Biology Evolution

Three Things Biologists Rarely Know About Biology

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I’ve talked to a number of biologists, and it seems like there are a number of important facts that are left out of a standard biological education.

The following things seem to be either skipped or glossed over in biology education. These are based on my interactions with biology majors, grad students, and even post docs. Nearly everyone either has either forgotten them (which means their professors just mentioned them in passing) or they were never covered in the first place.

    1. The pervasiveness of directed mutation. Most biologists do not realize that directed mutations even exist, much less the extent to which they exist. This is due both to a lack of knowledge about the mutational systems which are known, as well as to a lack of understanding of what it means for something to be directed. Most biologists are trained to think of mutations as being “undirected” if they aren’t 100% on-target. However, there are systems which reduce the mutational search space by well over 99%. Within the tiny space remaining, the search may be random, but it is directed because (a) it is triggered by a need of the organism, and (b) it skips a significant chunk of the genome which is not likely to carry the result.
    2. The significance in symbiosis in evolution. Most biologists are only trained to see mutations as being significant in evolution. That any change in form or interbreedability must be due to mutation. The one exception is at the beginning of Eukarya, they permit themselves to believe in endosymbiosis. However, as numerous areas of biology have shown, gaining or losing a symbiont can actually generate significant morphological change in a single generation.
    3. The importance of non-genetic inputs to the resulting morphology. Many differences in form, including heritable ones, can result from non-genetic inputs. The simplest of these is prions, where the shape of a protein affects the shape of later generated proteins. If a similar protein has a different conformation, it can alter the conformation of later proteins. This can cause phenotypic changes which are heritable, but are not in any way genetic.

In fact, the field of Ecological Developmental Biology has a number of examples of #2 and #3. Organisms can change morphologies merely due to the presence of pheromones in the environment. If those triggers persist after several generations, oftentimes the trait will the “stick” even without the environmental driver!

Anyway, I’ve found that evolution has essentially blinded numerous biologists and funneled them all into an understanding of evolution which is directly counter to how organisms are experimentally understood to change. Certainly there are many great biologists who understand these issues. However, I might go as far as to say that a majority of biologists are poorly informed on these points.

45 Replies to “Three Things Biologists Rarely Know About Biology

  1. 1
    caleb says:

    @johnnyb

    If you are going to make claims like these, you had better have references, and lots of them.

    1. I can take a guess as to what you are referring to but you make a number of misstatements along the way,

    “Most biologists are trained to think of mutations as being “undirected” if they aren’t 100% on-target. ” No they aren’t. They are taught that mutations occur without respect to the needs of the organism.

    “However, there are systems which reduce the mutational search space by well over 99%.”
    That’s a pretty good trick if it works. Are you thinking of Susan Rosenberg’s work? References?

    2. Endosymbiosis. Can you show examples of gaining or losing a symbiont? References? How many examples? If you want to claim this plays a significant role there had better be a lot.

    3. Non-genetic inputs. Prions are a pretty poor example of positive evolution. They are misfolded proteins that are toxic. And I doubt they are heritable. You pass on the tendency to develop prions but not the prions themselves. References?

    Presence or absence of pheromones can certainly trigger large scale changes, such as sex reversal in fish. But they aren’t going to be a pathway for evolution. Those are programmed responses necessary to create a new morphology, a program that is likely the product of design. How do you evolve a process to create a female fish when there is none? One of the males makes the change. How does that work? There is no reproduction until you get it right. But it’s never been done before and there are a lot of steps. That happens by evolution or by design?References?

    Maybe biologists haven’t heard of these mechanisms because they aren’t significant or heritable. Or because they aren’t as described here.

  2. 2
    cornu says:

    I think you should consider the possibility that biologists know more about these topics than you do. Take the first example

    I guess you are talking about somatic hypermutation when you are talking about “directed” mutations, but these are somatic (so irrelevant to evolution) and not directed.

  3. 3
    Bob O'H says:

    I think johnnyb’s point is that although these things are known by biologists as a whole, individual biologists don’t know them. Of course, there are a lot of things individual biologists don’t know about biology.

    The directed mutations point is something that I think is interesting in its own right, except is isn’t directed mutation, as johnnyb basically admits. I think it might be better not to resort to what looks like sophistry. Perhaps say that “evolution that looks like directed mutation is pervasive”. That way you can get to explaining some fascinating biology without looking like you have an agenda.

  4. 4
    bornagain77 says:

    As to:

    “I’ve found that evolution has essentially blinded numerous biologists and funneled them all into an understanding of evolution which is directly counter to how organisms are experimentally understood to change.”

