is: a ‘visual’ just-so story. Darwin applauded a keen imagination. ‘Just-so’ stories require it. And Klebba doesn’t disappoint.

  15. In this case I am going to defend Klebba. For the flagellum to be IC then there cannot be a plausible mutation/selection path.

    The model discussed here is far from complete in the detailed sense required to completely disprove IC; however it is not simply a made up solution. Significant work has been done to show that the major interum steps in the model are viable.

    This is than an argument about burden of proof. From a design side there is the perspecitve that IC must be disproven; however is it not the case rather that the assumption of IC requires taking on all challengers, and places the burden on IC to disprove any plausible (if incomplete) solutions?

  16. Allann:

    however is it not the case rather that the assumption of IC requires taking on all challengers, and places the burden on IC to disprove any plausible (if incomplete) solutions?

    I fail to see why IC should hold the burden of proof. It is the IC hypothesis that claims a falsification of NDE. As NDE is the established paradyme whose historicity has been challenged, it is NDE that carries the burden of proof.

    One thing is for sure — ID, in the form of the IC of the bacterial flagellum is not proving to be a research stopper, it is begging for a serious scientific research project.

  17. 17
    Benjamin L. Harville

    bFast: “I fail to see why IC should hold the burden of proof. It is the IC hypothesis that claims a falsification of NDE. As NDE is the established paradyme whose historicity has been challenged, it is NDE that carries the burden of proof.”

    It is the job of an advocate for a position or theory to make his case. He should not expect the other guy to make his case for him.

  18. In order for a putative Darwinian pathway to have any credibility the following questions must be answered:

    1) What specific mutations or other random changes to what genetic information would be required to engineer the intermediate forms?

    2) What is the probability of these random changes occurring and being fixed in the population, given the available number of individuals and generations?

    Without answers to these questions it’s all just woolgathering. Not only are these questions never answered, they are never even asked.

  19. No biologist or biochemist argues we understand all the mechanisms of nature.
    Clearly we don’t.
    However, we need not look to intelligent design for the explanation of these puzzles, but rather await the stepwise progress of human technology and knowledge.

    He seems to be summarizing how biologists train themselves to be blind based on myths about Progress and so on. Apparently biologists are indoctrinated, step by step, with imaginary notions of natural progress. They “need not look” or try to be aware of intelligence when simply imagining things about the tick and tock typical to technology, attributing their imaginings to the Blind Watchmaker is so much easier.

    Ironically “stepwise” progress will never come if biologists sit around waiting for their Mommy Nature to make the type of selections that they imagine come naturally to her. Given their indoctrination it seems that generally they’ll never admit to the quantifiable impact of sight on things like intelligent selection and the progress typical to technology. Indoctrination is not education, although those subject to it will fail to understand that. Sight is not blindness, although those who are blind may be confused on that point. Recognizing and seeing ID as a possible falsification of naturalism is only a science/knowledge stopper to those who want to act as if knowledge drawn mainly from their own imaginations is on a par with harder forms of science like physics which need not be propped up by or linked with philosophic naturalism.

    Note that as knowledge tends towards progress “stepwise” based on the use of technology which tends to progress in such a way what is being found is that philosophic naturalism is less and less tenable the more that can be observed. Yet somehow progress towards something other a philosophy of naturalism is apparently interpreted as being based on “gaps” in knowledge, as many biologists want to fill all gaps with their own imaginations instead of admitting that the work of a mind can have effects which can be known as such. They seem to close their mind of the synaptic gaps as a supposed matter of principle and then imagine that opening it again will be the end of all progress towards knowledge as we know it. Every biologist that I’ve ever debated has been quite the fearful fellow as a result of the notion of Progress that seems to come naturally to them, yet putting aside all the fear and reading between their lines it still seems that they have a little mind left even if it is trying to crawl back into the womb of their Mother Nature, step by imaginary step.

  20. “and when juxtaposed together, lead to a selectable trait. ”

    Yes, and wave your magic want and blow a little fairy dust.

    Personally, I’m not so much impressed with the parts (as impressive as they are) which may have been “precursor” as much as what it took to get them to assemble together in the right order at the right time.

