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Why Darwinian medicine is a dead loss

In “Darwinian Medicine and Proximate and Evolutionary Explanations,” at Evolution News & Views (June 25, 2011), neurosurgeon Mike Egnor makes a critical distinction between proximate explanations and evolutionary explanations,s they apply to medicine:

Proximate explanations are the description of the process itself. A proximate explanation of type 1 diabetes is that it is caused by lack of insulin. A proximate explanation of Duchenne muscular dystrophy is that it is a recessive X-linked genetic disease that causes muscle degeneration, weakness and death. Males are affected, though females can be carriers. It is caused by a mutation in the dystrophin gene on the X chromosome (Xp21).

As you can see, proximate explanations are what medical researchers would call the scientific explanation for a disease. Proximate explanations are medical science and provide the foundation for all medical treatments.

[ ... ]

The difficulty with evolutionary explanations in medicine is:

1) All of the relevant pathophysiology is provided by the proximate explanations, which are the only explanations useful for treatment.

There are other difficulties but that first one is the swish of Occam’s Razor, as far as medicine is concerned.

Takin’ it to the street: You tripped and sprained your ankle. What you need is a speculative history of the sprained ankle in vertebrates … not!

The principle question is, what is evolutionary medicine meant to do, given that it is no use in the normal sense?

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72 Responses to Why Darwinian medicine is a dead loss

  1. In my 30 years practicing medicine I have never found Darwinian evolution helpful in any way.

  2. 2
    Elizabeth Liddle

    The answer is that it is useful in research, not necessarily in clinical practice.

    In clinical practice, as Egnor says, all you need are proximal explanations.

    But distal explanations are often helpful in research for even arriving at proximal explanations.

  3. I am both a clinician and a researcher and have never found Darwinism of any use in my work. It’s not to say that it can’t be of any use ever but the current problem is funding and many different proximate routes to follow.
    Even in areas such as studying HIV resistance patterns we look at proximate explanations.

  4. 4
    Elizabeth Liddle

    To understand bacterial resistance without a “replication with variance plus natural selection” model seems pretty difficult.

    Also, the entire principle of “take the full course of antibiotics even though you may feel better before the end of the course” is predicated on the principle that failing to kill all the bugs will lead to selective survival of the most resistant, and thus to the evolution of multiply-resistant strains.

    Without the principle, you would have no basis for the advice, surely?

    I assume you give it?

  5. Micro-evolution is directly observable though. No one doubts this.

  6. 6
    Elizabeth Liddle

    Well, there you are. A practical and useful application of Darwinian evolution in the way patients are instructed to take their meds.

    Here are other examples: understanding the causes of obesity; lactose intolerance; stress-related disease in sedentary people; epidemiology of sickle cell disease; diabetes.

    In all these fields, an understanding of distal Darwinian evolutionary process can help make sense of proximal causes of disorders.

  7. Actually we’ve seen resistance emerge before any Darwinian explanations came along.

    In your other examples the payoff has always been in proximal research. Darwinian explanations follow later but are not really of much utility. Trust me, without proximal research and with only Darwinian evolution we’d be in the middle ages. Without Darwinian evolution we’d still be where we are, perhaps ahead for we’d have more resources for proximal work.

  8. 8
    Elizabeth Liddle

    Purugu: antibiotics were discovered well after Darwin’s theory was largely accepted.

    Darwin’s account explains why we see antibiotic resistance in bacteria, and why it is important to “finish the course”. My parents, both doctors, came into practice around the time when antibiotics came into widespread use (as an aside, my grandfather, an army pathologist, was the RAMC Major General responsible for deploying the scarces supplies of penicillin to troops during WWII!), and at my mother’s knee (literally) I learned that she was worried that over-subscription of penicillin would lead to antibiotic resistance strains emerging, and that that was why it was important to “finish the course”.

    As for your point about “proximal research” – of course it’s important! But your assertion that “without Darwinian evolution we’d still be where we are, perhaps ahead…” I strongly disagree. Genetics research, for example, has been hugely important in many disorders, and genetics is firmly based in a Darwinian framework. As I pointed out – look at the epidemiology of sickle cell, for example.

  9. Now, Lizzie, do you even know what “bacterial resistance” actually is? Careful now; you’ve strayed from your home turf.

  10. Why Do We Invoke Darwin?
    Evolutionary theory contributes little to experimental biology
    By: Philip S. Skell
    Excerpt: A.S. Wilkins, editor of the journal BioEssays, wrote in 2000 “Evolution would appear to be the indispensable unifying idea and, at the same time, a highly superfluous one.”

    I would tend to agree. Certainly, my own research with antibiotics during World War II received no guidance from insights provided by Darwinian evolution. Nor did Alexander Fleming’s discovery of bacterial inhibition by penicillin. I recently asked more than 70 eminent researchers if they would have done their work differently if they had thought Darwin’s theory was wrong. The responses were all the same: No.

    I also examined the outstanding biodiscoveries of the past century: the discovery of the double helix; the characterization of the ribosome; the mapping of genomes; research on medications and drug reactions; improvements in food production and sanitation; the development of new surgeries; and others. I even queried biologists working in areas where one would expect the Darwinian paradigm to have most benefited research, such as the emergence of resistance to antibiotics and pesticides. Here, as elsewhere, I found that Darwin’s theory had provided no discernible guidance, but was brought in, after the breakthroughs, as an interesting narrative gloss.

    In the peer-reviewed literature, the word “evolution” often occurs as a sort of coda to academic papers in experimental biology. Is the term integral or superfluous to the substance of these papers? To find out, I substituted for “evolution” some other word – “Buddhism,” “Aztec cosmology,” or even “creationism.” I found that the substitution never touched the paper’s core. This did not surprise me. From my conversations with leading researchers it had became clear that modern experimental biology gains its strength from the availability of new instruments and methodologies, not from an immersion in historical biology.
    http://www.discovery.org/a/2816

    Podcasts and Article of Dr. Skell
    http://www.evolutionnews.org/2.....40981.html

    Science Owes Nothing To Darwinian Evolution – Jonathan Wells – video
    http://www.metacafe.com/watch/4028096

    “Charles Darwin said (paraphrase), ‘If anyone could find anything that could not be had through a number of slight, successive, modifications, my theory would absolutely break down.’ Well that condition has been met time and time again. Basically every gene, every protein fold. There is nothing of significance that we can show that can be had in a gradualist way. It’s a mirage. None of it happens that way. – Doug Axe PhD. – video interview
    http://www.metacafe.com/watch/5347797/

    further note:

    Experimental Evolution in Fruit Flies – October 2010
    Excerpt: “This research really upends the dominant paradigm about how species evolve”.,,, as stated in regards to the 35 year experimental failure to fixate a single beneficial mutation within fruit flies.
    http://www.arn.org/blogs/index.....ruit_flies

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

    ==========================

    Whereas Intelligent Design, contrary to what many evolutionists will say publicly, does in fact make solid predictions for science that we can test:

    A Response to Questions from a Biology Teacher: How Do We Test Intelligent Design? – March 2010
    Excerpt: Regarding testability, ID (Intelligent Design) makes the following testable predictions:
    (1) Natural structures will be found that contain many parts arranged in intricate patterns that perform a specific function (e.g. complex and specified information).
    (2) Forms containing large amounts of novel information will appear in the fossil record suddenly and without similar precursors.
    (3) Convergence will occur routinely. That is, genes and other functional parts will be re-used in different and unrelated organisms.
    (4) Much so-called “junk DNA” will turn out to perform valuable functions.
    http://www.evolutionnews.org/2.....rom_a.html

    A Positive, Testable Case for Intelligent Design – Casey Luskin – March 2011 – several examples of cited research
    http://www.evolutionnews.org/2.....45311.html

    In the last part of this following audio, Casey Luskin lays the evidence out for a Professor of evolution, who who has the audacity to challenge his students to come up with ‘ANY’ evidence for Intelligent Design:

    Evidence for Intelligent Design – Casey Luskin – July 2010
    http://intelligentdesign.podom.....6_24-07_00

    I found this following paper particularly interesting for broadly outlining how evolution misses the mark for a true science and is, in reality, a pseudo-science:

    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

    C.S. Lewis: creationist and anti-evolutionist
    Excerpt: “In 1951 C S Lewis wrote that evolution was “the central and radical lie in the whole web of falsehood that now governs our lives” and modern civilization. Evolution, Lewis explained, is a picture of reality that has resulted from imagination and is “not the logical result of what is vaguely called ‘modern science’.”

  11. Elizabeth, antibiotic resistance was observed irrespective of Darwinian evolution or predictions. We do not need Darwinian explanations for it, we can observe it and extrapolate from that point. In that light Darwinism did not provide us anything new that we did not see ourselves empirically. Even if we never heard of TOE, we’d still have figured it out. We’d have, because we have microbiology, biochemistry, pharmacology, pathology, and other fields which do pretty well without TOE.

    Genetics per se is not based on a Darwinian framework. Genetics is an independent area of science. We owe more to Mendel in that department than Darwin.

    What we do need is more people to do proximal research and more funding.

  12. Elizabeth:

    Why Do We Invoke Darwin?
    Evolutionary theory contributes little to experimental biology
    By: Philip S. Skell
    Excerpt: A.S. Wilkins, editor of the journal BioEssays, wrote in 2000 “Evolution would appear to be the indispensable unifying idea and, at the same time, a highly superfluous one.”

    I would tend to agree. Certainly, my own research with antibiotics during World War II received no guidance from insights provided by Darwinian evolution. Nor did Alexander Fleming’s discovery of bacterial inhibition by penicillin. I recently asked more than 70 eminent researchers if they would have done their work differently if they had thought Darwin’s theory was wrong. The responses were all the same: No.

    I also examined the outstanding biodiscoveries of the past century: the discovery of the double helix; the characterization of the ribosome; the mapping of genomes; research on medications and drug reactions; improvements in food production and sanitation; the development of new surgeries; and others. I even queried biologists working in areas where one would expect the Darwinian paradigm to have most benefited research, such as the emergence of resistance to antibiotics and pesticides. Here, as elsewhere, I found that Darwin’s theory had provided no discernible guidance, but was brought in, after the breakthroughs, as an interesting narrative gloss.

