horizontal gene transfer News

Horizontal gene transfer: Jumping gene jumped to all three domains of life?

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From The Scientist:

Horizontal gene transfer—the passing of DNA from one organism to another—is a prevalent among bacteria, and has even occurred between distantly related organisms, such as animals and bacteria. In a study published in eLife last week (November 25), researchers demonstrated for the first time that an antibacterial gene family has made the rounds across the three domains of life, from bacteria to archaea and eukaryotes. More.

Here’s the abstract:

Though horizontal gene transfer (HGT) is widespread, genes and taxa experience biased rates of transferability. Curiously, independent transmission of homologous DNA to archaea, bacteria, eukaryotes, and viruses is extremely rare and often defies ecological and functional explanations. Here, we demonstrate that a bacterial lysozyme family integrated independently in all domains of life across diverse environments, generating the only glycosyl hydrolase 25 muramidases in plants and archaea. During coculture of a hydrothermal vent archaeon with a bacterial competitor, muramidase transcription is upregulated. Moreover, recombinant lysozyme exhibits broad-spectrum antibacterial action in a dose-dependent manner. Similar to bacterial transfer of antibiotic resistance genes, transfer of a potent antibacterial gene across the universal tree seemingly bestows a niche-transcending adaptation that trumps the barriers against parallel HGT to all domains. The discoveries also comprise the first characterization of an antibacterial gene in archaea and support the pursuit of antibiotics in this underexplored group. Open access

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50 Replies to “Horizontal gene transfer: Jumping gene jumped to all three domains of life?

  1. 1
    bornagain77 says:

    Of related note to ‘gene-transfer’, the gene transfering bacteriophage virus is far more complex than many people have ever imagined, as these following video clearly point out:

    Virus – Assembly Of A Nano-Machine – video
    https://www.youtube.com/watch?v=Ofd_lgEymto

    Bacteriophage T4 DNA Packing
    https://www.youtube.com/watch?v=wNQQz0NGUNQ

    Here is a short video of the Bacteriophage ‘landing’ on a bacterium:

    Bacteriophage T4 – landing – video
    https://www.youtube.com/watch?v=kdz9VGH8dwY

    The first thought I had when I first saw the bacteriophage virus is that it looks very similar to the lunar lander of the Apollo program. The comparison is not without merit considering some of the relative distances to be traveled and the virus must somehow possess, as of yet unelucidated, orientation, guidance, docking, unloading, loading, etc… mechanisms. And please remember this level of complexity exists in a world that is far too small to be seen with the naked eye.

    I don’t know much about other gene-transfer mechanisms, but clearly it beggars belief to think that this particular gene-transfer mechanism ‘happened by chance’. As well, it is, to put it mildly, un-parsimonious to think that genes are just being transferred in a haphazard fashion as Darwinists hold.

    Of related note. Bacteria also use photons to communicate information amongst themselves

    Cellular Communication through Light – 2009
    Excerpt: Information transfer is a life principle. On a cellular level we generally assume that molecules are carriers of information, yet there is evidence for non-molecular information transfer due to endogenous coherent light. This light is ultra-weak, is emitted by many organisms, including humans and is conventionally described as biophoton emission.
    http://www.plosone.org/article.....ne.0005086

    Cellular Communication through Light
    Excerpt: As there were significant differences when separating the populations with glass or quartz, it is suggested that the cell populations use two (or more) frequencies for cellular information transfer, which influences at least energy uptake, cell division rate and growth correlation. Altogether the study strongly supports a cellular communication system, which is different from a molecule-receptor-based system and hints that photon-triggering is a fine tuning principle in cell chemistry.
    http://www.plosone.org/article.....ne.0005086

    Electrical Communication in Bacteria – August 2010
    Excerpt: These responses occurred too quickly for any sort of chemical exchange or molecular process such as osmosis, says Nielsen. The most plausible option, his team reports in the 25 February issue of Nature, is that the bacteria are somehow communicating electrically by transmitting electrons back and forth. How exactly they do this is unclear,
    http://www.uncommondescent.com.....-bacteria/

    Biophoton Communication: Can Cells Talk Using Light? – May 2012
    Excerpt: The question he aims to answer is whether the stream of photons has any discernible structure that would qualify it as a form of communication.,, Biophoton streams consist of short quasiperiodic bursts, which he says are remarkably similar to those used to send binary data over a noisy channel.
    http://www.technologyreview.co.....alk-using/

    of note:

    Learning from Bacteria about Social Networking (Information Processing) – video
    Excerpt: I will show illuminating movies of swarming intelligence of live bacteria in which they solve optimization problems for collective decision making that are beyond what we, human beings, can solve with our most powerful computers. I will discuss the special nature of bacteria computational principles in comparison to our Turing Algorithm computational principles,
    http://www.youtube.com/watch?v=yJpi8SnFXHs

  2. 2
    Silver Asiatic says:

    This does wonders for the nested hierarchy. Jumping genes is exactly what evolution predicted, right? Plus, it predicted exactly the pattern of where the all genes would jump also, I guess. It’s an amazing theory.