    Otherwise known as Darwinian Cognitive Dissonance Disorder (DCDD).

    Yes folks, it is a mental disease. But there is hope:

    Cognitive Conditioning and the Distortion of Reality – Brian Miller – April 17, 2018
    Excerpt: On the bright side, I have found that the cognitive conditioning, (i.e. DCDD), can be overcome by those who have a very strong desire to know the truth. And people who leave philosophically oppressive academic institutions often find work in environments that are much more congenial to exploration. The conditioning can then wane, and their design-detection capacities and critical thinking can reengage. At that point, many describe a process where “scales seemed to fall from my eyes,” and the evidence for design in nature becomes self-evident, as does the logical incoherence of many materialist rationalizations to deny it.
    https://evolutionnews.org/2018/04/cognitive-conditioning-and-the-distortion-of-reality/

  5. 5
    News says:

    A big question is, how many biologists can even afford to know what is going on here? Consider what happened to Gunter Bechly: “Erased” paleontologist Bechly gets support from Science and Health Council

    Aren’t they safer as Aren’t I good? girls?

  6. 6
    Bob O'H says:

    ba77 – Brian Miller’s education is in physics, not psychiatry. I’m curious to know what psychiatric qualifications you have that make you feel competent to diagnose psychiatric conditions in others. Are you, for example, a member of the American Psychiatric Association?

  7. 7
    ET says:

    caleb:

    “Most biologists are trained to think of mutations as being “undirected” if they aren’t 100% on-target. ” No they aren’t.

    They are taught that all mutations are undirected- the result of chance alone.

    They are taught that mutations occur without respect to the needs of the organism.

    There are mutations which occur that do benefit the organism.

    If you want to read about the evidence for directed mutations read “Evolution: A View from the 21st Century” by James Shapiro

  8. 8
    bornagain77 says:

    Well Bob, since to experts you appealed to experts we will go:

    The following found that ALL people, especially including atheists, (i.e. people who have voiced a predisposition to believe that they are not really people at all but are really neuronal illusions 🙂 ), have a tendency to believe in God and also have an innate, deep-seated, ability to ‘detect design’:

    Predisposed to believe – July 2011
    Excerpt: Science Daily reports “A three-year international research project, directed by two academics at the University of Oxford, finds that humans have natural tendencies to believe in gods and an afterlife.” As my friend added, “This research was quite costly – they could have saved money by reading the Bible!”
    http://www.uncommondescent.com.....o-believe/

    Design Thinking Is Hardwired in the Human Brain. How Come? – October 17, 2012
    Excerpt: “Even Professional Scientists Are Compelled to See Purpose in Nature, Psychologists Find.” The article describes a test by Boston University’s psychology department, in which researchers found that “despite years of scientific training, even professional chemists, geologists, and physicists from major universities such as Harvard, MIT, and Yale cannot escape a deep-seated belief that natural phenomena exist for a purpose” ,,,
    Most interesting, though, are the questions begged by this research. One is whether it is even possible to purge teleology from explanation.
    http://www.evolutionnews.org/2.....65381.html

    The following video and studies found that the belief in God and/or Design is a ‘knee jerk’ reaction even for atheists. Moreover, in the video it is shown that atheists have to mentally work suppressing their innate design inference!

    Is Atheism a Delusion?
    https://www.youtube.com/watch?v=_Ii-bsrHB0o

    Richard Dawkins take heed: Even atheists instinctively believe in a creator says study – Mary Papenfuss – June 12, 2015
    Excerpt: Three studies at Boston University found that even among atheists, the “knee jerk” reaction to natural phenomenon is the belief that they’re purposefully designed by some intelligence, according to a report on the research in Cognition entitled the “Divided Mind of a disbeliever.”
    The findings “suggest that there is a deeply rooted natural tendency to view nature as designed,” writes a research team led by Elisa Järnefelt of Newman University. They also provide evidence that, in the researchers’ words, “religious non-belief is cognitively effortful.”
    Researchers attempted to plug into the automatic or “default” human brain by showing subjects images of natural landscapes and things made by human beings, then requiring lightning-fast responses to the question on whether “any being purposefully made the thing in the picture,” notes Pacific-Standard.
    “Religious participants’ baseline tendency to endorse nature as purposefully created was higher” than that of atheists, the study found. But non-religious participants “increasingly defaulted to understanding natural phenomena as purposefully made” when “they did not have time to censor their thinking,” wrote the researchers.
    The results suggest that “the tendency to construe both living and non-living nature as intentionally made derives from automatic cognitive processes, not just practised explicit beliefs,” the report concluded.
    The results were similar even among subjects from Finland, where atheism is not a controversial issue as it can be in the US.
    “Design-based intuitions run deep,” the researchers conclude, “persisting even in those with no explicit religious commitment and, indeed, even among those with an active aversion to them.”
    http://www.ibtimes.co.uk/richa.....dy-1505712