    In the peer-reviewed literature, the word “evolution” often occurs as a sort of coda to academic papers in experimental biology. Is the term integral or superfluous to the substance of these papers? To find out, I substituted for “evolution” some other word – “Buddhism,” “Aztec cosmology,” or even “creationism.” I found that the substitution never touched the paper’s core. This did not surprise me. From my conversations with leading researchers it had became clear that modern experimental biology gains its strength from the availability of new instruments and methodologies, not from an immersion in historical biology.
    http://www.discovery.org/a/2816

    Podcasts and Article of Dr. Skell
    http://www.evolutionnews.org/2.....40981.html

    Science Owes Nothing To Darwinian Evolution – Jonathan Wells – video
    http://www.metacafe.com/watch/4028096

    “Charles Darwin said (paraphrase), ‘If anyone could find anything that could not be had through a number of slight, successive, modifications, my theory would absolutely break down.’ Well that condition has been met time and time again. Basically every gene, every protein fold. There is nothing of significance that we can show that can be had in a gradualist way. It’s a mirage. None of it happens that way. – Doug Axe PhD. – video interview
    http://www.metacafe.com/watch/5347797/

    further note:

    Experimental Evolution in Fruit Flies – October 2010
    Excerpt: “This research really upends the dominant paradigm about how species evolve”.,,, as stated in regards to the 35 year experimental failure to fixate a single beneficial mutation within fruit flies.==

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

    New Research on Epistatic Interactions Shows “Overwhelmingly Negative” Fitness Costs and Limits to Evolution – Casey Luskin June 8, 2011
    Excerpt: In essence, these studies found that there is a fitness cost to becoming more fit. As mutations increase, bacteria faced barriers to the amount they could continue to evolve. If this kind of evidence doesn’t run counter to claims that neo-Darwinian evolution can evolve fundamentally new types of organisms and produce the astonishing diversity we observe in life, what does?
    http://www.evolutionnews.org/2.....47151.html

    ==========================

    Whereas Intelligent Design, contrary to what many evolutionists will say publicly, does in fact make solid predictions for science that we can test:

    A Response to Questions from a Biology Teacher: How Do We Test Intelligent Design? – March 2010
    Excerpt: Regarding testability, ID (Intelligent Design) makes the following testable predictions:
    (1) Natural structures will be found that contain many parts arranged in intricate patterns that perform a specific function (e.g. complex and specified information).
    (2) Forms containing large amounts of novel information will appear in the fossil record suddenly and without similar precursors.
    (3) Convergence will occur routinely. That is, genes and other functional parts will be re-used in different and unrelated organisms.
    (4) Much so-called “junk DNA” will turn out to perform valuable functions.
    http://www.evolutionnews.org/2.....45311.html

    In the last part of this following audio, Casey Luskin lays the evidence out for a Professor of evolution, who who has the audacity to challenge his students to come up with ‘ANY’ evidence for Intelligent Design:

    Evidence for Intelligent Design – Casey Luskin – July 2010
    http://intelligentdesign.podom.....6_24-07_00

    I found this following paper particularly interesting for broadly outlining how evolution misses the mark for a true science and is, in reality, a pseudo-science:

    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

    C.S. Lewis: creationist and anti-evolutionist
    Excerpt: “In 1951 C S Lewis wrote that evolution was “the central and radical lie in the whole web of falsehood that now governs our lives” and modern civilization. Evolution, Lewis explained, is a picture of reality that has resulted from imagination and is “not the logical result of what is vaguely called ‘modern science’.”

  13. 13
    Elizabeth Liddle

    I understand it to be the evolution of bacterial strains that are resistant to (i.e. are not killed or prevented from reproducing by) widely used antibiotics, as predicted, among others, by my mother.

    What is your understanding?

  14. 14
    Elizabeth Liddle

    Puragu:

    Elizabeth, antibiotic resistance was observed irrespective of Darwinian evolution or predictions. We do not need Darwinian explanations for it, we can observe it and extrapolate from that point. In that light Darwinism did not provide us anything new that we did not see ourselves empirically. Even if we never heard of TOE, we’d still have figured it out. We’d have, because we have microbiology, biochemistry, pharmacology, pathology, and other fields which do pretty well without TOE.

    That’s not making sense to me, Puragu. Obviously if you have a candidate mechanism for a process you make far faster progress in figuring it out than if you don’t. Darwinian evolution offered a clear prediction, that bacterial populations would evolve resistance to an environment in which antibiotics were part of the landscape. And they do. I’m not sure how you proposed that people would have come to that conclusion without actually having a mechanism to hand. If medicine had progressed by trial-and-error, without the germ theory of disease, it might have got to antibiotics in the end, but it would have taken a heck of a lot longer. As it was, because Chain and Florey knew that infection was caused by bacteria, they knew that if they could find an agent that killed bacteria they could cure infection. So they checked the literature and found Fleming’s paper.

    You need to be able to rack the microscope to lots of different focal lengths to do effective research! Not just proximal, not just distal.

    Genetics per se is not based on a Darwinian framework. Genetics is an independent area of science. We owe more to Mendel in that department than Darwin.

    I disagree. Genetics is about the mechanics of inheritance with variation. What we know about genetics depends in large part on an understanding of common descent, and the idea that populations adapt and diverge. I guess you could be a very narrow geneticist and ignore this, but you’d be very limited in what you could do.

    What we do need is more people to do proximal research and more funding.

    Well funding is good. But insisting on “proximal research” as a priority seems arbitrary to me, like insisting that, I dunno, chemists should stop worrying about quantum physics and just stick to molecules. Unless you are prepared to go from the near to the far – to look for both proximal and distal causes, you are crippling yourself for no good reason that I can see. Yes, medical research needs to be translated into practical patient care, and yes the translational process goes in both direction (from “proximal” clinical observation back to more “distal” science as well as the other way round) but to insist that all research occurs at the clinical seems to me not only arbitrary but bad clinical practice.

    My mother was using her knowledge of Darwinian evolution to sensibly modify her clinical practice well before antibiotic resistance was a widely known problem, to her patients’ benefit.

  15. Elizabeth, you, nor anyone else, is the least bit warranted to extrapolate the deleterious mutations, that are responsible for antibiotic resistance in bacteria, to the grand macro-evolutionary claims of neo-Darwinists that all life came from bacteria. It is simply a scientific felony to do as such!!! If any prediction has been confirmed, it is the fact that severe constraints are found to be in place which confirms the ‘variation within kind’ prediction of the Theistic model;

    Is Antibiotic Resistance evidence for evolution? – ‘The Fitness Test’ – video
    http://www.metacafe.com/watch/3995248

    Testing the Biological Fitness of Antibiotic Resistant Bacteria – 2008
    http://www.answersingenesis.or.....-drugstore

    Thank Goodness the NCSE Is Wrong: Fitness Costs Are Important to Evolutionary Microbiology
    Excerpt: it (an antibiotic resistant bacterium) reproduces slower than it did before it was changed. This effect is widely recognized, and is called the fitness cost of antibiotic resistance. It is the existence of these costs and other examples of the limits of evolution that call into question the neo-Darwinian story of macroevolution.
    http://www.evolutionnews.org/2.....s_wro.html

    List Of Degraded Molecular Abilities Of Antibiotic Resistant Bacteria:
    http://www.trueorigin.org/bacteria01.asp

    The following study surveys four decades of experimental work, and solidly backs up the preceding conclusion that there has never been an observed violation of genetic entropy:

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.(that is a net ‘fitness gain’ within a ‘stressed’ environment i.e. remove the stress from the environment and the parent strain is always more ‘fit’)
    http://behe.uncommondescent.co.....evolution/

    Testing Evolution in the Lab With Biologic Institute’s Ann Gauger – podcast with link to peer-reviewed paper
    Excerpt: Dr. Gauger experimentally tested two-step adaptive paths that should have been within easy reach for bacterial populations. Listen in and learn what Dr. Gauger was surprised to find as she discusses the implications of these experiments for Darwinian evolution. Dr. Gauger’s paper, “Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness,”.
    http://intelligentdesign.podom.....4_13-07_00

    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

    Dr. Behe states in The Edge of Evolution on page 135:

    “Generating a single new cellular protein-protein binding site (in other words, generating a truly beneficial mutational event that would actually explain the generation of the complex molecular machinery we see in life) is of the same order of difficulty or worse than the development of chloroquine resistance in the malarial parasite.”

    That order of difficulty is put at 10^20 replications of the malarial parasite by Dr. Behe. This number comes from direct empirical observation.

    Richard Dawkins’ The Greatest Show on Earth Shies Away from Intelligent Design but Unwittingly Vindicates Michael Behe – Oct. 2009
    Excerpt: The rarity of chloroquine resistance is not in question. In fact, Behe’s statistic that it occurs only once in every 10^20 cases was derived from public health statistical data, published by an authority in the Journal of Clinical Investigation. The extreme rareness of chloroquine resistance is not a negotiable data point; it is an observed fact.
    http://www.evolutionnews.org/2.....est_s.html

  16. further note:

    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....._edge.html

    Response from Ralph Seelke to David Hillis Regarding Testimony on Bacterial Evolution Before Texas State Board of Education, January 21, 2009
    Excerpt: He has done excellent work showing the capabilities of evolution when it can take one step at a time. I have used a different approach to show the difficulties that evolution encounters when it must take two steps at a time. So while similar, our work has important differences, and Dr. Bull’s research has not contradicted or refuted my own.
    http://www.discovery.org/a/9951

    Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) – October 2010
    Excerpt: “Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, “This research really upends the dominant paradigm about how species evolve,” said ecology and evolutionary biology professor Anthony Long, the primary investigator.
    http://www.arn.org/blogs/index.....ruit_flies

    Static evolution: is pond scum the same now as billions of years ago?
    Excerpt: But what intrigues (paleo-biologist) J. William Schopf most is lack of change. Schopf was struck 30 years ago by the apparent similarities between some 1-billion-year-old fossils of blue-green bacteria and their modern microbial microbial. “They surprisingly looked exactly like modern species,” Schopf recalls. Now, after comparing data from throughout the world, Schopf and others have concluded that modern pond scum differs little from the ancient blue-greens. “This similarity in morphology is widespread among fossils of [varying] times,” says Schopf. As evidence, he cites the 3,000 such fossils found;
    http://www.thefreelibrary.com/.....a014909330

    The Paradox of the “Ancient” (250 million year old) Bacterium Which Contains “Modern” Protein-Coding Genes:
    “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;

  17. I never said that all of medicine is done on a trial and error basis. So please don’t suggest that. However, before you can study a given mechanism of resistance you need actual resistant bacteria, and those we isolated or at least recognised as early as 1946.

    I don’t think the type of research I mention is arbitrary. It has proven most beneficial in easing suffering. That’s my primary aim in medicine.

    We recognise micro-evolution in medicine but to figure out the actual mechanisms proximal work.

    What measures did your Mother introduce to protect her patients from antibiotic resistance? Do you have evidence that they were in any way effective?

  18. Elizabeth:

    You DO realize that Ernst Chain, who shared the 1945 Nobel Prize in Physiology or Medicine with Alexander Fleming and Howard Florey, was an ardent anti-Darwinian, don’t you?

    See here.

    Concerning the materialistic theory of evolution, Ernst Chain (who could be described as a theistic, anti-Darwinian evolutionist) stated:

    “I would rather believe in fairies than in such wild speculation.