    Sheesh. Gimme a break.

  21. “Reminds me of the old adage applied to fundamentalist preachers — “Argument weak, shout here!”

    The way I remember it is “argument weak, pound pulpit here”, but the effect is the same. ;)

  22. Gosh you are picky!! Seriously, knowing that such a thing is virtually impossible are you saying that effectively you will never concede?

    I can’t answer for him but I would be happy if Darwinists lived up to some of their own propaganda. For example, if Darwinian reasoning is the equivalent of Newtonian reasoning and/or merely a summary of basic empirical facts like the earth revolving around the sun then what trajectory of adaptation has been predicted based on the language of mathematics being used to encode Darwinian logic, etc… and then verified or falsified by observing the evolution of a group of organisms? Apparently Darwinian theory is a theory and gravity is a theory so they’re pretty much the same in the minds of many biologists, so where has the comparison been supported with based on the language of mathematics and empirical evidence?

    All I’ve ever found are metaphors which describe or trace back to blindness, nonsense, a lack of sense rooted in the hypothetical goo typical to those stupid or ignorant enough to begin to cite their own subjective imaginations as the equivalent of objective geometric/objective and empirical evidence. Perhaps I’ll try to imagine that biologists are not just stupid while I wait to debate one that is intelligent.

  23. It is the IC hypothesis that claims a falsification of NDE.

    Not in total. Behe himself said way back in 1996 that the only way for Darwinian mechanisms to evolve an IC machine was through Indirect pathways! The issue is not whether the flagellum is IC. It is. Stating something to be IC is NOT a claim that it cannot evolve in principle. The real issue is whether Indirect pathways are realistic.

    I think it interesting that ellazimm says that merely coming up with a hypothetical scenario for an indirect pathway that is consistent with reality, engineering principles, and the practical demands of Darwinism in itself is “virtually impossible”. Why should this be? We’re not asking to observe such a scenario happening, we’re just asking for it to be documented. I for one think it should be possible to imagine such indirect pathways for any type of problem. Of course, if no one is even capable of imagining a scenario then how could it occur in reality? If people object to such a simple request, then how can Darwinism even be labeled a hypothesis?

    He also says: “are you saying that effectively you will never concede?” So you think that imagining a scenario is enough? Personally I would want positive evidence that such categories of scenarios are observed to occur in nature, and are capable of producing 500 informational bits. It need not be directly observed with the flagellum…that’s why I said “categories of scenarios”. For example, I can document the physics behind the pathway for flipping a quarter and getting heads millions of times in a row. Describing a hypothetical won’t make it happen.

    Without answers to these questions it’s all just woolgathering. Not only are these questions never answered, they are never even asked.

    I noticed the same trend with that recent article on flying squirrels. All the obvious questions seemed to be overlooked, or at least pushed off to the future.

  24. I disagree. For centuries, naturalism has worked very well in explaining the natural world. There’s no reason to think it will stop working now.

    Yes there is, because we know way more than we used to. It seems the whole shootin’ match is controlled by extremely complex biological software. It was much easier to have complete confidence in a materialistic cosmos when we thought the cell was a “blob of protoplasm”.

  25. Benjamin L. Harville

    bornagain77: “To presume a purely materialistic answer prior to investigation is just plain wrong.”

    “I disagree. For centuries, naturalism has worked very well in explaining the natural world. There’s no reason to think it will stop working now.”

    And I ask you sir, If God is actually part of this world through some process like quantum mechanics does Theism then fall under your definition of naturalism/materialism? If not why not?
    Plus since naturalism/materialism has clearly revealed Theism to be viable as a hypothesis in science since Theism is clearly shown to be more powerful in predictive power than naturalism/materialism (as it is currently defined) should not the proper course of science be to include Theistic predictions in future predictions of scientific inquiry? If not why not?

    ellazimm stated:

    “BA77 wrote: Yet Theism would have naturally expected this level of complexity in the DNA code.

    I guess I would have thought that Theism would have predicted a much more straight forward and concise code; could you explain your reasoning?”