    Scientists discover that atheists might not exist, and that’s not a joke By Nury Vittachi | July 6th 2014
    Excerpt: “atheism is psychologically impossible because of the way humans think,” says Graham Lawton, an avowed atheist himself, writing in the New Scientist. “They point to studies showing, for example, that even people who claim to be committed atheists tacitly hold religious beliefs, such as the existence of an immortal soul.”
    This shouldn’t come as a surprise, since we are born believers, not atheists, scientists say.,,,
    This feeling of having an awareness of another consciousness might simply be the way our natural operating system works.,,,
    Of course these findings do not prove that it is impossible to stop believing in God. What they do indicate, quite powerfully, is that we may be fooling ourselves if we think that we are making the key decisions about what we believe, and if we think we know how deeply our views pervade our consciousnesses.,,,
    http://www.science20.com/write.....oke-139982

    It is not that Atheists do not see Design in nature, it is that they, for whatever severely misguided reason, live in denial of the Design that they themselves see.

    “Biologists must constantly keep in mind that what they see was not designed, but rather evolved.”
    – Francis Crick, in What Mad Pursuit, p. 138 (1990)

    I hold the preceding studies (and quote) to be confirming evidence for Romans 1:19-20

    Romans 1:19-20
    For what can be known about God is plain to them, because God has shown it to them. For his invisible attributes, namely, his eternal power and divine nature, have been clearly perceived, ever since the creation of the world, in the things that have been made. So they are without excuse.

    Of further note: The following studies found that this ‘knee jerk’ instinct to believe in God and/or Design is with us from childhood:

    Children are born believers in God, academic claims – 24 Nov 2008
    Excerpt: “Dr Justin Barrett, a senior researcher at the University of Oxford’s Centre for Anthropology and Mind, claims that young people have a predisposition to believe in a supreme being because they assume that everything in the world was created with a purpose.”
    http://www.telegraph.co.uk/new.....laims.html

    As to the fact that the Atheist’s suffer mentally and physically as a result of suppressing their natural belief in God, I cite this book from Professor Andrew Sims former President of the Royal College of Psychiatrists

    “I maintain that whatever else faith may be, it cannot be a delusion.
    The advantageous effect of religious belief and spirituality on mental and physical health is one of the best-kept secrets in psychiatry and medicine generally. If the findings of the huge volume of research on this topic had gone in the opposite direction and it had been found that religion damages your mental health, it would have been front-page news in every newspaper in the land.”
    – Professor Andrew Sims former President of the Royal College of Psychiatrists – Is Faith Delusion?: Why religion is good for your health – preface
    https://books.google.com/books?id=PREdCgAAQBAJ&pg=PR11#v=onepage&q&f=false
    “In the majority of studies, religious involvement is correlated with well-being, happiness and life satisfaction; hope and optimism; purpose and meaning in life; higher self-esteem; better adaptation to bereavement; greater social support and less loneliness; lower rates of depression and faster recovery from depression; lower rates of suicide and fewer positive attitudes towards suicide; less anxiety; less psychosis and fewer psychotic tendencies; lower rates of alcohol and drug use and abuse; less delinquency and criminal activity; greater marital stability and satisfaction… We concluded that for the vast majority of people the apparent benefits of devout belief and practice probably outweigh the risks.”
    – Professor Andrew Sims former President of the Royal College of Psychiatrists – Is Faith Delusion?: Why religion is good for your health – page 100
    https://books.google.com/books?id=PREdCgAAQBAJ&pg=PA100#v=onepage&q&f=false

    And the detrimental physical effects on the health of Atheists is found to b rather pronounced in the following study.

    Can attending church really help you live longer? This study says yes – June 1, 2017
    Excerpt: Specifically, the study says those middle-aged adults who go to church, synagogues, mosques or other houses of worship reduce their mortality risk by 55%. The Plos One journal published the “Church Attendance, Allostatic Load and Mortality in Middle Aged Adults” study May 16.
    “For those who did not attend church at all, they were twice as likely to die prematurely than those who did who attended church at some point over the last year,” Bruce said.
    https://www.usatoday.com/story/news/nation-now/2017/06/02/can-attending-church-really-help-you-live-longer-study-says-yes/364375001/

    Verse:

    Romans 1:28
    Furthermore, just as they did not think it worthwhile to retain the knowledge of God, so God gave them over to a depraved mind, so that they do what ought not to be done.

