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Here's another possibility for the IM issue;-"What has become increasingly clear in the past 10 years is that this liberal genetic exchange is definitely not limited to the DNA of the microscopic world. It likewise happens to genes that belong to animals, fungi and plants, collectively known as eukaryotes because they boast nuclei in their cells. The ancient communion between ferns and hornworts is the latest in a series of newly discovered examples of horizontal gene transfer: when DNA passes from one organism to another generally unrelated one, rather than moving vertically' from parent to child. In fact, horizontal gene transfer has happened between all kinds of living things throughout the history of life on the planet - not just between species, but also between different kingdoms of life. Bacterial genes end up in plants; fungal genes wind up in animals; snake and frog genes find their way into cows and bats. It seems that the genome of just about every modern species is something of a mosaic constructed with genes borrowed from many different forms of life."-http://aeon.co/magazine/science/how-horizontal-gene-transfer-changes-evolutionary-theory/

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Here's another possibility for the IM issue;
> 
> "What has become increasingly clear in the past 10 years is that this liberal genetic exchange is definitely not limited to the DNA of the microscopic world. It likewise happens to genes that belong to animals, fungi and plants, collectively known as eukaryotes because they boast nuclei in their cells. The ancient communion between ferns and hornworts is the latest in a series of newly discovered examples of horizontal gene transfer: when DNA passes from one organism to another generally unrelated one, rather than moving vertically' from parent to child. In fact, horizontal gene transfer has happened between all kinds of living things throughout the history of life on the planet - not just between species, but also between different kingdoms of life. Bacterial genes end up in plants; fungal genes wind up in animals; snake and frog genes find their way into cows and bats. It seems that the genome of just about every modern species is something of a mosaic constructed with genes borrowed from many different forms of life."
> 
> http://aeon.co/magazine/science/how-horizontal-gene-transfer-changes-evolutionary-theor... can see Sheldrake's morphic field and the holographic universe fitting well with the above information. Like minds coming from different angles (with words) toward the same information/images.

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http://aeon.co/magazine/science/how-horizontal-gene-transfer-changes-evolutionary-theor... 
> bbella: I can see Sheldrake's morphic field and the holographic universe fitting well with the above information. Like minds coming from different angles (with words) toward the same information/images.-It is an amazing possibility

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DAVID: Here's another possibility for the IM issue;
" In fact, horizontal gene transfer has happened between all kinds of living things throughout the history of life on the planet - not just between species, but also between different kingdoms of life. Bacterial genes end up in plants; fungal genes wind up in animals; snake and frog genes find their way into cows and bats. It seems that the genome of just about every modern species is something of a mosaic constructed with genes borrowed from many different forms of life."-http://aeon.co/magazine/science/how-horizontal-gene-transfer-changes-evolutionary-theory/-A very illuminating post, for which many thanks. You will certainly have noted that the pioneer in this research was Barbara McClintock, who called for further investigation into the way cells think. The emphasis laid by her and Margulis on the way in which cells cooperate is obviously highly relevant here, and the whole article seems to me to confirm the hypothesis of the inventive mechanism.-QUOTE: Horizontal gene transfer opens the possibility of a creature instantaneously acquiring a gene-trait combo that its own genome would have been unlikely to invent by itself. 
 
You could hardly have a clearer confirmation of the idea that innovations are caused by cooperation between the inventive mechanisms of different cells/cell communities. The instantaneous reference offers an obvious explanation for the lack of so-called transitional forms, and is especially significant for the Cambrian Explosion.-QUOTE: Rather than evolving from a last universal ancestor all life arose from a communal pool of primitive cells with unbridled zeal for exchanging DNA. -Presumably this means Darwin's few forms rather than one, with ever increasing complexity as more and more combinations came into play. Such a process would clearly have led to the higgledy-piggledy bush which is such a problem for your anthropocentrism.
 
QUOTE: We did not invent gene transfer; DNA did. Genes are concerned with only one thing above all: self-perpetuation [...] Species barriers might protect the integrity of a genome as a whole, but when an individual gene has a chance to advance itself by breaking those boundaries, it will not hesitate.-You can still hold onto the fact that this whole mechanism is too complex to have arisen by chance, but if you accept these observations, I don't see how you can continue to cling to the idea that the unbridled zeal with which cells form new combinations coincides with your God's meticulous planning of a path leading from bacteria to humans. (See also the quote under Negative atheism?)-BBELLA: I can see Sheldrakes morphic field and the holographic universe fitting well with the above information. Like minds coming from different angles (with words) toward the same information/images.-I'd be interested to know the extent to which you see morphic fields and the holographic universe fitting in with the panpsychist hypothesis that all things have their own form of quasi-consciousness or intelligence (inverted commas, because this should not be equated with human consciousness and intelligence).

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> dhw: You could hardly have a clearer confirmation of the idea that innovations are caused by cooperation between the inventive mechanisms of different cells/cell communities. The instantaneous reference offers an obvious explanation for the lack of so-called transitional forms, and is especially significant for the Cambrian Explosion.-Agreed. At issue is the source of the horizontal transfer mechanism (HTM). It occurs, but how did it start, and is it a mechanism coded into the original DNA coding when life started? We do not know the answer, so we are left with: did HTM appear de novo through cellular invention or was it set in place in advance?-
> dhw: Such a process would clearly have led to the higgledy-piggledy bush which is such a problem for your anthropocentrism.-The h-p bush is your problem not mine. Please think for yourself, as I think the drive for humans to appear is perfectly compatible with the bush of life, as I have previously explained many times citing the balance of nature being a natural and also required condition for life in general. 
> 
> dhw: QUOTE: We did not invent gene transfer; DNA did. Genes are concerned with only one thing above all: self-perpetuation [...] Species barriers might protect the integrity of a genome as a whole, but when an individual gene has a chance to advance itself by breaking those boundaries, it will not hesitate.-Nice atheistic quote. Perhaps God invented DNA? Sounds like Dawkins.
> 
> dhw: You can still hold onto the fact that this whole mechanism is too complex to have arisen by chance, but if you accept these observations, I don't see how you can continue to cling to the idea that the unbridled zeal with which cells form new combinations coincides with your God's meticulous planning of a path leading from bacteria to humans. -As stated above, the whole arrangement can have come from God's planning.
> 
> BBELLA: I can see Sheldrakes morphic field and the holographic universe fitting well with the above information. Like minds coming from different angles (with words) toward the same information/images.
> 
> dhw: I'd be interested to know the extent to which you see morphic fields and the holographic universe fitting in with the panpsychist hypothesis that all things have their own form of quasi-consciousness or intelligence (inverted commas, because this should not be equated with human consciousness and intelligence).-I accept Sheldrake's human consciousness work, having studied his findings, but his morphic fields as well as holographic universe theories are just proposals, without any basis in study. And yes, cells under the guidance of their genomes do appear to act intelligently, or perhaps they have been intelligently planned to act that way.

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dhw: Such a process would clearly have led to the higgledy-piggledy bush which is such a problem for your anthropocentrism.
DAVID: The h-p bush is your problem not mine. Please think for yourself, as I think the drive for humans to appear is perfectly compatible with the bush of life, as I have previously explained many times citing the balance of nature being a natural and also required condition for life in general. -I'm not aware of anyone doing my thinking for me, though I know some lovely people who give it a good try! I'm glad you think the higgledy-piggledy bush and the extinction of 99% of species and the ever changing balance of nature are all compatible with your God having planned humans from the start of evolution. That will save you from thinking any more about it.-dhw: You can still hold onto the fact that this whole mechanism is too complex to have arisen by chance, but if you accept these observations, I don't see how you can continue to cling to the idea that the unbridled zeal with which cells form new combinations coincides with your God's meticulous planning of a path leading from bacteria to humans. 
DAVID: As stated above, the whole arrangement can have come from God's planning.-Yes, indeed. Your God could have planned a mechanism that would autonomously and with unbridled zeal create its own combinations (some successful, some unsuccessful).-BBELLA: I can see Sheldrakes morphic field and the holographic universe fitting well with the above information. Like minds coming from different angles (with words) toward the same information/images.
dhw: I'd be interested to know the extent to which you see morphic fields and the holographic universe fitting in with the panpsychist hypothesis that all things have their own form of quasi-consciousness or intelligence (inverted commas, because this should not be equated with human consciousness and intelligence).-DAVID: I accept Sheldrake's human consciousness work, having studied his findings, but his morphic fields as well as holographic universe theories are just proposals, without any basis in study. And yes, cells under the guidance of their genomes do appear to act intelligently, or perhaps they have been intelligently planned to act that way.-Your first cause, eternally conscious energy is just a proposal, without any basis in study. And cells that appear to act intelligently may be intelligent, and perhaps their intelligence was designed to act autonomously.

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> dhw: I'm not aware of anyone doing my thinking for me, though I know some lovely people who give it a good try! I'm glad you think the higgledy-piggledy bush and the extinction of 99% of species and the ever changing balance of nature are all compatible with your God having planned humans from the start of evolution. That will save you from thinking any more about it.-Just don't think for my construction of a reasonable theory for me. I keep watching the literature, and will change my mind if a demonstrable lead appears. Note I do it most days of the week.
> DAVID: the whole arrangement can have come from God's planning.
> 
> dhw: Yes, indeed. Your God could have planned a mechanism that would autonomously and with unbridled zeal create its own combinations (some successful, some unsuccessful).-Thank you. That is my concept.-> 
> dhw: Your first cause, eternally conscious energy is just a proposal, without any basis in study. And cells that appear to act intelligently may be intelligent, and perhaps their intelligence was designed to act autonomously.-All true. It is a logical proposal based on the resultant reality we see.. The genome, designed with intelligent planning will then act intelligently.

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The first exchanges come under Negative atheism? but I am combining them here, as the discussion is more relevant to the inventive mechanism.-dhw: And how does a blob of eternal energy acquire a planning consciousness? -DAVID: Because the eternal energy has always been conscious. For a proper first cause to have the potential to create complexity it has to have always been that way.
dhw: I find that just as difficult to imagine as consciousness evolving through ever changing matter, which would also produce the attributes we see.
DAVID: So do I.-And so there is no has to have been. Inexplicable, causeless eternal consciousness is no more imaginable (and in my view no more likely) than inexplicable evolving consciousness. It's a matter of faith, not logic.-dhw: As far as planning is concerned, I have explained many times that it would come from within countless, ever evolving intelligences working together.
DAVID: Where do your intelligences come from? Do they plan as a committee? Or could they be different aspects of one universal intelligence, which panpsychism might represent.-Horizontal gene transfer is a clear example of what I have called intelligent cooperation between cells. No need for anthropomorphic committee meetings. I do not know where the intelligences came from initially, but they might be different aspects of a single intelligence (most panpsychist theories are theistic). That makes no difference to the inventive mechanism hypothesis I offer as an alternative to your theory that 3.7 billion years ago your God preprogrammed the first cells with every innovation from bacteria to humans.
 
The article showed that some experiments worked and others didn't, which suggests higgledy-piggledy, balanced or unbalanced D-I-Y by the genes themselves rather than the anthropocentric advanced planning so dear to your heart.
DAVID: H-P [higgledy-piggledy] is required.
dhw: Which is like saying that if you plan to make an omelette, you must make a Yorkshire pudding, a shepherd's pie, and a cheesecake as well. (And then throw them away.)
DAVID: Anthropomorphic reasoning. We are discussing evolving life, a marked level above acting as a chef.-So we'll drop the image. God's purpose was to make humans, and in order to do so he was apparently required to make trilobites and dinosaurs and millions of other diddly-squats which then went extinct. I don't buy it, and it would seem that there has also been a subtle shift now in your own reasoning :-D AVID: the whole arrangement can have come from God's planning.
dhw: Yes, indeed. Your God could have planned a mechanism that would autonomously and with unbridled zeal create its own combinations (some successful, some unsuccessful).
DAVID: Thank you. That is my concept.-My thanks go to you. After months of insisting that God had preplanned everything, and cells were mere automatons obeying his instructions (though perhaps with the ability to make minor adaptations of their own), you now appear to accept the possible autonomy of the inventive mechanism. I do not ask for more.-dhw: Your first cause, eternally conscious energy is just a proposal, without any basis in study. And cells that appear to act intelligently may be intelligent, and perhaps their intelligence was designed to act autonomously.
DAVID: All true. It is a logical proposal based on the resultant reality we see. The genome, designed with intelligent planning will then act intelligently.-I have at all times made the concession that the cells' intelligence MAY have been designed by your God. Since you now accept the possible autonomy of cellular (genomic) intelligence, we are in agreement at last.-**********-I shall need time to digest the new posts from yourself and Tony, whose return I greet with great pleasure.

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> dhw: Inexplicable, causeless eternal consciousness is no more imaginable (and in my view no more likely) than inexplicable evolving consciousness. It's a matter of faith, not logic.-It is a matter of logically realizing that only a competent planning consciousness can be the only first cause. First logic, then faith. An inexplicable evolving consciousness must be endowed with potentiality somehow to do what you profess to think might be possible. What makes your ideal IEC evolve? -> 
> dhw:Horizontal gene transfer is a clear example of what I have called intelligent cooperation between cells. No need for anthropomorphic committee meetings. I do not know where the intelligences came from initially, but they might be different aspects of a single intelligence (most panpsychist theories are theistic).-You like panpsychism, or at least you use it as a starting point for your theories. Can it be you are entertaining a switch to theism? -> 
> dhw: My thanks go to you. After months of insisting that God had preplanned everything, and cells were mere automatons obeying his instructions (though perhaps with the ability to make minor adaptations of their own), you now appear to accept the possible autonomy of the inventive mechanism. I do not ask for more.-But you push too far. Semi-autonomy is only as far as I will ever go.
 
> dhw: I have at all times made the concession that the cells' intelligence MAY have been designed by your God. Since you now accept the possible autonomy of cellular (genomic) intelligence, we are in agreement at last. -Make it semi-autonomy and we are in synch.