    “I have said for years that speculations about the origin of life lead to no useful purpose as even the simplest living system is far too complex to be understood in terms of the extremely primitive chemistry scientists have used in their attempts to explain the unexplainable that happened billions of years ago. God cannot be explained away by such naive thoughts.”

    (Chain, as cited in The Life of Ernst Chain: Penicillin and Beyond, by Ronald W. Clark, London, Weidenfeld & Nicolson, 1985, 147-148).

    Chain described “the divine spark which manifests itself so evidently in the spiritual creation of man” thus:

    “Any speculation and conclusions pertaining to human behaviour drawn on the basis of Darwinian evolutionary theories from animal ethological studies, and in particular ethological studies on primates, must be treated with the greatest caution and reserve.

    “It may be amusing for those engaged in the task to describe their fellow man as naked apes, and a less discriminating section of the public may enjoy reading about comparisons between the behaviour of apes and man, but this approach – which, by the way, is neither new nor original – does not really lead us very far.

    “We do not need to be expert zoologists, anatomists or physiologists to recognise that there exist some similarities between apes and man, but surely we are much more interested in the differences than the similarities. Apes, after all, unlike man, have not produced great prophets, philosophers, mathematicians, writers, poets, composers, painters and scientists. They are not inspired by the divine spark which manifests itself so evidently in the spiritual creation of man and which differentiates man from animals.”

    (Chain, 1971, “Social Responsibility and the Scientist in Modern Western Society,” Perspectives in Biology and Medicine, Spring 1971, Vol. 14, No. 3, p. 368).

    Here’s another quote:

    “Only one theory has been advanced to make an attempt to understand the development of life – the Darwin-Wallace theory of evolution. And a very feeble attempt it is, based on such flimsy assumptions, mainly of morphological-anatomical nature that it can hardly be called a theory.”

    (Chain, as cited in The Life of Ernst Chain: Penicillin and Beyond, by Ronald W. Clark, London, Weidenfeld & Nicolson, 1985, p. 147.)

    Chain also made it clear that he was very concerned about the effect of Darwinism on human behavior:

    Any speculation and conclusions pertaining to human behaviour drawn on the basis of Darwinian evolutionary theories…must be treated with the greatest caution and reserve….a less discriminating section of the public may enjoy reading about comparisons between the behaviour of apes and man, but this approach–which, by the way, is neither new nor original–does not really lead us very far…. Apes, after all, unlike man, have not produced great prophets, philosophers, mathematicians, writers, poets, composers, painters and scientists. They are not inspired by the divine spark which manifests itself so evidently in the spiritual creation of man and which differentiates man from animals.

    (Chain, Social Responsibility and the Scientist in Modern Western Society, London: The Council of Christians and Jews, p. 26.)

  19. 19
    Elizabeth Liddle

    No, I didn’t in fact, vjtorley, but I realised that my paragraph was potentially misleading. Let me emend it here:

    That’s not making sense to me, Puragu. Obviously if you have a candidate mechanism for a process you make far faster progress in figuring it out than if you don’t. Darwinian evolution offered a clear prediction, that bacterial populations would evolve resistance to an environment in which antibiotics were part of the landscape. And they do. I’m not sure how you proposed that people would have come to that conclusion without actually having a mechanism to hand.

    As another example of where a theoretical mechanism informed a major clinical discovery, if medicine had progressed by trial-and-error, without the germ theory of disease, it might have got to antibiotics in the end, but it would have taken a heck of a lot longer. As it was, because Chain and Florey knew that infection was caused by bacteria, they knew that if they could find an agent that killed bacteria they could cure infection. So they checked the literature and found Fleming’s paper.

    I didn’t mean to imply that Chain got there by adopting Darwinian theory, but by adopting another “distal” theory, the germ theory of disease.

    Apologies for any confusion!

  20. I agree that not all ‘distal’ theories are equal.

  21. 21
    Elizabeth Liddle

    I never said that all of medicine is done on a trial and error basis. So please don’t suggest that. However, before you can study a given mechanism of resistance you need actual resistant bacteria, and those we isolated or at least recognised as early as 1946.

    Right. And given that such resistance variants were discovered to be possible, the possiblity of the evolution of resistant populations became a strong likely result of widespread antibiotic use, as predicted by Darwinian theory.

    I don’t think the type of research I mention is arbitrary. It has proven most beneficial in easing suffering. That’s my primary aim in medicine.

    Excellent :) No, I’m sure it isn’t arbitrary. What I’m saying is that both proximal and distal mechanisms inform our understanding of what causes disease and disorders, and that if we (in a reductio ad absurdum) abandoned all but proximal observations, we would make much slower progress than if we said, for instance “we know this condition is caused by bacteria – if we find a toxic agent for this bacteria, then we might be able to cure the condition”, or, on the other hand, “we know this condition is caused by bacteria, but this is a patient who has been taking long-term antibiotics, and so it is possible that she has an endemic population of penicillin-resistant bacteria; we had better see whether we can find an alternative approach to treating the infection”. And, specifically, the clinician (or, more likely, researchers aware of the problem) might find out the mechanism of resistance, and search for a class of antibiotic that suppressed bacterial multiplication by a different mechanism. Again, the whole logical thought process is informed by theory.

    We recognise micro-evolution in medicine but to figure out the actual mechanisms proximal work.

    Well, I’m delighted that you recognise micro-evolution! But micro-evolution is Darwinian. So it’s an example of Darwinian theory being relevant.

    What measures did your Mother introduce to protect her patients from antibiotic resistance? Do you have evidence that they were in any way effective?

    She tried not to treat any condition with an antibiotic until she had a lab report that identified what the bacteria was sensitive to; she insisted that her patients “finish the course”; she avoided prescribing antibiotics for conditions likely to resolve spontaneously.

    I have no systematic evidence that it benefited her patients, although ironically, she herself suffered from not being treated by as good a physician as she was, and ended up with chronic kidney infections by multiply resistant bacteria. Eventually she died from brain haemorrhages resulting from amyloid angiopathy, possibly caused by chronic infection.

    Now, regarding the epidemiology of sickle-cell disease…. :)

  22. 22
    Elizabeth Liddle

    I agree that not all ‘distal’ theories are equal.

    Cool :)

    Also, it’s a continuum. I mean death is caused, in a distal sense, by birth :) But that’s not very useful.

    What matters, I suggest, is what is useful. I contend that an understanding of Darwinian processes is – or at least can be – useful in medicine.

    It’s certainly useful in my own work (mental health research).

  23. EL:

    “She tried not to treat any condition with an antibiotic until she had a lab report that identified what the bacteria was sensitive to; she insisted that her patients “finish the course”; she avoided prescribing antibiotics for conditions likely to resolve spontaneously.”

    I am sorry to hear about your mother.

    She seems to have had access to pretty modern medicine e.g. sensitivity results, for 1945.

    Those are pretty much conditions in which current 1st World physicians practice.

    However, for the most part I disagree about understanding of underlying Darwinian processes being helpful, it’s not, in fact it deflects attention from the problem at hand. We have a population of human beings we can work with already. Darwinian processes are able to suggest stories on how some mutation emerged in some ancestor or was passed down, but these stories are usually too vague, not clinically significant, change with the times and rely on proximal data, not vice versa.

  24. 24
    Elizabeth Liddle

    She practised medicine for several decades, Puragu!

    In any case, we seem to agree that microevolution is relevant to antibiotic resistance. So I hope we can agree that in that instance, Darwinian evolutionary theory is relevant.

    However, for the most part I disagree about understanding of underlying Darwinian processes being helpful, it’s not, in fact it deflects attention from the problem at hand.

    Clinically, you may well be right that Darwinian processes aren’t usually especially relevant, although I’d like to see an example them “deflect[ing] attention from the problem in hand”.

    We have a population of human beings we can work with already. Darwinian processes are able to suggest stories on how some mutation emerged in some ancestor or was passed down, but these stories are usually too vague, not clinically significant, change with the times and rely on proximal data, not vice versa.

    So what about the epidemiology of sickle cell disease?

    I’m not saying: by understanding how we evolved we can understand disease. That would be silly. What I am saying is that by viewing human beings in a Darwinian framework, we can understand all kinds of things, and predict all kinds of things, that we would not be able to do without that framework. I gave some examples above.

  25. Elizabeth, the neo-Darwinian framework, being a pack of lies that it is, is absolutely useless for truly ‘understanding all kinds of things’. And indeed, if followed, will consistently lead to false predictions for science.

    Darwin’s Predictions
    http://www.darwinspredictions.com/

    not to mention tragic consequences for man,,,

    From Darwin to Hitler
    http://www.youtube.com/watch?v=w_5EwYpLD6A

    ,,

  26. 26
    Elizabeth Liddle

    Well, it isn’t “a pack of lies” ba77.

    The basic Darwinian principle is simple logic. Demonstrating that that logic is actually implemented in living things has been demonstrated at many scales in many ways.

    That it has been used as an excuse for atrocity has no bearing on whether it is true or not, any more than the fact that atomic bombs were dropped on Japan has any bearing on whether e=mc^2 or not.

    As for your linked “predictions” – that site appears to me to be based on a profound misunderstanding both of evolutionary theory and the nature of scientific hypothesis testing.

    There are certainly unsolved issues in accounting for the appearance of life on earth, not least being the appearance of the first modern-type cell. There are also intriguing questions about the evolvability of evolvability – whether mutation rates, for example, are optimised at a population selection level, and whether the mechanisms of variance-production themselves evolved. And we know now that the role of drift is far greater than Darwin would have been aware of. Then there is the whole burgeoning field of “evo-devo” which has hugely enhanced our understanding of how allelic variance produces phenotypic effects.

    So evolutionary science is far from static – predictions are constantly being made, some are falsified and some confirmed. It’s how science works. But the basic Darwinian structure remains intact. We know it works because we can see it happening, in the lab and in the field.

  27. Elizabeth states:

    ‘Well, it isn’t “a pack of lies” ba77.’

    ,,,In the spirit of Elizabeth’s reference-less rebuttal,,,

    Yes it is a pack of lies!!!

  28. 28
    Elizabeth Liddle

    So how do I know that your references aren’t “a pack of lies” ba77?

    References themselves require evaluation.

    What I provided, in any case, rather than references, was a logical argument. What do you find wrong with my logic?

    And if you want references, I can provide some if you are interested.