  9. 9
    johnnyb says:

    I don’t have time to respond in detail at the moment, but thought I would point to a few resources:

    (1) I did a video many years ago summarizing some really interesting new areas in mutation studies:

    https://www.youtube.com/watch?v=YJwWhhpua_o&list=PLED30A9B8304C8C21

    (2) You might also check out the series I did for UD many years ago on directed mutation:

    Responding to Merlin

    (3) On symbiosis, check out this evolution of a cecal valve due to a new novel symbiotic association:

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2290806/

    To see the blindness of biologists to the effects of symbiosis, check out this quote by Lynn Margulis from her book Symbiotic Planet:

    I once asked the eloquent and personable paleontologist Niles Eldredge whether he knew of any case in which the formation of a new species had been documented. I told him I’d be satisfied if his example were drawn from the laboratory, from the field, or from observations from the fossil record. He could muster only one good example. Theodosius Dobzhansky’s experiments with Drosophila, the fruit fly. In this fascinating experiment, populations of fruit flies, bred at progressively hotter temperatures, became genetically separated. After two years or so the hot-bred ones bould no longer produce fertile offspring with their cold-breeding brethren. “But,” Eldredge quickly added, “that turned out to have something to do with a parasite!” Indeed, it was later discovered that the hot-breeding flies lacked an intracellular symbiotic bacterium found in the cold breeders. Eldredge dismissed this case as an observation of speciation because it entailed a microbial symbiosis! He had been taught, as we all have, that microbes are germs, and when you have germs, you have a disease, not a new species. And he had been taught that evolution through natural selection occurs by the gradual accumulation, over eons, of single gene mutations…

    (4) As for the importance of non-genetic inputs to morphology, what I really had in mind was Jonathan Wells’ work, but I didn’t then (and don’t now) have the time to look it up. If someone wants to link to it I would appreciate it. I don’t even think it originated with Wells, but he has made it more prominent.

  10. 10
    groovamos says:

    This has been publicized in the popular press since 1986 or before, when I read about it. This type of intentional cover up in the textbooks should be a major scandal in any field of study; for some reason biology is tolerant of this type of thing. Here is a piece from 1990: https://www.newscientist.com/article/mg12717342-900-science-can-bacteria-direct-their-own-evolution/

  11. 11
    ET says:

    Bob:

    Brian Miller’s education is in physics, not psychiatry.

    And? Does that mean that unlike psychiatrists and psychologists he can actually back up his claims?

    Or do you actually think that being a psychiatrist means something?

  12. 12
    Bob O'H says:

    ba77 @ 8 – OK, so I guess that means that you aren’t a psychiatrist, and can’t cite any psychiatrists to beck up a diagnosis of mental illness.

    ET @ 11 – ba77 was making a diagnosis of mental illness. Being a psychiatrist means that at least one has experience in dealing with mental health issues.

  13. 13
    ET says:

    Bob:

    Being a psychiatrist means that at least one has experience in dealing with mental health issues.

    The same can be said about being a parent. 😎

  14. 14
    bornagain77 says:

    HUH??? Cite Professor Andrew Sims former President of the Royal College of Psychiatrists about the detrimental effects of atheism on mental and physical health and Bob (and weave) responds with,,, “I guess that means that you aren’t a psychiatrist, and can’t cite any psychiatrists to beck up a diagnosis of mental illness.”,,,

    DUH!!!

    I guess I could cite Bob’s response itself as confirming evidence that atheists suffer acutely from Darwinian Cognitive Dissonance Disorder (DCDD). 🙂

    But anyways here are Prof. Sims credentials:

    Is Faith Delusion?: Why Religion is Good for Your Health
    About the author (2009)
    For more than twenty years, Andrew Sims was Professor of Psychiatry in the University of Leeds. He was consecutively Dean (1987-1990), President (1990-93) and the first Director of Continuing Professional Development (1993-97) of the Royal College of Psychiatrists. He edited Advances in Psychiatric Treatment from its inception in 1993 until 2003, and was founder editor of Developing Mental Health (2002-5). He has chaired the Spirituality and Psychiatry Special Interest Group of the Royal College of Psychiatrists and has also served on the General Medical Council. The author of 12 books and over 200 papers, he has published and spoken widely on the interface between religious faith and mental illness.
    https://books.google.com/books/about/Is_Faith_Delusion.html?id=jdPUAwAAQBAJ

  15. 15
    caleb says:

    @johnnyb and others
    If you want to be taken seriously you need to provide real references to research papers, or books by biologists like Shapiro. (Did he claim that the search space is reduced by 99%? Where did that come from?) Quotes from your own youtube videos don’t cut it. (I will take a look though.)