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Dhw (under Negative atheism?): And so I see rational cause for NOT believing one way or the other (God, chance). It was a conclusion I reached in my late teens (only later did I discover that Darwin himself was an agnostic), and although I feel I have learned a great deal since, what I have learned has so far not clarified any of these major issues.
DAVID: And I thought I was getting closer to convincing you! My teaching entries are quite clear.-Your teaching entries are wonderfully clear in relation to the complexities of life and lifestyles. It's your conclusions that are so murky, though you state them with great authority! -dhw: Inexplicable, causeless eternal consciousness is no more imaginable (and in my view no more likely) than inexplicable evolving consciousness. It's a matter of faith, not logic.
DAVID: It is a matter of logically realizing that only a competent planning consciousness can be the only first cause. First logic, then faith. An inexplicable evolving consciousness must be endowed with potentiality somehow to do what you profess to think might be possible. What makes your ideal IEC evolve? -Round and round we go. What makes your ideal first-cause energy conscious? You can't answer, except by stating authoritatively that first-cause energy has to be conscious. Maybe non-conscious first cause energy has been transmuting itself into matter for ever and ever, and at long last its billions of universes have spawned life by chance. You are fond of quoting mathematical odds against chance. Well, given eternity and an infinite number of universes, what are the odds? Is this a fantasy? You might ask yourself what your eternally conscious God might have been doing with himself for the eternity that preceded our time. Whatever may be the first cause, it must have the potential to create universes by the billion. No, I don't believe in chance. Nor do I believe in an uncaused conscious mind that creates and encompasses universes. But not believing is not the same as disbelieving.
 
dhw: Horizontal gene transfer is a clear example of what I have called intelligent cooperation between cells. No need for anthropomorphic committee meetings. I do not know where the intelligences came from initially, but they might be different aspects of a single intelligence (most panpsychist theories are theistic).
DAVID: You like panpsychism, or at least you use it as a starting point for your theories. Can it be you are entertaining a switch to theism?-I use it as an alternative to your God and to chance. Somewhere along the line, there has to be intelligence, but we just don't know where it begins. You say that somehow intelligence has always been there. Perhaps George will argue that somehow it evolved through life on earth, which began by chance. Most panpsychist theories are along the lines that particles of God somehow end up in all things, but mine is that somehow intelligence evolved through changing matter, which would result in billions of intelligences, not one. Hence evolution through cooperation between different forms (which I confess I find vastly more credible in the organic than in the inorganic world). But all of these somehow options remain open. I am exploring, not preaching.-dhw: My thanks go to you. After months of insisting that God had preplanned everything, and cells were mere automatons obeying his instructions (though perhaps with the ability to make minor adaptations of their own), you now appear to accept the possible autonomy of the inventive mechanism. I do not ask for more.
DAVID: But you push too far. Semi-autonomy is only as far as I will ever go.-Why ever? Why not stick to not knowing the extent of its autonomy, which leaves open the possibility that it extends far beyond minor adaptations? Don't close your mind.

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dhw:It's your conclusions that are so murky, though you state them with great authority!-It is crystal-clear to me!
 
> dhw: Round and round we go. ... You might ask yourself what your eternally conscious God might have been doing with himself for the eternity that preceded our time.- Amazingly as an agnostic you love to imagine what God might think or might do for entertainment. I never do that, since for me God just IS. ->dhw I don't believe in chance. Nor do I believe in an uncaused conscious mind that creates and encompasses universes. But not believing is not the same as disbelieving.-Just be careful as you spin round and round that your body doesn't end up in a circular anastomosis. -> DAVID: Can it be you are entertaining a switch to theism?[/i]
> 
> dhw: I use it as an alternative to your God and to chance. Somewhere along the line, there has to be intelligence, but we just don't know where it begins. You say that somehow intelligence has always been there. ... Most panpsychist theories are along the lines that particles of God somehow end up in all things, but mine is that somehow intelligence evolved through changing matter, which would result in billions of intelligences, not one.... I am exploring, not preaching.-Yes, exploring. Please explore the issue I keep mentioning. The start of the universe and the start of life both require information, which then comes across as your term 'intelligence'. See the discussion about George's assertion we can have something from nothing.-> DAVID: But you push too far. Semi-autonomy is only as far as I will ever go [re an IM].
> 
> dhw:Why ever? Why not stick to not knowing the extent of its autonomy, which leaves open the possibility that it extends far beyond minor adaptations? Don't close your mind.-I'm not close-minded. But at the present time we do not know the extent of an IM's ability. Currently we are discussing it in the realm of supposition. If we find proof of total autonomy I will change my mind. But semi-autonomous fits my concept of theistic evolution. You see my mind works authoritatively. You are the fuzzy one, with options in every possible direction.

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dhw: It's your conclusions that are so murky, though you state them with great authority!
DAVID: It is crystal-clear to me!-He who sees clearly sees not the whole picture. (New Taunton proverb)-dhw: Round and round we go. ... You might ask yourself what your eternally conscious God might have been doing with himself for the eternity that preceded our time.
DAVID: Amazingly as an agnostic you love to imagine what God might think or might do for entertainment. I never do that, since for me God just IS. -Amazingly for someone who claims never to imagine what God might think, you tell us that he preprogrammed all the innovations and complex lifestyles 3.7 billion years ago for the purpose of creating humans (but you've now decided he didn't dabble), and you know that God likes to hide. He tests. He cannot be tested. (Falsifiability, 19 December at 00.53) But we mustn't ask ourselves what he might have done before he created this universe.-dhw I don't believe in chance. Nor do I believe in an uncaused conscious mind that creates and encompasses universes. But not believing is not the same as disbelieving.
DAVID: Just be careful as you spin round and round that your body doesn't end up in a circular anastomosis.-Luckily for me, I don't know what that means, and dictionary definitions don't help much, except that they all involve making connections. That is one of the eye-opening things about our forum: everybody looks at the world, and makes different connections.
 
Dhw: I am exploring, not preaching.
DAVID: Yes, exploring. Please explore the issue I keep mentioning. The start of the universe and the start of life both require information, which then comes across as your term 'intelligence'. See the discussion about George's assertion we can have something from nothing.-I have explicitly stated many times, including in my post of yesterday, that I do not accept the something from nothing theory. (My thanks to you and Tony for your illuminating comments on the article George referred us to.) We have discussed umpteen times the fact that the universe and life require information, but you are only willing to explore one explanation of its origins, and when you are confronted with the sheer unimaginableness and totally unscientific nature of that explanation, your response is: One must jump the chasm to faith. -DAVID: But you push too far. Semi-autonomy is only as far as I will ever go [re an IM].
dhw: Why ever? Why not stick to not knowing the extent of its autonomy, which leaves open the possibility that it extends far beyond minor adaptations? Don't close your mind.
DAVID: I'm not close-minded. But at the present time we do not know the extent of an IM's ability. Currently we are discussing it in the realm of supposition. If we find proof of total autonomy I will change my mind.-I suggested that you stick to not knowing the extent, and you reply that we do not know the extent! On the basis of that, you say that semi-autonomy is only as far as you will EVER go. This sounds pretty closed to me, though of course everyone will change their mind if they are confronted with proof. Even an atheist would become a theist if we found proof of God's existence.-DAVID: But semi-autonomous fits my concept of theistic evolution. You see my mind works authoritatively. You are the fuzzy one, with options in every possible direction.-Yes, I see different options. My "fuzziness" is due to the fact that I do not have a fixed concept to which I can try to fit the evidence. I look at the evidence and try to find concepts that fit. Alas, so far none of them do.

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dhw;Amazingly for someone who claims never to imagine what God might think, you tell us that he preprogrammed all the innovations and complex lifestyles 3.7 billion years ago for the purpose of creating humans.... But we mustn't ask ourselves what he might have done before he created this universe.-We can only know about God's probable intentions from the point where time began. There we have a degree of evidence. I'm glad you can think about the pre-time era. You do it either to get confused about issues or to keep your mind occupied. To me it makes no sense to go back there.
> 
> dhw: Luckily for me, I don't know what that means, and dictionary definitions don't help much, except that they all involve making connections. That is one of the eye-opening things about our forum: everybody looks at the world, and makes different connections.-Don't ask. It is a medical school joke involving an impossible ano-buccal anastomosis.-
> dhw: I have explicitly stated many times, including in my post of yesterday, that I do not accept the something from nothing theory.-Only desperate atheists do it. -> dhw but you are only willing to explore one explanation of its origins, and when you are confronted with the sheer unimaginableness and totally unscientific nature of that explanation, your response is: One must jump the chasm to faith.-That is why is described as a chasm.
 
> DAVID: But semi-autonomous fits my concept of theistic evolution. You see my mind works authoritatively. You are the fuzzy one, with options in every possible direction.
> 
> dhw: Yes, I see different options. My "fuzziness" is due to the fact that I do not have a fixed concept to which I can try to fit the evidence. I look at the evidence and try to find concepts that fit. Alas, so far none of them do.-You still have it bass-ackwards. The evidence strongly points to a planning consciousness.

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DAVID: ...you love to imagine what God might think [...] I never do that, since for me God just IS.
dhw: Amazingly for someone who claims never to imagine what God might think, you tell us that he preprogrammed all the innovations and complex lifestyles 3.7 billion years ago for the purpose of creating humans.... But we mustn't ask ourselves what he might have done before he created this universe.
DAVID: We can only know about God's probable intentions from the point where time began. There we have a degree of evidence. I'm glad you can think about the pre-time era. You do it either to get confused about issues or to keep your mind occupied. To me it makes no sense to go back there.-You claim never to imagine what God might think, and yet you know about his (probable) intentions! In order to explain our universe, you inevitably have to consider what preceded it, and you have come up with first cause conscious energy. Some atheists say it makes no sense to go back there, because there was nothing before the Big Bang. Why are you so frightened of even considering the possibility that this was not the first ever universe?-dhw: ...but you are only willing to explore one explanation of its origins, and when you are confronted with the sheer unimaginableness and totally unscientific nature of that explanation, your response is: One must jump the chasm to faith.-DAVID: That is why is described as a chasm.-And yet you claim that science IS finding God, and that there is no other logical explanation, although you know yourself that this hypothesis is as unimaginable and as unscientific as any other.-DAVID: But semi-autonomous fits my concept of theistic evolution. You see my mind works authoritatively. You are the fuzzy one, with options in every possible direction.
dhw: Yes, I see different options. My "fuzziness" is due to the fact that I do not have a fixed concept to which I can try to fit the evidence. I look at the evidence and try to find concepts that fit. Alas, so far none of them do.
DAVID: You still have it bass-ackwards. The evidence strongly points to a planning consciousness.-That is the subject of our ongoing discussions. But the particular reference here was to the autonomy of the IM, and that actually allows for a planning consciousness. My point was that you have a fixed concept concerning theistic evolution (anthropocentric, preprogrammed 3.7 billion years ago) and refuse to acknowledge that evidence such as the higgledy-piggledy bush and research into cellular intelligence is open to a different interpretation.

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DHW: Amazingly for someone who claims never to imagine what God might think, you tell us that he preprogrammed all the innovations and complex lifestyles 3.7 billion years ago for the purpose of creating humans (but you've now decided he didn't dabble), and you know that God likes to hide. He tests. He cannot be tested. (Falsifiability, 19 December at 00.53) But we mustn't ask ourselves what he might have done before he created this universe.
> -Hrmm, but the concept of God, at least from my perspective, is falsifiable. Both by science, Archaeology, and Philosophy. I am not going to hijack this thread derailing into that statement, but yes, there is a means to falsify god, and ironically, God provides the means to falsify him.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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> 
> Tony: Hrmm, but the concept of God, at least from my perspective, is falsifiable. Both by science, Archaeology, and Philosophy. I am not going to hijack this thread derailing into that statement, but yes, there is a means to falsify god, and ironically, God provides the means to falsify him.-Please give us your approach. This is an instructional and learning website.

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> > 
> > Tony: Hrmm, but the concept of God, at least from my perspective, is falsifiable. Both by science, Archaeology, and Philosophy. I am not going to hijack this thread derailing into that statement, but yes, there is a means to falsify god, and ironically, God provides the means to falsify him.
> 
>David: Please give us your approach. This is an instructional and learning website.-The Bible's claim is that it is 100% true. That gives three sets of predictions:-The statements regarding science will be 100% accurate. 
The Statements regarding history will be 100% accurate. -Neither one of those, in of itself prove anything divine, but they do build a record of reliability.-The on the proves divine influence is prophecy. Since prophecy, particularly specific prophecies over large time scales have no rational explanation, a 100% accuracy rating is the test of falsifiability.-The only scientific statement that I know for certain has yet to be proven is the Flood account. There is a lot of archaeological evidence, but there is a lot of argument over the flood, which, ironically, fulfills a prophecy. :P

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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> > > 
> > > Tony: Hrmm, but the concept of God, at least from my perspective, is falsifiable. Both by science, Archaeology, and Philosophy. I am not going to hijack this thread derailing into that statement, but yes, there is a means to falsify god, and ironically, God provides the means to falsify him.
> > 
> >David: Please give us your approach. This is an instructional and learning website.-David, what is your take on this-
http://www.grisda.org/origins/24002.htm-Particularly, note the following:-"Occasionally stumps and logs show driftwood-like abrasion or broken and reduced root systems...
Careful examination of the top few centimeters of the broken tops of erect stumps sometimes shows the wood tissue to be twisted and smashed, not from the breakage of the tree trunk, but from subsequent abrasion, perhaps by rocks and colliding trees."-" Note the wide range of habitats and ecological requirements. The fossil wood and leaves have been identified to modern genera that live in widely differing habitats and environments."- "In this research, gross identification of the wood specimens in the organic levels was undertaken. Trees were classified as pine-type (resin ducts present), sequoia-type (no resin ducts), and deciduous (vessels present). Leaves and needles in the organic levels were identified using the same categories.
 
