Monday, March 17, 2008

A Challenge to Jonathan Wells

 
On February 29th Jonathan Wells published a short review of a scientific paper by Maurice et al. (2008). You can read the original Wells posting at: The Irrelevance of Darwinian Evolution to Antibiotic Resistance.

Wells was trying to make a point. Concerning the work from Dardel's lab (Maurice et al, 2008), Wells claimed ...
Yet Darwinian evolution had nothing to do with it.

First, some bacteria happen to have a very complex enzyme (acetyltransferase), the origin of which Darwinism hasn’t really explained. Come to think of it, most cases of antibiotic resistance (including resistance to penicillin) involve complex enzymes, and the only “explanations” for them put forward by Darwinists are untestable just-so stories about imaginary mutations over unimaginable time scales.

Second, the acetyltransferase story is about minor changes in an existing species of bacteria. But Darwin’s theory isn’t really about how existing species change over time. People had been observing those long before 1859, and most of the new insights we’ve gained since then have come from genetics, not Darwinism. Yet Mendel’s theory of genetics contradicted Darwin’s, and Darwinists rejected Mendelian genetics for half a century. And although an understanding of genetics is important when dealing with antibiotic resistance, Darwin’s theory of the origin of species by natural selection is not.

Third, Dardel and his colleagues made their discovery using protein crystallography. They were not guided by Darwinian evolutionary theory; in fact, they had no need of that hypothesis.
We all know how creationists use the word "Darwinism." Most of the time, it's a synonym for evolution. All of the time, it's an attempt to obfuscate and confuse their audience. What Wells is saying is that evolution had nothing to do with the paper. All that happened was a bit of genetics. According to Wells, "Darwin's theory of the origin of species by natural selection" was not involved.

The senior author of the paper posted a comment on Pharyngula saying, "Actually, we did indeed use darwinian evolution within this work (something unusual in structural biology)." [see Why the Right People Hate IDiots, and links within that posting].

Michael Egnor gallops to the defense of his hero. Today he posted a rebuttal to my criticism of him and Wells [Dr. Larry Moran, Darwinism, and Vicious Personal Invective]. Here's what Egnor says,
Dr. Wells pointed out that research on antibiotic resistance wasn’t guided by Darwinian evolutionary theory. That evolution occurred — that is, that the population of bacteria changed over time — is obviously true, and obviously was relevant to the antibiotic resistance research. Dr. Wells made the observation that the research owed little to Darwin’s theory that all biological complexity arose by natural selection without teleology.
This is an incredible admission from a creationist. Egnor admits that the bacteria evolved. He then goes on to define some bizarre version of "Darwin's theory."1 But the cat is out of the bag. What we see here folks, is the recognition that there is a distinction between Darwinism and evolution by natural selection. We're still not clear about the difference but it seems that bacteria can evolve resistance to antibiotics.

Egnor admits that the paper used evolution but it just wasn't Darwinism.

Now let's see if Jonathan Wells agrees. I'll apologize to Wells if he will post a comment here, or on Evolution News & Views, agreeing to the following ..
I, Jonathan Wells, agree that Maurice et al. (2006) employed evolution by natural selection in their methodology. My position is that evolution by natural selection is not what I mean when I use the word Darwinian.
Note that I'm not asking him to agree that "Darwinism" was involved in the paper. All he has to do is admit that evolution by natural selection is not what he means when he uses the word "Darwinian."

Michael Egnor has indicated that this is what Wells actually means. Now let's see if Wells himself will admit it.


1. The standard version of Darwin's Theory of Evolution by Natural Selection is that populations evolve due to the differential survival of individuals with a fitter genotype.

Maurice, F., Broutin, I., Podglajen, I., Benas, P., Collatz, E. and Dardel, F. (2008) Enzyme structural plasticity and the emergence of broad-spectrum antibiotic resistance. EMBO Rep. 2008 Feb 22 [Epub ahead of print] [PubMed]

30 comments:

  1. "The senior author of the paper posted a comment on Pharyngula"
    Actually, Dardel's comment appeared on pandasthumb.

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  2. I think you're going to get their usual obfuscation of concepts, with a pretty strawberry on top.

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  3. According to Wells himself, Darwinism IS the best natural explanation for what we see in the world. From the Discovery Institute podcast of 20th of July, 2006.

    "When we look at the evidence for Darwinian evolution, its pathetic.
    Its not overwhelming, its underwhelming. And as soon as people learn that they will realize that Darwinism is not good science, what it is is the best natural explanation for what we see, but that doesn't make it the real explanation for what we see. Its artificially constrained by this materialistic philosophy that inspired this radical redefinition of science in 2001. Without that radical redefinition of science, if people are encouraged to follow the evidence, Darwinism will fall."