  29. Elizabeth, so you are not going to take my word for it that neo-Darwinian evolution is a pack of lies??? :)

    Dang it!!! Well, here is a bit more formal way to show that neo-Darwinian evolution is a pack of lies;

    Neo-Darwinian evolution purports to explain all the wondrously amazing complexity of life on earth by reference solely to chance and necessity processes acting on energy and matter (i.e. purely material processes). In fact neo-Darwinian evolution makes the grand materialistic claim that the staggering levels of unmatched complex functional information we find in life, and even the ‘essence of life’ itself, simply ‘emerged’ from purely material processes. And even though this basic scientific point, of the ability of purely material processes to generate even trivial levels of complex functional information, has spectacularly failed to be established, we now have a much greater proof, than this stunning failure for validation, that ‘put the lie’ to the grand claims of neo-Darwinian evolution. This proof comes from the fact that it is now shown from quantum mechanics that ‘information’ is its own unique ‘physical’ entity. A physical entity that is shown to be completely independent of any energy-matter space-time constraints, i.e. it does not ‘emerge’ from a material basis. Moreover this ‘transcendent information’ is shown to be dominant of energy-matter in that this ‘information’ is shown to be the entity that is in fact constraining the energy-matter processes of the cell to be so far out of thermodynamic equilibrium.

    notes:

    Falsification of neo-Darwinism;

    First, Here is the falsification of local realism (reductive materialism).

    Here is a clip of a talk in which Alain Aspect talks about the failure of ‘local realism’, or the failure of reductive materialism, to explain reality:

    The Failure Of Local Realism – Reductive Materialism – Alain Aspect – video
    http://www.metacafe.com/w/4744145

    The falsification for local realism (reductive materialism) was recently greatly strengthened:

    Physicists close two loopholes while violating local realism – November 2010
    Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview.
    http://www.physorg.com/news/20.....alism.html

    Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009
    Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables.
    http://www.sciencedaily.com/re.....142824.htm

    (of note: hidden variables were postulated to remove the need for ‘spooky’ forces, as Einstein termed them — forces that act instantaneously at great distances, thereby breaking the most cherished rule of relativity theory, that nothing can travel faster than the speed of light.)

    And yet, quantum entanglement, which rigorously falsified local realism (reductive materialism) as the complete description of reality, is now found in molecular biology on a massive scale!

    Quantum Information/Entanglement In DNA & Protein Folding – short video
    http://www.metacafe.com/watch/5936605/

    Quantum entanglement holds together life’s blueprint – 2010
    Excerpt: When the researchers analysed the DNA without its helical structure, they found that the electron clouds were not entangled. But when they incorporated DNA’s helical structure into the model, they saw that the electron clouds of each base pair became entangled with those of its neighbours (arxiv.org/abs/1006.4053v1). “If you didn’t have entanglement, then DNA would have a simple flat structure, and you would never get the twist that seems to be important to the functioning of DNA,” says team member Vlatko Vedral of the University of Oxford.
    http://neshealthblog.wordpress.....blueprint/

    The relevance of continuous variable entanglement in DNA – July 2010
    Excerpt: We consider a chain of harmonic oscillators with dipole-dipole interaction between nearest neighbours resulting in a van der Waals type bonding. The binding energies between entangled and classically correlated states are compared. We apply our model to DNA. By comparing our model with numerical simulations we conclude that entanglement may play a crucial role in explaining the stability of the DNA double helix.
    http://arxiv.org/abs/1006.4053v1

    Quantum Information confirmed in DNA by direct empirical research;

    DNA Can Discern Between Two Quantum States, Research Shows – June 2011
    Excerpt: — DNA — can discern between quantum states known as spin. – The researchers fabricated self-assembling, single layers of DNA attached to a gold substrate. They then exposed the DNA to mixed groups of electrons with both directions of spin. Indeed, the team’s results surpassed expectations: The biological molecules reacted strongly with the electrons carrying one of those spins, and hardly at all with the others. The longer the molecule, the more efficient it was at choosing electrons with the desired spin, while single strands and damaged bits of DNA did not exhibit this property.
    http://www.sciencedaily.com/re.....104014.htm

    Information and entropy – top-down or bottom-up development in living systems? A.C. McINTOSH
    Excerpt: This paper highlights the distinctive and non-material nature of information and its relationship with matter, energy and natural forces. It is proposed in conclusion that it is the non-material information (transcendent to the matter and energy) that is actually itself constraining the local thermodynamics to be in ordered disequilibrium and with specified raised free energy levels necessary for the molecular and cellular machinery to operate.
    http://journals.witpress.com/paperinfo.asp?pid=420

    i.e. It is very interesting to note that quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints, should be found in molecular biology on such a massive scale, for how can the quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy space/time) ’cause’ when the quantum entanglement ‘effect’ falsified material particles as its own ‘causation’ in the first place? (A. Aspect) Appealing to the probability of various configurations of material particles, as neo-Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the energy/matter particles themselves to supply! To give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time
    and space! i.e. Put more simply, you cannot explain a effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘specified’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place!
    ,,,To refute this falsification of neo-Darwinism, one must falsify Alain Aspect, and company’s, falsification of local realism (reductive materialism)!

  30. f/n

    ,,, As well, appealing to ‘non-reductive’ materialism (multiverse or many-worlds) to try to explain quantum non-locality in molecular biology ends up destroying the very possibility of doing science rationally;

    BRUCE GORDON: Hawking’s irrational arguments – October 2010
    Excerpt: For instance, we find multiverse cosmologists debating the “Boltzmann Brain” problem: In the most “reasonable” models for a multiverse, it is immeasurably more likely that our consciousness is associated with a brain that has spontaneously fluctuated into existence in the quantum vacuum than it is that we have parents and exist in an orderly universe with a 13.7 billion-year history. This is absurd. The multiverse hypothesis is therefore falsified because it renders false what we know to be true about ourselves. Clearly, embracing the multiverse idea entails a nihilistic irrationality that destroys the very possibility of science.
    http://www.washingtontimes.com.....arguments/

    ,,,Michael Behe has a profound answer to the infinite multiverse (non-reductive materialism) argument in “Edge of Evolution”. If there are infinite universes, then we couldn’t trust our senses, because it would be just as likely that our universe might only consist of a human brain that pops into existence which has the neurons configured just right to only give the appearance of past memories. It would also be just as likely that we are floating brains in a lab, with some scientist feeding us fake experiences. Those scenarios would be just as likely as the one we appear to be in now (one universe with all of our experiences being “real”). Bottom line is, if there really are an infinite number of universes out there, then we can’t trust anything we perceive to be true, which means there is no point in seeking any truth whatsoever.

    “The multiverse idea rests on assumptions that would be laughed out of town if they came from a religious text.” Gregg Easterbrook

    =================

    Alain Aspect and Anton Zeilinger by Richard Conn Henry – Physics Professor – John Hopkins University
    Excerpt: Why do people cling with such ferocity to belief in a mind-independent reality? It is surely because if there is no such reality, then ultimately (as far as we can know) mind alone exists. And if mind is not a product of real matter, but rather is the creator of the “illusion” of material reality (which has, in fact, despite the materialists, been known to be the case, since the discovery of quantum mechanics in 1925), then a theistic view of our existence becomes the only rational alternative to solipsism (solipsism is the philosophical idea that only one’s own mind is sure to exist). (Dr. Henry’s referenced experiment and paper – “An experimental test of non-local realism” by S. Gröblacher et. al., Nature 446, 871, April 2007 – “To be or not to be local” by Alain Aspect, Nature 446, 866, April 2007

  31. as to buttress Dembski and Marks work on Conservation of Information,,,

    “LIFE’S CONSERVATION LAW: Why Darwinian Evolution Cannot Create Biological Information”: Dembski – Marks
    http://evoinfo.org/publication.....ation-law/

    ,,,It is now shown that ‘classical information’ is a subset of quantum information;,,,

    This following research provides solid falsification for Rolf Landauer’s contention that information encoded in a computer is merely physical (merely ‘emergent’ from a material basis) since he believed it always required energy to erase it;

    Quantum knowledge cools computers: New understanding of entropy – June 2011
    Excerpt: No heat, even a cooling effect;
    In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy.
    Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.”
    http://www.sciencedaily.com/re.....134300.htm

    ,,,and here is the empirical confirmation for ‘conservation of quantum information’,,,

    Quantum no-hiding theorem experimentally confirmed for first time
    Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment. (This experiment provides experimental proof that the teleportation of quantum information in this universe must be complete and instantaneous.)
    http://www.physorg.com/news/20.....tally.html

  32. Elizabeth Liddle @13:

    Darwinian evolution offered a clear prediction/b>, that bacterial populations would evolve resistance to an environment in which antibiotics were part of the landscape.

    This is false. You’ve made a very similar claim in the past and I pointed out why it was false then as well. So why do you persist?

    And they do.

    Except when they don’t. Which is also a “prediction” of Darwinian theory. Amazing theory.

    Darwinian evolution offered a clear prediction, that bacterial populations would evolve resistance to an environment in which antibiotics were part of the landscape.

    Darwinian theory does not and cannot predict that any species will survive in the face of conditions [read fitness landscape] which can bring about the death [read anti biotic] of that species, much less conditions designed to bring about the death of that species.

    Consider all the extinct species.

    If Darwinism predicts they would have evolved and survived, then Darwinism has been falsified.

    Consider sterilization, or heating things to a temperature which is lethal to life [anti biotic].

    Darwinism does not and cannot predict that any species will evolve to survive in deadly conditions.

    The claim that Darwinian theory predicts that any species will evolve and survive rather than perish is rubbish, plain and simple. It is false.

    Please stop repeating it.

    Darwinian theory does not predict what any “fitness landscape” is going to look like.

    Therefore it is incapable of predicting whether a species will survive or perish in the face of conditions hostile to life.

    fyi – anti biotic = anti life.

  33. Elizabeth Liddle @25:

    As for your linked “predictions” – that site appears to me to be based on a profound misunderstanding both of evolutionary theory and the nature of scientific hypothesis testing.

    Cornelius G. Hunter is a graduate of the University of Illinois where he earned a Ph.D. in Biophysics and Computational Biology. He is Adjunct Professor at Biola University and author of the award-winning Darwin’s God: Evolution and the Problem of Evil. Hunter’s other books include Darwin’s Proof, and his newest book Science’s Blind Spot (Baker/Brazos Press). Dr. Hunter’s interest in the theory of evolution involves the historical and theological, as well as scientific, aspects of the theory. His website is http://www.DarwinsPredictions.com.

  34. 34
    Elizabeth Liddle

    Mung:

    Elizabeth Liddle @13:

    Darwinian evolution offered a clear prediction, that bacterial populations would evolve resistance to an environment in which antibiotics were part of the landscape.

    This is false. You’ve made a very similar claim in the past and I pointed out why it was false then as well. So why do you persist?

    I don’t recall you pointing out that it was false, and I don’t think it is. I guess that’s why I persist. :)

    Perhaps you’d better “point out” again why you think it is false.

    It’s certainly not false that it is what Darwinian theory predicts. It predicts that either the population will go extinct or adapt, i.e. evolve to survive in the new + antibiotic environment.

    It is also not false that they have adapted.

    So what part is false?

    And they do.

    Except when they don’t. Which is also a “prediction” of Darwinian theory. Amazing theory.

    What?