 Taxonomic sorting of the constituents in the organic bands (needles and leaves not mixed together) was noticed early in the research. Under normal conditions leaves, needles, cones, limbs, bark, etc., fall as a well-mixed litter onto the forest floor year by year as the seasons pass and the trees grow. A flotation experiment involving aspen and poplar leaves and fir needles in a tank of water showed that the needles became saturated and sank to the bottom first. Thus flotation in water is a possible explanation for the observed taxonomic sorting in the "soil" levels."-"That these trees in Oregon have a similar origin and history to those of Yellowstone is a reasonable assumption. An example from an organic level from this Oregon formation shows similar size sorting of the inorganic particles among or between leaves (Figure 13)."-"Despite much study of the Yellowstone Petrified Forests, no animal fossils have been found. Why are animal remains absent from the plant fossil-bearing levels of Yellowstone? Because forests would be expected to harbor a wide variety of animals, some of which would be buried by the successive mud slides, the absence of animal fossils has been a mystery. Volcanic activity could have caused larger forest animals to flee elsewhere, but flight cannot be used as an explanation for the absence of all animal remains because many animals could not or would not leave their forest habitats. "

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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> > > > 
> > > > Tony: Hrmm, but the concept of God, at least from my perspective, is falsifiable. Both by science, Archaeology, and Philosophy. I am not going to hijack this thread derailing into that statement, but yes, there is a means to falsify god, and ironically, God provides the means to falsify him.
> > > 
> > >David: Please give us your approach. This is an instructional and learning website.
> 
> Tony: David, what is your take on this-Fascinating study. Yellowstone, which I have visited several times, is a huge caldera with marvelous features. That it was part of Noah's flood is an interesting conjecture. At least there were termites in the petrified trees, if no other animals found so far. -As far as floods are concerned, it seems pretty obvious to me the great Black Sea flood after the last glacial period, is the basis for the Noachian Flood story. What supports your point of view is the recent suggestion that Earth's mantel contains a huge amount of water. In the story 'much of the water rose from the depths'. Perhaps it could be proposed it receded back there during the miracle. I can see how your thinking runs, but I'm still convinced of a local flood to explain the story. Now if the Ark could be found on Mt. Ararat, we could stop this website.

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> > > > > 
> > > > > Tony: Hrmm, but the concept of God, at least from my perspective, is falsifiable. Both by science, Archaeology, and Philosophy. I am not going to hijack this thread derailing into that statement, but yes, there is a means to falsify god, and ironically, God provides the means to falsify him.
> > > > 
> > > >David: Please give us your approach. This is an instructional and learning website.
> > 
> > Tony: David, what is your take on this
> 
>David: Fascinating study. Yellowstone, which I have visited several times, is a huge caldera with marvelous features. That it was part of Noah's flood is an interesting conjecture. At least there were termites in the petrified trees, if no other animals found so far. 
> 
> As far as floods are concerned, it seems pretty obvious to me the great Black Sea flood after the last glacial period, is the basis for the Noachian Flood story. What supports your point of view is the recent suggestion that Earth's mantel contains a huge amount of water. In the story 'much of the water rose from the depths'. Perhaps it could be proposed it receded back there during the miracle. I can see how your thinking runs, but I'm still convinced of a local flood to explain the story. Now if the Ark could be found on Mt. Ararat, we could stop this website.-Actually, the part that makes it interesting is that 
A) That area is more than 5000 feet above sea level.
B) The trees are not native to that area, so they had to come from somewhere (some were native to SE Asia)
C) There were mirror sites in Oregon near the same elevations containing the same type of layers and fauna.-How did trees from Asia end up 5000 + feet above sea level in the U.S. in layered strata in a short amount of time?

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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> Tony: Actually, the part that makes it interesting is that 
> A) That area is more than 5000 feet above sea level.
> B) The trees are not native to that area, so they had to come from somewhere (some were native to SE Asia)
> C) There were mirror sites in Oregon near the same elevations containing the same type of layers and fauna.
> 
> How did trees from Asia end up 5000 + feet above sea level in the U.S. in layered strata in a short amount of time?-The flood was supposed to cover all the mountains. Everest is 29,000+ feet or thereabouts. That makes your point very interesting. My maim problem is the ark. How did Noah get kangaroos and llamas on board, as two examples of far distant animals from the site of where the ark landed.

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> Tony: Actually, the part that makes it interesting is that 
> A) That area is more than 5000 feet above sea level.
> B) The trees are not native to that area, so they had to come from somewhere (some were native to SE Asia)
> C) There were mirror sites in Oregon near the same elevations containing the same type of layers and fauna.
> 
> How did trees from Asia end up 5000 + feet above sea level in the U.S. in layered strata in a short amount of time?-You make a good point about the elevation of the forest. The story tells that the water covered all the mountains, which with Everest at 29,000+ feet or thereabouts, would certainly reach Yellowstone. I read the article carefully. What it does not mention is trees from Asia. but that aside, what really makes me raise questions is the Ark which was not that large. How did Noah get kangaroos and llamas in his region of the world, as examples of species far afield from where the Ark landed. All of the animals boarded at the same time. Also two by two makes for a terrible genetic pool for each species. And what happened to all of the plant vegetation that drowned? None were taken on the Ark and the flood lasted 150 days. -From your comments to dhw you have done an amazing amount of study. Very admirable to me. I'm glad you responded to my request for more material from your point of view. Dhw thinks I am closed-minded. I'm not, but I can't know everything, and I work to conclusions from the material I've had time to cover.

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Cinnamonum ...	cinnamon-Cinnamomum camphora is native to China south of the Yangtze River, Taiwan, southern Japan, Korea, and Vietnam, and has been introduced to many other countries.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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> > Tony: Actually, the part that makes it interesting is that 
> > A) That area is more than 5000 feet above sea level.
> > B) The trees are not native to that area, so they had to come from somewhere (some were native to SE Asia)
> > C) There were mirror sites in Oregon near the same elevations containing the same type of layers and fauna.
> > 
> > How did trees from Asia end up 5000 + feet above sea level in the U.S. in layered strata in a short amount of time?
> 
> David: You make a good point about the elevation of the forest. The story tells that the water covered all the mountains, which with Everest at 29,000+ feet or thereabouts, would certainly reach Yellowstone. I read the article carefully. What it does not mention is trees from Asia. but that aside, what really makes me raise questions is the Ark which was not that large. How did Noah get kangaroos and llamas in his region of the world, as examples of species far afield from where the Ark landed. All of the animals boarded at the same time. Also two by two makes for a terrible genetic pool for each species. And what happened to all of the plant vegetation that drowned? None were taken on the Ark and the flood lasted 150 days. 
> 
> From your comments to dhw you have done an amazing amount of study. Very admirable to me. I'm glad you responded to my request for more material from your point of view. Dhw thinks I am closed-minded. I'm not, but I can't know everything, and I work to conclusions from the material I've had time to cover.-
Well, as far as how he got them there, a Pangea is not a biblical concept, but it does have a lot of supporting evidence. That would, perhaps, at least explain them being on one continent, which is also in line with Genesis where it talks about the animals being brought to Adam to be named. That also gives us the 'how'. If God could cause the animals to gather in one location to be named, then he could certainly manage for Noah. It never says Noah actually rounded them up himself. -As far as the space requirements, that is an issue, I admit, and one of the reasons I am intensely curious about speciation vs. adaptation. Taking two dogs with perfect bloodlines would carry all the genetic material needed for all many varieties on the planet, but because our current taxonomy is definitely wrong (by a genetic standpoint) it is very difficult to say which creatures would have had to have been on board. I don't pretend to have an easy answer to every problem.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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> 
> tony: Well, as far as how he got them there, a Pangea is not a biblical concept, but it does have a lot of supporting evidence. That would, perhaps, at least explain them being on one continent,-Pangea is about 60 myo. What is your timeline for Noah? You must be an Old Earth type believer. -> Tony: As far as the space requirements, that is an issue, I admit, and one of the reasons I am intensely curious about speciation vs. adaptation.... I don't pretend to have an easy answer to every problem.-Thanks for your honesty.

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Even if the biblical timeline for Noah is accurate, i.e. 6000+/-, it would not necessarily disprove the old earth, merely OUR timeline for the pangea expansion.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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Tony: Even if the biblical timeline for Noah is accurate, i.e. 6000+/-, it would not necessarily disprove the old earth, merely OUR timeline for the pangea expansion.-I accept the Pangea age as scientifically stated.

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> > > 
> > > Tony: Hrmm, but the concept of God, at least from my perspective, is falsifiable. Both by science, Archaeology, and Philosophy. I am not going to hijack this thread derailing into that statement, but yes, there is a means to falsify god, and ironically, God provides the means to falsify him.
> > 
> >David: Please give us your approach. This is an instructional and learning website.
> 
> The Bible's claim is that it is 100% true. That gives three sets of predictions:
> 
> The statements regarding science will be 100% accurate. 
> The Statements regarding history will be 100% accurate. 
> 
> Neither one of those, in of itself prove anything divine, but they do build a record of reliability.
> 
> The on the proves divine influence is prophecy. Since prophecy, particularly specific prophecies over large time scales have no rational explanation, a 100% accuracy rating is the test of falsifiability.
> 
> The only scientific statement that I know for certain has yet to be proven is the Flood account. There is a lot of archaeological evidence, but there is a lot of argument over the flood, which, ironically, fulfills a prophecy. :P-Tony, I agree with most of what you say here, though there is one idea I would like to explore more fully. Your claim is that if prophecies have been fulfilled 100% of the time, there is no other "rational" explanation than divine influence. This "rationality" completely hinges on your belief in a divine, biblical God. I've done much study and research as well on the biblical prophecies and agree, from a biblical believer/researcher's standpoint, their fulfillment's do appear to be near 100% - allowing for those yet to be fulfilled. -But, is there really no other "rational" explanation for what appears as prophecies fulfilled over long time scales than a divine, biblical God created all there is and knows all there is and so has divinely inspired a book to prove it? In my mind there are other just as rational explanations. If a mind is open to possibilities (that anything is possible) and looks elsewhere for explanations of how these things can be so, the Ancient Alien, time travel, Angels as Aliens, a connection to the Akashic/Hall of Records, and many more theories seem just as rational to me, if not more rational to me than a divine biblical creator of all that is, comes down in time and inspires stories and prophecies to a tiny new race of humans in all the universe to prove his existence. And then asks for worship and belief, as well as followers. -Unless we know for a fact these other (or any other) possibilities are not so, we cannot know for a fact the Bible is "divinely" written (from a deity) with inspired words. They may seem divinely inspired to us earth humans, because we as a new race, have less knowledge and understanding than those who inspired the writers to write them. Those that inspired them could have been an alien race, a future race, or humans that connected with the Hall of Records - or something else. -What seems rational and divine to one may not be rational or divine to another, so your belief in a divinely inspired God explanation is not the only possibility. But being brought up in this belief definitely makes it feel more comfortable for many.

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From a statistical standpoint, just the prophecies about the life of Christ being fulfilled 100% are beyond the point being of statistically impossible. -Let's me phrase the question this way. In science, if a theory were to have even a 70% success rate, we would question our thinking if we found something that did not agree with the theory. Evolution has a FAR poorer success rate than that. Even supposed "facts" such as the theory of gravity has a far poorer success rate. Yet, in science, if we find something that doesn't agree with a well supported theory, we tend to question our findings or assume that we are missing something or ignorant of something before we just discard the theory altogether.-If you consider the bible as a scientific theory, why does it not enjoy the same degree of trust that we would give any other scientific theory that has demonstrated such a high degree of success?

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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If you consider the bible as a scientific theory, why does it not enjoy the same degree of trust that we would give any other scientific theory that has demonstrated such a high degree of success?-I completely agree about the Bible having full authority (in my opinion) of true stories that have factual archaeological and prophetic proof, as well as life changing guidance. -And I have no qualms recognizing the supernatural hand (to my human view) at work within it's pages and stories. The Bible Code alone is enough to accept there is something "otherworldly" at work here, though my belief in it's authority came long before I studied the Bible Code. My questioning has nothing to do with its validity or truth. My question is the WHO behind the inspired hand.

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I hate to be the devil's advocate here (ok, I lie, I don't hate it.) but there are a fair number of rather large speculative gaps here. Lot's of "could have's" and "possibly's" with no real actual scientific data. -
"The mite regularly parasitises both D melanogaster and D willistoni, using its needling mouthparts to suck up nutrients from fruit fly eggs and larvae. Such a parasite could conceivably transfer DNA from the egg of one fruit fly species to another." (Note that they didn't say it has been proven to happen)-"Thus exposed, the fern's gametes could easily come into contact with the similarly liberated sperm and eggs of hornworts, which tend to congregate in the same moist spots on the forest floor. If damaged or malformed gametes from both plants found one another, they could have traded DNA across their broken membranes before fusing with one of their own kind."-They then went on to compare the likely hood of a process they have not witnessed to viral transmissions which are on a totally different level. What I see when I read this is: -"We find a lot of stuff that doesn't agree with the theory of evolution. In order to save the theory of evolution, we have to create some new method that can be neither proved nor disproved to support the theory."

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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> Tony: They then went on to compare the likely hood of a process they have not witnessed to viral transmissions which are on a totally different level. What I see when I read this is: 
> 
> "We find a lot of stuff that doesn't agree with the theory of evolution. In order to save the theory of evolution, we have to create some new method that can be neither proved nor disproved to support the theory."-My point is HGT is accepted as happening. Perhaps God arranged for it when life's genomes were set up.