    So apparently if people follow natural evidence (like scientific empiricism) then Darwinism is the best explanation. However, if you follow non-natural evidence (like, say, hmmm...religion perhaps? - then Darwinism collapses - what a surprise!)

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  4. Repeating what I have said on Abbie's blog.

    Shorter Michael Egnor (in the style of Kenny Craig from Little Britain):

    "Look into my eyes, look into my eyes, the eyes, the eyes, not around the eyes, don't look around my eyes, look into my eyes, you're under.

    Wells did not say that the research had nothing to do with evolution, at all. Of course we at the Discovery Institute accept that life evolved.


    *sound of creo's fainting the world over*

    We are simply questioning the role of Natural Selection as the principle mechanism, that's all. In that sense we are just like Larry Moran.

    Three, two, one... You're back in the room."

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  5. Where's the controversy? Dardel's research involved microevolution, which creationists and ID'ers have long accepted.

    Also, there are different kinds of artificial evolution: (1) selective breeding, (2) inducing random mutations by massive doses of radiation or by chemical means, and (3) creating environmental stresses that favor particular mutations.

    BTW, there was once an outfit called the Station for Experimental Evolution. LOL. It merged with the Eugenics Record Office in 1920 to form the Carnegie Institute's Dept. of Genetics.

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  6. "Larry Fafarman" !!!

    (The previous commenter) is on PZ's killfile, for being mentally ill - he's also banned from Panda's thumb.
    Anything he says is trash.

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  7. He's also a holocaust denier.

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  8. "This is an incredible admission from a creationist. Egnor admits that the bacteria evolved."

    No, O unsurprisingly dishonest one, he didn't. He admitted that bacteria change over time. But guess what - they remain, as always, bacteria. He's not admitting that bacteria or any other species change so much over time that they become new species.

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  9. "Anything he says is trash."

    But he IS funny. No no, seriously, it's such a coincidence that I LOL'd at the EXACT SAME TIME that Larry did after reading "the Station for Experimental Evolution." Oh man, I'm still wiping away the tears. I think, I think it's the relevancy that makes it work.

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  10. jason wrote:

    He's not admitting that bacteria or any other species change so much over time that they become new species.

    Just curious regarding what happens when living things formerly considered as belonging to a single species are reclassified as two species, or living things formerly classified as two species are reclassified as belonging to a single species. Does someone (the Designer, perhaps?) somehow inform them that it is now OK/not OK to evolve? "All right, you're now two distinct species. Everyone out of the gene pool!"

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  11. No, O unsurprisingly dishonest one, he didn't. He admitted that bacteria change over time. But guess what - they remain, as always, bacteria. He's not admitting that bacteria or any other species change so much over time that they become new species.

    Jinxy! Hooray! Things haven't been the same since you and your heterosexual life partner Minn left us.

    (I am aware this will be meaningless to everyone but Jason and I - apologies for this)

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  12. Jason,
    Only one species of bacteria exists?

    ReplyDelete
  13. G. Tingey driveled,

    >>>>>"Larry Fafarman" !!!

    (The previous commenter) is on PZ's killfile, for being mentally ill - he's also banned from Panda's thumb.
    Anything he says is trash. <<<<<<

    "G. Tingey"!!! A stupid fathead. Anything he says is trash.

    See? It is easy to make insults and ad hominem attacks. Anyone can do it.

    Has it ever occurred to you, dunghill, that Sleazy PZ and Pander's Thumb could be wrong and I could be right?

    It is the cogent opposing comments and commenters that are censored. Unpersuasive opposing comments are allowed to remain as examples of the supposed weakness of the opposition.

    ReplyDelete
  14. "Has it ever occurred to you, dunghill, that Sleazy PZ and Pander's Thumb could be wrong and I could be right?"

    If I may be so bold as to answer for g.tingey - No

    ReplyDelete
  15. Second the motion. Larry, we have absolute confidence that no sane, rational person could ever make the serious mistake of thinking you could be right about anything concerning evolution.

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  16. Oh, and my prediction is that the answer to the question "what happens when living things formerly considered as belonging to a single species are reclassified as two species will be something along the lines of "Doesn't matter, as we've never seen it happen".

    Which is a lie, of course, but that's my prediction of the ID creationist answer.

    Oh, and that's one more prediction than ID has.

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  17. Larry F, it appears that you do not understand or "believe" in macroevolution. This must mean that you dismiss the entire fossil record (as it does not support your beliefs) and the hard work of all paleontologists. And you wonder why no one in the scientific community takes you seriously?

