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Antibiotic resistance: The non-Darwin truth

In “Evolutionary Lessons From Superbugs” (Huffington Post, January 8, 2012), James Shapiro, author of Evolution: A View from the 21st Century (FT Press Science), talks about how Darwinism misled scientists who were trying to understand antibiotic resistance:

In the early days of molecular biology, bacterial geneticists applied conventional evolutionary concepts from the pre-DNA period to explain the evolution of antibiotic resistance. The theory was that mutations could alter the structure of cell components and either block entry of the drugs into the bacteria or prevent their action on cellular targets, such as the enzymes essential to cell wall synthesis. Even if the initial mutation did not confer a high degree of resistance, accumulation of several sequential changes would result in resistance to the antibiotic levels used in clinical medicine. Indeed, a wide variety of laboratory experiments confirmed this theory, and bacterial geneticists isolated the predicted mutant strains. In virtually all cases, the resistant mutants grew less well than the parental sensitive bacteria, leading to the comforting conclusion that resistant bacteria would not significantly accumulate in nature. The degree of confidence was so great that the U.S. Surgeon General in 1967 declared that “the war against infectious diseases has been won” (Fauci 2001).

There were problems both with the science and the new public health policy based on it. The Surgeon General “misunderestimated” the bacteria, which followed their own evolutionary rules and did not listen to what the scientists said they should do. Although experimentally confirmed, the mutation theory of antibiotic resistance failed to account for most cases in the real world. Resistance continued to spread among bacteria isolated in clinics around the globe. Even more ominously, different strains of pathogenic bacteria increasingly displayed resistance to more than one antibiotic at a time. Research pioneered in Japan found that multiple antibiotic resistances could be transferred simultaneously from one bacterial species to another (Watanabe 1967). The DNA agents responsible for this transfer are circular molecules that are called multidrug resistance plasmids, which can move from one cell to another (Clowes 1973; Novick 1980). Moreover, the resultant multiply resistant bacteria were not altered in their cellular structures or inhibited in their growth properties. Rather, they had acquired new biochemical activities that could destroy or inactivate the antibiotics, chemically alter their targets, or remove them from the bacterial cell (Davies 1979; Levy 1998).

Multiple antibiotic resistance clearly represented genome change and evolution of a type unimagined in the pre-DNA period. DNA molecules could be transferred “horizontally” between unrelated cells rather than inherited from ancestral cells. Moreover, horizontally transferred DNA could carry complex sets of genetic information encoding multiple distinct biochemical activities. Evolutionary leaps involving several characteristics at once could occur through horizontal DNA transfer.

We wonder how many people out there took the long walk out of research just for saying what they knew, and how many others just kept quiet.

And the dull-witted docent went on telling the public that antibiotic resistance proves that Darwin was right.

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12 Responses to Antibiotic resistance: The non-Darwin truth

  1. But just what can neo-Darwinism do even with the very non-Darwinian ‘natural genetic engineering’ (Shapiro’s term not mine) of HGT at its disposal:

    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

    A review of The Edge of Evolution: The Search for the Limits of Darwinism
    The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155).
    http://creation.com/review-mic.....-evolution

    “The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable.”
    Michael J. Behe PhD. (from page 146 of his book “Edge of Evolution”)

    Nature Paper,, Finds Darwinian Processes Lacking – Michael Behe – Oct. 2009
    Excerpt: Now, thanks to the work of Bridgham et al (2009), even such apparently minor switches in structure and function (of a protein to its supposed ancestral form) are shown to be quite problematic. It seems Darwinian processes can’t manage to do even as much as I had thought. (which was 1 in 10^40 for just 2 binding sites)
    http://www.evolutionnews.org/2.....hes_t.html

    The Sheer Lack Of Evidence For Macro Evolution – William Lane Craig – video
    http://www.metacafe.com/watch/4023134

    Dr. Behe’s empirical research also agrees with the extreme difficulty encountered if scientists try to purposely (intelligently) design a 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. Sick!
    http://www.reasons.org/viral-b.....-sick-cool

    Moreover, there is, ‘surprisingly’, found to be ‘rather low’ conservation of Domain-Domain Interactions occurring in Protein-Protein interactions:

    A Top-Down Approach to Infer and Compare Domain-Domain Interactions across Eight Model Organisms
    Excerpt: Knowledge of specific domain-domain interactions (DDIs) is essential to understand the functional significance of protein interaction networks. Despite the availability of an enormous amount of data on protein-protein interactions (PPIs), very little is known about specific DDIs occurring in them.,,, Our results show that only 23% of these DDIs are conserved in at least two species and only 3.8% in at least 4 species, indicating a rather low conservation across species.,,,
    http://www.plosone.org/article.....ne.0005096

    Off topic music, verse and picture:

    What pi sounds like when out to music – cool video
    http://www.youtube.com/watch?v=YOQb_mtkEEE

    Proverbs 8:26-27
    While as yet He had not made the earth or the fields, or the primeval dust of the world. When He prepared the heavens, I was there, when He drew a circle on the face of the deep,

    Picture of CMBR
    https://webspace.utexas.edu/reyesr/SolarSystem/cmbr.jpg

    Hillsong – Mighty to Save – With Subtitles/Lyrics
    http://www.youtube.com/watch?v=-08YZF87OBQ

  2. Yes! Shame on Darwin for not anticipating research that would take place more than a hundred years later.

    And shame on researchers for drawing a reasonable conclusion based on the evidence available at the time:

    In virtually all cases, the resistant mutants grew less well than the parental sensitive bacteria, leading to the comforting conclusion that resistant bacteria would not significantly accumulate in nature.