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> > Tony: They then went on to compare the likely hood of a process they have not witnessed to viral transmissions which are on a totally different level. What I see when I read this is: 
> > 
> > "We find a lot of stuff that doesn't agree with the theory of evolution. In order to save the theory of evolution, we have to create some new method that can be neither proved nor disproved to support the theory."
> 
>David: My point is HGT is accepted as happening. Perhaps God arranged for it when life's genomes were set up.-Which is more likely, that genes were swapped like baseball cards and every organism managed to make them do something useful, of that the "gene pool" is nothing more than a standard collection of function libraries which were used to program similar functions wherever they were needed?

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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> >David: My point is HGT is accepted as happening. Perhaps God arranged for it when life's genomes were set up.
> 
>Tony: Which is more likely, that genes were swapped like baseball cards and every organism managed to make them do something useful, of that the "gene pool" is nothing more than a standard collection of function libraries which were used to program similar functions wherever they were needed?-Which is why I brought up the issue of primary patterns, which is something you first pointed out in programming comparisons. I think you are right, but it may in part be due in part to horizontal transfers. Some animals come with organs for that purpose.

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TONY: I hate to be the devil's advocate here (ok, I lie, I don't hate it.) but there are a fair number of rather large speculative gaps here. Lot's of "could have's" and "possibly's" with no real actual scientific data. -"The mite regularly parasitises both D melanogaster and D willistoni, using its needling mouthparts to suck up nutrients from fruit fly eggs and larvae. Such a parasite could conceivably transfer DNA from the egg of one fruit fly species to another." (Note that they didn't say it has been proven to happen)-The next sentence is: Follow up studies showed that mites feeding on fruit flies did indeed harbor the P element. Here is another quote from the same article: -Scientists have known for many decades that prokaryotes such as bacteria and other microorganisms - which lack a protective nucleus enveloping their DNA - swap genetic material with each other all the time. Researchers have also documented countless cases of viruses shuttling their genes into the genomes of animals, including our own.
What has become increasingly clear in the past 10 years is that this liberal genetic exchange is definitely not limited to the DNA of the microscopic world. It likewise happens to genes that belong to animals, fungi and plants, collectively known as eukaryotes because they boast nuclei in their cells. (My bold)-Definitely could hardly be more factual, and David says it is accepted as happening (I presume he means by the scientific community). You wrote: In order to save the theory of evolution, we have to create some new method that can be neither proved nor disproved to support the theory. I would say that if HGT is an established fact, it's not unreasonable to investigate the extent to which it might be responsible for major innovations that lead to new species. A theist can always argue, as David does, that it's all part of the mechanism God devised in the first place. As I have pointed out ad nauseam, evolution is not an atheistic theory. -However, the problem you raise is very significant for non-scientists like myself, and can be extended to most walks of life in which we ourselves are not proficient. We simply don't know how far we can trust the so-called experts. That's why we so rarely get consensus on any of the subjects that we discuss here!

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DHW: Definitely could hardly be more factual, and David says it is accepted as happening (I presume he means by the scientific community). You wrote: In order to save the theory of evolution, we have to create some new method that can be neither proved nor disproved to support the theory. I would say that if HGT is an established fact, it's not unreasonable to investigate the extent to which it might be responsible for major innovations that lead to new species. A theist can always argue, as David does, that it's all part of the mechanism God devised in the first place. As I have pointed out ad nauseam, evolution is not an atheistic theory. 
> 
> However, the problem you raise is very significant for non-scientists like myself, and can be extended to most walks of life in which we ourselves are not proficient. We simply don't know how far we can trust the so-called experts. That's why we so rarely get consensus on any of the subjects that we discuss here!-Note that I did not say HGT does not happen. We know from experimental data that virus's do in fact copy dna to/from it's host. We also know that during sexual reproduction genetic material is transferred in the blending of genes from both parents into the final child life form. My main point was that the other methods of transmission were clearly, by the wording of the author, speculation, not the result of experimental data which would have been cited had it existed.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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> Tony: They then went on to compare the likely hood of a process they have not witnessed to viral transmissions which are on a totally different level. What I see when I read this is: 
> 
> "We find a lot of stuff that doesn't agree with the theory of evolution. In order to save the theory of evolution, we have to create some new method that can be neither proved nor disproved to support the theory."-What I found was a review essay. I could not check references to check the studies alluded to. But the author says this:-"The fact that horizontal gene transfer happens among eukaryotes does not require a complete overhaul of standard evolutionary theory, but it does compel us to make some important adjustments. According to textbook theories of evolution, the major route of genes moving between organisms is parent to child - whether through sex or asexual cloning - not this sneaky business of escorting genes between unrelated organisms. We must now acknowledge that, even among the most complex organisms, vertical is not the only direction in which genes travel."-http://aeon.co/magazine/science/how-horizontal-gene-transfer-changes-evolutionary-theory/-I've re-read the essay. I find it very positively presented, and damaging to Darwin theory, as God could have set this up as part of His evolutionary program.-Here is another example;-http://www.sciencedaily.com/releases/2014/11/141124125430.htm-"Bacteria compete for resources in the environment by injecting deadly toxins into their rivals. Researcher have now discovered that many animals steal toxins from bacteria to fight unwanted microbes growing on them. Genes for these toxins have jumped from bacterial to animals. These genes are now permanently incorporated into the genomes of these animals. Deer ticks, which can carry Lyme disease, are one of the many diverse organisms in which toxin gene transfers from bacteria to animal has occurred."

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Mice carry endogenous retroviral DNA from previous ancestors to help build antibodies when necessary;-http://www.the-scientist.com//?articles.view/articleNo/41707/title/Repurposed-Retroviruses/-"Retroviral sequences in mammalian genomes are the remnants of old viral infections and, for the most part, their expression is suppressed. But a report published today (December 18) in Science suggests that, in B cells, a particular type of antigen can stimulate transcription of these viral relics, which in turn prompts cell proliferation and antibody production.-"The work is a tour de force, said Michael Cancro, a professor of pathology and laboratory medicine at the University of Pennsylvania Perelman School of Medicine who was not involved in the study. It may well be the seminal paper in resolving this long-standing conundrum of exactly what is a TI-2 antigen doing to get these B cells to kick off.-"TI-2 antigens are so named because they can stimulate B cells to produce antibodies in a T cell-independent (TI) manner. Unlike protein antigenswhich need T helper cells to interact with and stimulate the B cell in which they are being processedTI antigens can stimulate B cells on their own. TI-2 antigens tend to be large polysaccharides with repetitive structures, such as those that encapsulate certain bacteria and viruses. It is known that they interact via multiple crosslinks with B cell receptors, but the subsequent pathway to antibody production was a mystery.-"It turned out that TI-2 stimulated B cells to produce a wide range of endogenous retrovirus (ERV) RNA transcripts from across the genome. These transcripts were then also reverse-transcribed into DNA. Indeed, the team showed that treating the mice with drugs that inhibit reverse transciptase not only reduced ERV-derived DNA, but also the production of TI-2-induced antibodies."

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A very clear-cut study showing how viruses that live in bacteria (bacteriophages) play a major role during gut infections by bacteria:

http://www.the-scientist.com/?articles.view/articleNo/48833/title/Inflammation-Drives-G...

"Intestinal inflammation caused by Salmonella infection activates bacteriophages within the bacteria to spread genes throughout the colony. The findings reveal how genetic traits encoded in the viruses, such as increased virulence, can rapidly emerge in pathogenic bacteria during infection.

***

"Some bacteriophages—bacteria-infecting viruses—kill their hosts immediately. Others take up residence long-term. These temperate phages ensure their retention within a bacterial host by providing the bug with one or more genetic benefits, such as antibiotic resistance or increased virulence. But when the host bacterium is in trouble, it’s a different matter: the phage rapidly replicates, kills the host cell, and heads off to infect nearby healthy bacteria. By transferring their beneficial genes to new hosts in this way, the viruses “play a key role in bacterial evolution,” wrote James. (my bold)

***

"Hardt and colleagues infected mice with two strains of Salmonella bacteria. One strain (donor) contained a phage that encodes a virulence factor, SopE, which helps the bacteria invade host gut cells. The other (recipient) did not. The team introduced small, equal doses of the two strains into the animals to produce an intestinal infection. After as few as 24 hours, phage transfer of the sopE gene from the donor to the recipient strain was apparent. “It was super efficient,” said Hardt.

"So what prompted the transfer? Inside an animal’s gut, Salmonella “gets a severe beating” from the host innate immune system, said Hardt. “They are in real trouble.”
His team therefore hypothesized that the inflammatory environment might be the phage’s signal to escape. To test this idea, the researchers created non-virulent versions of the two Salmonella strains. These strains were able to colonize the gut for approximately three days before causing inflammation, Hardt explained. During this non-inflammatory period, sopE transfer was dramatically reduced, the team showed.

"Furthermore, vaccination of the mice with inactivated Salmonella also significantly repressed phage transfer upon later Salmonella infection. (Vaccination ensures that subsequent infecting bacteria are neutralized by host antibodies rather than innate inflammation.)

“'The study suggests that vaccination can not only protect against bacterial disease; but also reduce the ability of bacteria in the body to transfer genetic material that might enhance virulence or resistance to treatment,” wrote James.

"This previously unappreciated benefit of vaccination should be considered in future immunology studies, Hardt suggested."

Comment: This study shows how viruses take a major role in horizontal gene transfer. Note the bolded sentence. That viruses can be part of an inventive mechanisms that drove evolution has been discussed in other entries previously presented.

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TONY: Note that I did not say HGT does not happen. We know from experimental data that virus's do in fact copy dna to/from it's host. We also know that during sexual reproduction genetic material is transferred in the blending of genes from both parents into the final child life form. My main point was that the other methods of transmission were clearly, by the wording of the author, speculation, not the result of experimental data which would have been cited had it existed.-DAVID (quoting): "The fact that horizontal gene transfer happens among eukaryotes does not require a complete overhaul of standard evolutionary theory, but it does compel us to make some important adjustments. According to textbook theories of evolution, the major route of genes moving between organisms is parent to child - whether through sex or asexual cloning - not this sneaky business of escorting genes between unrelated organisms. We must now acknowledge that, even among the most complex organisms, vertical is not the only direction in which genes travel."-http://aeon.co/magazine/science/how-horizontal-gene-transfer-changes-evolutionary-theory/-I've re-read the essay. I find it very positively presented, and damaging to Darwin theory, as God could have set this up as part of His evolutionary program.
-No matter what mechanism drives evolution, a theist can argue that God could have set it up, so that can hardly be said to damage the theories of common descent and natural selection. HGT illustrates cooperation between autonomous organisms (using their own inventive intelligence). As such it offers a far more convincing explanation of innovations than random mutations, and it goes against gradualism, but we have already long since agreed that Darwin probably got that wrong. Ah well, I know how you love to flog dead horses!

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New discovery in mice:-"But now, a new study in mice by researchers at Washington University School of Medicine in St. Louis has shown that the DNA of bacteria that live in the body can pass a trait to offspring in a way similar to the parents' own DNA. According to the authors, the discovery means scientists need to consider a significant new factor -- the DNA of microbes passed from mother to child -- in their efforts to understand how genes influence illness and health.-"Eventually, the scientists learned that one of the culprits likely responsible for the spread of low antibody levels is a bacterium called Sutterella. This bacterium and others found in the low-IgA mice could explain both ways that decreased antibody levels were spreading: Mice that were housed together acquired low antibody levels through normal spread of the bacteria, and mouse mothers passed the same bacteria to their descendants.-"The latter explanation involves a major change in thinking because it suggests that traits affected by bacteria can pass from mothers to their offspring in the same manner as traits affected by mouse DNA."-http://www.sciencedaily.com/releases/2015/02/150216125425.htm

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Another very good explanatory article about horizontal gene transfer with great graphics:

http://www.the-scientist.com/?articles.view/articleNo/47151/title/Lateral-Gene-Transfer...

The article:

http://www.the-scientist.com/?articles.view/articleNo/47125/title/Bacteria-and-Humans-H...

"Before we understood that DNA was the genetic code, scientists knew that bacteria transferred it between cells. In 1928, 25 years before the structure of DNA was solved, British bacteriologist Frederick Griffith demonstrated that live, nonvirulent bacteria could transform into virulent microbes after being incubated with a heat-killed virulent strain. Fifteen years later, a trio of researchers at the Rockefeller Institute for Medical Research (now Rockefeller University), Oswald Avery, Colin MacLeod, and Maclyn McCarty, demonstrated that this transformation was mediated by DNA. Even dead bacteria, it seemed, could share their genes.

"This DNA-sharing process, known as horizontal or lateral gene transfer (LGT), is now understood to occur by the direct movement of DNA between two organisms. Almost all bacterial genomes show evidence of past LGT events, and the phenomenon is known to have profound effects on microbial biology, from spreading antibiotic resistance genes to creating new pathways for degrading chemicals. But LGT is not limited to bacteria. Scientists now recognize that microbes transfer DNA to the plants, fungi, and animals they infect or reside in, and conversely, human long interspersed elements (LINEs) have been found in bacterial genomes. Moreover, researchers have documented LGT from fungi to insects and from algae to sea slugs. There is reason to believe that any two major groups of organisms—including humans—can share their genetic codes.

***

"Bacteria are a genomically promiscuous bunch. They do not reproduce sexually but are among the most genetically varied species because they are constantly exchanging bits of their genetic code via LGT. Their diversity has allowed them to adapt to every ecological niche on the planet, from deep-sea hydrothermal vents to the frozen lakes of Antarctica, from rock crevices to our own intestines. LGT between bacteria has been categorized as transformation by free DNA (genetic material is released into the environment by bacteria and taken up by living microbes, as in Griffith’s experiment), transduction by viruses, and direct cell-cell transfer through conjugation.