    Yet the DNA code is optimal from a engineering perspective:

    “The genetic code could well be optimized to a greater extent than anything else in biology and yet is generally regarded as the biological element least capable of evolving.”

    http://www.pnas.org/cgi/content/full/103/28/10696

    These “parallel codes” include binding sequences for regulatory and structural proteins, signals for splicing, and RNA secondary structure. Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes.

    http://www.genome.org/cgi/cont.....t/17/4/405

    The data compression (multiple meanings) of some stretches of human DNA is estimated to be up to 12 codes thick (Trifonov, 1989)! No line of computer code ever written by man approaches that level of data compression (poly-functional complexity).

    So ellazimm if you can do better at making a functional code than that go for it buddy!

    But as for myself I am very impressed at the complexity and optimality we are finding in DNA!

  26. But surely the burden of proof lies with the challenger?

    It seems to me that the burden of proof lies with those who claim that their theory is like the theory of gravity, claim that there is overwhelming evidence behind what they say, argue that the State must support their position and only their position, dictate that all parents must use their education dollars to teach their position and only their position, etc.

    Also note that if someone is allowed to cite their own imagination as if it is evidence or proof then the burden of proof is itself imaginary. If ID types keep trying to specify a falsifiable definition and specification for Darwinism instead of joining Darwinists in blurring essential specifications then technology will naturally be on their side. Ironically, it will most likely keep evolving, step by step, to lift the burden for them with respect to revealing a number of highly essential specifications in the origin of the Cosmos, to the origin of life and perhaps even to the origin of specifications observed in many “species.”

  27. By the evolution of technology I mean things like microscopes, telescopes, etc. I.e. it seems that technology will tend to reveal more specifications favorable to the ID hypothesis, naturally.

  28. elazimm:

    Gosh you are picky!! Seriously, knowing that such a thing is virtually impossible are you saying that effectively you will never concede?

    I fail to see why this is all that impossible. Bacteria are easy to raise in a laboratory. We begin with a bacterium that has a functioning system that is not a flagellum, we prove that the non-flagellum is fully functional, we then induce a mutational event that crosses the rubicon, producing a flagellum. We don’t need to wait until nature reproduces the required mutational event, we just have to limit ourselves to a single event that nature could reasonably produce. This is not all that unachievable.

    That seems to me to be a level of proof much greater than that to which you hold ID accountable. Or have I got that wrong?

    You have that wrong. If you read what I have said about ID, you will see that I still use the term hypothesis. That said, I am rather impressed with the stress-test that Behe presents in “Edge of Evolution”. He makes a pretty intense case, demonstrating the testing of more organisms than all of the mammals that ever existed.

    But surely the burden of proof lies with the challenger?

    If the burden of proof lies with the challenger, then the burden of proof lies with Klebba and his ilk — after all they are challenging Behe’s IC hypothesis are they not?

  29. “Evolutionary dreamers…”

    The perfect description of what we’re dealing with. I’m really amazed at what can pass peer review where darwin is concerned; it’s shameful. Just come up with a plausible explanation, and poof, it becomes fact. I would be downright embarrassed to be associated with the entire darwin party if I was a biologist. Most people who have actually designed and/or built something using the creative power of their own mind know that fanciful evolutionary tales about the flagellum are completely bogus. Everywhere we turn in nature, we find design – it screams at us. Even if darwinism survives for 500 more years, it will still be dead wrong and a really, really dumb idea to base your worldview on.

  30. [...] Here is Klebba’s essay. Here is Dembski’s response. [...]

  31. This argument put fourth by Klebba remind me of debating my little brother on Christianity (me for it, him against it). I know I really made a good point when gets mad and says “YOu don’t even know as much about the bible as I do, you don’t read it enough.” Every time he does that I say 1 point for me. Maybe Bill should start doing that!

  32. Just come up with a plausible explanation, and poof, it becomes fact.

    Plausibility is not the issue, because none of the proposed Darwinian pathways are plausible. Almost any old thing will do, because evidence doesn’t matter. The conclusion has been reached in advance of evaluating the evidence.