    Two examples of symbiotic change are not overwhelming. And I still need a reference. The Drosophila one I already know about. The Drosophila symbiont in question is Wolbachia. It has coopted an essential process in germ cells–it’s more like a parasitic disease than symbiosis in most cases.

    The reason for the sterility is because Wolbachia causes incompatibility between infected males and non-infected males, and other things as well. Read Wikipedia at the very least, for heavens sake, before claiming speciation. https://en.wikipedia.org/wiki/Wolbachia

    My goal here is not to diss you. It is to raise the level of discussion. Wild claims need clear evidence. If you are going to say that you have knowledge of biology that other biologists lack, you had better be able to substantiate it by references to the primary literature or quotes from books.

    And my comments are aimed not just at you but at many other posters. Take it as friendly criticism from a biologist. Raise your game.

  16. 16
    Mung says:

    caleb:

    Wild claims need clear evidence.

    He didn’t make any wild claims.

    caleb:

    If you are going to say that you have knowledge of biology that other biologists lack, you had better be able to substantiate it by references to the primary literature or quotes from books.

    He didn’t say he had knowledge of biology that other biologists lack. He’s not even a biologist afiak.

  17. 17
    groovamos says:

    I’m curious to know what psychiatric qualifications you have that make you feel competent to diagnose psychiatric conditions in others. Are you, for example, a member of the American Psychiatric Association?

    Now there’s professional field rife with long term political scandal. Most members of said organization are philosophical materialists who believe psychiatric conditions in total are the signs and symptoms of organic brain disease. Without ever having any proof and without ever having found a cure for a single category. A group which for decades included homosexuality in its diagnostic manual, and miraculously found a political cure for that organic disease in 1974.

  18. 18
    bornagain77 says:

    too funny,,, if just more citations are provided then Darwinists might start to take ID more seriously! 🙂

    The problem is not that there is not already abundant evidence against Darwinian claims. The problem is that Darwinian evolution is basically, especially when compared to other fields of science, an unfalsifiable pseudoscience that is impervious to empirical falsification.

    Darwinian evolution is a pseudoscience (Popper and Lakatos) – March 2018
    https://uncommondescent.com/intelligent-design/coursera-vid-by-darwinism-is-wrong-prof-banned-from-youtube/#comment-655046

    Moreover, the falsification criteria that were set forth by Charles Darwin himself have all been met by Michael Behe, by Douglas Axe, by Stephen Meyer, and by Lee Spetner. Yet, despite each of Darwin’s own falsification criteria being met, Darwinists STILL refuse to accept empirical falsification of their theory (which is still yet more proof that we are dealing with a pseudoscience instead of a real science.)
    https://uncommondescent.com/intelligent-design/ohia-only-human-intelligence-allowed/#comment-655865

    Since falsifiability/testability is considered the gold standard by which to judge whether a theory is scientific or not, I want to delve a little more into falsifiability/testability. (and apply it to the basic precepts of the reductive materialism that undergirds Darwinian thought) – April 2018
    https://uncommondescent.com/intelligent-design/ohia-only-human-intelligence-allowed/#comment-655886

    Moreover, although the Darwinist firmly believes he is on the terra firma of science, the fact of the matter is that Darwinists are adrift in an ocean of fantasy and imagination with no discernible anchor for reality to grab on to:

    Basically the atheist claims he is merely a ‘neuronal illusion’ (Coyne, Dennett), who has the illusion of free will (Harris), who has illusory perceptions of reality (Hoffman), who, since he has no real time empirical evidence substantiating his grandiose claims for Darwinian evolution, must make up illusory “just so stories” with the illusory, and impotent, ‘designer substitute’ of natural selection (Behe, Gould, Sternberg), so as to ‘explain away’ the appearance (i.e. illusion) of design (Crick, Dawkins), and who must make up illusory meanings and purposes for his life since the reality of the nihilism inherent in his atheistic worldview is too much for him to bear, and who must also hold morality to be subjective and illusory since he has rejected God.
    Bottom line, nothing is real in the atheist’s worldview, least of all, morality, meaning and purposes for life.
    https://uncommondescent.com/intelligent-design/the-ubiquitin-system-functional-complexity-and-semiosis-joined-together/#comment-655355

    It would be hard to fathom a worldview more antagonistic to modern science than Atheistic Materialism has turned out to be.