    Darwinian evolution offered a clear prediction, that bacterial populations would evolve resistance to an environment in which antibiotics were part of the landscape.

    Darwinian theory does not and cannot predict that any species will survive in the face of conditions [read fitness landscape] which can bring about the death [read anti biotic] of that species, much less conditions designed to bring about the death of that species.

    You seem confused. Obviously I am using “antibiotic” in the specific sense of a class of drugs that are toxic to bacteria, specifically those originally derived from fungi. And a “species” doesn’t die, it goes extinct. A population may also go extinct.

    And if a population doesn’t adapt (evolve) to survive in a newly hostile environment it will go extinct. Therefore Darwinian theory predicts that unless you manage to kill of the entire population of bacteria in a human carrier, you risk adaptation occurring; in other words, you risk the population evolving resistance to the hostile agent. Which is why you must “finish the course”.

    Consider all the extinct species.

    If Darwinism predicts they would have evolved and survived, then Darwinism has been falsified.

    Mung, I do tend to assume that readers of my posts use some common sense. Yes, of course, some populations will go extinct, rather than adapt. The vast majority of populations do. However, if you introduce a new hostile agent to a population of bacteria, you run the risk that instead of rendering that population extinct, you will trigger the evolution of an adapted population with resistance to your hostile agent.

    Which is exactly what has happened: as Darwinian theory enabled us to predict, widespread use of antibiotics has resulted in the evolution of multiply resistant populations. Because we know which of our actions is likely to cause this, we can take some steps to minimise the risk. This is important, and it’s a direct practical application of Darwinian theory to clinical practice. Incidentally, the same also applies to the widespread use of bactericidal work-top cleaners.

    Consider sterilization, or heating things to a temperature which is lethal to life [anti biotic].

    Exactly. And a much better approach, because that way you can kill the bacteria before they even enter the patient, by a broad spectrum method that you can’t use in vivo.

    Darwinism does not and cannot predict that any species will evolve to survive in deadly conditions.

    Obviously not.

    The claim that Darwinian theory predicts that any species will evolve and survive rather than perish is rubbish, plain and simple. It is false.

    Please stop repeating it.

    Mung, I am not capable of predicting what straw man you will erect from my posts. As I said, I mostly assume that my readers will use their common sense.

    Obviously, just as I thought it was clear on that other thread that I was using “advantageous” in the sense in which it is used in population genetics (seeing as we were talking about population genetics) I took it as read that my readers would understand that “antibiotic resistance will evolve” was virtually footnoted by “unless the whole population dies”, particularly as I kept on repeating “which is why you have to ‘finish the course’”. That’s the Whole Point. If you manage to have the whole population go extinct, then it won’t adapt. duh.

    So the danger is: IF you don’t take the whole course, or IF some of the population survive anyway, THEN you will get the evolution of resistance.

    Unfortunately it has proved impossible to render our pathogenic bacteria extinct, and so, as a predictable (from Darwinian theory) result, we are now faced with resistant populations.

    Is that clear now? Because really, if it wasn’t before, you must have been skimming my posts rather than reading them for meaning.

    Darwinian theory does not predict what any “fitness landscape” is going to look like.

    Obviously not.

    Therefore it is incapable of predicting whether a species will survive or perish in the face of conditions hostile to life.

    True, O King.

    fyi – anti biotic = anti life.

    “Antibiotic” has a widely agreed specific meaning, and it should have been (indeed was) abundantly clear in which sense I was using it.

    If you picket an abortion clinic with a placard saying “antibiotic”, don’t blame me if you get some odd looks.

  35. Darwinism is the modern narrative, and the spell cast by this narrative is so powerful that it covers over a multitude of logical sins, as seen in the tales being spun about antibacterial resistance.

    First of all, the concept of resistance among strains of bacteria is not dependent on Darwin. In fact the old understanding of “antibacterial resistance” was that some strains of bacteria were more resistant to antibiotics than others. These strains do not have to “evolve.” They were there all the time but came to the fore and flourished as other bacteria were destroyed.

    No evolution occurs in this case except in sense of change in the overall character of the bacterial colony. And by the way, this was the standard explanation as recently as 20 years ago. Emergence, not evolution, is what institutions like the NIH were telling the public before the Darwinists decided to seize upon bacterial resistance as their cause célèbre.

    Now everywhere you go you hear that the resistant bacteria “evolve” according to selection pressures. First of all, no one has ever quantified in vivo the degree to which antibacterial resistance is attributable to “evolved” resistance or to emergent resistance. As far as we know, most of the observed resistance could be due to emergent strains coupled with gene transfer.

    But let’s grant that the contribution made by genetic change is significant, as claimed. First of all, these bacteria cannot be said to “evolve” in the sense that Darwin used the term. Information must be added in order for more complex forms to emerge and species to develop. That is not what is seen in bacteria, where resistance develops due to a loss of information.

    So the analogy that some try to draw between between antibacterial resistance and Darwinism is misleading at best. But the question remains—does the clinician need to have Darwin in mind in order to see bacterial resistance and devise effective strategies for minimizing it? Do doctors need Darwin to be good doctors? Is it really true that “nothing makes sense” in biology apart from Darwin’s theory?

    The answer is a simple “no.” A physician may have Darwin in mind, and the frame provided by Darwin’s theory may help him to give logical order to what he observes in his patients—but this framework is not necessary. Physicians do not need the concept of Natural Selection to recognize resistance. Nor does Natural Selection dictate the strategy they use to minimize resistance, which is simply to use restraint.

    Actually the world of medicine should be a treasure-trove for ID. We are still waiting for the day when the management at UD discovers the myriad medical journals that publish bread-and-butter research in microbiology. Guess what, Darwin’s theory virtually never finds its way into the Methods of these studies, as would be the case if Dobzhansky were actually onto something.

    That’s because the theory does not have the explanatory power to account for the miracles in engineering that are being uncovered every day.

  36. Michael Egnor, whom I believe is a professor at a college of medicine, weighs in on the ‘non-value’ of neo-Darwinian explanations for medicine:

    The difficulty with evolutionary explanations in medicine is:

    1) All of the relevant pathophysiology is provided by the proximate explanations, which are the only explanations useful for treatment.

    2) Evolutionary explanations are based on proximate explanations — scientists understand a disease, and then, based on the detailed proximate explanation for the disease, evolutionary biologists concoct speculations as to how the disease evolved. Evolutionary explanations are always dependent on proximate explanations, not the other way around.

    3) Evolutionary explanations do not provide a substantial basis for therapy. Even in situations in which evolutionary biologists claim that an evolutionary explanation has provided therapeutic insight, actual scientific confirmation of the effect of the therapy (i.e.- the proximate explanation) is needed to actually implement the theory.

    4) Evolutionary explanations by themselves are worthless to medicine. All medical treatments are based on detailed proximate explanations

    5) Even in areas of medicine in which evolutionary insight is claimed to be important (such as the development of antibiotic resistance in bacteria), the necessary expertise — microbiology, cell biology, molecular biology, molecular genetics, population biology, pharmacology, pathology, etc. — is already an integral part of medical education and research. Evolutionary biology has contributed nothing of substance in the past, except to point out that bacteria that are not killed by antibiotics are not killed by antibiotics, which is sole insight provided by ‘natural selection’ to antibiotic resistance.

    6) As evolutionary biologists readily acknowledge, there are very few evolutionary biologists in medical schools, and modern medicine has progressed rapidly and far without evolutionary speculations about disease.

    7) Evolutionary speculations about disease belong in departments of evolutionary biology, not in medical schools. Any genuine insight provided by such evolutionary speculation can be communicated to medical researchers through the normal process of communication (a brief e-mail, a paper presented at a scientific meeting, etc)

    8) The incorporation of evolutionary biology in medical school curricula is a waste of valuable resources. It is the actual proximate scientific explanations for disease that guides medical research. Speculation about biological origins already has a scientific home, and provides little help to medicine.
    http://www.evolutionnews.org/2.....47701.html

  37. 37
    Elizabeth Liddle

    Bornagain77 @ 28:

    :D

    Thanks for trying :) Seriously.

    Cheers

    Lizzie

  38. Elizabeth Liddle:

    It [Darwinian theory] predicts that either the population will go extinct or adapt…

    Which is precisely why many of us here (most of us?) consider Darwinian theory to be vacuous.

    Review time:

    YOU: Darwinian evolution offered a clear prediction, that bacterial populations would evolve resistance to an environment in which antibiotics were part of the landscape. And they do.

    ME: Except when they don’t. Which is also a “prediction” of Darwinian theory.

    YOU: What?

    YOU: It predicts that either the population will go extinct or adapt, i.e. evolve to survive in the new + antibiotic environment.

    ‘Nuff said.

  39. If you picket an abortion clinic with a placard saying “antibiotic”, don’t blame me if you get some odd looks.

    Hey. Not a bad idea! :)

    I wonder if they got FDA approval for using their antibiotics.

  40. It [Darwinian theory] predicts that either the population will go extinct or adapt…

    Allow me to belabor the point.

    If the population does not die out, it obviously adapted, and that is what Darwinian theory predicted would happen.

    If the population does die out, it obviously did not adapt, and that is what Darwinian theory predicted would happen.

    O Blessed Theory
    Thy pow’r be praised
    despite thy faults
    We remain unfazed.

  41. Elizabeth Liddle:

    I have enjoyed this thread and have a question for you (I hope I’m not too late!). And I’m not a scientist (they didn’t teach much about Darwin in my accounting courses), so please bear with me.

    In #4 and #8, you explain how bacteria evolve due to antibiotics. I think I understand your explanation, but it doesn’t seem to explain what actually happens. Allanius (#35) explains that there is no real evolution, that there were already different strains before the antibiotic was administered, which to me makes more sense.

    So… are you saying that, immediately before the antibiotic is ingested, there were no resistant bacteria, but then they somehow instantly evolved due to interaction with the antibiotic so that some would survive?? If you are NOT saying this, then how do the bacteria evolve any resistance that wasn’t there?

    If none were resistant to the antibiotic, they would all be killed, wouldn’t they? It seems that evolution, in the way you think about it, didn’t actually do anything, but rather the antibiotics just selected for a variant that was naturally — and already — there, well before the antibiotic was introduced.

    My understanding matches what I think Allanius explained, that the bacteria have been pre-programmed to produce descendants that are continually different in subtle ways for the purposes of increasing the odds of some offspring remaining after any environmental threat. And these changes are ALWAYS restricted in some way, so that no matter how many generations occur, and no matter how many variations occur, they are always the same species. (It seems to me, from what I’ve read, that the bacteria make changes in MICRO ways that never change the basic kind of bacteria, but these changes are never MACRO in a way that creates a new bacteria.)

    So, if you could, please explain for me how it is that the antibiotic causes evolution (rather than simply eliminating most varieties, but ignoring those that had already been modified before the bacteria ever saw the antibiotic).