  33. If we have learned anything at all from Geosynclinal theory it’s that anyone can look at patterns in nature and impose a vision of how they came about. It is the words like randomness, purposeless, chance and simple unguided “Natural” selection that are the abracadabra of Darwinian evolution. Anyone can look at something and devise a creation story. The unscientific part of DE is that once the community decides that a given version of the creation tale is right, the rest of the world better walk along in lock step or face persecution. Why is Darwinian evolution not held to any of the mathematical standards that we would hold a fortune 500 company to? Why is DE allowed to write greater promissory notes than those that earned the Enron cohorts jail time? Why is it that DE is allowed to dodge explanation of the first life and along with that the digital code in DNA which is the most sophisticated language in the known universe?

    The answer is what Phillip Johnson said along time ago in Darwin on Trial that “Darwinian Evolution is not an explanation of how origins evolved it is merely a weak description.”

  34. bornagain77, in post 5, said “Yet Theism would have naturally expected this level of complexity in the DNA code.”

    I’m unsure of the basis of this claim. Common forms of theism predicted that the code of life, at least for man, might have the complexity “of the dust of the ground” (Genesis 2:7) Is there a source that you could provide regarding a theistic prediction of the more complex DNA?

  35. Q — I think he is simply referring to the idea that the bible says repeatedly that man is made in the image of god and as god is the omnipotent and is capable of designing the heavens would logically be very complex in the ability to account for the universe a least by our standards based on expierence of design. The super complexity found in humans is eerily transient in this view. While the rest of the universe is certainly complex the human mind and DNA for its size is unbelievably so displaying vast complexity an specification. SC. ID in no free lunch transforms complexity into information or intelligence, showing that DNA and such can be understood as non material information. The information it would take to account for the universe and the diversity of life therein is almost unbelievable (except for there being no other explanation) and therefore, one can see that information is a good way of comparing man’s complexity with the father’s. Even stranger the bible says that the father will be known through his word. Information- super complex in humans, is only to be trumped by that of the entire cosmos and/or the possible super mind our representation of god displays. Hence through experience we can find his true nature and DNA is loaded with this informational genius.

    Not that ID is dependent on religion or God but it is clearly compatible.

  36. bfast:
    “If the burden of proof lies with the challenger, then the burden of proof lies with Klebba and his ilk — after all they are challenging Behe’s IC hypothesis are they not?”

    No. Behe has proposed an alternative to the more commonly accepted model. There is data supporting the accepted model; that’s how it came to be accepted. It’s up to Behe (or you) to present something more than hypotheticals in support of the hypothesis. Because most scientists don’t find Behe’s proposal plausible on the face of it, or in detail, it will require very strong evidence to convince them Behe is right.

  37. Q you asked:

    bornagain77, in post 5, said “Yet Theism would have naturally expected this level of complexity in the DNA code.”

    I’m unsure of the basis of this claim. Common forms of theism predicted that the code of life, at least for man, might have the complexity “of the dust of the ground” (Genesis 2:7) Is there a source that you could provide regarding a theistic prediction of the more complex DNA?

    A few that come to mind:

    “I praise you because I am fearfully and wonderfully made” – Psalm 139:14

    (That sure doesn’t sound like we should expect the “dust of the ground” to be put together in a simple fashion to me.)

    As will as this scripture for the breathtaking interrelated complexity we are finding at the molecular level as well as at the macroscopic level.

    “For you formed my inmost being. You knit me together in my mother’s womb.” Psalm 139:13

    As far as the complex specified information (CSI) we find in cosmology and biology, That is a simple Theistic prediction to find;

    John 1:1-3

    1.In the beginning was the Word (Logos), and the Word was with God, and the Word was God.

    2.The same was in the beginning with God.

    3.All things were made by him; and without him was not any thing made that was made.

  38. GilDodgen said: “Plausibility is not the issue, because none of the proposed Darwinian pathways are plausible.”

    You are correct of course. I should have said, “plausible according to darwinian standards.” Which means any old fairy tale will do. They seem to be stuck in a fantasy world where “anything is possible” The problem is that the real world – the universe we live in – just doesn’t work like that.

  39. Bill,
    It’s very easy to refute you:
    You are a Christian.

    There! That pretty much shows that ID is bogus, and evolution is true.