    Verses

    2 Corinthians 10:5
    Casting down imaginations, and every high thing that exalteth itself against the knowledge of God, and bringing into captivity every thought to the obedience of Christ;

    Matthew 7:24-27
    “Everyone then who hears these words of mine and does them will be like a wise man who built his house on the rock. And the rain fell, and the floods came, and the winds blew and beat on that house, but it did not fall, because it had been founded on the rock. And everyone who hears these words of mine and does not do them will be like a foolish man who built his house on the sand. And the rain fell, and the floods came, and the winds blew and beat against that house, and it fell, and great was the fall of it.”

  19. 19
    Nonlin.org says:

    ET@7

    Can you summarize the evidence for: “There are mutations which occur that do benefit the organism.” if any?

    References are fine for support, but should not replace a strong argument.

    bornagain77,

    Maybe I’m not the first to ask… How do you manage to write so much and with so many links? Thanks.

  20. 20
    ET says:

    Nonlin-

    The mutations that confer an advantage for bacteria which are being subjected to antibiotics, come to mind.

  21. 21
    bornagain77 says:

    Nonlin.org

    ‘Maybe I’m not the first to ask… How do you manage to write so much and with so many links? Thanks”

    I’ve kept semi-organized notes for the past 10 years or so.

  22. 22
    bornagain77 says:

    ET, I’m pretty sure that you are aware of the caveat that Dr. Behe and others have pointed out: “Break or blunt any functional coded element whose loss would yield a net fitness gain.”

    “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.
    http://behe.uncommondescent.co.....evolution/

    List Of Degraded Molecular Abilities Of Antibiotic Resistant Bacteria:
    Table 1 excerpt:
    Actinonin – Loss of enzyme activity
    Ampicillin – SOS response halting cell division
    Azithromycin – Loss of a regulatory protein
    Chloramphenicol – Reduced formation of a porin or a regulatory protein
    Ciprofloxacin – Loss of a porin or loss of a regulatory protein
    Erythromycin – Reduced affinity to 23S rRNA or loss of a regulatory protein
    Fluoroquinolones – Loss of affinity to gyrase
    Imioenem – Reduced formation of a porin
    Kanamycin – Reduced formation of a transport protein
    Nalidixic Acid – Loss or inactivation of a regulatory protein
    Rifampin – Loss of affinity to RNA polymerase
    Streptomycin – Reduced affinity to 16S rRNA or reduction of transport activity
    Tetracycline – Reduced formation of a porin or a regulatory protein
    Zittermicin A – Loss of proton motive force
    http://www.trueorigin.org/bacteria01.asp

    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

    Helping an Internet Debater Defend Intelligent Design – Casey Luskin – May 3, 2014
    Excerpt: antibiotic resistance entails very small-scale degrees of biological change.,,,
    antibiotic resistant bacteria tend to “revert” to their prior forms after the antibacterial drug is removed. This is due to a “fitness cost,” which suggests that mutations that allow antibiotic resistance are breaking down the normal, efficient operations of a bacterial cell, and are less “advantageous.
    http://www.evolutionnews.org/2.....85171.html

    Is Antibiotic Resistance evidence for evolution? – ‘The Fitness Test’ – video
    https://www.youtube.com/watch?v=rYaU4moNEBU

    A Tale of Two Falsifications of Evolution – September 2011
    Excerpt: “Scientists were surprised at how fast bacteria developed resistance to the miracle antibiotic drugs when they were developed less than a century ago. Now scientists at McMaster University have found that resistance has been around for at least 30,000 years.”
    http://crev.info/content/11090....._evolution

    (Ancient) Cave bacteria resistant to antibiotics – April 2012
    Excerpt: Antibiotic-resistant bacteria cut off from the outside world for more than four million years have been found in a deep cave. The discovery is surprising because drug resistance is widely believed to be the result of too much treatment.,,, “Our study shows that antibiotic resistance is hard-wired into bacteria. It could be billions of years old, but we have only been trying to understand it for the last 70 years,” said Dr Gerry Wright, from McMaster University in Canada, who has analysed the microbes.
    http://www.scotsman.com/news/h.....1-2229183#

    Antibiotic resistance genes are essentially everywhere – May 8, 2014
    Excerpt: The largest metagenomic search for antibiotic resistance genes in the DNA sequences of microbial communities from around the globe has found that bacteria carrying those vexing genes turn up everywhere in nature that scientists look for them,,
    http://www.sciencedaily.com/re.....121347.htm

  23. 23
    Nonlin.org says:

    ET@20

    “The mutations that confer an advantage for bacteria which are being subjected to antibiotics, come to mind.”