***

"In 2001, the first draft sequence of the human genome was suggested to have 223 LGT-derived regions that were not present in other species’ genomes that had been sequenced at that time.4 Some researchers quickly disputed this number as an overestimate, even suggesting that all of the proposed LGTs were more likely explained through alternative mechanisms such as gene loss or convergent evolution.5 A new analysis published last year by Alastair Crisp of the University of Cambridge and colleagues found more than 130 traces of possible LGT events in the human genome—including the presence of fungal hyaluronan synthases, a fat mass and obesity associated gene (FTO), and the gene responsible for blood types (ABO). But most, if not all, of the identified events predate the human and primate lineages and were identified because the researchers chose to no longer limit the results to LGTs that exist only in humans and not in other animal species.

"In order for a nonhuman gene to appear in the genomes of many people, however, the LGT needs to occur in the germline so that it can be passed to future generations; and it has to confer some benefit to the host."

Comment: It is obvious that evolution can advance with the phenomenon of HGT. It can be debated whether the first cells had this ability or whether it developed later, which brings us back to pre-programming or dabbling by God. This is a very long and interesting article about the research recently performed, but I've out the major evolutionary thrust of the HGT ability.

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A virus has been found using the gene black widow spiders use to make their poison:

https://www.newscientist.com/article/2108671-virus-steals-black-widow-poison-gene-to-he...

"In one of the most unexpected genetic thefts ever, a virus that infects bacteria appears to have stolen the gene coding for the poison of the black widow spiders. The virus, named WO, probably uses the gene to help it attack its targets.

"Viruses often steal genes from their hosts. But because bacterial viruses – also called bacteriophages – only attack bacteria, genes from other domains of life are usually beyond their reach. That would include higher organisms known as eukaryotes, which have cells that contain a nucleus.

"WO, however, faces an unusual challenge: its targets are Wolbachia bacteria living within the cells of insects, spiders, and some other animals. That means that for it to infect new bacterial cells, WO has to escape not only from its existing Wolbachia host, but also from the eukaryotic cell – and then the virus particles have to evade the eukaryote’s powerful immune system.

***

"They found several genes closely related to ones found in eukaryotes, including the gene for latrotoxin, the poison used by black widow spiders. It kills by poking holes in cell membranes, making it a plausible tool for a virus needing to escape from a eukaryotic cell. WO also had other genes like those in eukaryotes, and these may help it evade the immune system.

"This is the first time eukaryotic genes have turned up in a bacterial virus. What’s more, the eukaryote genes make up almost half of WO’s genome.

“'For a phage to devote about half its genome to these eukaryotic-like genes, they must be important to the phage function,” says Sarah Bordenstein. WO probably picks up the eukaryote DNA after breaking out of a Wolbachia cell into the animal cell."

Comment: Another neat say to provide changes in evolution. Was this mechanism present in initial life or developed later? Did God act or provide the mechanism early on?

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My Comment: It is obvious that evolution can advance with the phenomenon of HGT. It can be debated whether the first cells had this ability or whether it developed later, which brings us back to pre-programming or dabbling by God. This is a very long and interesting article about the research recently performed, but I've out the major evolutionary thrust of the HGT ability.

Needs a correction in my garbled typing. The bolded sentence should read, I've brought out the major evolutionary thrust in the article of the HGT ability.

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This is not the usual event, since the plants are highly complex as compared to HGT in bacteria:

https://www.sciencedaily.com/releases/2016/10/161024170709.htm

:In a study, researchers detected 52 incidents of the nonsexual transfer of DNA -- known as horizontal gene transfer, or HGT -- from a host plant that later became functional into members of a parasitic plant family known as the broomrapes, said Claude dePamphilis, professor of biology, Penn State. The transferred genes then became functional in the parasitic species. Although considered rare in more plants and other complex species, like plants, HGT may thus occur in some parasitic plants.

***

"While horizontal gene transfers in less complex species, such as bacteria, is are common, most evolution in more complex organisms is driven by the sexual exchange of DNA, along with mutation and natural selection. However, the researchers suggest that the close feeding connections of parasitic plants with their hosts may increase the chances of intact genes traveling from the host to the parasite's genome where it can quickly become functional.

"'Parasitic plants seem to have a far greater rate of horizontal gene transfer than non-parasitic plants and we think this is because of their very intimate connection they have with their host," said dePamphilis.

"The roots of the parasite contact and enter the host, and then begin extracting water, sugars, mineral nutrients and even nucleic acids, including DNA and RNA, he added.

"'So, they are stealing genes from their host plants, incorporating them into the genome and then turning those genes back around, very often, as a weapon against the host," said dePamphilis.

***

"The researchers focused on transcriptomes -- expressed gene sequences -- of three parasitic plants:,

***

" Because the researchers considered mRNA, which can move between hosts and their parasites, as a possible source of the transfers, they tested and re-tested the data to rule out the experimental host as the source of the genetic material. Instead, they found that the foreign sequences had been derived from entire genes of past host plants and incorporated into the parasitic plants genomes."

Comment: It is becoming apparent that HGT is present all through various branches of life. Remember even human genomes show elements of various viruses. This is one of the inventive mechanisms used in advancing evolution. Knowing it happens does not tell us how it is allowed to happen. The mechanisms need to be discovered. Did God do it? By this I mean is it such a highly complex mechanism that chance evolutionary development is unlikely and therefore agency or saltation is required.

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A new study shows one example of how it probably works:

http://phys.org/news/2016-12-mechanism-successful-horizontal-gene-divergent.html

"The transfer of genes from one organism to another is potentially a rapid way for evolution to occur and for complicated novel functions to emerge. However, even when the two organisms in question are in close proximity to each other, such as in a symbiotic or parasitic relationship, the transfer of genetic material and its introduction into a new genome only marks the initial step for successful horizontal gene transfer. It is also necessary for the gene to be expressed in a way that benefits the new host and ensures that it is passed down through the generations.

***

"The team focused on marine filter feeders called ascidians and their cellulose synthase gene. This gene encodes a protein that helps form an external protective coating, the loss of which leads to a lack of cellulose production and has adverse effects on these organisms. This gene is specifically expressed in the protective outer layer of cells called the epidermis, which was suggested to be key to its coating-related function.

"'We showed that a region adjacent to the cellulose synthase gene is responsible for its specific epidermal expression," study coauthor Yosuke Ogura says. "Sequence analysis revealed that this region contains a binding site of a transcription factor called AP-2 and, when we induced mutations in this binding site, the expression of cellulose synthase in the ascidian epidermis disappeared."

"Although all DNA sequences consists of the four letters or bases of A, C, G, and T, their proportions differ depending on the organism. For example, in actinobacteria , over 70% of the DNA consists of Gs and Cs, while the genome of ascidians has an abundance of As and Ts. The AP-2 binding site in ascidians is actually GC-rich, suggesting it originated from another species. It turns out that this GC bias may have been key to its functional integration.

"'AP-2 inherently binds to GC-rich regions, so it was already primed to start interacting with the bacterial GC-rich DNA once it had integrated into the ascidian genome," first author Yasunori Sasakura says. "The GC-specificity and epidermal expression of AP-2 meant that the introduced cellulose synthase gene could immediately be expressed in its new surroundings in a beneficial way."

"These findings provide interesting insight into one way in which the conditions in the new host can facilitate expression of a newly transferred gene and its integration into the host's functions, reducing the improbability that a randomly inserted foreign gene could actually be beneficial."

Comment: This seems like a very special circumstance in which everything necessary fits. I'm not sure it is close to explaining generalized horizontal transfer, but perhaps each type of transfer has elements of this example. That seems logical.

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Just how it picks out the correct DNA portion is still unknown:

https://phys.org/news/2018-06-scientists-bacteria-harpoon-dna-evolution.html

"Using methods invented at IU, researchers recorded the first images of bacterial appendages—over 10,000 times thinner than human hair—as they stretched out to catch DNA. These DNA fragments can then be incorporated into bacteria's own genome through a process called DNA uptake or "horizontal gene transfer."

***

"The bacterium used in the study was Vibrio cholerae, the microbe that causes cholera. The bacterial structures used to catch DNA in the environment are extremely thin, hair-like appendages called pili.

"Although scientists were aware that pili play a role in DNA uptake, Dalia said that direct evidence demonstrating how they work was lacking until this study. In order to observe pili in action, the scientists used a new method invented at IU to "paint" both the pili and DNA fragments with special glowing dyes.

***

"The new study uses these dyes to reveal that pili act like microscopic "harpooners" that cast their line through pores in the cell's wall to "spear" a stray piece of DNA at the very tip. The pili then "reel" the DNA into the bacterial cell through the same pore.

"Dalia said the pore is so small that the DNA would need to fold in half to fit through the opening in the cell.

***

"'It's like threading a needle," said Ellison, who is first author on the study. "The size of the hole in the outer membrane is almost the exact width of a DNA helix bent in half, which is likely what is coming across. If there weren't a pilus to guide it, the chance the DNA would hit the pore at just the right angle to pass into the cell is basically zero."

"Next, Dalia said the team wants to study exactly how pili "hook" onto the DNA at just the right spot, especially since the protein involved in the process appears to interact with DNA in an entirely new way. They also look forward to applying their pili labeling method to study other functions played by these diverse bacterial structures."

Comment: An amazing mechanism which would facilitate evolution. Looks designed to me.

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Horizontal gene transfer is an active system in bacteria, and is controlled by a specific agent in DNA:

https://phys.org/news/2018-06-road-gene-written-dna.html

"A new discovery suggests that bacteria's ability to transfer genes, like those associated with antibiotic resistance, are governed by a previously unknown set of rules that are written in the DNA of the recipient.

***

"'In nature, bacteria are constantly exchanging genetic material, even between distant relatives, in a process called horizontal gene transfer, where genetic material is transferred between different species," Dr. Hendrickson says. "The genetic material donated from one bacterium to another may carry novel traits like metabolic pathways, virulence genes and even antibiotic resistance elements."
These "rules" are governed by architecture imparting sequences (AIMS), which are in all bacterial chromosomes. The team discovered that if sets of AIMS are well matched between a donor and recipient genome, then the DNA moving between those genomes can be maintained. The opposite is true if they are not well matched, effectively establishing the "rules of transfer".

"Dr. Henrickson says that when it comes to horizontal gene transfer, AIMS are a little like blood groups for genetic exchange between bacterial species.
"AIMS are most likely to be similar in closely-related bacteria, but when it comes to distant transfer events, there were some surprises. For example, one of our findings was that some species have sequence structures that make them good general donors but very selective recipients, a little like people with group O-blood types."

"Critically, AIMS are easily recognised in all bacterial chromosomes, making possible the prediction of routes of likely gene transfer."

Comment: Horizontal gene transfer is a non-Darwinian way to advance evolution. It looks built-in to drive the process of advancing evolution.

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DAVID’s comment: Horizontal gene transfer is a non-Darwinian way to advance evolution. It looks built-in to drive the process of advancing evolution.

Yes, it fits in perfectly with the idea that evolution advances through the cooperation of cells. It was Lynn Margulis who pioneered the idea that symbiosis was a major factor, and it is worth noting that she was also a firm believer in bacterial intelligence, and did not consider consciousness to be synonymous with self-awareness:

https://www.astrobio.net/.../bacterial-intelligence

AM: Can you explain how you view bacteria as being intelligent?

LM: If you look up consciousness in the dictionary, it says, "awareness of the world around you," and that’s because you lose it somehow when you become unconscious, right? Well, you can show that microorganisms, or bacteria, are certainly conscious. They will orient themselves, they will work together to make structures. They’ll do a lot of things. This ability to respond specifically to the environment and to act creatively, in the sense that that precise action has never been taken before, is a property of life. Of course, it has to be moving life, or you can’t tell. You can’t tell if a plant is thinking, but in organisms that move, you can tell their intelligence.

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DAVID’s comment: Horizontal gene transfer is a non-Darwinian way to advance evolution. It looks built-in to drive the process of advancing evolution.

dhw: Yes, it fits in perfectly with the idea that evolution advances through the cooperation of cells. It was Lynn Margulis who pioneered the idea that symbiosis was a major factor, and it is worth noting that she was also a firm believer in bacterial intelligence, and did not consider consciousness to be synonymous with self-awareness:

https://www.astrobio.net/.../bacterial-intelligence

AM: Can you explain how you view bacteria as being intelligent?

LM: If you look up consciousness in the dictionary, it says, "awareness of the world around you," and that’s because you lose it somehow when you become unconscious, right? Well, you can show that microorganisms, or bacteria, are certainly conscious. They will orient themselves, they will work together to make structures. They’ll do a lot of things. This ability to respond specifically to the environment and to act creatively, in the sense that that precise action has never been taken before, is a property of life. Of course, it has to be moving life, or you can’t tell. You can’t tell if a plant is thinking, but in organisms that move, you can tell their intelligence.

From the Britannica:

Consciousness, a psychological condition defined by the English philosopher John Locke as “the perception of what passes in a man’s own mind.”

It depends on the authority you quote. I'm referring to human consciousness, and no other organism has it!

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AM: Can you explain how you view bacteria as being intelligent?

LM [Lynn Margulis]: If you look up consciousness in the dictionary, it says, "awareness of the world around you," and that’s because you lose it somehow when you become unconscious, right? Well, you can show that microorganisms, or bacteria, are certainly conscious. They will orient themselves, they will work together to make structures. They’ll do a lot of things. This ability to respond specifically to the environment and to act creatively, in the sense that that precise action has never been taken before, is a property of life. Of course, it has to be moving life, or you can’t tell. You can’t tell if a plant is thinking, but in organisms that move, you can tell their intelligence.

David: From the Britannica:
Consciousness, a psychological condition defined by the English philosopher John Locke as “the perception of what passes in a man’s own mind.”
It depends on the authority you quote. I'm referring to human consciousness, and no other organism has it!

Of course no organism other than humans has human consciousness! And of course the meaning of the word depends on which authority you quote. But you understand perfectly well what Margulis means by the term. There is no need to argue about definitions. The question is whether other organisms have a degree of awareness/intelligence – not whether they have the same thoughts as humans!

