Darwinism horizontal gene transfer Intelligent Design science education

Horizontal gene transfer: Cholera bacterium steals 150 genes at once

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From ScienceDaily:

In 2015, EPFL researchers led by Melanie Blokesch published a seminal paper in Science showing that the bacterium responsible for cholera, Vibrio cholerae, uses a spring-loaded spear to literally stab neighboring bacteria and steal their DNA. They identified the spear mechanism to be the so-called “type VI secretion system” or T6SS, also used for interbacterial competition by many other bacteria.

V. cholerae uses its T6SS to compete with other bacteria in its aquatic environment and acquire new genetic material, which the pathogen absorbs and exchanges against some parts of its own genome. This mode of “horizontal gene transfer” leads to rapid evolution and pathogen emergence. The pathogen V. cholerae has caused seven major cholera pandemics since 1817 and, according to current WHO data, still kills more than 100,000 people each year and infects up to 4 million others, mostly in poor or underdeveloped countries.

Now, Blokesch’s group has discovered the extent of DNA that V. cholerae can steal in a single attack: more than 150,000 nucleic acid base pairs, or roughly 150 genes in one go (the cholera bacterium carries around 4,000 genes in total). The researchers calculated this number by sequencing the entire genome of almost 400 V. cholerae strains before and after stealing DNA from their neighboring bacteria…

The authors conclude that the environmental “lifestyle” of V. cholerae enables exchange of genetic material with enough coding capacity that it can significantly accelerate the evolution of the bacterium.

“This finding is very relevant in the context of bacterial evolution,” says Blokesch. “It suggests that environmental bacteria might share a common gene pool, which could render their genomes highly flexible and the microbes prone to quick adaption.” Paper. (open access) – Noémie Matthey, Sandrine Stutzmann, Candice Stoudmann, Nicolas Guex, Christian Iseli, Melanie Blokesch. Neighbor predation linked to natural competence fosters the transfer of large genomic regions in Vibrio cholerae. eLife, 2019; 8 DOI: 10.7554/eLife.48212 More.

Relevant in more ways than one. Remember that recent Atlantic article where the writer was grousing that her school didn’t teach “evolution” (Darwinism)?:

[Glenn] Branch [of NCSE, the Darwin-in-the-schools lobby] says lacking a knowledge of human evolution might make it harder for, say, doctors to understand superbugs, or for farmers to understand the nuances of agriculture. I’m a little skeptical of that argument. There are great doctors in Texas, and certainly plenty of great farmers too. The internet wasn’t as ubiquitous when I was in high school, but it was still possible to read and explore on one’s own. Today, that’s even easier.

Olga Khazan, “I Was Never Taught Where Humans Came From” at The Atlantic

She’s right to be skeptical and it’s even worse than she thinks: Dangerous bacteria like cholera seem to use methods much faster than Darwinism to do their stuff. But how many “evolution” lobbies besiege school boards to teach horizontal gene transfer? Is that because they can’t use it the way they can use Darwinism, to front the idea that humans are just animals? Nah. Must be something else…


See also: A cry from grievance culture: She never learned Darwinism in school. If Darwinists had been in charge of Khazan’s education, she would mainly have a bunch of stuff to unlearn.

and

Horizontal gene transfer: Sorry, Darwin, it’s not your evolution any more

29 Replies to “Horizontal gene transfer: Cholera bacterium steals 150 genes at once

  1. 1
    hazel says:

    I’m curious: why is horizontal gene transfer not part of “Darwinism” (assuming by that you just mean evolution.)?

  2. 2
    ET says:

    No, hazel, your assumption is unwarranted especially given the last sentence. The issue would be does it happen by chance or is it an intelligently designed mechanism for rapid adaptation?

  3. 3
    hazel says:

    I’m not interested in that question, ET. My question is isn’t horizontal gene transfer a widely known and accepted way by which genomes change?

  4. 4
    Ed George says:

    Hazel

    My question is isn’t horizontal gene transfer a widely known and accepted way by which genomes change?

    It has certainly been known about and researched for a long time. In and of itself it is perfectly consistent with Darwinian evolution.

  5. 5
    anthropic says:

    Sure it’s perfectly consistent with Darwinian evolution. Everything is, once the theory has been adjusted.

  6. 6
    ET says:

    hazel:

    My question is isn’t horizontal gene transfer a widely known and accepted way by which genomes change?