    Thanks,

    EJR

  42. 42
    Elizabeth Liddle

    Mung:

    Allow me to belabor the point.

    If the population does not die out, it obviously adapted, and that is what Darwinian theory predicted would happen.

    If the population does die out, it obviously did not adapt, and that is what Darwinian theory predicted would happen.

    O Blessed Theory
    Thy pow’r be praised
    despite thy faults
    We remain unfazed.

    Mung, you are stuck in the rut of thinking everything is about proving Darwinism right or wrong.

    It isn’t.

    In the case of antibiotic resistance, it’s about risk minimisation.

    Because Darwinian theory says that if you assault a population with a toxin and fail to kill it, the remaining population will be biased in favour of the resistant members, and subsequent generations will be resistant to the toxin.

    For this reason, from the beginning, my mother, and others, warned that over-use of penicillin would tend to result in a population of penicillin-resistant bacteria, and that a) penicillin should not be lightly prescribed, b) where possible, the bacteria’s sensitivity to penicillin should first be confirmed and c) people should finish the course.

    This was a direct application of Darwinian theory to clinical practice.

    It does not confirm that Darwin was correct.

    But it was a correct prediction, and indeed, penicillin resistant bacteria have become a major problem, and, with the proliferation of antibiotics, multiply resistant bacteria are also a problem.

    In other words, because the best survivors of a population in a given environment are those whose progeny dominate subsequent generations, antibiotic resistance is a real problem.

    You actually don’t need Darwin to understand that, but that’s because Darwin’s principle is pretty obvious!

    In fact probably many people who think that Darwin was the silly guy who thought we all recently swung from trees, still would use common sense to arrive at Darwin’s conclusion when it comes to antibiotic resistance.

    Even Michael Egnor, and Puragu. Indeed, Puragu has explictly said he accepts microevolution. Well, Darwinian evolution is what explains microevolution.

    ergo, Darwinian evolution has practical application to many aspects of medicine.

  43. 43
    Elizabeth Liddle

    Hi EJR!

    In #4 and #8, you explain how bacteria evolve due to antibiotics. I think I understand your explanation, but it doesn’t seem to explain what actually happens. Allanius (#35) explains that there is no real evolution, that there were already different strains before the antibiotic was administered, which to me makes more sense.

    It is quite possible, indeed probable, that before the antibiotic was administered, some bacteria were already resistant, i.e. had some allele or alleles that meant that they had better-than-average resistance to penicillin. However, prior to the introduction of penicillin these alleles were approximately “neutral” in effect – i.e. they conferred no reproductive advantage, and so their prevalence in the bacterial population remained low.

    However, once the population is in an environment containing penicillin, those resistant alleles now become highly advantageous, and so their prevalence in subsequent generations (descendent populations) becomes very much higher.

    “Micro evolution” (indeed all evolution in some sense) can be described as “a change in allele frequence over time”, and this is exactly what happens when an environment changes, and alleles change in the degree to which they confer reproductive advantage.

    So allanius is correct, but that doesn’t mean that no evolution took place! By the above definition, it did.

    However, what happens next is that if penicillin continues to be used, and the surviving bacteria move to new hosts and become endemic in the human population, the danger is that that the frequency of resistant alleles in that endemic population becomes higher and higher, and with repeated penicillin treatments, or other treatments, new alleles from time to time emerge as well, and as well as the antibiotics effectively “filtering in” those alleles that already existed and happened to confer antibiotic resistance, we now have strong “selective pressure” on any new alleles that might work even better.

    This is why it is important to find out, when we meet a multiply resistant bacteria, to find out what, in its genome, is conferring the resistance, and how. That informs development of new drugs that can attack it where it is weakest.

    So… are you saying that, immediately before the antibiotic is ingested, there were no resistant bacteria, but then they somehow instantly evolved due to interaction with the antibiotic so that some would survive?? If you are NOT saying this, then how do the bacteria evolve any resistance that wasn’t there?

    Well,there are two parts to evolutionary theory: one is the creation of variance; the second is the selection of beneficial variants. I don’t think allanius, or anyone else here doubts that selection of beneficials take place. The controversy is whether any new, potentially beneficial, alleles are created by mutation alone, or whether somehow they are already either present in some members of a population, or there as “silent” alleles to be “switched on” by some means, when the environment requires it. But you’d have to ask an IDist how they think useful alleles are produced – I don’t know! I think they arise from various mutation mechanisms that occur during reproduction.

    If none were resistant to the antibiotic, they would all be killed, wouldn’t they? It seems that evolution, in the way you think about it, didn’t actually do anything, but rather the antibiotics just selected for a variant that was naturally — and already — there, well before the antibiotic was introduced.

    Yes. Probably several variants that conferred resistance to varying degrees. However, that doesn’t mean that subsequent new variants, conferring even greater resistance won’t appear, and, of course, if they do, because the environment now favours such alleles (renders them beneficial) they will tend to propagate rapidly through the population.

    My understanding matches what I think Allanius explained, that the bacteria have been pre-programmed to produce descendants that are continually different in subtle ways for the purposes of increasing the odds of some offspring remaining after any environmental threat. And these changes are ALWAYS restricted in some way, so that no matter how many generations occur, and no matter how many variations occur, they are always the same species. (It seems to me, from what I’ve read, that the bacteria make changes in MICRO ways that never change the basic kind of bacteria, but these changes are never MACRO in a way that creates a new bacteria.)

    Well, I’m not sure how this is supposed to work. You’d have to ask someone who believes it! But I do think it’s likely that mutational mechanisms themselves have evolved, so that the kinds of variants that tend to appear during replication are biased in favour of the kinds of variants that may give rise to mostly near neutral, rather than disastrous, mutations, some of which will tend to be beneficial in some circs. Those kinds of mechanisms would render populations more robust, and therefore tend to be selected at population level (populations with healthy variance-producing mechanisms will have less chance of going extinct when they meet a new hostile environment).

    So, if you could, please explain for me how it is that the antibiotic causes evolution (rather than simply eliminating most varieties, but ignoring those that had already been modified before the bacteria ever saw the antibiotic).

    Thanks,

    EJR

    Hope that helps at least in understanding the “Darwinian” position! The IDists will have to help out with the alternative :)

  44. Is Antibiotic Resistance evidence for evolution? – ‘The Fitness Test’ – video
    http://www.metacafe.com/watch/3995248

  45. 45
    Elizabeth Liddle

    ba77: your video simply confirms what I am saying – that Darwinian evolution results in bacterial resistance.

    What the video also says is that this “doesn’t go far enough” because it doesn’t account for “new species”.

    Well, I’m not, here, saying it does (though I think it does!) – I’m merely pointing out that Darwinian evolution is a good model for bacterial resistance, and directly informs clinical practice.

    Re speciation: it has, in fact, been observed, whatever Jonathan Wells claims, in that non-interbreeding descendent populations from a single ancestral population have been observed.

    However, obviously you won’t see this in bacterial populations because bacteria don’t actually interbreed. In fact, tbh, I don’t know how “species” is defined as a concept in regard to populations that only reproduce by cloning.

    And, in any case, “speciation” doesn’t mean that daughter species from a single ancestral population are a different “species” from ancestral population. It’s a mostly meaningless concept because that ancestral population no longer exists.

    However, what is probably true is that when a population speciates, resulting in two non-interbreeding population, one of those two may tend to remain more similar to the ancestral population than the other, and, theoretically at least, could interbreed with it if it could be thawed out and reanimated (you could at least try this out with sexually reproducing plants).

    However, if, for example, modern dogs end up speciating (as they almost have), it won’t make either the chihuahua lineage, or the Great Dane lineage “not dogs”. In both lineages (from the ancestral wild dog) what we would be observing (if we had the data) would be changes in allele frequency in the population over time. It’s just that you’d have to plot the frequency changes twice, once for each lineage, and you’d get two lineages of changes.

    This is why the micro-but not macro- argument is flawed. Yes, other factors affect whether a population splits or not (i.e. whether speciation occurs, or simply “vertical” evolution) but for any one lineage, the “micro” definition of evolution will apply.

  46. Elizabeth, pass the test then you will have a legitimate ‘scientific’ leg to stand on.

  47. 47
    Elizabeth Liddle

    Also, the guy with the test tube makes an error.

    He says, when he replaces the resistant bacteria in an environment with the original that he has “removed selection”. He hasn’t. He has changed the environment, so that now, the resistance allele is deleterious.

    Obviously, every time you change the environment, you will tend to get a change in allele frequency. In this experimental set up, the frequency oscillates depending on the environment.

    However, let the resistant strain evolve in an environment in which the ancestral non-resistant strain are not present, and fitness is likely to increase. This is what Lenski’s experiments showed – that given an ancestral population in a given environment, fitness will tend to increase, relative to the ancestral population.

    But you have to control the environment – if you change that too, then you will get a meaningless answer, as in this video.

  48. 48
    Elizabeth Liddle

    What “fitness test”? ba77? I see a video that makes errors.

    Also, Scott Minnich claims that resistant bacteria “never regain the fitness of the original”, even though he accepts that “compensatory mutations” occur.

    Apart from the fact that he is comparing the “fitness” of the evolved resistant strain with the “fitness” of the ancestral strain in an environment without antibiotics (which would be like comparing the “fitness” of a cow and a whale in a field, and claiming that the whale had never “regained” the fitness it lost when it lost its back legs and exchanged them for “compensatory” fins), no reference is given for this claim.

    It is possibly true – that resistant bacteria, which are hugely “successful” and therefore a major threat to people, are “less fit” than non-resistant bacteria when placed in an antibiotic-free environment, but it may not be. I don’t know. I don’t suppose anyone has tested it because it’s completely irrelevant to the problem of antibiotic resistance.

    Or, indeed,to evolutionary theory. “Adaptation” is the process by which populations become best fitted, by Darwinian mechanisms that no-one disputes, it seems (not the people in that video anyway) to the current environment. Nobody expects Darwinian theory to explain why whales are unfit when placed in a field, nor cows unfit when placed in the ocean. Both are well-fitted to their environment, which was Darwin’s entire point.

  49. Elizabeth you seem to have this figured out (ha); but I’m still kind of a ‘shaky convert’,,, do you mind evolving just a single molecular machine for me so as to ease my doubts in the almighty power of evolution???

    Astonishingly, actual motors, which far surpass man-made motors in ‘engineering parameters’, are now being found inside ‘simple cells’.

    Articles and Videos on Molecular Motors
    http://docs.google.com/Doc?doc.....#038;hl=en

    Michael Behe – Life Reeks Of Design – 2010 – video
    http://www.metacafe.com/watch/5066181

    And in spite of the fact of finding molecular motors permeating the simplest of bacterial life, there are no detailed Darwinian accounts for the evolution of even one such motor or system.