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AM: Can you explain how you view bacteria as being intelligent?

LM [Lynn Margulis]: If you look up consciousness in the dictionary, it says, "awareness of the world around you," and that’s because you lose it somehow when you become unconscious, right? Well, you can show that microorganisms, or bacteria, are certainly conscious. They will orient themselves, they will work together to make structures. They’ll do a lot of things. This ability to respond specifically to the environment and to act creatively, in the sense that that precise action has never been taken before, is a property of life. Of course, it has to be moving life, or you can’t tell. You can’t tell if a plant is thinking, but in organisms that move, you can tell their intelligence.

David: From the Britannica:
Consciousness, a psychological condition defined by the English philosopher John Locke as “the perception of what passes in a man’s own mind.”
It depends on the authority you quote. I'm referring to human consciousness, and no other organism has it!

dhw; Of course no organism other than humans has human consciousness! And of course the meaning of the word depends on which authority you quote. But you understand perfectly well what Margulis means by the term. There is no need to argue about definitions. The question is whether other organisms have a degree of awareness/intelligence – not whether they have the same thoughts as humans!

Awareness is not equal to intelligence. Plants react intelligently to noxious events. That can simply be an intelligently designed programmed event as with other organisms without brains. Brained organisms obviously have awareness and intelligence.

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AM: Can you explain how you view bacteria as being intelligent?

LM [Lynn Margulis]: If you look up consciousness in the dictionary, it says, "awareness of the world around you," and that’s because you lose it somehow when you become unconscious, right? Well, you can show that microorganisms, or bacteria, are certainly conscious. They will orient themselves, they will work together to make structures. They’ll do a lot of things. This ability to respond specifically to the environment and to act creatively, in the sense that that precise action has never been taken before, is a property of life. Of course, it has to be moving life, or you can’t tell. You can’t tell if a plant is thinking, but in organisms that move, you can tell their intelligence.

David: From the Britannica:
Consciousness, a psychological condition defined by the English philosopher John Locke as “the perception of what passes in a man’s own mind.”
It depends on the authority you quote. I'm referring to human consciousness, and no other organism has it!

dhw; Of course no organism other than humans has human consciousness! And of course the meaning of the word depends on which authority you quote. But you understand perfectly well what Margulis means by the term. There is no need to argue about definitions. The question is whether other organisms have a degree of awareness/intelligence – not whether they have the same thoughts as humans!

DAVID: Awareness is not equal to intelligence. Plants react intelligently to noxious events. That can simply be an intelligently designed programmed event as with other organisms without brains. Brained organisms obviously have awareness and intelligence.

You have echoed the Margulis quote above, except that her criterion is movement, not brains. “Of course it has to be moving life, or you can’t tell. You can’t tell if a plant is thinking, but in organisms that move, you can tell their intelligence.” And that includes bacteria. I know you don’t agree, but the fact of the matter is that even when organisms have brains, you refuse to believe that they are capable of intelligently working out their own natural wonders. Your God has to dabble or design a special programme for every one, including my favourite example: the weaverbird’s nest.

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AM: Can you explain how you view bacteria as being intelligent?

LM [Lynn Margulis]: If you look up consciousness in the dictionary, it says, "awareness of the world around you," and that’s because you lose it somehow when you become unconscious, right? Well, you can show that microorganisms, or bacteria, are certainly conscious. They will orient themselves, they will work together to make structures. They’ll do a lot of things. This ability to respond specifically to the environment and to act creatively, in the sense that that precise action has never been taken before, is a property of life. Of course, it has to be moving life, or you can’t tell. You can’t tell if a plant is thinking, but in organisms that move, you can tell their intelligence.

David: From the Britannica:
Consciousness, a psychological condition defined by the English philosopher John Locke as “the perception of what passes in a man’s own mind.”
It depends on the authority you quote. I'm referring to human consciousness, and no other organism has it!

dhw; Of course no organism other than humans has human consciousness! And of course the meaning of the word depends on which authority you quote. But you understand perfectly well what Margulis means by the term. There is no need to argue about definitions. The question is whether other organisms have a degree of awareness/intelligence – not whether they have the same thoughts as humans!

DAVID: Awareness is not equal to intelligence. Plants react intelligently to noxious events. That can simply be an intelligently designed programmed event as with other organisms without brains. Brained organisms obviously have awareness and intelligence.

dhw: You have echoed the Margulis quote above, except that her criterion is movement, not brains. “Of course it has to be moving life, or you can’t tell. You can’t tell if a plant is thinking, but in organisms that move, you can tell their intelligence.” And that includes bacteria. I know you don’t agree, but the fact of the matter is that even when organisms have brains, you refuse to believe that they are capable of intelligently working out their own natural wonders. Your God has to dabble or design a special programme for every one, including my favourite example: the weaverbird’s nest.

I believe those with brains can work out simple traits on their own. My dog does. At the single cell level it still remains 50/50: it can be explained by automatic activity due to a codex of instructions or very simple autonomous responses. If one is theistic, the anser is obvious.

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DAVID: Awareness is not equal to intelligence. Plants react intelligently to noxious events. That can simply be an intelligently designed programmed event as with other organisms without brains. Brained organisms obviously have awareness and intelligence.

dhw: You have echoed the Margulis quote above, except that her criterion is movement, not brains. “Of course it has to be moving life, or you can’t tell. You can’t tell if a plant is thinking, but in organisms that move, you can tell their intelligence.” And that includes bacteria. I know you don’t agree, but the fact of the matter is that even when organisms have brains, you refuse to believe that they are capable of intelligently working out their own natural wonders. Your God has to dabble or design a special programme for every one, including my favourite example: the weaverbird’s nest.

DAVID: I believe those with brains can work out simple traits on their own. My dog does. At the single cell level it still remains 50/50: it can be explained by automatic activity due to a codex of instructions or very simple autonomous responses. If one is theistic, the anser is obvious.

The answer is not obvious at all. I am happy with your acknowledgement that organisms with brains can work out simple traits on their own, but not with your assumption that they cannot be intelligent enough to work out any of the natural wonders you describe (e.g. the weaverbird’s nest). I am satisfied with your acknowledgement that single cells may (50/50) be capable of autonomous responses, which for me are good enough odds to warrant very serious discussion about the possible implications (as with the 50/50 existence of your God). I see absolutely no reason why theists should not believe that their God is capable of giving all these organisms different degrees of intelligence through a brain or brain equivalent, and this actually seems to me far more likely than the theory that their God preprogrammed every natural wonder 3.8 billion years ago or gave personal tuition to each organism involved.

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DAVID: Awareness is not equal to intelligence. Plants react intelligently to noxious events. That can simply be an intelligently designed programmed event as with other organisms without brains. Brained organisms obviously have awareness and intelligence.

dhw: You have echoed the Margulis quote above, except that her criterion is movement, not brains. “Of course it has to be moving life, or you can’t tell. You can’t tell if a plant is thinking, but in organisms that move, you can tell their intelligence.” And that includes bacteria. I know you don’t agree, but the fact of the matter is that even when organisms have brains, you refuse to believe that they are capable of intelligently working out their own natural wonders. Your God has to dabble or design a special programme for every one, including my favourite example: the weaverbird’s nest.

DAVID: I believe those with brains can work out simple traits on their own. My dog does. At the single cell level it still remains 50/50: it can be explained by automatic activity due to a codex of instructions or very simple autonomous responses. If one is theistic, the answer is obvious.

dhw: The answer is not obvious at all. I am happy with your acknowledgement that organisms with brains can work out simple traits on their own, but not with your assumption that they cannot be intelligent enough to work out any of the natural wonders you describe (e.g. the weaverbird’s nest). I am satisfied with your acknowledgement that single cells may (50/50) be capable of autonomous responses, which for me are good enough odds to warrant very serious discussion about the possible implications (as with the 50/50 existence of your God). I see absolutely no reason why theists should not believe that their God is capable of giving all these organisms different degrees of intelligence through a brain or brain equivalent, and this actually seems to me far more likely than the theory that their God preprogrammed every natural wonder 3.8 billion years ago or gave personal tuition to each organism involved.

We can all assume we know what God can do with his powers, but none of us really know what God can do. We can only judge by analyzing His works and making individual conclusions, which should not include any form of wishful thinking. And we do not know if God's logic is the same as human logic.

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dhw: I see absolutely no reason why theists should not believe that their God is capable of giving all these organisms different degrees of intelligence through a brain or brain equivalent, and this actually seems to me far more likely than the theory that their God preprogrammed every natural wonder 3.8 billion years ago or gave personal tuition to each organism involved.

DAVID: We can all assume we know what God can do with his powers, but none of us really know what God can do. We can only judge by analyzing His works and making individual conclusions, which should not include any form of wishful thinking. And we do not know if God's logic is the same as human logic.

All agreed, but (a) if we are going to discuss these subjects, we have no choice other than to use our human logic, and (b) that does not mean our human logic is wrong! The theistic suggestion that God created the mechanism for an evolutionary free-for-all, though always with the option of dabbling, arises out of consideration of his works, the history of which gives the appearance of an evolutionary free-for-all. Where’s the wishful thinking? The view that every innovation, lifestyle and natural wonder has been precisely pre-programmed or dabbled by your God, though 99% of species have disappeared, and somehow they were all specially designed to keep life going until he could produce the brain of Homo sapiens, seems less logical to me, and you can hardly blame me for being dissatisfied with the response that maybe God’s logic is different from ours.

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dhw: I see absolutely no reason why theists should not believe that their God is capable of giving all these organisms different degrees of intelligence through a brain or brain equivalent, and this actually seems to me far more likely than the theory that their God preprogrammed every natural wonder 3.8 billion years ago or gave personal tuition to each organism involved.

DAVID: We can all assume we know what God can do with his powers, but none of us really know what God can do. We can only judge by analyzing His works and making individual conclusions, which should not include any form of wishful thinking. And we do not know if God's logic is the same as human logic.

dhw: All agreed, but (a) if we are going to discuss these subjects, we have no choice other than to use our human logic, and (b) that does not mean our human logic is wrong! The theistic suggestion that God created the mechanism for an evolutionary free-for-all, though always with the option of dabbling, arises out of consideration of his works, the history of which gives the appearance of an evolutionary free-for-all. Where’s the wishful thinking? The view that every innovation, lifestyle and natural wonder has been precisely pre-programmed or dabbled by your God, though 99% of species have disappeared, and somehow they were all specially designed to keep life going until he could produce the brain of Homo sapiens, seems less logical to me, and you can hardly blame me for being dissatisfied with the response that maybe God’s logic is different from ours.

When the current end point of evolution is the human brain, it looks more purposeful than a free-for-all. Your dissatisfaction comes from your point of view, and God's logic still might not be ours, since we must interpret His works from our point of view.

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DAVID: We can all assume we know what God can do with his powers, but none of us really know what God can do. We can only judge by analyzing His works and making individual conclusions, which should not include any form of wishful thinking. And we do not know if God's logic is the same as human logic.

dhw: All agreed, but (a) if we are going to discuss these subjects, we have no choice other than to use our human logic, and (b) that does not mean our human logic is wrong! The theistic suggestion that God created the mechanism for an evolutionary free-for-all, though always with the option of dabbling, arises out of consideration of his works, the history of which gives the appearance of an evolutionary free-for-all. Where’s the wishful thinking? The view that every innovation, lifestyle and natural wonder has been precisely pre-programmed or dabbled by your God, though 99% of species have disappeared, and somehow they were all specially designed to keep life going until he could produce the brain of Homo sapiens, seems less logical to me, and you can hardly blame me for being dissatisfied with the response that maybe God’s logic is different from ours.

DAVID: When the current end point of evolution is the human brain, it looks more purposeful than a free-for-all.

I like "current". My theistic proposal allows for your God to dabble, which of course he would do purposefully. The lack of logic concerns the need for him to design millions of extinct innovations, lifestyles and natural wonders in order to keep life going until he could produce our brain.

DAVID: Your dissatisfaction comes from your point of view, and God's logic still might not be ours, since we must interpret His works from our point of view.

Of course my dissatisfaction comes from my point of view, but if the only defence you can offer for your own theory is that God’s logic might be different from mine and yours (= ours), perhaps you might consider the possibility that your illogical view might be wrong and my logical view might be right!

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DAVID: When the current end point of evolution is the human brain, it looks more purposeful than a free-for-all.

dhw:I like "current". My theistic proposal allows for your God to dabble, which of course he would do purposefully. The lack of logic concerns the need for him to design millions of extinct innovations, lifestyles and natural wonders in order to keep life going until he could produce our brain.

And I've explained that logically as the need for a balance of nature which supplies the food energy for such a long process.

DAVID: Your dissatisfaction comes from your point of view, and God's logic still might not be ours, since we must interpret His works from our point of view.

dhw: Of course my dissatisfaction comes from my point of view, but if the only defence you can offer for your own theory is that God’s logic might be different from mine and yours (= ours), perhaps you might consider the possibility that your illogical view might be wrong and my logical view might be right!

We've agreed here and there. With no disagreement there would be no website!

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That is the finding in the latest study:

https://cosmosmagazine.com/biology/jumping-gene-flash-horizontal-transfer-is-a-major-ev...

"scientists are finding that genes are jumping around all over the place, in a phenomenon known as Horizontal Gene Transfer (HGT).

"New research published in the journal Genome Biology has focussed on genes called retrotransposons, also known transposable elements (TEs), or, more colloquially, “jumping genes”. TEs are genes that can change position on the chromosome, and were first uncovered by the Nobel prize-winning cytogeneticist Barbara McClintock.

"TEs, however, can jump a lot further and do so far more regularly than anyone imagined.
In the largest study of its kind, lead researcher David Adelson, Director of the University of Adelaide’s Bioinformatics Hub and a team of University of Adelaide scientists have sifted through the genomes of 759 species of plants, animals and fungi, tracking two jumping genes, known as L1 and BovB.