    I don’t care about that question, hazel. And neither does News.

  7. 7
    ET says:

    Ed George:

    In and of itself it is perfectly consistent with Darwinian evolution.

    In what way? Darwinian evolution did NOT predict it. Darwinian evolution can’t even account for it.

  8. 8
    Latemarch says:

    Hazel@3,

    My question is isn’t horizontal gene transfer a widely known and accepted way by which genomes change?

    Sure. So answer me this.
    Why, after millions of generations of hot swapping genes, is V. cholerae still V. cholerae?
    A Hundred Year Old Strain of Cholera Bacteria Has Been Decoded
    Note in the article they use terms like “distantly related”. So distantly related that it’s still the same genus and species! Really the only thing that has changed is the subtype. There is no evolution going on here. Only adaption.

    Edited for broken link.

  9. 9
    Ed George says:

    Anthropology

    Sure it’s perfectly consistent with Darwinian evolution. Everything is, once the theory has been adjusted.

    HGT is perfectly consistent with Darwin’s theory even before the new synthesis. Darwin’s theory required that traits be heritable, that there be a source of variation and that selection acts on this variation. HGT provides a source of variation to a population, it is heritable, and can result in differential reproduction. All of the boxes are checked without the need to alter his theory

  10. 10
    ET says:

    Ed George:

    HGT is perfectly consistent with Darwin’s theory even before the new synthesis.

    Except for the facts that it wasn’t predicted and cannot be accounted for via blind and mindless processes.

    Darwin’s theory required that traits be heritable, that there be a source of variation and that selection acts on this variation.

    Darwin required that the variation be that of chance. That is a happenstance occurrence due to some accident, error or mistake.

    That you keep ignoring that important fact is very telling.

  11. 11
    News says:

    Darwinism is natural selection acting on random mutation. Horizontal gene transfer is not a random mutation; it is the adoption of alien genes. It’s quite clear from the literature that the extent of HGT is quite unexpected. More reasons that people don’t face career ruin for abandoning Darwincentic evolution.

  12. 12
    Ed George says:

    ET

    Darwin required that the variation be that of chance. That is a happenstance occurrence due to some accident, error or mistake.

    Do you have a reference for this? Since did not know about DNA and mutations, and since he did not rule out Lamarckian processes, which are decidedly not chance or happenstance, I suspect he never said what you claim he did.

  13. 13
    Ed George says:

    News

    Darwinism is natural selection acting on random mutation.

    Where in Origin of Species did Darwin say this?

  14. 14
    hazel says:

    My merely layperson’s understanding is that Darwin said natural selection acting upon variation among individuals, but he knew nothing about genes and mutation, and I don’t know if he speculated on the cause of variability.

    And I really don’t understand why it is so critical what Darwin thought: there has been about 150 years of further biological knowledge since his time. Why don’t people say the theory of evolution instead of Darwinism? For instance, NEWS says, “Darwinism is natural selection acting on random mutation.” Where is that definition? If one writes, “The theory of evolution is natural selection acting on random mutation,” I think one could reasonably reply that the modern theory includes different ways, including HGT, that produce variability, which is the key idea.

  15. 15
    Ed George says:

    Hazel

    Why don’t people say the theory of evolution instead of Darwinism?

    For the same reason that ID is referred to as Creationism in a cheap tuxedo. Both tactics are nothing more than cheap parlour tricks.

  16. 16
    ET says:

    Ed George:

    Do you have a reference for this? Since did not know about DNA and mutations, and since he did not rule out Lamarckian processes, which are decidedly not chance or happenstance, I suspect he never said what you claim he did.

    Read the book, Ed. Count how many times the word “chance” appears in “On the Origins of Species…”, and note the context. Darwin’s entire concept was all about chance and nature eliminating those who were deficient in some manner- either with respect to their environment or regardless of environment.

    In “What Evolution Is”, Ernst Mayr wrote:

    The first step in selection, the production of genetic variation, is almost exclusively a chance phenomenon except that the nature of the changes at a given locus is strongly constrained. Chance plays an important role even at the second step, the process of elimination of the less fit individuals. Chance may be particularly important in the haphazard survival during periods of mass extinction.

    So you figure it out, Ed.