    But those mutations disappear from the population when the stimulus is removed. They are trade-off, not beneficial mutations.

    Anything else?

  24. 24
    ET says:

    What? Those mutations definitely benefit the organisms that have them when antibiotics are present. That was my claim:

    There are mutations which occur that do benefit the organism.

  25. 25
    ET says:

    Sickle-cell trait is a benefit for the humans who have it and live in malaria zones.

  26. 26
    ET says:

    Yes, bornagain77, I am aware that “beneficial” can mean “loss of function/ loss of specificity”.

    What is beneficial is all relative. And that the fittest bacteria is still a bacteria. The fittest clown fish is still a clown fish. The fittest of any population is still the same species as that population. There isn’t any known mechanism capable of going beyond that.

  27. 27
    Nonlin.org says:

    ET,

    What? Those mutations definitely benefit the organisms that have them when antibiotics are present. That was my claim:

    There are mutations which occur that do benefit the organism.

    Would you give up something beneficial? Yet the bacteria give up AB-resistance after the stimulus is removed. Same goes for Sickle-cell trait – these are clearly trade-offs that most modern carriers would gladly give up.

    Definitely not the Darwinist fairy tale of “beneficial mutations that spread throughout the population resulting in the transmutation of species”. Get it?

    Also, there’s no such thing as “fitness” or “natural selection” for that matter: http://nonlin.org/natural-selection/.

  28. 28
    Allan Keith says:

    Nonlin,

    Can you summarize the evidence for: “There are mutations which occur that do benefit the organism.” if any?

    References are fine for support, but should not replace a strong argument.

    Apolipoprotein AI-Milano

    LRP5

  29. 29
    jdk says:

    Off topic, but maybe of interest: https://blogs.scientificamerican.com/observations/on-darwinism/

    I don’t have any place to post new material, so I just posted this here. Sorry.

  30. 30
    ET says:

    Nonlin- Stop moving the goalposts.

    Thank you

  31. 31
    ET says:

    Yes, Jack, it is of interest but not in the way that you think. There is a huge difference between mere evolution and Darwinism (not an insult by the way). Darwinism is evolution by means of blind and mindless processes.

    Dr Behe made it clear in his ignored testimony tat there is a difference and that ID only argues against evolution by means of blind and mindless processes 9which is an untestable position).

    It seems the norm that evos equivocate and then play the victim. Pathetic

  32. 32
    rna says:

    bornagain #22

    your list is a bit one-sided.

    ampicillin resistance: a specialized enzyme called b-lactamase inactivating ampicillin

    kanamycin/neomycin: a specialized phosphotransferase enzyme that chemically modifies kanamycin and neomycin so they become ineffective

    tetracyclin: specialized ribosome binding proteins such as TetO that actively remove tetracycline from the ribosome

    chloramphenicol: a specialized enzyme that transfers an acetyl group to chloramphenicol thereby inactivating it


    in many other cases specialized enzymes modify ribosomal rnas by adding methyl groups

    So one wonders why Behe so exclusively focused on those mechanisms where he did not need to mention that they are carried out by specialized proteins that have an often exclusive role in actively conferring antibiotic resistance. I am conviced that he knows them because they are often used as genetic markers in genetic engineering experiments.

  33. 33
    bornagain77 says:

    rna, You have to get into the weeds for the specifics with Dr. Behe on that one.,,, He had three classifications. Loss of Function, Modification of Function and Gain of Function.

    Myself, glancing over your list, and since antibiotic resistance is now shown to be ancient, I would safely assume all those examples to be classified as ‘modification of (preexisting) function’.

    (Ancient) Cave bacteria resistant to antibiotics – April 2012
    Excerpt: Antibiotic-resistant bacteria cut off from the outside world for more than four million years have been found in a deep cave. The discovery is surprising because drug resistance is widely believed to be the result of too much treatment.,,, “Our study shows that antibiotic resistance is hard-wired into bacteria. It could be billions of years old, but we have only been trying to understand it for the last 70 years,” said Dr Gerry Wright, from McMaster University in Canada, who has analysed the microbes.
    http://www.scotsman.com/news/h.....1-2229183#

    Antibiotic resistance genes are essentially everywhere – May 8, 2014
    Excerpt: The largest metagenomic search for antibiotic resistance genes in the DNA sequences of microbial communities from around the globe has found that bacteria carrying those vexing genes turn up everywhere in nature that scientists look for them,,
    http://www.sciencedaily.com/re.....121347.htm

    The main point being, Darwinists originally thought they had stunning proof for evolution in action with antibiotic resistant bacteria. And indeed Darwinists taught it as supposedly undeniable proof for Darwinian evolution for decades to gullible students. But the fact of the matter is that ‘antibiotic resistance is hard-wired into bacteria’, and Darwinists were found to be falsely using an evidence that actually points to the elegant Design of bacteria as a pseudo-proof for their pseudoscientific theory.