  40. For centuries, naturalism has worked very well in explaining the natural world.-Benjamin L. Harville

    Well it certainly cannot explain the origin of nature (natural processes only exist in nature and therefore cannot account for its origins), the origin of the laws that govern nature nor the origin of living organisms.

    So now I am curious- what does naturalism explain?

    For the flagellum to be IC then there cannot be a plausible mutation/selection path.-Alann

    That is false. It is not mutation/ selection that is agrued against. It is the type of mutation/ selection that is argued against.

    For example if the bac flag were designed to evolve then the mutations would be non-random and nature would not be the (sole) selector.

    Also no one has been able to demonstrate that even if all the right proteins were together that a bac flag would be assembled. And assembly isn’t the only issue- there is still command and control.

    IOW once assembled there still needs to be a communication pathway that controls the spin rate and direction. It would also be a good thing to be able to stop when the organism reaches the food supply.

  41. Stop the discussion! This just in…The chair of the Dept. of Physics and Astronomy at ISU has stated that ID is not falsifiable, so attempts to show that the BF is not IC are pointless.

    See his comments below and here: http://www.evolutionnews.org/2.....f_isu.html

    [O]n numerous occasions, Dr. Gonzalez has stated that Intelligent Design is a scientific theory and someday would be taught in science classrooms. This is confirmed by his numerous postings on the Discovery Institute Web site. The problem here is that Intelligent Design is not a scientific theory. … A valid scientific theory should plant the seeds of its own destruction and be falsifiable.

  42. MacT:

    There is data supporting the accepted model; that’s how it came to be accepted.

    The ID community generally rejects this statement on its face. It would appear rather that there is no data supporting the accepted model, but that the accepted model came to be accepted because it fits the preferred metaphysics.

    Alas, as I watch the debate on the topic, I see ID rejected primarily on the grounds of metaphysics. I see very little in the line of an evidenciary case rejecting ID.

    Please humor me by showing me the evidenciary case for the neo-darwinian evolution of the bacterial flagellum or any other complex organ. Please don’t waste my time with “just-so stories”. Ideally an experimental proof — we took an organism, we induced an individual mutational event, we got this new organism that has a new organ making it better than its predecessors.

  43. bfast:

    “The ID community generally rejects this statement on its face. It would appear rather that there is no data supporting the accepted model, but that the accepted model came to be accepted because it fits the preferred metaphysics.”

    If that statement is true, then it is not surprising ID is finding it hard to gain traction in the scientific community. Appearances, supposition, hypotheticals . . . these are not evidence in support of a theory.

    ID is rejected on the grounds that it does not meet the criteria of scientific inquiry, not metaphysics.

    Here’s an example of the evidence you request. It isn’t the entire case, of course, but it’s a good place to start.

    Bierne, Helene, Cossart, Pascale
    Listeria monocytogenes Surface Proteins: from Genome Predictions to Function
    Microbiol. Mol. Biol. Rev. 2007 71: 377-397

    EDIT: Note from the moderator.

    Unfortunately, it later became apparent this reference was a literature bluff.

    See here:

    http://www.uncommondescent.com.....ent-155309

  44. “To presume a purely materialistic answer prior to investigation is just plain wrong.”

    It is probably even worse than that. In many other venues such behavior would have the person labeled a “fundamentalist” or some other culturally approved pejorative.

  45. MacT: “Behe has proposed an alternative to the more commonly accepted model. There is data supporting the accepted model; that’s how it came to be accepted.”

    The “commonly accepted” model is presumably cooption schemes like Klebba’s. It is commonly accepted because it appears to make the problem of the IC of macromolecular machines go away. They wish.

    Mike Gene posted a very interesting and exhaustively detailed series of articles on the flagellum issue at http://www.idthink.net/biot/flag1/index.html. A summary:

    1. The design problem for a flagellum makes it optimal for it to be based around a protein transport system. So there is no reason to give this any significance in theories of origin.

    2. Human imagination can come up with endless simpler theoretical origin models for designed systems like automobiles and airplanes, so being able it imagine simpler states in general is rather meaningless.