    “There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject.”
    James Shapiro – Molecular Biologist

    The following expert doesn’t even hide his very unscientific preconceived philosophical bias against intelligent design,,,

    ‘We should reject, as a matter of principle, the substitution of intelligent design for the dialogue of chance and necessity,,,

    Yet at the same time the same expert readily admits that neo-Darwinism has ZERO evidence for the chance and necessity of material processes producing any cellular system whatsoever,,,

    ,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.’
    Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205.
    *Professor Emeritus of Biochemistry, Colorado State University, USA

    Michael Behe – No Scientific Literature For Evolution of Any Irreducibly Complex Molecular Machines
    http://www.metacafe.com/watch/5302950/

    “The response I have received from repeating Behe’s claim about the evolutionary literature, which simply brings out the point being made implicitly by many others, such as Chris Dutton and so on, is that I obviously have not read the right books. There are, I am sure, evolutionists who have described how the transitions in question could have occurred.” And he continues, “When I ask in which books I can find these discussions, however, I either get no answer or else some titles that, upon examination, do not, in fact, contain the promised accounts. That such accounts exist seems to be something that is widely known, but I have yet to encounter anyone who knows where they exist.”
    David Ray Griffin – retired professor of philosophy of religion and theology

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.(that is a net ‘fitness gain’ within a ‘stressed’ environment i.e. remove the stress from the environment and the parent strain is always more ‘fit’)
    http://behe.uncommondescent.co.....evolution/

    Michael Behe talks about the preceding paper on this podcast:

    Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time – December 2010
    http://intelligentdesign.podom.....3_46-08_00

    What I find very persuasive, to the suggestion that the universe was designed with life in mind, is that physicists find many processes in a cell operate at the ‘near optimal’ capacities allowed in any physical system:

    William Bialek – Professor Of Physics – Princeton University:
    Excerpt: “A central theme in my research is an appreciation for how well things “work” in biological systems. It is, after all, some notion of functional behavior that distinguishes life from inanimate matter, and it is a challenge to quantify this functionality in a language that parallels our characterization of other physical systems. Strikingly, when we do this (and there are not so many cases where it has been done!), the performance of biological systems often approaches some limits set by basic physical principles. While it is popular to view biological mechanisms as an historical record of evolutionary and developmental compromises, these observations on functional performance point toward a very different view of life as having selected a set of near optimal mechanisms for its most crucial tasks.,,,The idea of performance near the physical limits crosses many levels of biological organization, from single molecules to cells to perception and learning in the brain,,,,”
    http://www.princeton.edu/~wbialek/wbialek.html

  50. 50
    Elizabeth Liddle

    ba77:

    Elizabeth you seem to have this figured out (ha); but I’m still kind of a ‘shaky convert’,,, do you mind evolving just a single molecular machine for me so as to ease my doubts in the almighty power of evolution???

    I’ll do my best, ba77 :)

    In the mean time, you’ll have to make do with micro-evolution, which clearly occurs, because it’s been observed, and maybe speciation, on a small scale, as well.

  51. And though I would be impressed by the ‘evolution’ of ANY molecular machine by neo-Darwinian processes, I would be particularly interested if you could falsify Behe on the flagellum by ‘evolving’ one of those:

    Bacterial Flagellum – A Sheer Wonder Of Intelligent Design – video
    http://www.metacafe.com/watch/3994630

    Bacterial Flagellum: Visualizing the Complete Machine In Situ
    Excerpt: Electron tomography of frozen-hydrated bacteria, combined with single particle averaging, has produced stunning images of the intact bacterial flagellum, revealing features of the rotor, stator and export apparatus.
    http://www.sciencedirect.com/s.....tImgPref=F

    Electron Microscope Photograph of Flagellum Hook-Basal Body
    http://www.skeptic.com/eskepti.....gure03.jpg

    Biologist Howard Berg at Harvard calls the Bacterial Flagellum

    “the most efficient machine in the universe.”

    The flagellum has steadfastly resisted all attempts to elucidate its plausible origination by Darwinian processes, much less has anyone ever actually evolved a flagellum from scratch in the laboratory;

    Stephen Meyer – T3SS Derived From Bacterial Flagellum (Successful ID Prediction) – video
    http://www.youtube.com/watch?v=3c-EAzJ8_4U

    Genetic Entropy Refutation of Nick Matzke’s TTSS (type III secretion system) to Flagellum Evolutionary Narrative:
    Excerpt: Comparative genomic analysis show that flagellar genes have been differentially lost in endosymbiotic bacteria of insects. Only proteins involved in protein export within the flagella assembly pathway (type III secretion system and the basal-body) have been kept…
    http://mbe.oxfordjournals.org/.....t/msn153v1

    Phylogenetic Analyses of the Constituents of Type III Protein Secretion Systems
    Excerpt: We suggest that the flagellar apparatus was the evolutionary precursor of Type III protein secretion systems.
    http://www.horizonpress.com/jmmb/v2/v2n2/02.pdf

    “One fact in favour of the flagellum-first view is that bacteria would have needed propulsion before they needed T3SSs, which are used to attack cells that evolved later than bacteria. Also, flagella are found in a more diverse range of bacterial species than T3SSs. ‘The most parsimonious explanation is that the T3SS arose later,” Howard Ochman – Biochemist – New Scientist (Feb 16, 2008)

    Michael Behe on Falsifying Intelligent Design – video
    http://www.youtube.com/watch?v=N8jXXJN4o_A

    Genetic analysis of coordinate flagellar and type III – Scott Minnich and Stephen Meyer
    Molecular machines display a key signature or hallmark of design, namely, irreducible complexity. In all irreducibly complex systems in which the cause of the system is known by experience or observation, intelligent design or engineering played a role the origin of the system.
    http://www.discovery.org/scrip.....php?id=389

  52. Michael Behe Hasn’t Been Refuted on the Flagellum – March 2011
    http://www.evolutionnews.org/2.....44801.html

    Bacterial Flagella: A Paradigm for Design – Scott Minnich – Video
    http://www.vimeo.com/9032112

    Flagellum – Sean D. Pitman, M.D.
    http://www.detectingdesign.com/flagellum.html

    The Bacterial Flagellum – Truly An Engineering Marvel! – December 2010
    http://www.uncommondescent.com.....ng-marvel/

  53. Dang it Elizabeth you state;

    ‘In the mean time, you’ll have to make do with micro-evolution, which clearly occurs, because it’s been observed, and maybe speciation, on a small scale, as well.’

    Man I’m really weak in my blind devotion to Darwin here Elizabeth, you see those doggone IDists have come along and said that ALL those micro-evolutionary events are occurring at a loss of functional information,,, moreover they attack my faith again by saying that all sub-speciation events are the result of reproductive isolation brought about by loss of information.,,, I relly need me a ‘miracle’ Elizabeth or I might go back to my heathen IDists ways

  54. 54
    Elizabeth Liddle

    Well, you could try checking out some of those Lenski papers, ba77, and see whether Scott Minnich is really correct when he says that when a beneficial mutation appears, it is always “at a cost” and compensatory mutations are never enough for it to reach the fitness of its ancestral population.

    I’m pretty sure you will find they are wrong, so that should keep your spirits up until I manage to evolve a bacterial flagellum for you :)

    OK, better get back to my lab….

  55. Elizabeth, if the flagellum is too hard for you, perhaps you could ‘lay hands’ on your flask and evolve me the ‘simpler’ ATP synthase so as to restore me to the fold of the Darwinian faithful:

    Evolution vs ATP Synthase – Molecular Machine – video
    http://www.metacafe.com/watch/4012706

    The ATP Synthase Enzyme – exquisite motor necessary for first life – video
    http://www.youtube.com/watch?v=W3KxU63gcF4

    ATP synthase: majestic molecular machine made by a mastermind – November 2010
    http://creation.com/atp-synthase

    Fine-Tuning Found in Life’s Rotary Engine – August 2010
    Excerpt: ATP synthases are among the most abundant and important proteins in living cells. These rotating nano-machines produce the central chemical form of cellular energy currency, ATP (adenosine triphosphate), which is used to meet the energy needs of cells. For example, human adults synthesize up to 75 kg (165 lbs.) of ATP each day under resting conditions and need a lot more to keep pace with energy needs during strenuous exercise or work. The turbine of the ATP synthase is the rotor element, called the c-ring. This ring is 63 A [Angstroms] in diameter (6.3 nm, or 6.3 millionths of a millimeter) and completes over 500 rotations per second during ATP production. 500 rotations per second amounts to, in the terminology of more familiar motors, some 30,000 RPM. Since three ATP molecules are synthesized for each rotation, one of these motors can generate just short of 100,000 ATP per minute – and your body has quadrillions of them working all your life, even in your sleep.
    http://www.creationsafaris.com.....#20100804a

    =================

  56. Elizabeth these videos are not helping either:

    Powering the Cell: Mitochondria – video
    http://www.youtube.com/watch?v=RrS2uROUjK4

    Molecular Biology Animations – Demo Reel
    http://www.metacafe.com/w/5915291/

  57. Elizabeth, your in that whole psychology thing aren’t you??? Do you think I need to be ‘deprogrammed’ so that I can be a faithful Darwinbot once again???

    1984 Apple’s Macintosh Commercial – video
    http://www.youtube.com/watch?v=OYecfV3ubP8

  58. 58
    Elizabeth Liddle

    BTW, made some enquiries about the concept of “species” with regard to bacteria. It seems that Lynn Margulis agrees with me, that “species” is not a relevant or helpful term for bacteria.

    http://www.astrobio.net/interv.....ve-species

    In that case, I’d really like to know what Jonathan Wells meant when he claimed that even though bacterial populations evolve antibiotic resistance, no new “species” have been observed.

    It seems to me that that is a fairly meaningless claim. What is important is that new strains evolve and, unfortunately flourish, in response to widespread antibiotic use.

    That doesn’t prove that Darwinian evolution can account for the whole variety of life on earth, but it a) confirms that the principle works and b) stands as an example of how Darwinian principles are relevant to clinical practice.

  59. Elizabeth, I KNOW YOU are sold on the whole antibiotic thing, but I just can’t buy it.

  60. Mung, you are stuck in the rut of thinking everything is about proving Darwinism right or wrong.

    It isn’t.

    You’re mistaken Elizabeth. Modern evolutionary theories are incoherent. As in not even wrong.

    Darwinism isn’t falsifiable. It’s basic tenet is a tautology.

    It would be a waste of my time to try to prove it’s wrong.

    If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case.

    If you want to believe, like Darwin, I cannot stop you. But it’s not on me to disprove the theory.

    You need demonstrate that Darwinian mutation/selection can actually bring about the effects attributed to it’s power.

    Good luck.

  61. Elizabeth Liddle:

    So allanius is correct, but that doesn’t mean that no evolution took place! By the above definition, it did.

    But you don’t equivocate, do you.

  62. Because Darwinian theory says that if you assault a population with a toxin and fail to kill it, the remaining population will be biased in favour of the resistant members, and subsequent generations will be resistant to the toxin.