    As Dr Wells pointed out in his book “ICONS of Evolution”, and in his subsequent book “Zombie Science”, this tendency of Darwinists to use false evidence for their theory is the norm rather than the exception.

  34. 34
    Nonlin.org says:

    ET@30

    Moving the goalposts? It’s all linked and you brought up “fittest” @26.

    Allan Keith @28

    That’s ET’s quote. Ask him.

  35. 35
    ET says:

    No, it isn’t all linked. There are mutations tat benefit the organism. Period.

    Allan Keith brought up another beneficial mutation in 28. Look it up

  36. 36
    Allan Keith says:

    Nonlin,

    That’s ET’s quote. Ask him.

    I know. I was responding to your subsequent request of him. I seldom agree with ET, but in this case he is correct.

  37. 37
    es58 says:

    Ba77@21 what format do you store your notes in spreadsheets onenote that you can do easily find and retrieve them , database?

  38. 38
    Bob O'H says:

    HUH??? Cite Professor Andrew Sims former President of the Royal College of Psychiatrists about the detrimental effects of atheism on mental and physical health and Bob (and weave) responds with,,, “I guess that means that you aren’t a psychiatrist, and can’t cite any psychiatrists to beck up a diagnosis of mental illness.”,,,

    DUH!!!

    I was specifically asking about this comment by you @4:

    Otherwise known as Darwinian Cognitive Dissonance Disorder (DCDD).

    Yes folks, it is a mental disease.

    Sims doesn’t say he’s describing a mental disease, still less a Cognitive Dissonance Disorder. He is also not talking about Darwinism.

  39. 39
    bornagain77 says:

    Well Bob (and weave), having to convince a person, who holds a worldview that tells him that he might not actually exist as a real person, but may very well be be a neuronal illusion, that his worldview leads to cognitive dissonance is a bit like trying to convince someone who is under the belief he is Napoleon, that he is not the Napoleon, 🙂

    But your delusional thinking is particularly acute, because you are in double denial. You are in denial of the denial inherent in your atheistic materialism.

    As touched upon here

    Right here on the pages of UD, Bob (and weave) O’Hara and Allan Keith have repeatedly strenuously objected to being called ‘neuronal illusions’, and claimed that, (despite the fact they were shown that many leading atheists themselves claim to be illusions),
    https://uncommondescent.com/intelligent-design/progressives-eating-their-own/#comment-656813

  40. 40
    bornagain77 says:

    es58, I use google doc. and Libre Office.

  41. 41
    Nonlin.org says:

    ET@35
    Allan Keith@28 and 36

    As seen, antibiotic resistance fails as does sickle cell. You must acknowledge!

    Apolipoprotein AI-Milano and LRP5 are at best insufficiently studied, but the fact they can only be found in small populations goes to show they are not universally beneficial and in fact are trade-offs like everything else.

    Apo-A1 promisses have fizzled: http://blogs.sciencemag.org/pi.....-a1-milano

    Wikipedia: “Mutations in LRP5 cause polycystic liver disease”

    You both must acknowledge you have nothing. And do your research before replying with more nonsense.

  42. 42
    ET says:

    As seen, antibiotic resistance fails as does sickle cell

    Fails at what?

  43. 43
    Allan Keith says:

    Nonlin,

    Apolipoprotein AI-Milano and LRP5 are at best insufficiently studied, but the fact they can only be found in small populations goes to show they are not universally beneficial and in fact are trade-offs like everything else.

    They have to start somewhere. That is how evolution works.

  44. 44
    ET says:

    Allan Keith:

    That is how evolution works.

    Except there isn’t any evidence that evolution works the way you need it to.

  45. 45
    Nonlin.org says:

    ET & AK

    Antibiotic resistance and sickle cell are trade-off mutations hence fail as examples of beneficial mutation. The other two fail as well as shown and you’re left with no such thing as “beneficial mutation”. Did you conveniently forget what the argument was?!?

    What’s the point of continuing the discussion if you won’t admit clear evidence? Typical Darwinist nonsense.

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