    And:

    Subsequent research has bolstered Sonea and Paniset’s initially outlandish idea.

    Those idiot Darwinists should have embraced the outlandish idea, knowing that future research would corroborate it.

    It’s a good thing we have clairvoyant ID proponents who can predict every relevant future scientific discovery.

  3. Actually ‘Darwinism’ is not even scientific in the first place:

    Science and Pseudoscience – Imre Lakatos – exposing Darwinism as a ‘degenerate science program’
    https://docs.google.com/document/d/1LpGd3smTV1RwmEXC25IAEKMjiypBl5VJq9ssfv4JgeM/edit?hl=en_US

    “nobody to date has yet found a demarcation criterion according to which Darwin can be described as scientific” – Imre Lakatos (November 9, 1922 – February 2, 1974) a philosopher of mathematics and science, , quote was as stated in 1973 LSE Scientific Method Lecture
    http://en.wikipedia.org/wiki/I.....27s_theory

    Is evolution pseudoscience?
    Excerpt:,,, Thus, of the ten characteristics of pseudoscience listed in the Skeptic’s Dictionary, evolution meets nine. Few other?pseudosciences — astrology, astral projection, alien abduction, crystal power, or whatever — would meet so many.
    http://creation.com/is-evolution-pseudoscience

  4. From Shapiro’s blog:

    Since the Intelligent Design (ID) advocates point to the bacterial flagellum as an example of an “irreducibly complex” structure that could not have evolved by Darwinian evolutionary processes (Behe 1996), they need to address how such intricate and clearly related biological inventions have come to be diversified for so many different uses. Certainly, the ID argument is greatly undermined if it has to invoke supernatural intervention for the origin of each modified adaptive structure. At the same time, it is fair to recognize that the evolutionary science community is also challenged to come up with detailed explanations for the origin and diversification of a basic complex functional design.

    It’s refreshing to have a scientist raising serious challenges both to ID and to mainstream science, without insulting either.

  5. as to:

    Certainly, the ID argument is greatly undermined if it has to invoke supernatural intervention for the origin of each modified adaptive structure. At the same time, it is fair to recognize that the evolutionary science community is also challenged to come up with detailed explanations for the origin and diversification of a basic complex functional design.

    Reminds me of this recent article:

    Evolution and the Illusion of Randomness – Talbott – Fall 2011
    Excerpt: The situation calls to mind a widely circulated cartoon by Sidney Harris, which shows two scientists in front of a blackboard on which a body of theory has been traced out with the usual tangle of symbols, arrows, equations, and so on. But there’s a gap in the reasoning at one point, filled by the words, “Then a miracle occurs.” And the one scientist is saying to the other, “I think you should be more explicit here in step two.”
    In the case of evolution, I picture Dennett and Dawkins filling the blackboard with their vivid descriptions of living, highly regulated, coordinated, integrated, and intensely meaningful biological processes, and then inserting a small, mysterious gap in the middle, along with the words, “Here something random occurs.”
    This “something random” looks every bit as wishful as the appeal to a miracle. It is the central miracle in a gospel of meaninglessness, a “Randomness of the gaps,” demanding an extraordinarily blind faith. At the very least, we have a right to ask, “Can you be a little more explicit here?”
    http://www.thenewatlantis.com/.....randomness

    foot note:

    Blackholes – The neo-Darwinian ‘god of entropic randomness’ which can create all things (at least according to them)
    https://docs.google.com/document/d/1fxhJEGNeEQ_sn4ngQWmeBt1YuyOs8AQcUrzBRo7wISw/edit?hl=en_US

  6. Jon:

    I agree it is refreshing. Shapiro is a good scientist. About is specific objection to ID:

    Certainly, the ID argument is greatly undermined if it has to invoke supernatural intervention for the origin of each modified adaptive structure.

    I would say, why supernatural?

    The phrase, is so modified:

    “Certainly, the ID argument is greatly undermined if it has to invoke a design intervention for the origin of each functionally complex modified adaptive structure.”

    really makes little sense.

  7. gpuccio – yes, that was my reaction, too. But at least it’s a challenege one can counter, rather than an ad hominem attack.

    So that just leaves his challenge to the evolutionary science community. Shapiro himself would probably say – “I’m working on it.” Others, I suspect, if they commented at all, would say, “You’re just lacking in imagination,” with a side-swipe at him for being heterodox.

  8. Can anyone explain how the article supports ID?

  9. Well one way to support one’s position is by showing your opponet’s position is bogus. And it just so happens that it is mandatory for all design inferences to eliminate chance and necessity.

  10. Well one way to support one’s position is by showing your opponet’s position is bogus.

    LOL:
    Mr X: I believe that penguins can fly.
    Joe: This evidence demonstrates conclusively that they can’t fly … This refutation of your position supports my own position that penguins can teleport instantly between different galaxies.

  11. Way to take what i said, not only out-of-context, but to some absolute idiotic extreme.

  12. So Darwin knew nothing about genetics or the mechanics of variation. Since his theory wasn’t based on the mechanics of variation, discovering new processes says nothing about Darwinian evolution.

    Discovering new sources of variation say nothing about evolution unless one observes the Designer in action. Shapiro admits that variation does not have foresight or knowledge of what’s needed by a population. At most, microbes increase their rate of mutation under stress.

    I’m sure everyone at UD downloaded the free Shapiro book and noticed that.

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