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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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Comments
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.Zachriel
December 9, 2014
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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)wd400
December 9, 2014
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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.ppolish
December 9, 2014
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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?ppolish
December 9, 2014
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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?ppolish
December 9, 2014
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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.wd400
December 9, 2014
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ppolish: Poor excuse for a tree It's topologically a tree. http://darwin-online.org.uk/converted/published/1872_Origin_F391/1872_Origin_F391_figdiagram.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
Zachriel
December 9, 2014
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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,ppolish
December 9, 2014
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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?wd400
December 9, 2014
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Darwin saw Nature as a Tangled Brush, more like a Jackson Pollock painting: http://m.newser.com/story/199153/jackson-pollock-master-of-physics.html The whole "Tree of Life" is a misnomer, a bad science misnomer at that.ppolish
December 9, 2014
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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.Mung
December 9, 2014
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Designophobia ... or in this case, Design-er-phobiaSilver Asiatic
December 9, 2014
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The designer (our glorious leader) obviously took a mechanical engineering course before putting ATP synthase
AVS is obviously just a strawman erecting ignoramus.Joe
December 9, 2014
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How was it determined that nylonase is the result of unguided evolution? Zachriel will never say.Joe
December 9, 2014
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We have a robust explanation, including for adaptation.
That is your opinion. However it is not supported by the evidence.Joe
December 9, 2014
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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.Zachriel
December 9, 2014
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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?AVS
December 9, 2014
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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?
keith s
December 8, 2014
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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.keith s
December 8, 2014
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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?????tjguy
December 8, 2014
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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.Zachriel
December 8, 2014
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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?Box
December 8, 2014
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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.Mung
December 8, 2014
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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.Zachriel
December 8, 2014
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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.Box
December 8, 2014
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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.Mung
December 8, 2014
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Mung:
Isn’t this the exact thing Keith S claimed “the designer” never did?
No. Silly Mung.keith s
December 8, 2014
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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.Zachriel
December 8, 2014
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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.Zachriel
December 8, 2014
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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/Mung
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