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  18. Re Larry Fafarman

    Attached is a commentary from Ed Brayton relative to Mr. Fafarman.

    "The upshot of all this is clear: Larry Fafarman needs serious therapy. His obsessive compulsive nature subverts any chance his mind has of forming even a mildly accurate picture of reality. He creates these bizarre legal theories, none of which have ever won anything in court, and he sits in his house all day long desperate for people to listen to him. So he spams every blog and forum with his lunatic ideas and gets banned, then in his mind he is converted into Don Quixote, bravely tilting at all the dragons windmills that do him such injustice. He doesn't have delusions of grandeur so much as he has delusions of relevance. And he convinces himself that he's on the verge of winning against we who torment him so. He's gonna be added to the legal team that is threatening to sue me and bring me down, or he's going to convince ScienceBlogs to fire me. It's alternately amusing and sad, and sad only because there is a real person at the other end of this pathetic behavior and he really is nuts. Not just a little clueless or "kooky" but genuinely mentally ill and in need of psychological help."

    Mr. Fafarman is indeed a sad case.

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  19. Anonymous said,
    >>>>>> Larry F, it appears that you do not understand or "believe" in macroevolution. <<<<<<

    Macroevolution is not the issue here -- the issue here is whether Dardel's research is a study of microevolution, which creationists and ID'ers have long accepted.

    SLC driveled,
    >>>>>> Attached is a commentary from Ed Brayton relative to Mr. Fafarman. <<<<<<

    Fatheaded Ed Brayton is an unscrupulous BVD-clad blogger who "wins" debates by censoring comments.

    Anonymous driveled,
    >>>>> Larry, we have absolute confidence that no sane, rational person could ever make the serious mistake of thinking you could be right about anything concerning evolution. <<<<<<

    Just for that, I am going to unleash my theory of co-evolution of total co-dependence of two different kinds of organisms -- e.g., bees and flowering plants. In such co-evolution, unlike in evolutionary adaptation to widespread fixed physical features of the environment, e.g., land, water, and air, there may be nothing to adapt to because the corresponding co-dependent trait in the other organism is likely to be locally absent. When corresponding co-dependents traits in both organisms are fatal in such absence, co-evolution by means of random mutation is virtually impossible, and even when the co-dependent traits are not fatal or harmful in such absence, the appearance of only one of the corresponding co-dependent traits would be of no benefit in natural selection. Also, there may be irreducibly complex multiple sets of pairs of corresponding traits involving multiple organs — for example, a bee must not only be able to digest nectar but must also be able to find the flowers.

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  20. "All he has to do is admit that evolution by natural selection is not what he means when he uses the word "Darwinian."

    "Evolution by natural selection" is a vague, untestable belief.
    Changes in gene frequency is not evolution. It's simply a variation, which doesn't say how the system itself came into existence. Before Darwin knew that animals "change over time". However, Darwin didn't come to explain how animals change over time, but how animals came into existence. Using situations where "change over time" happens as suporting the notion that dinosaurs turned into birds it.....well.....nonsense.

    Essencially, belief that biological systems are the result of an unguided, impersonal, undirected natural force was not necessary in the experiment. Atheists need that. Scientists don't.

    ReplyDelete
  21. SLC driveled (quoting Ed Brayton) --
    >>>>> He's gonna be added to the legal team that is threatening to sue me and bring me down, or he's going to convince ScienceBlogs to fire me. <<<<<<

    BTW, I don't understand how Fatheaded Ed Brayton was ever accepted by ScienceBlogs and Panda's Thumb. He has no credentials in any technical field (science, engineering, mathematics, and computer science). He admitted that he is not even a college grad. He is just a fast-talking storyteller.

    ReplyDelete
  22. Larry, Larry, Larry (or PC2, PC2, PC2, or ______)

    Your postings are extremely rambling, distorted and display an abysmal of understanding of science and scientific method. I have conferred with a number of colleagues and friends with expertise in a variety of medical sciences, physical sciences and education, and, as we have concern for your mental health and general well-being, we offer the following suggestions to assist you:

    Education is good, so we recommend that you enroll in a properly accredited educational institution (a grade 5 or 6 level would likely be appropriate).

    Seek qualified psychiatric help.

    Perhaps there is a medical procedure that can reverse the effects of that nasty frontal lobotomy. We have heard rumors to the effect that those Scientology guys have some sure-fire medical cures, based on state-of-the-art science that is every bit as good as the “science” promoted by creationists (YEC, OEC and IDC).