  17. 17
    ET says:

    hazel:

    Why don’t people say the theory of evolution instead of Darwinism?

    Two reasons, hazel:
    1- There isn’t any scientific theory of evolution
    2- Darwinism refers to evolution by means of blind, mindless and purposeless processes, aka blind watchmaker evolution.

    And natural selection is defined as the result of heritable random mutations and fecundity. It is nothing more than differential reproduction due to heritable random variation. Read any college textbook on evolution.

  18. 18
    Ed George says:

    ET

    Read the book, Ed. Count how many times the word “chance” appears in “On the Origins of Species…”, and note the context.

    The word “chance” appears 61 times, none of them suggesting that the variation that selection acts on is the result of chance or happenstance. “Happenstance” is not mentioned once. You obviously do not have a reference where Darwin says that the variation that selection acts on is the result of chance or happenstance.

    In “What Evolution Is”, Ernst Mayr wrote:

    You are quoting a book published 120 years after Darwin died, 143 after Darwin published his theory. A quote about genetic variation, a subject that Darwin knew nothing about when he proposed his theory.

  19. 19
    ET says:

    LoL! Ernst Mayr was one of the architects of the modern synthesis, Ed. What he said followed directly from what Darwin wrote, it just ADDED the genetic component. That was the whole point of the modern synthesis, Ed. “What Evolution Is” just summed up the state of the mainstream at the time it was published.

    Ed:

    You obviously do not have a reference where Darwin says that the variation that selection acts on is the result of chance or happenstance.

    Unlike you, Ed, I have actually read an understood the text. You obviously missed the following:

    In such case, every slight modification, which in the course of ages chanced to arise, and which in any way favoured the individuals of any of the species, by better adapting them to their altered conditions, would tend to be preserved; and natural selection would thus have free scope for the work of improvement.- Charles Darwin, Chapter IV Natural Selection

    The whole point of natural selection was the appearance of design absent a plan or designer. It was to counter Paley’s argument- that was Dawkins’ point with “the Blind Watchmaker”. Dawkins was only promoting what Darwin first wrote in the 19th century.

    Only ID is OK with directed variation, ie changes that aren’t chance events.

  20. 20
    ET says:

    There’s MOAR!

    Mere chance, as we may call it, might cause one variety to differ in some character from its parents, and the offspring of this variety again to differ from its parent in the very same character and in a greater degree; but this alone would never account for so habitual and large an amount of difference as that between varieties of the same species and species of the same genus. – Charles Darwin (divergence of character)

    My knowledge trumps your frantic internet searches, Eddie Bogart spearshake

  21. 21
    ET says:

    And MOAR!- Clearly Ed has never read the book:

    If, however, an isolated area be very small, either from being surrounded by barriers, or from having very peculiar physical conditions,thetotalnumberoftheindividualssupportedonitwillnecessarilybe very small; and fewness of individuals will greatly retard the production of new species through natural selection, by decreasing the chance of the appearance of favourable variations.

    and

    Throughout a great and open area, not only will there be a better chance of favourable variations arising from the large number of individuals of the same species…

    and

    Furthermore, the species which are most numerous in individuals will have the best chance of producing within any given period favourable variations.

    and

    I have hitherto sometimes spoken as if the variations—so common and multiform in organic beings under domestication, and in a lesser degree in those in a state of nature—had been due to chance.

    and

    firstly, because new varieties are very slowly formed, for variation is a very slow process, and natural selection can do nothing until favourable variations chance to occur…

  22. 22
    ET says:

    Ed George:

    The word “chance” appears 61 times, none of them suggesting that the variation that selection acts on is the result of chance or happenstance.

    Liar

  23. 23
    john_a_designer says:

    Historical evidence abounds that as Darwin envisioned his theory it did not allow any rooms for providence or teleology. Nature + nature’s law’s + chance are all that were necessary and sufficient to explain the evolution of life according to his theory. And while Darwin did not claim the origin of life could be explained naturalistically, he did speculate about it and proclaim, “But if (& oh what a big if) we could conceive in some warm little pond with all sorts of ammonia & phosphoric salts,—light, heat, electricity…” Here is an excerpt of a book review of a book (Curtis Johnson: Darwin’s dice: the idea of chance in the thought of Charles Darwin. New York: Oxford University Press, 2015,) which makes the argument quite persuasively that Darwin was a thorough going materialist who believed chance could do things that appear to be miraculous.