    3. The Type III secretion (protein transport) system is almost certainly much later in origin than the flagellum, so it could hardly have been “coopted” in building the flagellum. This system is used by certain bacteria to inject toxins into its host which is a metazoan, and most likely evolved from a flagellum mostly by loss of parts.

    4. None of the other existing bacterial transport/secretion systems have formed the core of a eubacterial flagellum, so not just “any” transporter will work. It is the origin of the flagellum’s Type III export machinery that needs to be explained by cooption, and there is no plausible existing candidate.

    3. The whole cooption hypothesis makes numerous vague, extremely implausible speculations glossing over the details of the real biology of the process, so that the scheme falls apart on close examination. For just a small part of the problems, consider the notion that the protein transport system somehow had a single mutation event that caused certain appropriate export proteins to stick to themselves and to to the outer parts of the export machinery. This is supposed to somehow have resulted in a proto-filament that had selective functional value.

    “….this poses a huge problem for the hypothesis. What is to prevent the exported proteins from aggregating before they are transported? What’s to prevent them from sticking to something else not in the basic story? What’s to prevent them from being degraded? And what’s to prevent them from clogging up the transport channel during any stage of the transport process? And what if this mutant export-protein polymerized like HbS filaments and formed a solid core? Then, we’d seal off the export machinery, which presumably is important for other reasons. Thus, it would seem the EFM hypothesis is relying on deleterious mutations to evolve this filament, unless of course, it is relying on a special mutation that just happens to perfectly fit the story.”

    4. The Type III secretion system is itself IC, with perhaps 10 parts. The correct assembly of the machine is required for it to work as a secretion pump and to produce the effector molecules. So the Klebba type of scheme fails to account for the origin of the protein transport mechanism itself. It has to assume IC in order to explain an example of IC.

    6. The bacterial nonmotile filament itself (supposedly somehow coopted into building the flagellum) and its assembly process are highly IC themselves. The simplest filament formed in bacteria (P pilus), with 13 genes, is on its own a fundamentally sophisticated complex machine with multiple interdependent parts. So the Klebba type of scheme also fails to account for the pilli filaments. Again it has to assume IC in order to explain an example of IC.

    7. The pilium and other bacterial filaments are assembled bottom-up, but the flagellar filament is built top-down (the flagellar proteins travel up the hollow core to build the tip).

    8. Actual generation of rotation and the necessary torque requires very specific interactions between stator and rotor, and three specialized proteins, where any mutation of the sites involved results in loss of motility. This construction had to come about by pure chance, a microscopic minority of all possible changes. Another aspect of the IC of the entire molecular machine.

    9. Because of their very small size, bacteria are continually being buffeted by the Brownian motion of water molecules which knocks them off-course on the average after 3-4 seconds. The hypothesis has to assume that motility developed in tiny steps from some kind of primitive “proto-motility”, but some minimal proto-wiggle would hardly be any advantage in this environment. Also, such a proto-wiggle would be useless without a directional ability toward food and away from noxious substances. So the motility function would need to already be sophisticated in order to have a selective benefit.

  46. Would you say that the recent targeted discovery of the Tiktaalik fossil was a verification of evolution’s predictive strength?

    First off, ID is compatible with universal common descent and you’ll find a lot of supporters of such hypotheses on UD. This is despite the fact that Darwinists claim that “As such, it [Tiktaalik] will be a blow to proponents of intelligent design, who claim that the many gaps in the fossil record show evidence of some higher power.” Here is how Bill Dembski put it:

    ““Intelligent design does not so much challenge whether evolution occurred but how it occurred. In particular, it questions whether purposeless material processes–as opposed to intelligence–can create biological complexity and diversity.”

