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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
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.Box
December 8, 2014
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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.Mung
December 8, 2014
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Mapou: Suppose this were true. And therefore what? Where does this nonsense come from? William of Ockham.Zachriel
December 8, 2014
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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.Mapou
December 8, 2014
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Zachriel said:
What “unprovable negative”?
ROFL!William J Murray
December 8, 2014
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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 conditionsZachriel
December 8, 2014
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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?Box
December 8, 2014
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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.William J Murray
December 8, 2014
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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.Edward
December 8, 2014
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"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? https://uncommondescent.com/intelligent-design/why-doesnt-animal-germ-cell-formation-bear-much-relationship-to-the-alleged-tree-of-life/ http://darwins-god.blogspot.com/2013/06/contradictory-trees-evolution-goes-0.html https://uncommondescent.com/tree-of-life/evolutionary-biologists-say-darwins-tree-of-life-is-wrong/ https://uncommondescent.com/genetics/problems-with-using-rna-to-build-tree-of-life/ http://darwins-god.blogspot.com/2014/06/more-fossil-molecule-contradictions-now.html http://www.evolutionnews.org/2014/03/cosmos_episode_083331.html http://darwins-god.blogspot.com/2014/03/guess-evidence-for-early-evolution.html http://darwins-god.blogspot.com/2012/07/evolutionist-plants-are-driving-me-nuts.htmlgeoffrobinson
December 8, 2014
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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.Joe
December 8, 2014
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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"JDH
December 8, 2014
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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.Zachriel
December 8, 2014
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geoffrobinson- All unguided evolution has going for it are the equivocations, lies and exaggerations of its supporters. Sad, but true.Joe
December 8, 2014
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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. ;-)Silver Asiatic
December 8, 2014
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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.geoffrobinson
December 8, 2014
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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.Joe
December 8, 2014
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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.Zachriel
December 8, 2014
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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.Silver Asiatic
December 8, 2014
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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/info%3Adoi%2F10.1371%2Fjournal.pone.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/info%3Adoi%2F10.1371%2Fjournal.pone.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, https://uncommondescent.com/intelligent-design/electrical-communication-in-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.com/view/427982/biophoton-communication-can-cells-talk-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=yJpi8SnFXHsbornagain77
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