    Darwinian evolution… [makes the] proposal that life and the cosmos based upon chance ends God’s providence. An advanced degree in theology is not necessary to see the problem. ‘‘God is no absentee landlord,’’ says one layman’s guide to Christian orthodoxy. God’s providence demonstrates it. Providence ‘‘refers to the preservation, care, and government of God over all his creation…. That is, God sees all creation heading for some kind of historical culmination’’ (Cantelon 2007, 129). As such, providence is inherently teleological. If chance is to be understood in its normal, ordinary sense, it would stand in direct contradiction to God’s providence. This is often misunderstood. Thompson (2015), for example, thinks that Darwinian evolution is only in tension with literal, young-earth interpretations of scripture (190–198). This, however, is logically and historically false. A chance-driven world cannot by its very nature entail a designed, providential world since intentionality is the defining distinction between naturalistic chance on the one hand and theistic providence on the other. Furthermore, one need not be a bible-thumping literalist to have problems with Darwin’s enthronement of chance in nature. Historical examples abound, but two will suffice. Alfred Russel Wallace(1823–1913), co-discoverer of the theory of natural selection, an ardent supporter of common descent by means of natural selection who was not a Christian, questioned the ability of that mechanism to account for the special mental (and even some physical) attributes of human beings and instead called upon some‘ ‘Overruling Intelligence’’ to explain its source. When an appalled Darwin sought support from the uniformitarian geological gradualist Lyell (1797–1875)—hardly a young earth biblical literalist!—he got little sympathy. Instead, Lyell (1881) told Darwin, ‘‘I rather hail Wallace’s suggestion that there may be a Supreme Will and Power which may not abdicate its functions of interference, but may guide the forces and laws of Nature e’’ (442). But this is precisely what Darwin’s chance precludes. Thus, Thompson is correct in thinking that evolution broadly speaking is compatible with some interpretations of scripture and theism generally, but not Darwinian evolution. No matter what interpretation of Genesis one invokes the tension between Darwin’s chance and God’s providence will be there.

    https://www.readcube.com/articles/10.1007/s11016-016-0139-9?author_access_token=0r13nyyB8B8tVZPAqsPPS_e4RwlQNchNByi7wbcMAY7v18zbQ6uC_SRUFQbxpvNs6VMV9EjKNUJWMhqoKDhISYDQo4TGS0gmKxz4ny_P6d1LW2SarfRffBW1Bnj3CCVUv11jJzijZbBoXmayUifFaQ%3D%3D

  24. 24
    bornagain77 says:

    If I might add to the discussion, the word ‘chance’, as it is used by Darwinists, is not an appeal to any known mathematical probability but is, in reality, a placeholder for ignorance. As Robert C. Sproul points out: “By calling the unknown cause ‘chance’ for so long, people begin to forget that a substitution was made. . . . The assumption that ‘chance equals an unknown cause’ has come to mean for many that ‘chance equals cause.’”

    What Is Chance? – Nicholas Nurston
    Excerpt: “The vague word ‘chance’ is used as a substitute for a more precise word such as ’cause’. “To personify ‘chance’ as if we were talking about a causal agent,” notes biophysicist Donald M. MacKay, “is to make an illegitimate switch from a scientific to a quasi-religious mythological concept.”
    Similarly, Robert C. Sproul points out: “By calling the unknown cause ‘chance’ for so long, people begin to forget that a substitution was made. . . . The assumption that ‘chance equals an unknown cause’ has come to mean for many that ‘chance equals cause.’” Others who reasoned in this fashion, Nobel laureate Jacques Monod, for one, used this chance equals cause line of reasoning. “Absolutely free but blind, (is) at the root of the stupendous edifice of evolution,”…
    https://books.google.com/books?id=bQ5OAAAAQBAJ&pg=PT25&lpg=PT25

    Although the word “chance” is usually defined as the mathematical probability of something happening, such as the chance involved in flipping a coin, when Darwinists use the word ‘chance’, they are not appealing to any known probability of something happening but are in fact appealing to an unknown cause which, as Wolfgang Pauli himself pointed out, is more or less synonymous with the word ‘miracle’.