    Second, despite the hype surrounding Tiktaalik I believe it’s prudent to consider the evidence fully.

    tiktaalik

    The origin of major tetrapod features has remained obscure for lack of fossils that document the sequence of evolutionary changes. Scientists speculate that the front fins of the Tiktaalik allowed the creature to hoist itself up and possibly drag its tail behind. Unfortunately, lacking living representatives, scientists are unable to tell for certain what the fin bones actually were used for (other than the obvious one of swimming). Side-by-side comparisons do not look that informative, especially when there are no soft parts and no evidence for how the creature actually lived. It must be remembered, for instance, that Coelacanth was long considered a transitional form because of its bony fins, but when discovered alive, the fish did not use them for walking or raising itself up in any way. The same thing happened to “Lucy” last year when more evidence was discovered in Dikika, Ethiopia, since “all three lines of evidence suggest that the locomotion of A. afarensis was unlikely to have been restricted to walking on two feet” (‘Palaeoanthropology: A precious little bundle’ Nature 443(7109):278–281, 21 September 2006.”) and thus was demoted and placed in a separate lineage. The general conclusion seems to be it may have been capable of walking upright some of the time—as does the living pygmy chimp (bonobo)–but “[i]t is now recognized widely that the australopithecines are not structurally closely similar to humans, that they must have been living at least in part in arboreal environments, and that many of the later specimens were contemporaneous or almost so with the earlier members of the genus Homo.” (C.E. Oxnard, Nature 258:389–395) The latest evidence seems to indicate that an arboreal lifestyle is even more likely.

    Back to Tiktaalik. Although these small distal bones bear some resemblance to tetrapod digits in terms of their supposed function and range of movement, they are still very much components of a fin. There remains a large morphological gap between them and digits as seen in, for example, Acanthostega: if the digits evolved from these distal bones, the process must have involved considerable developmental repatterning. The implication is that function changed in advance of morphology…assuming the storytelling about Tiktaalik’s lifestyle are true, of course.

    In particular we have almost no information about the step between Tiktaalik and the earliest tetrapods, when the anatomy underwent the most drastic changes, or about what happened in the following Early Carboniferous period, after the end of the Devonian, when tetrapods became fully terrestrial.

    So, no, despite being a potential transitional (notice that I’m not immediately rejecting it, but being cautious, which is prudent given the examples of the Coelacanth and A. afarensis) overall I don’t see this example as being particularly strong considering it largely rides on the storytelling and the base assertion (hype) that it is a major find, and not the evidence itself. The usual lack of details is also present. Would the minor ability to supposedly drag itself along the ground give enough selective pressure to evolve into a tetrapod? The ability to soak up sun in the arctic, as I’ve also seen speculated? It’s speculated that it might be capable of escaping predators by dragging itself onto land, although how large of a factor this would be is unknown. Sounds squirrelly to me. Also, what exactly was predicted (not “predicting” after the fact) about the Tiktaalik that they’d find…that’s one thing I did not see discussed when I read about the Tiktaalik.

    The major issue is that Darwinian mechanisms do not have any positive evidence to say they are capable of providing such a transition. Intelligent evolution (whatever the mechanism) would at least be capable. With intelligent evolution the changes can also be quite rapid, as well, conforming to the evidence better. Not to mention, the true evolutionary lineage for tetrapods might not even include the Tiktaalik at all. Scientists thought tetrapods evolved in the northern hemisphere (Tiktaalik was found in the arctic) but examples like the Gogonasus, which shares some similarities with Tiktaalik, was found in Australia. Convergent evolution or frontloading or are both dead ends for investigation into tetrapod evolution?

    Henry Gee, editor of Nature, on the feasibility of reconstructing phylogenetic trees from fossils: “To take a line of fossils and claim that they represent a lineage is not a scientific hypothesis that can be tested, but an assertion that carries the same validity as a bedtime story — amusing, perhaps even instructive, but not scientific.”

  47. ID is rejected on the grounds that it does not meet the criteria of scientific inquiry, not metaphysics.-MacT

    Of course ID meets the criteria of scientific inquiry.

    1- It is based on observation

    2- It can be tested (CSI & IC are testable concepts)

    3- It can be falsified (both concepts can be falsified if it demonstrated that purely stochastic processes can account for them)

    Now just how can one test the premise that say chimps and humans shared a common ancestor and that the physiological and anatomical differences observed arose via purely stochastic processes?

    1- It has NEVER been observed

    2- It canNOT be tested.

    3- It canNOT be falsified, short of PROVING ID or Creation.