  3. 3
    Zachriel says:

    Silver Asiatic: This does wonders for the nested hierarchy.

    While Darwin didn’t have modern data, he was well aware that the nested hierarchy wouldn’t be perfect. Hybridization and convergence can confound the nested hierarchy.

    The nested hierarchy is strongly supported across most taxa, however, the root of the tree is problematic. Even then, many conserved genes show a single tree. This suggests that there was a single most recent common ancestor, but that there was rampant horizontal exchange both before and after that time.

    Silver Asiatic: Plus, it predicted exactly the pattern of where the all genes would jump also, I guess. It’s an amazing theory.

    The Theory of Evolution doesn’t predict specific histories from first principles. The basic pattern is branching descent, though Darwin wasn’t sure if there was one or more than one tree. Modern findings are that all life is related by common descent, and that life branches mostly but not entirely by vertical descent.

  4. 4
    Joe says:

    Darwin didn’t say anything about a nested hierarchy because he knew that gradual evolution would not produce one.

    Zachriel doesn’t know jack about nested hierarchies.

  5. 5

    So basically common descent by purely non-intelligent causes is unfalsifiable. If the molecular analysis to produce a Tree of Life doesn’t line up, it must have been horizontal gene transfer.

  6. 6
    Silver Asiatic says:

    If the molecular analysis to produce a Tree of Life doesn’t line up, it must have been horizontal gene transfer.

    Exactly. And if there wasn’t one tree of life there were multiple. If multiple, then multiple origins. Similar features in non-ancestral forms? No problem. They all evolved the same thing independently. The origin of life occurred several times exactly the same way and created different trees of life? No problem. We’re all related because we’re all carbon-based life forms. 😉

  7. 7
    Joe says:

    geoffrobinson- All unguided evolution has going for it are the equivocations, lies and exaggerations of its supporters. Sad, but true.

  8. 8
    Zachriel says:

    geoffrobinson: So basically common descent by purely non-intelligent causes is unfalsifiable.

    It’s difficult to prove a negative, however, an intelligent cause is superfluous.

    geoffrobinson: If the molecular analysis to produce a Tree of Life doesn’t line up, it must have been horizontal gene transfer.

    The basic tree is strongly supported, and that evidence doesn’t go away because of certain anomalies. In addition, we observe horizontal gene transfer, as well as hybridization.

    Silver Asiatic: And if there wasn’t one tree of life there were multiple. If multiple, then multiple origins.

    The evidence since Darwin has largely supported a single tree with a single common ancestral population.

    Silver Asiatic: The origin of life occurred several times exactly the same way and created different trees of life?

    The evidence doesn’t support that claim.

  9. 9
    JDH says:

    Zachriel

    The evidence doesn’t support that claim.

    You left out the part: “But if future evidence supports that claim, this incredible theory is flexible enough that it would predict that”

  10. 10
    Joe says:

    It’s difficult to prove a negative, however, an intelligent cause is superfluous.

    Only if “superfluous” means required.

    The evidence since Darwin has largely supported a single tree with a single common ancestral population.

    And yet Darwin said he didn’t know if it were one nor a few- nor a few thousand for all he knew.

    And as “evolution” doesn’t say anything about the origin of life, including how many times life arose from the chemical soup, no one can say anything about any singular tree. This is a clear case of post-hoc reasoning.

  11. 11

    “The basic tree is strongly supported, and that evidence doesn’t go away because of certain anomalies. In addition, we observe horizontal gene transfer, as well as hybridization.”

    So when scientists try to create a tree based on a particular molecule they get one tree. And then they get conflicting trees when they study something else. How many anomalies do you need to have before something is a bunch of epicycles instead of strongly supported?

    http://www.uncommondescent.com.....e-of-life/

    http://darwins-god.blogspot.co.....oes-0.html

    http://www.uncommondescent.com.....-is-wrong/

    http://www.uncommondescent.com.....e-of-life/

    http://darwins-god.blogspot.co.....s-now.html

    http://www.evolutionnews.org/2.....83331.html

    http://darwins-god.blogspot.co.....ution.html

    http://darwins-god.blogspot.co.....-nuts.html

  12. 12
    Edward says:

    Ok. If we have horizontal gene transfer, how do we know genes are conserved from a common base? 3 1/2 billion years is very long time for horizontal gene transfer to occur between multiple roots, and mess up the data. A very long time.