    Again, that is not true. Darwinian theory does not predict that the members who survived did so because they were resistant.

    It could in fact be that case that they survived because they were not subjected to the toxin at all.

    That’s why you “finish the course,” as you call it.

    It makes no sense to “finish the course” if the course doesn’t kill the resistant bacteria.

  63. Elizabeth:

    Thank you again for taking the time to respond. But I was surprised at a couple of things in your response @43: You stated:

    “Micro evolution” (indeed all evolution in some sense) can be described as “a change in allele frequence over time”, and this is exactly what happens when an environment changes, and alleles change in the degree to which they confer reproductive advantage.

    Defining evolution as “a change in allele frequence over time” seems totally useless to me. Every single time there is a descendent due to sexual reproduction, this occurs, whether the change is beneficial, neutral, or harmful. So if evolution simply means that descendents will always become slightly different, that is not helpful, and that is NOT what I think most people mean when they use the term “evolution.”

    So with that definition, if my daughter has dark hair (mine’s light brown), she evolved. And since her son has light brown hair, he evolved too – although his hair is just like mine (and this is exactly what has happened in my family). And I have no clue whether hair color produces any kind of reproductive advantage (well, my son-in-law obviously liked dark hair, and I suspect my grandson will eventually find someone who likes light-brown hair, once he learns to talk and walk a bit better!). And yet with all of us evolving, we are still exactly the same species, the same kinds of living thing. So I can’t accept “allele frequency change” as a helpful definition of evolution.

    And so your statement that by using your definition, evolution occurred, does not seem helpful. It seems to me that “evolution” as used by most people would incorporate what I had mentioned @41, in that it is a change that leads to a new kind of living thing, not just one with different hair color or eye color.

    Also, my understanding about bacterial resistance is this: when there is any kind of mutation during reproduction, it is never the kind that has been seen to produce a new kind of living thing. It’s simply a new strain, (as you mentioned @58), and we don’t see bacteria developing wings or sonar or anything complex, beyond rather simple changes that make them resistant to an antibiotic.

    You mention:

    Well,there are two parts to evolutionary theory: one is the creation of variance; the second is the selection of beneficial variants. I don’t think allanius, or anyone else here doubts that selection of beneficials take place. The controversy is whether any new, potentially beneficial, alleles are created by mutation alone, or whether somehow they are already either present in some members of a population, or there as “silent” alleles to be “switched on” by some means, when the environment requires it. But you’d have to ask an IDist how they think useful alleles are produced – I don’t know! I think they arise from various mutation mechanisms that occur during reproduction.

    My understanding is that bacteria have been “pre-programmed”, if you will, to vary their descendants during reproduction such that the descendants all have slightly different abilities to adapt to changing environments. They always do that, whether in the presence of an antibiotic or not. And that makes a few of them likely to survive an antibiotic treatment, the same as some are more likely to survive with other changes in the environment. And I’ve read that when some threat such as an antibiotic is present, they can vary more quickly, but the variances are in specific areas and not throughout the entire genome. That tells me the changes are likely NOT truly random, which Darwinian evolution requires, but rather they occur due to some genetic programming already existing in their genome.

    The fact that some survive doesn’t mean much, especially since, as I’ve read, when these “super” strains combine with normal strains over a period of a few months, they revert to the normal strain. These changes never create a fundamentally new type of bacteria; they are always just a new strain of the same species.

    I’ve read Genetic Entropy by John Sanford, where he shows that beneficial mutations that might occur will usually be “shouted down” by the environmental noise, such that there is little evidence that beneficial mutations can propagate rapidly. And I’m not concerned about hair color, or the wing color of moths, or the size of beaks, which although they are changes in allele frequency, those frequencies always go up and down and fluctuate, but none of them gives a unique feature, and they have always been observed to stay within certain limits.

    So what I’m looking for but haven’t seen is concrete evidence of a real new feature that evolved that created a new kind of living thing, not just another color or strain. I’ve read lots of ID and evolution books, and I’ve read lots of evidence from the ID side showing that these types of major changes have never happened in bacterial colonies, but I haven’t seen any refutation of what the ID side claims (specifically, books by Behe: The Edge of Evolution and by Meyer: Signature in the Cell).

    So until I can see real scientific evidence showing that macro evolution can really occur, I think I have to vote with the ID camp. From my layman’s view, it seems that the “science” behind evolution is more on theoretical paper arguments than in the actual physical evidence, while on the other hand, the ID side seems to be squarely and firmly centered on the scientific evidence.

    But… I would love to see some evidence, for example, of a true beneficial mutation. And not sickle cell anemia, please. My daughter’s sister-in-law unfortunately has that disease and will succomb to it in a few more years. I have never understood how people could claim this fatal mutation as an example of how beneficial mutations are upward improvements supporting evolutionary theory, despite providing some certain benefit against malaria.

    Regards,

    EJR

  64. Elizabeth:

    One additional thought comes to mind.

    You said @ 58 that the term “species” is not a relevant or helpful term for bacteria. If that is so, then how could they have been the precursors of any species? At what point does a strain become a species? Because as I see it, if they can’t ever create a new species, evolution kinda stops at the bacteria level – correct?

    Again, thanks for your time.

    Regards,

    EJR

  65. Elizabeth Liddle:

    “Darwinian evolution offered a clear prediction/b>, that bacterial populations would evolve resistance to an environment in which antibiotics were part of the landscape.”

    Mung:
    “This is false. You’ve made a very similar claim in the past and I pointed out why it was false then as well. So why do you persist?”
    ===

    Perhaps this will put it into perspective as to the reason and motive behind such incessant ideological rantings in the face of real world observation and logic. This article back in May 2008 in New Scientist online journal addressing the same ideological motives as your opponent above. Prof Randolph Nesse is a well known advocate of so-called evolutionary applications medicine was quoted in this article and proving not only how ignorant such a worldview can be as far as deadly consequences, but the last paragraph shows what truly motivates these political agenda pimping shills.

    Randolph Nesse:
    ” . . progress is being hampered by the fact that many medics still think of the body as a machine designed by an engineer, when in fact it is a “bundle of compromises … designed to maximise reproduction, not health”.

    So how many here want a doctor with the flawed worldview of your body being nothing more than a bundle of compromises, or one who truly is interested in the science of viewing your amazing construct as designed by an engineer ???
    Now notice in the very last paragraph of this article sums up that ultimately it is NOT about the science so much as it’s about the ideology and philosophy for directing politics and worldview.

    New Scientist:
    “There is no question about the importance of applied evolution. The trouble is, if biologists themselves are only just waking up to how relevant and crucial evolution can be, what hope is there of educating the leaders and policy makers who need to understand and act upon this research? Not much, I fear.”

    So what do leaders and policy makers have to do with science ??? Oh that’s right, they don’t!

  66. Here’s that link to the article I forgot to reference above.

    http://www.newscientist.com/ar.....ad_dn13839

  67. How does a bacterium evolve resistance to an antibiotic?

    How does a population of bacteria evolve resistance to an antibiotic?

    Any room for equivocation here?

    Does Darwinism predict that either of these will happen?

    Does Darwin’s account explain why we see antibiotic resistance in bacteria?

    Does Darwinian evolution offer a clear prediction that bacterial populations will evolve resistance to an environment in which antibiotics are part of the landscape.

  68. Mung:

    “How does a bacterium evolve resistance to an antibiotic?”

    “How does a population of bacteria evolve resistance to an antibiotic?”
    ===

    This an easy one. It doesn’t evolve anything, it engineers itself using purpose and intent with the genetic informational tools it has in it’s possion. An easy way to understand what and how they do it is to read up on your own immune system and how it functions and works when the body is attacked. It re-engineers itself for defensive measures never encountered before and it keeps records of past attacks.

    EXAMPLE: People around after WWII who not only survived the war, but also the Spanish Influenza. Those survivors today if any, still contain memory cells in their immune system which were engineered way back when. Though it’s an older book, “THE BODY VICTORIOUS” [I believe written in the 1980s by Lennart Nilsson, with Jan Lindberg] beautifully illustrated just how sophisticated and engineered our immune system is.

    The cells just aren’t manufactured and sent out to search and destroy, they first get sent to the lymph system to go to school, that is to be specifically engineered with certain weaponry to deal with the specific and unique new invader of the body never encountered before. Memory cells are kept in existance over a life time for the individual who had the experience. Bacteria, though more simple than us, though still extremely complex engineer in similar ways. But by all means find, obtain and read that book.

    Mung:

    “Any room for equivocation here?”
    ===

    You bet there is. For education and entertainment value, please read Cornelius Hunter’s arguement with hardcore evolutionary diehards who won’t own up to anything, especially when they run in packs.

    http://darwins-god.blogspot.co.....st-of.html

    Enjoy!!!

  69. An easy way to understand what and how they do it is to read up on your own immune system and how it functions and works when the body is attacked.

    You mean they employ an essentially stochastic function with selection?

  70. Mung:

    “You mean they employ an essentially stochastic function with selection?”
    ====

    Hardly, get the book and READ it. Not at all difficult to understand unless worldview is diliberately allowed to stochastically get in the way and fuzzy it for you.

    *wink*

  71. I don’t need to get the book and read it. I’ve been interested in the immune system for a while. I have textbooks on immunology. It really is pretty cool.

    But it does start out as a rather stochastic process. The body doesn’t know what sort of pathogen it might encounter so it generates all sorts of “sentries” to be on the lookout.

    And if one is triggered it is favored over the others and more of it’s kind are generated. It’s like the body has a built-in GA.

  72. Mung:

    “I don’t need to get the book and read it. I’ve been interested in the immune system for a while. I have textbooks on immunology. It really is pretty cool.”
    ===

    Agreed, it is pretty kool. The only reason the book is a beautiful read is it’s use of illustrations and metaphors for helping the average person appreciate just how brilliantly complex and sophisticated the entire process actually is. Nothing random about it.

    Mung:

    “But it does start out as a rather stochastic process. The body doesn’t know what sort of pathogen it might encounter so it generates all sorts of “sentries” to be on the lookout.”
    ===

    I would say it would be stochastic or random if the the T-Cells and B-Cells just came out of the bone marrow and went off to wage war and hopefully one or two of them got lucky. However as the book pointed out, they are actually sent to a college of sorts or military academy for specialized training. Their weaponry is ultramodern. High-tech training is mandatory before they take to the field. The T cells will be involved in biological warfare. B cells will be specializing in guided missiles. They get their training for this in the technical colleges of the immune system. Again, very sophisticated and technical and hardly the makings of blind pointless unguided processes.

    Mung:

    “It’s like the body has a built-in GA.”
    ===

    Yes I believe Genetic algorithms and a host of other sophisticated componants are a work here, even other things we have yet to discover. As you state it is truly amazing.

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