"What they found is startling. The genes have jumped from species to species, even phylum to phylum, regularly throughout evolutionary history.

“'Jumping genes … copy and paste themselves around genomes, and in genomes of other species,” says Adelson.

“'How they do this is not yet known although insects like ticks or mosquitoes or possibly viruses may be involved – it’s still a big puzzle.”

"One of the genes tracked, L1, is a TE long thought only to pass vertically from parent to offspring, but was found in abundance across animals and plants, in 74% of species studied.
Ubiquitous in so-called therian mammals – those which give birth to live young – L1 almost certainly entered the lineage in a horizontal gene transfer event not long after the group’s divergence from monotremes. (Egg-laying mammals, the platypus and echidna, from which L1 is utterly absent.)

"The effect of the introduction of TEs into mammals was striking. “We think the entry of L1s into the mammalian genome was a key driver of the rapid evolution of mammals over the past 100 million years,” says Adelson. (my bold)

"The specific genes that jump are not so important, Adelson continues; rather “it’s the fact that they introduce themselves into other genomes and cause disruption of genes and how they are regulated.”

"Despite being the largest study of HGT to date, Adelson believes they have “only begun to scratch the surface of horizontal gene transfer. There are many more species to investigate and other types of jumping genes.'”

Comment: This was not anticipated in the theoretical discussions by Darwin. Is this the inventive mechanism used by God or is it another version of chance evolution? Note the effect on mammalian evolution.

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That is the finding in the latest study:

https://cosmosmagazine.com/biology/jumping-gene-flash-horizontal-transfer-is-a-major-ev...

"scientists are finding that genes are jumping around all over the place, in a phenomenon known as Horizontal Gene Transfer (HGT).

"New research published in the journal Genome Biology has focussed on genes called retrotransposons, also known transposable elements (TEs), or, more colloquially, “jumping genes”. TEs are genes that can change position on the chromosome, and were first uncovered by the Nobel prize-winning cytogeneticist Barbara McClintock.

"TEs, however, can jump a lot further and do so far more regularly than anyone imagined.
In the largest study of its kind, lead researcher David Adelson, Director of the University of Adelaide’s Bioinformatics Hub and a team of University of Adelaide scientists have sifted through the genomes of 759 species of plants, animals and fungi, tracking two jumping genes, known as L1 and BovB.

"What they found is startling. The genes have jumped from species to species, even phylum to phylum, regularly throughout evolutionary history.

“'Jumping genes … copy and paste themselves around genomes, and in genomes of other species,” says Adelson.

“'How they do this is not yet known although insects like ticks or mosquitoes or possibly viruses may be involved – it’s still a big puzzle.”

"One of the genes tracked, L1, is a TE long thought only to pass vertically from parent to offspring, but was found in abundance across animals and plants, in 74% of species studied.
Ubiquitous in so-called therian mammals – those which give birth to live young – L1 almost certainly entered the lineage in a horizontal gene transfer event not long after the group’s divergence from monotremes. (Egg-laying mammals, the platypus and echidna, from which L1 is utterly absent.)

"The effect of the introduction of TEs into mammals was striking. “We think the entry of L1s into the mammalian genome was a key driver of the rapid evolution of mammals over the past 100 million years,” says Adelson. (my bold)

"The specific genes that jump are not so important, Adelson continues; rather “it’s the fact that they introduce themselves into other genomes and cause disruption of genes and how they are regulated.”

"Despite being the largest study of HGT to date, Adelson believes they have “only begun to scratch the surface of horizontal gene transfer. There are many more species to investigate and other types of jumping genes.'”

David Comment: This was not anticipated in the theoretical discussions by Darwin. Is this the inventive mechanism used by God or is it another version of chance evolution? Note the effect on mammalian evolution.

It is predicted by my hypothesis, though, because it is an common element in the programming language.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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David: from the rticle:

> "The effect of the introduction of TEs into mammals was striking. “We think the entry of L1s into the mammalian genome was a key driver of the rapid evolution of mammals over the past 100 million years,” says Adelson. (my bold)

"The specific genes that jump are not so important, Adelson continues; rather “it’s the fact that they introduce themselves into other genomes and cause disruption of genes and how they are regulated.”

"Despite being the largest study of HGT to date, Adelson believes they have “only begun to scratch the surface of horizontal gene transfer. There are many more species to investigate and other types of jumping genes.'”

David Comment: This was not anticipated in the theoretical discussions by Darwin. Is this the inventive mechanism used by God or is it another version of chance evolution? Note the effect on mammalian evolution.

Tony: It is predicted by my hypothesis, though, because it is an common element in the programming language.

You are implying whoever designed the program was an excellent programmer.

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David: from the rticle:
"The effect of the introduction of TEs into mammals was striking. “We think the entry of L1s into the mammalian genome was a key driver of the rapid evolution of mammals over the past 100 million years,” says Adelson. (my bold)

"The specific genes that jump are not so important, Adelson continues; rather “it’s the fact that they introduce themselves into other genomes and cause disruption of genes and how they are regulated.”

"Despite being the largest study of HGT to date, Adelson believes they have “only begun to scratch the surface of horizontal gene transfer. There are many more species to investigate and other types of jumping genes.'”

David Comment: This was not anticipated in the theoretical discussions by Darwin. Is this the inventive mechanism used by God or is it another version of chance evolution? Note the effect on mammalian evolution.

Tony: It is predicted by my hypothesis, though, because it is an common element in the programming language.

David: You are implying whoever designed the program was an excellent programmer.

Well....yes. However, I think that much of the complexity is self-inflicted simply because we refuse to see it for what it is.

If we need a screw for a machine, most any machine, we don't reinvent the darn screw, we just determine the circumference and the rate of ascent of the inclined plane. We match those to the needs of the socket. Why would ANY designer reinvent the code ever time they needed to do something similar?

Their discovery actively disproves evolution by common descent, and instead of accepting that they invent more fairy tales to explain why the evidence does not fit their theory.

Does it make sense that a designer would reuse code when needed?
Absolutely!

Is there evidence to support that hypothesis?
Absolutely!

Could my hypothesis be tested in a repeatable fashion?
Absolutely! And has been. The fact that they are able to programmatically rewrite DNA supports my hypothesis.

Will it ever be accepted by mainstream science?
Never.

There are too many scientists who have staked their career and funding on evolution, first and foremost. However, admitting that the life and/or the universe has a designers makes them feel small and insignificant, raising a bunch of uncomfortable questions.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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David Comment: This was not anticipated in the theoretical discussions by Darwin. Is this the inventive mechanism used by God or is it another version of chance evolution? Note the effect on mammalian evolution.

Tony: It is predicted by my hypothesis, though, because it is an common element in the programming language.

David: You are implying whoever designed the program was an excellent programmer.

Tony: Well....yes. However, I think that much of the complexity is self-inflicted simply because we refuse to see it for what it is.

If we need a screw for a machine, most any machine, we don't reinvent the darn screw, we just determine the circumference and the rate of ascent of the inclined plane. We match those to the needs of the socket. Why would ANY designer reinvent the code ever time they needed to do something similar?

Their discovery actively disproves evolution by common descent, and instead of accepting that they invent more fairy tales to explain why the evidence does not fit their theory.

Does it make sense that a designer would reuse code when needed?
Absolutely!

Is there evidence to support that hypothesis?
Absolutely!

Could my hypothesis be tested in a repeatable fashion?
Absolutely! And has been. The fact that they are able to programmatically rewrite DNA supports my hypothesis.

Will it ever be accepted by mainstream science?
Never.

There are too many scientists who have staked their career and funding on evolution, first and foremost. However, admitting that the life and/or the universe has a designers makes them feel small and insignificant, raising a bunch of uncomfortable questions.

You don't seem believe in common descent, but based on your discussion of rearranging parts, doesn't that imply each stage came from the past stage?

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QUOTES: "New research published in the journal Genome Biology has focussed on genes called retrotransposons, also known transposable elements (TEs), or, more colloquially, “jumping genes”. TEs are genes that can change position on the chromosome, and were first uncovered by the Nobel prize-winning cytogeneticist Barbara McClintock.

"The effect of the introduction of TEs into mammals was striking. “We think the entry of L1s into the mammalian genome was a key driver of the rapid evolution of mammals over the past 100 million years,” says Adelson. (David’s bold)

DAVID: Is this the inventive mechanism used by God or is it another version of chance evolution? Note the effect on mammalian evolution.

Firstly, it’s worth remembering that Barbara McClintock was a firm believer in cellular intelligence. What seems clear to me is that there IS an inventive mechanism. I myself remain unconvinced that it operates by chance, and find it far more likely that it operates through the autonomous intelligence of the cell communities themselves. It may or may not have been designed by your God.

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QUOTES: "New research published in the journal Genome Biology has focussed on genes called retrotransposons, also known transposable elements (TEs), or, more colloquially, “jumping genes”. TEs are genes that can change position on the chromosome, and were first uncovered by the Nobel prize-winning cytogeneticist Barbara McClintock.

"The effect of the introduction of TEs into mammals was striking. “We think the entry of L1s into the mammalian genome was a key driver of the rapid evolution of mammals over the past 100 million years,” says Adelson. (David’s bold)

DAVID: Is this the inventive mechanism used by God or is it another version of chance evolution? Note the effect on mammalian evolution.

dhw: Firstly, it’s worth remembering that Barbara McClintock was a firm believer in cellular intelligence. What seems clear to me is that there IS an inventive mechanism. I myself remain unconvinced that it operates by chance, and find it far more likely that it operates through the autonomous intelligence of the cell communities themselves. It may or may not have been designed by your God.

Or the cells run on intelligent information planning and therefore look as if they have innate intelligence..

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A study compares Earth's grasses and finds similar genes and presumes horizontal transfer:

https://phys.org/news/2019-02-thieves-survive.html

"Scientists have discovered that grasses are able to short cut evolution by taking genes from their neighbours. The findings suggest wild grasses are naturally genetically modifying themselves to gain a competitive advantage.

"Understanding how this is happening may also help scientists reduce the risk of genes escaping from GM crops and creating so called "super-weeds—which can happen when genes from GM crops transfer into local wild plants, making them herbicide resistant.

"Since Darwin, much of the theory of evolution has been based on common descent, where natural selection acts on the genes passed from parent to offspring. However, researchers from the Department of Animal and Plant Sciences at the University of Sheffield have found that grasses are breaking these rules. Lateral gene transfer allows organisms to bypass evolution and skip to the front of the queue by using genes that they acquire from distantly related species.

***

"Scientists looked at grasses—some of the most economically and ecologically important plants on Earth including many of the most cultivated crops worldwide such as: wheat, maize, rice, barley, sorghum and sugar cane.

***

"Studying the genome of the grass Alloteropsis semialata - which is found across Africa, Asia and Australia—researchers were able to compare it with approximately 150 other grasses (including rice, maize, millets, barley, bamboo etc.). They identified genes in Alloteropsis semialata that were laterally acquired by comparing the similarity of the DNA sequences that make up the genes.

"'We also collected samples of Alloteropsis semialata from tropical and subtropical places in Asia, Africa and Australia so that we could track down when and where the transfers happened," said Dr. Dunning.

"'Counterfeiting genes is giving the grasses huge advantages and helping them to adapt to their surrounding environment and survive—and this research also shows that it is not just restricted to Alloteropsis semialata as we detected it in a wide range of other grass species'"

Comment: They found similar genes and ASSUMED the plants made copies. Really? Where is the proof. Read articles critically. Similar genes Are found in many different species and may be doing different controlling roles.

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It can be physically obtained by needling another bacterium and seizing DNA:

https://www.nature.com/articles/s41564-018-0174-y

" Abstract:

"Natural transformation is a broadly conserved mechanism of horizontal gene transfer in bacterial species that can shape evolution and foster the spread of antibiotic resistance determinants, promote antigenic variation and lead to the acquisition of novel virulence factors. Surface appendages called competence pili promote DNA uptake during the first step of natural transformation1; however, their mechanism of action has remained unclear owing to an absence of methods to visualize these structures in live cells. Here, using the model naturally transformable species Vibrio cholerae and a pilus-labelling method, we define the mechanism for type IV competence pilus-mediated DNA uptake during natural transformation. First, we show that type IV competence pili bind to extracellular double-stranded DNA via their tip and demonstrate that this binding is critical for DNA uptake. Next, we show that type IV competence pili are dynamic structures and that pilus retraction brings tip-bound DNA to the cell surface. Finally, we show that pilus retraction is spatiotemporally coupled to DNA internalization and that sterically obstructing pilus retraction prevents DNA uptake. Together, these results indicate that type IV competence pili directly bind to DNA via their tip and mediate DNA internalization through retraction during this conserved mechanism of horizontal gene transfer."

Comment: Bacteria can alter their responses with this mechanism, but, for example, E. coli will stay E. coli. Doesn't solve speciation.

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Usually not seen at this level of complexity:

https://cosmosmagazine.com/biology/parasitic-plants-steal-genes-to-become-better-parasi...

“;In this study, we present the most dramatic case known of functional horizontal gene transfer ever found in complex organisms."

***

"plays a positive role in plant-plant communication

"Like other parasites it cannot live on its own; rather, it uses structures called haustoria to tap into a host plant's supply of water and nutrients. It wraps itself around its host plant, growing into its vascular tissue, and often feeds on multiple plants at one time.

"'Parasitic plants live very intimately in connection with their host, extracting nutrients," says dePamphilis. "But they also get genetic material in the process, and sometimes they incorporate that material into their genome.

“'Previous studies focused on single transferred genes. Here, we used genome-scale datasets about gene expression to determine whether the large amount of genetic material coming over through horizontal gene transfer is actually being used."

"The research team identified 108 genes that have been added to dodder's genome by horizontal gene transfer and now seem to be functional in the parasite. Eighteen of these appear in all dodder species, suggesting, the researchers say, that these genes were originally stolen by the ancestral form of dodder and are maintained in modern species.