  13. 13

    Zachriel said:

    It’s difficult to prove a negative,..

    Then perhaps Darwinists shouldn’t assert an unprovable negative in the first place. This is hilarious; Darwinists assert an unprovable negative, IDist challenge the assertion, then the Darwinist responds “it’s difficult to prove a negative.”

    Well, gee.

  14. 14
    Box says:

    Zachriel: It’s difficult to prove a negative, however, an intelligent cause is superfluous.

    Superfluous? Why? Because unguided evolution does such a great job explaining enzymes or anything else related to information?

  15. 15
    Zachriel says:

    JDH: “But if future evidence supports that claim, this incredible theory is flexible enough that it would predict that”

    As we said, evolutionary theory doesn’t predict particular histories from first principles. For that matter the standard theory of animal reproduction doesn’t predict particular histories from first principles.

    geoffrobinson: So when scientists try to create a tree based on a particular molecule they get one tree.

    See Theobald A formal test of the theory of universal common ancestry, Nature 2010.

    Edward: If we have horizontal gene transfer, how do we know genes are conserved from a common base? 3 1/2 billion years is very long time for horizontal gene transfer to occur between multiple roots, and mess up the data.

    For most of the tree, there is no ambiguity. For example, there’s no reasonable doubt that mice nest within rodents which nest within mammals which nest within amniotes which nest within tetrapods which nest within gnathostomes which nest within vertebrates which nest within craniates which nest within chordates which nest within bilateria which nest within metazoa which nest within eukaryotes.

    William J Murray: Darwinists assert an unprovable negative

    What “unprovable negative”?

    Box: Because unguided evolution does such a great job explaining enzymes or anything else related to information?

    There is ample evidence of enzyme evolution. We have the strong support for common ancestry in protein families, plus we have direct evidence of enzymes evolving in response to environmental conditions

  16. 16

    Zachriel said:

    What “unprovable negative”?

    ROFL!

  17. 17
    Mapou says:

    Zacky:

    an intelligent cause is superfluous.

    Suppose this were true. And therefore what? Therefore the only explanation is a non-intelligent cause? Where does this nonsense come from?

    This is another example of the mediocre and deceptive mentality that permeates Darwinism.

  18. 18
    Zachriel says:

    Mapou: Suppose this were true. And therefore what? Where does this nonsense come from?

    William of Ockham.

  19. 19
    Mung says:

    Isn’t this the exact thing Keith S claimed “the designer” never did? Yet another claim of keiths falsified by the evidence. Facts are such stubborn things.

  20. 20
    Box says:

    Zachriel: There is ample evidence of enzyme evolution.

    As in “unguided evolution”? Nope, zilch.

    Zachriel: We have the strong support for common ancestry in protein families, (…)

    As in evolved by Darwinian mechanisms? Nope, diddly-squat.

    Zachriel: (…) plus we have direct evidence of enzymes evolving in response to environmental conditions.

    As in evolving new functions by unguided means? Nope, zippo. And don’t start about stuff like nylonase.

  21. 21
    Mung says:

    Zachriel: “William of Ockham.”

    DDD #xx.

    The misuse and abuse of Ockham’s Razor.

    Let me again quote, for the record:

    Still, Ockham’s “nominalism,” in both the first and the second of the above senses, is often viewed as derived from a common source: an underlying concern for ontological parsimony. This is summed up in the famous slogan known as “Ockham’s Razor,” often expressed as “Don’t multiply entities beyond necessity.”[31] Although the sentiment is certainly Ockham’s, that particular formulation is nowhere to be found in his texts. Moreover, as usually stated, it is a sentiment that virtually all philosophers, medieval or otherwise, would accept; no one wants a needlessly bloated ontology. The question, of course, is which entities are needed and which are not.

    Ockham’s Razor, in the senses in which it can be found in Ockham himself, never allows us to deny putative entities; at best it allows us to refrain from positing them in the absence of known compelling reasons for doing so. In part, this is because human beings can never be sure they know what is and what is not “beyond necessity”; the necessities are not always clear to us. But even if we did know them, Ockham would still not allow that his Razor allows us to deny entities that are unnecessary. For Ockham, the only truly necessary entity is God; everything else, the whole of creation, is radically contingent through and through. In short, Ockham does not accept the Principle of Sufficient Reason.