    Whenever you feel the urge to post another rambling, irrational diatribe against evolution/science, take a deep breath and read any of the excellent material by Miller, Gould, Dawkins, Ruse, Coyne, Rosenhouse, Matzke, Forrest, Padian, Kitcher, etc. that explains in great detail how evolution works and why it is high quality science (and also points out the fatal flaws of creationism, and explains why no form of creationism is science).

    As additional reading assignments, we strongly recommend (for your summer reading pleasure) the following excellent books and websites on science and scientific method that can act as an antidote to the insidious antiscience creationism viral infection:

    Park, R. L. (2000): Voodoo Science: The Road from Foolishness to Fraud. Oxford University Press, New York, 230 pp.

    Plait, P. C. (2002): Bad Astronomy: Misconceptions and Misuses Revealed, from Astrology to the Moon Landing “Hoax”. John Wiley & Sons, New York, 277 pp.
    http://www.badastronomy.com/

    Sagan, C. (1997): The Demon-Haunted World – Science as a Candle in the Dark. Ballantine Books, 457 p

    Schick, T. and L. Vaughn (2002): How to Think about Weird Things – Critical Thinking for a New Age. McGraw-Hill, 310 pp.

    Shermer, M. (2001): The Borderlands of Science: Where Science Meets Nonsense. Oxford University Press, New York, 360 pp.

    Shermer, M. (2002): Why People Believe in Weird Things: Pseudoscience, Superstition and other Confusions of our Time. Henry Holt/Owl Books, New York, 349 pp (revised & expanded).

    Wynn, C. M. and A. W. Wiggins (2001): Quantum Leaps in the Wrong Direction: Where Real Science Ends - and Pseudoscience Begins. The National Academies Press, 240 pp.

    Coker, R. (2001): Distinguishing Science and Pseudoscience.
    http://www.quackwatch.org/01QuackeryRelatedTopics/pseudo.html


    Caringly Yours

    ReplyDelete
  23. Anonymous --

    Giving a list of publications is not a satisfactory answer to my comments. I could just as easily give you a list of publications written by Michael Behe, William Dembski, Jonathan Wells, Phillip Johnson, Denyse O'Leary, etc..

    I invite you to explain how the co-evolution of total co-dependence works.

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  24. Quoth Jason:
    No, O unsurprisingly dishonest one, he didn't. He admitted that bacteria change over time.

    and Anonymous wrote:
    Changes in gene frequency is not evolution. It's simply a variation

    Back when I had time to read talk.origins, it seemed that about once a month, some creationist would make a comment that boiled down to "That's not evolution! That's just allele frequency change over time in a population!"

    I'm glad to see that this tradition is alive and well.

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  25. Still no answer to my arguments about the co-evolution of total co-dependence. Anyone? Anyone? Bueller?

    "I'm always kicking their butts -- that's why they don't like me."
    -- Gov. Arnold Schwarzenegger

    ReplyDelete
  26. Ah yes, Behe, Dembski, Wells, Johnson, O'Leary, etc., the ultimate in creationist scientific illiterati. Where's the science??? They provide an exquisite mangled mess of misinterpreted science, bad philosophy, and the poorest quality math and statistics, liberally mixed with dogmatic, marginalized religious fundamentalism. What more could one ask for as a perfect demonstration that creationism is not science?? Thank you Larry for bringing this up; it demonstrates that if these heroes of yours are your best source for "science" you are scientifically illiterate. And you still wonder why no one takes you seriously?

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  27. >>>>>> Thank you Larry for bringing this up; it demonstrates that if these heroes of yours are your best source for "science" you are scientifically illiterate. And you still wonder why no one takes you seriously? <<<<<<

    You obviously missed my point, that point being that just giving a random list of publications is not a valid answer to an argument.

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  28. Larry said: < "This is an incredible admission from a creationist. Egnor admits that the bacteria evolved. He then goes on to define some bizarre version of "Darwin's theory."1 But the cat is out of the bag. What we see here folks, is the recognition that there is a distinction between Darwinism and evolution by natural selection." >


    Why is what he said an "incredible admission"? He said "That evolution occurred — that is, that the population of bacteria changed over time — is obviously true". This is the definition of evolution that you claimed not to understand and do not accept.

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  29. anthony022071 said...

    >>>>>Larry said: < "This is an incredible admission from a creationist . . . . . <<<<<<

    That quote was from Larry Moran. There is another Larry here, me -- Larry Fafarman. Please be specific about which Larry you are talking about.

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  30. Voice in the UrbannessSaturday, May 31, 2008 4:54:00 PM

    > There is another Larry here, me -- Larry Fafarman. Please be specific about which Larry you are talking about. <

    Perhaps you should be addressed as Larry "Dunghill" Fafarman as it is one of your favorite words.

    ReplyDelete