    The currentyly accepted theory of evolution is well beyond science. The ONLY evidence for universal common descent is genetic similarities. There isn’t anything in the theory to test whether or not the physiological and anatomical DIFFERENCES observed can be obtained via any amount of accumulated genetic accidents.

    And back to the OP- just how can one test the premise that the bacterial flagellum “evolved” via culled genetic accidents? How can that premise be falsified?

  48. Amen Joe- not to mention that the cambrian has already disproven one of darwins hypotheses being that all life evolved over long perions of time by smal steps. But dotn count on any of them admitting this because Darwinsism has become the new definition of science and therefore cannot be challanged.

  49. The Tiktaalik is an interesting fossil but if it is a missing link then the before and after so far are 10′s of million years in either direction. Hardly, a transitional from anything to anything.

    This may change with new findings but as of now it is just a fossil, actually I believe half a fossil. The area where it was found is only available for work a few months each year so it may be hard slugging to see what else is in the same strata.

  50. Re. Tiktaalik, whether or not it is a genuine transitional, in my opinion it should be recognized that the fossil record still shows a clear pattern of progression, of apparent descent with major innovation and elaboration based on the previous stage. Despite being mostly characterized by long periods of stasis interspersed by abrupt innovational jumps. This is on the large scale of classes and orders within classes and tens of millions of years.

    It seems to be the most reasonable inference from the available evidence. A good example is the progression from primitive jawless fish through amphibians to reptiles.
    - Class Ostracodermata; jawless, covered by bony plate except for tail region, cartilaginous notochord (Beginning in early Cambrian, 510 Ma)
    - Class Placodermata; functional jaws but no teeth, armored over most of body, bony skeleton (beginning in late Silurian, 400 Ma)
    - Class Osteichthyes (bony fish), includes Ctossopterygian lobe-finned fishes (beginning early to mid Devonian, 390-380 Ma)
    - Various forms physiologically intermediate between crossopterygians and early amphibians (mid to late Devonian, 380-360 Ma). Tiktaalik fits in this group.
    - First amphibians – quite fishlike, for example family Acanthostega (late Devonian, 360-370 Ma)
    - Subclass Labyrinthodonta; larger amphibians with more upright tetrapod characteristics (late Devonian – early Mississippian, 370-350 Ma)
    - Order Anthracosauria; early reptiles with some amphibian characteristics (late Mississippian, 330-320 Ma)
    - Order Cotylosauria; primitive reptiles with all basic reptile characters (early Pennsyvanian, 320-310 Ma)

    As can be seen, the temporal order in which these forms appeared in the fossil record and their general level of advancement clearly indicate common descent with progressive modification as the most reasonable inference. But this general pattern includes the fact that these class and order appearances occur mostly suddenly with no transitionals. The geological dating methods seem very solid to me (primarily based on radioactive decay product analysis), as are the characterizations of overall morphological form. Any hypothesis including ID needs to explain all these features of the record.

    Behe’s point has been that “Common descent is one thing. Random mutation and natural selection (explaining it) is something completely different”. In other words, these abrupt transitions represent his “edge of (NDE) evolution”.

    I am presently reading Dembski and Wells’ The Design of Life, and I think they give a balanced view of this problem. They discuss other examples cited by Darwinists, such as the supposed descent of the mammalian ear-bones from the jaw in the order therapsida (mammal-like reptiles), and apparent whale intermediates like genus Rhodocetus. These examples are still innovational jumps at the level of order and genus and still pose a serious difficulty for RV + NS. They state what to me is the bottom line on this: “The case for Darwinian evolution would be greatly strengthened if scientists could demonstrate (rather than merely gesture at) a plausible mechanism for producing macroevolution. But they have been unable to do so. Even if we assume that a structural progression such as the therapsid-to-mammal sequence is an evolutionary lineage, the fact remains that we know of no material mechanism capable of producing it.”

  51. [...] I replied to him that Collins makes this statement without citation, and that Collins can’t justify it — that he’s “bluffing.” I suggested that he contact Collins himself and also look at the following piece that I posted here at UD some time back: response to Philip Klebba. [...]

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