    Nevertheless, we do sometimes have sufficient methodological grounds for positively affirming the existence of certain things. Ockham acknowledges three sources for such grounds (three sources of positive knowledge). As he says in Sent. I, dist. 30, q. 1: “For nothing ought to be posited without a reason given, unless it is self-evident (literally, known through itself) or known by experience or proved by the authority of Sacred Scripture.”

    http://plato.stanford.edu/entries/ockham/#4.1

    See also:

    http://plato.stanford.edu/entries/simplicity/

  22. 22
    Zachriel says:

    Box: As in evolved by Darwinian mechanisms? As in evolved by Darwinian mechanisms?

    Let’s start with the nested hierarchy supporting branching descent.

    Box: And don’t start about stuff like nylonase.

    Nylonase certainly represents enzymatic evolution.

  23. 23
    Zachriel says:

    Mung: The question, of course, is which entities are needed and which are not.

    That’s right, and an unevidenced designer is superfluous when there are adequate alternative explanations, which Mapou granted arguendo.

  24. 24
    keith s says:

    Mung:

    Isn’t this the exact thing Keith S claimed “the designer” never did?

    No. Silly Mung.

  25. 25
    Mung says:

    Right you are keiths.

    You were whining about why “the designer” didn’t do this (re-use of designs by transfer).

    But it amounts to the same thing though.

  26. 26
    Box says:

    Zachriel: Let’s start with the nested hierarchy supporting branching descent. Let’s start with the nested hierarchy supporting branching descent. Let’s start with the nested hierarchy supporting branching descent.

    Okay. Okay already! What about it?

    Box: As in evolving new functions by unguided means? Nope, zippo.

    Zachriel: Nylonase certainly represents enzymatic evolution.

    It does not represent the evolution of a new kind of function in any meaningful way. The bacteria already had the ability to break down a similar chemical. When they encountered nylon, it was a small step to break that down.

  27. 27
    Zachriel says:

    Box: What about it {branching descent}?

    It provides a history of enzymatic change over time. The generally incremental change is consistent with direct observations of evolutionary rates via mutation, and shows that large changes result from a series of smaller changes.

    Box: It does not represent the evolution of a new kind of function in any meaningful way.

    The function is the ability to eat an entirely novel food source. For the bacteria, it’s a matter of life and death.

  28. 28
    Mung says:

    Mung: The question, of course, is which entities are needed and which are not.

    Zachriel: That’s right, and an unevidenced designer is superfluous when there are adequate alternative explanations, which Mapou granted arguendo.

    So if we assume that a designer is not necessary Ockham’s Razor tells us that a designer is not necessary?

    I’m going to apply Ockham’s Razor to that and claim that Ockham’s Razor is superfluous.

  29. 29
    Box says:

    Zachriel: It provides a history of enzymatic change over time. The generally incremental change is consistent with direct observations of evolutionary rates via mutation, and shows that large changes result from a series of smaller changes.

    Rubbish, you are a liar for Darwin.

    Zachriel: The function is the ability to eat an entirely novel food source.

    Nylonase does not represent the evolution of a entirely novel function, which was the subject at hand.
    I’m tired of you lies and distortions. Why don’t you go annoy someone else?

  30. 30
    Zachriel says:

    Box: you are a …

    Handwaving. You asked what could we determine from branching descent. We provided an answer.

    Box: Nylonase does not represent the evolution of a entirely novel function, which was the subject at hand.

    The ancestral strain couldn’t digest nylon-byproducts. The new strain could. It’s novel, by definition.

  31. 31
    tjguy says:

    Zachriel @15

    As WE said, evolutionary theory doesn’t predict particular histories from first principles. For that matter the standard theory of animal reproduction doesn’t predict particular histories from first principles.

    Zachriel, are you two people or something?

    Who in the world are you talking about when you say “As WE said,….”

    We?????

  32. 32
    keith s says:

    tjguy to Zachriel,

    Who in the world are you talking about when you say “As WE said,….”

    We?????

    His name is Legion, for he is many.

  33. 33
    keith s says:

    Here’s what I actually said, Mung:

    Speaking of lateral transfers, why do you suppose your designer doesn’t do more of them? I know we’re not allowed to make assumptions about him, but he does seem like an odd bird, doesn’t he? For example:

    It’s interesting that KF’s preferred example of design — the Abu 6500 C3 fishing reel, with which he bores us to death — is full of gears, yet only one case of gearing has ever been found in nature.

    Did God the Designer finally get around to taking a mechanical engineering course before designing Issus coleoptratus?