    Pauli’s ideas on mind and matter in the context of contemporary science – Harald Atmanspacher
    Excerpt: “In discussions with biologists I met large difficulties when they apply the concept of ‘natural selection’ in a rather wide field, without being able to estimate the probability of the occurrence in a empirically given time of just those events, which have been important for the biological evolution. Treating the empirical time scale of the evolution theoretically as infinity they have then an easy game, apparently to avoid the concept of purposesiveness. While they pretend to stay in this way completely ‘scientific’ and ‘rational,’ they become actually very irrational, particularly because they use the word ‘chance’, not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word ‘miracle.’”
    Wolfgang Pauli (pp. 27-28)
    https://pdfs.semanticscholar.org/234f/4989e039089fed5ac47c7d1a19b656c602e2.pdf

    Likewise, as Talbott points out in the following article, the way in which Darwinists use the word ‘random’ is also more or less synonymous with the word ‘miracle’.

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

    Thus, whenever you hear a Darwinist say that something happened randomly, or that it happened by chance, he is not appealing to any realistic mathematically defined probability but is in fact appealing to an unknown cause which is more or less synonymous with the world miracle. i.e. The Darwinist, when he uses the word chance, is, in fact, appealing to his ignorance of the actual cause. Which, (i.e. postulating an unknown cause as an actual cause), is just about as unscientific as one can get.

  25. 25
    ET says:

    Even Darwin wrote about “chance” just being a call to ignorance:

    I have hitherto sometimes spoken as if the variations—so common and multiform in organic beings under domestication, and in a lesser degree in those in a state of nature—had been due to chance. This, of course, is a wholly incorrect expression, but it serves to acknowledge plainly our ignorance of the cause of each particular variation. Chapter V

    I agree with a caveat of the word “chance” encompassed those phenomena that were not planned, whatever they were. All the changes were accidents, errors or mistakes that just happened and just happened to not be a detriment. Or even better just happened to be of some benefit even if the benefit was actually a loss of some function or functionality.

  26. 26
    DATCG says:

    Hmmmm…
    Darwin said, “…Natural selection acts ONLY(caps for emphasis) by taking advantage of slight successive variations; she can never take a great and sudden leap, but must advance by short and sure, though slow steps.”
    Darwin said, “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.”

    HGT is not Darwinian. But then, neither is life in general – thus a reason for ideas proposed like Punctuated Equilibrium:
    “… hypothesis that evolutionary development is marked by isolated episodes of rapid speciation between long periods of little or no change”

    Non-Darwinian = Horizontal, Darwinian = Vertical

    If life forms were created based upon Darwinian gradualist foundation, why the need for Stephen Gould and Niles Eldredge to propose Punctuated Equilibrium? Suddenly, new life forms appear after long periods of silence. Why is PE required?

    Why a need for Junk DNA? JUNK DNA was not evidenced based, so why declare the vast majority of DNA to be JUNK?

    And yet, today, in 2019… this was posted in August, a mention to Dan Graur at “Discover” Magazine
    Dan Graur’s Junk DNA – 75%

    JUNK DNA is falling apart, but they still reference angry Dan Graur.

    Could it be that Life does not follow Darwin’s gradualist, chance theory?

  27. 27
    DATCG says:

    BA77 #24,

    Nice quote by Sproul of Jacques Monod, with a bit of Editing to clarify the stupendousness…
    “Absolutely free but blind(ness), (is) at the root of the stupendous edifice of evolution,”

    Agree, a stupendous theory of blindness on the edge of a cliff 😉
    At the root of a false tree of life.

  28. 28
    tommy hall says:

    I would argue that HGT is Lamarckian. It’s certainly acquired characteristics. And the transferred genes/traits can be subsequently inherited by future generations. Also, this happens within individuals, not populations. “Evolution” only happens in populations. Via random mutation plus selection This is the fundamental naturalistic mechanism that forms the foundation for the materialistic, mechanistic Modern Synthesis.

    Within the Modern Synthesis, all traits are assumed to arise randomly and then get fixed into a population if they increase fitness. This mechanism is what keeps teleology/intelligence out of the biological sciences. Which was it’s whole point from inception. It was philosophical in nature.

  29. 29
    es58 says:

    It seems that hgt is evo by stealth bc it gives you a new, complex change in the current organism w/o having to explain how it originally arose in the source organism, the origin / existence of which you get to assume for free.

    On chance: davescot used to refer to “chance worshippers” which seems accurate

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