  34. 34
    AVS says:

    The designer (our glorious leader) obviously took a mechanical engineering course before putting ATP synthase and the bacterial flagellum together, then changed his mind when putting the archaeal flagellum together. Then he retook the class (it was required for his major) before putting together the eukaryotic flagellum and some insect legs.

    The only question is: did the great creator (our glorious leader)go to a christian college?

  35. 35
    Zachriel says:

    Mung: So if we assume that a designer is not necessary Ockham’s Razor tells us that a designer is not necessary?

    We have a robust explanation, including for adaptation. As for the assumption, Mapou made that for the sake of argument in order to explore the possibility that a designer could be involved even if we have a reasonable natural explanation. However, it would be considered an extraneous entity.

    Even if we don’t have a robust explanation, without entailments, the assertion of a designer is scientifically sterile. It’s no better than positing angels to explain the specified complexity of planetary movements.

  36. 36
    Joe says:

    We have a robust explanation, including for adaptation.

    That is your opinion. However it is not supported by the evidence.

  37. 37
    Joe says:

    How was it determined that nylonase is the result of unguided evolution? Zachriel will never say.

  38. 38
    Joe says:

    The designer (our glorious leader) obviously took a mechanical engineering course before putting ATP synthase

    AVS is obviously just a strawman erecting ignoramus.

  39. 39
    Silver Asiatic says:

    Designophobia …

    or in this case, Design-er-phobia

  40. 40
    Mung says:

    keiths:

    Speaking of lateral transfers, why do you suppose your designer doesn’t do more of them?

    The designer doesn’t do enough lateral transfers to satisfy keiths. Therefore there is no designer. QED.

  41. 41
    ppolish says:

    Darwin saw Nature as a Tangled Brush, more like a Jackson Pollock painting:
    http://m.newser.com/story/1991.....ysics.html

    The whole “Tree of Life” is a misnomer, a bad science misnomer at that.

  42. 42
    wd400 says:

    The only figure in The Origin is a tree, ppolish. Are you confusing Darwin’s comment about “an entangled bank” with his ideas about the history of species?

  43. 43
    ppolish says:

    Poor excuse for a tree if he even called it that.
    “It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us.”

    Although “guided by” instead of “produced by” would have been accurate. But he’s Victorian Era and deserved a pass on that,

  44. 44
    Zachriel says:

    ppolish: Poor excuse for a tree

    It’s topologically a tree.
    http://darwin-online.org.uk/co.....iagram.jpg

    ppolish: if he even called it that.

    The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during former years may represent the long succession of extinct species. At each period of growth all the growing twigs have tried to branch out on all sides, and to overtop and kill the surrounding twigs and branches, in the same manner as species and groups of species have at all times overmastered other species in the great battle for life. The limbs divided into great branches, and these into lesser and lesser branches, were themselves once, when the tree was young, budding twigs; and this connexion of the former and present buds by ramifying branches may well represent the classification of all extinct and living species in groups subordinate to groups.

    Darwin, On the Origin of Species, 6th Edition

  45. 45
    wd400 says:

    Well,it’s a tree by definition (there are no cycles), and the quote you reproduce isn’t about how species relate to each other. In fact, if it meant to tell us anything about biology it’s about ecology and not evolution.

  46. 46
    ppolish says:

    Zachriel, read the Darwin “Entangled Bank” quote I posted and the “Warlike Tree” quote you just did. Which one rings truer today? Which one seems lame today?

  47. 47
    ppolish says:

    Zachriel, that image you linked to is a tangled brush not a tree, especially if all 10 trunks were drawn out instead of only 2. You see a tree?

  48. 48
    ppolish says:

    Zachriel, that image you linked to is a tangled brush not a tree, especially if all 10 trunks were drawn out instead of only 2. You see a tree?

    WD, a tree by definition? Who defined? Not Darwin – he used metaphor and simile.

  49. 49
    wd400 says:

    A tree is a graph in which any two nodes are connected by exactly one path. No “tangles”, just like that tree has no tangles/cycles.

    (the only way you could reasonably argue Darwin didn’t believe in a tree relates to the fact he wasn’t sure life arose only once. If it arose more than one times you’ve have several trees, but non of them tangled)

  50. 50
    Zachriel says:

    ppolish: read the Darwin “Entangled Bank” quote I posted and the “Warlike Tree” quote you just did.

    There seems to be some confusion. The Tree of Life refers to the taxonomy of organisms.

    ppolish: that image you linked to is a tangled brush not a tree, especially if all 10 trunks were drawn out instead of only 2.

    It’s apparent from the diagram that A-L probably converge to a single trunk. If you don’t think A-L join, then you have disjoint trees, but trees nonetheless.

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