"The genes contribute to haustoria structure, defence responses, and amino acid metabolism.

"One even produces small segments of RNA – known as micro RNA – that are sent back into the host plant, acting as weapons that may play a role in silencing host defence genes.

"The team also identified 42 regions in the dodder genome that appear to result from horizontal gene transfer, but do not have any functional genes.

"'Because such a huge quantity of genetic material has come over through horizontal gene transfer, we suspect that the parasitic plants cannot filter what is coming in," says dePamphilis"

Comment: This shows that horizontal gene transfer is not limited to just simple organisms.

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Horizontal gene transfer in bacteria is necessary for bacteria to evolve and add new functions. It is under highly complex controls, not yet fully understood:

https://phys.org/news/2019-08-block-unwanted-genetic.html

"Random mutations add some diversity, but there's a much faster way for bacteria to reshuffle their genes and confer evolutionary advantages like antibiotic resistance or pathogenicity.

"Known as horizontal gene transfer, this process permits bacteria to pass pieces of DNA to their peers, in some cases allowing those genes to be integrated into the recipient's genome and passed down to the next generation.

"The Grossman lab in the MIT Department of Biology studies one class of mobile DNA, known as integrative and conjugative elements (ICEs). While ICEs contain genes that can be beneficial to the recipient bacterium, there's also a catch—receiving a duplicate copy of an ICE is wasteful, and possibly lethal. The biologists recently uncovered a new system by which one particular ICE, ICEBs1, blocks a donor bacterium from delivering a second, potentially deadly copy.

***

"Although plasmids are perhaps the best-known mediators of horizontal transfer, ICEs not only outnumber plasmids in most bacterial species, they also come with their own tools to exit the donor, enter the recipient, and integrate themselves into the recipient's chromosome. Once the donor bacterium makes contact with the recipient, the machinery encoded by the ICE can pump the ICE DNA from one cell to the other through a tiny channel.

"For horizontal transfer to proceed, there are physical barriers to overcome, especially in so-called Gram-positive bacteria, which boast thicker cell walls than their Gram-negative counterparts, despite being less widely studied. According to Davis, the transfer machinery essentially has to "punch a hole" through the recipient cell.

***

"Sure, ICEs are "selfish bits of DNA" that persist by spreading themselves as widely as possible, but in order to do so they must not interfere with their host cell's ability to survive. As Avello explains, ICEs can't just disseminate their DNA "without certain checks and balances."

***

"In this most recent study, they've identified the mysterious blocking mechanism as a type of "entry exclusion," whereby the ICE in the recipient cell encodes molecular machinery that physically prevents the second copy from breaching the cell wall. Scientists had observed other mobile genetic elements capable of exclusion, but this was the first time anyone had witnessed this phenomenon for an ICE from Gram-positive bacteria, according to Avello.

"The Grossman lab determined that this exclusion mechanism comes down to two key proteins. Avello identified the first protein, YddJ, expressed by the ICEBs1 in the recipient bacterium, forming a "protective coating" on the outside of the cell and blocking a second ICE from entering.

***

"Cell-cell signaling allows a cell to spread the word to its neighbors that it already has a copy of ICEBs1, so there's no need to bother assembling the transfer machinery. If this fails, exclusion kicks in to physically block the transfer machinery from penetrating the recipient cell. If that proves unsuccessful and the second copy enters the recipient, immunity will initiate and prevent the second copy from being integrated into the recipient's chromosome.

"'Each mechanism acts at a different step, because none of them alone are 100 percent effective," Grossman says. "That's why it's helpful to have multiple mechanisms."
They don't know all the details of this transfer machinery just yet, he adds, but they do know that YddJ and ConG are key players.

"'This initial description of the ICEBs1 exclusion system represents the first report that provides mechanistic insights into exclusion in Gram-positive bacteria, and one of only a few mechanistic studies of exclusion in any conjugation system," says Gary Dunny, a professor of microbiology and immunology at the University of Minnesota who was not involved in the study.
"This work is significant medically because ICEs can carry "cargo" genes such as those conferring antibiotic resistance, and also of importance to our basic understanding of horizontal gene transfer systems and how they evolve.'"

Comment: This complex transfer system with precise controls cannot develop stepwise by chance. It must be designed and created all at once as an initial step.

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HGT does control the advances of evolution, and may have been active in very early life:

https://aeon.co/essays/genes-that-jump-species-does-this-shake-the-tree-of-life?utm_sou...

"Every creature that ever existed presumably ‘descended from some one primordial form’, as Charles Darwin put it in 1859. And genes ostensibly flow in one direction: up from the trunk.

"Scientists such as Ford Doolittle and Carl Woese at the University of Illinois have argued that this portrayal is an oversimplification. Rather than rising from a single trunk, they say, the tree of life stands on an interweaving root system. Rather than evolving from one ‘last universal ancestor’, all life arose from a communal pool of primitive cells with unbridled zeal for exchanging DNA. For relatively simple cells with only a handful of genes each, swapping DNA was an excellent strategy for acquiring and preserving the best adaptations around.

"At some point, Woese proposed, cells reached a certain threshold of complexity at which it became detrimental to embrace a bombardment of foreign genes. A primordial cell harbouring a small group of genes can potentially gain a lot by adding new genes to its repertoire; but a more sophisticated cell with hundreds or thousands of genes risks imbalancing an intricate genome fine-tuned by a longer period of natural selection. So, complex eukaryotic cells evolved new ways to protect their DNA and expunge genetic invaders.

"However, as has become clear in the past decade, horizontal gene transfer did not halt among eukaryotes and their microbial denizens. A mischievous breeze continued to blow DNA this way and that, from one branch on the tree of life to another. Wolbachia, pea aphids and hornworts all encourage us to accept a truth that seems unsettling at first, but ultimately invites us into greater communion with all life on the planet.

***

"Genes are concerned with one thing above all else: self-perpetuation. If such preservation requires a particular gene to adapt to a genome it has never encountered before – if riding a parasite from one species to another turns out to be an extremely successful way of guaranteeing perpetuity – so be it. Species barriers might protect the integrity of a genome as a whole, but when an individual gene has a chance to advance itself by breaching those boundaries, it will not hesitate.

"That’s the thing about DNA: its true loyalty is to itself. We tend to think of any one species’s genome as belonging to that species. We have a strong sense of ownership over our genes in particular – an understanding that, even though our genome overlaps with that of other creatures, it is still singular, is still ‘the human genome’. So strong is our possessiveness that the mere idea of mixing our DNA with another creature’s – of any two species intermingling genes – immediately repulses us. As far as DNA is concerned, however, the supposed walls between species are not nearly so impermeable. Up in the branches of the great tree of life, we are no longer immersed in the ancient communal pool that watered its tangled roots. Yet we cannot escape the winds of promiscuity. Even today – as was true from the start – ‘our’ genes are not ours alone."

Comment: No question horizontal gene transfer is a major contributor to the course of evolution. The vast library of genes is standardized across life and all different organisms c an use them and modify their outputs. Woese, the discoverer of Archaea is a deeper thinker who may have a major point about early life. There is no top-down history of genes as Darwin and early Darwinists assumed.

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QUOTES: Rather than evolving from one ‘last universal ancestor’, all life arose from a communal pool of primitive cells with unbridled zeal for exchanging DNA. For relatively simple cells with only a handful of genes each, swapping DNA was an excellent strategy for acquiring and preserving the best adaptations around.
"Genes are concerned with one thing above all else: self-perpetuation. If such preservation requires a particular gene to adapt to a genome it has never encountered before – if riding a parasite from one species to another turns out to be an extremely successful way of guaranteeing perpetuity – so be it. Species barriers might protect the integrity of a genome as a whole, but when an individual gene has a chance to advance itself by breaching those boundaries, it will not hesitate.

DAVID: No question horizontal gene transfer is a major contributor to the course of evolution.

And so we begin the process with cells cooperating in order to enhance their chances of survival. Between us we have come up with three separate theories as to how this cooperation has led to evolution: 1) David’s God preprogrammed every single new combination of cells; 2) David’s God personally manipulated each new combination as and when he felt like it (dabbling); 3) (theistic version) David’s God designed the cells with the intelligence to work out their own ways of cooperating. This particular article uses interesting language: “unbridled zeal”, “excellent strategy”, “are concerned with”, “a chance to advance itself…it will not hesitate”. Sounds like (3) to me!

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QUOTES: Rather than evolving from one ‘last universal ancestor’, all life arose from a communal pool of primitive cells with unbridled zeal for exchanging DNA. For relatively simple cells with only a handful of genes each, swapping DNA was an excellent strategy for acquiring and preserving the best adaptations around.
"Genes are concerned with one thing above all else: self-perpetuation. If such preservation requires a particular gene to adapt to a genome it has never encountered before – if riding a parasite from one species to another turns out to be an extremely successful way of guaranteeing perpetuity – so be it. Species barriers might protect the integrity of a genome as a whole, but when an individual gene has a chance to advance itself by breaching those boundaries, it will not hesitate.

DAVID: No question horizontal gene transfer is a major contributor to the course of evolution.

dhw: And so we begin the process with cells cooperating in order to enhance their chances of survival. Between us we have come up with three separate theories as to how this cooperation has led to evolution: 1) David’s God preprogrammed every single new combination of cells; 2) David’s God personally manipulated each new combination as and when he felt like it (dabbling); 3) (theistic version) David’s God designed the cells with the intelligence to work out their own ways of cooperating. This particular article uses interesting language: “unbridled zeal”, “excellent strategy”, “are concerned with”, “a chance to advance itself…it will not hesitate”. Sounds like (3) to me!

Or the 'intelligence of cells' is the programmed information from God. 1,2, and 3 may all be the same.

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DAVID: No question horizontal gene transfer is a major contributor to the course of evolution.

dhw: And so we begin the process with cells cooperating in order to enhance their chances of survival. Between us we have come up with three separate theories as to how this cooperation has led to evolution: 1) David’s God preprogrammed every single new combination of cells; 2) David’s God personally manipulated each new combination as and when he felt like it (dabbling); 3) (theistic version) David’s God designed the cells with the intelligence to work out their own ways of cooperating. This particular article uses interesting language: “unbridled zeal”, “excellent strategy”, “are concerned with”, “a chance to advance itself…it will not hesitate”. Sounds like (3) to me!

DAVID: Or the 'intelligence of cells' is the programmed information from God. 1,2, and 3 may all be the same.

I don’t know why you have to bring in the term “information”, when the alternatives are already perfectly clear. There is no way divine preprogramming (fixed beforehand), divine dabbling (fixed on the spot) and autonomous cooperation (fixed by the cells themselves) could possibly be the same.

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DAVID: No question horizontal gene transfer is a major contributor to the course of evolution.

dhw: And so we begin the process with cells cooperating in order to enhance their chances of survival. Between us we have come up with three separate theories as to how this cooperation has led to evolution: 1) David’s God preprogrammed every single new combination of cells; 2) David’s God personally manipulated each new combination as and when he felt like it (dabbling); 3) (theistic version) David’s God designed the cells with the intelligence to work out their own ways of cooperating. This particular article uses interesting language: “unbridled zeal”, “excellent strategy”, “are concerned with”, “a chance to advance itself…it will not hesitate”. Sounds like (3) to me!

DAVID: Or the 'intelligence of cells' is the programmed information from God. 1,2, and 3 may all be the same.

dhw: I don’t know why you have to bring in the term “information”, when the alternatives are already perfectly clear. There is no way divine preprogramming (fixed beforehand), divine dabbling (fixed on the spot) and autonomous cooperation (fixed by the cells themselves) could possibly be the same.

You have always resented the concept of information contained in DNA. Of course it is information. That is what codes contain, and 1,2 and 3 are an exchange or development of new information, instructions.

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DAVID: No question horizontal gene transfer is a major contributor to the course of evolution.

dhw: And so we begin the process with cells cooperating in order to enhance their chances of survival. Between us we have come up with three separate theories as to how this cooperation has led to evolution: 1) David’s God preprogrammed every single new combination of cells; 2) David’s God personally manipulated each new combination as and when he felt like it (dabbling); 3) (theistic version) David’s God designed the cells with the intelligence to work out their own ways of cooperating. This particular article uses interesting language: “unbridled zeal”, “excellent strategy”, “are concerned with”, “a chance to advance itself…it will not hesitate”. Sounds like (3) to me!

DAVID: Or the 'intelligence of cells' is the programmed information from God. 1,2, and 3 may all be the same.

dhw: I don’t know why you have to bring in the term “information”, when the alternatives are already perfectly clear. There is no way divine preprogramming (fixed beforehand), divine dabbling (fixed on the spot) and autonomous cooperation (fixed by the cells themselves) could possibly be the same.

DAVID: You have always resented the concept of information contained in DNA. Of course it is information. That is what codes contain, and 1,2 and 3 are an exchange or development of new information, instructions.

You are simply saying that if cellular intelligence (3) was in fact information provided by God (1) or (2), it would be the same as (1) or (2). You are juggling with the term “information” to blur the distinction between an autonomous mechanism that uses information and a mechanism which is preprogrammed with the information that enables it to use information according to an existing programme of information. This is a silly game. There is no way an autonomous mechanism can be the same as a preprogrammed mechanism or a mechanism that is directly dabbled with by the hand of your God.

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DAVID: No question horizontal gene transfer is a major contributor to the course of evolution.

dhw: And so we begin the process with cells cooperating in order to enhance their chances of survival. Between us we have come up with three separate theories as to how this cooperation has led to evolution: 1) David’s God preprogrammed every single new combination of cells; 2) David’s God personally manipulated each new combination as and when he felt like it (dabbling); 3) (theistic version) David’s God designed the cells with the intelligence to work out their own ways of cooperating. This particular article uses interesting language: “unbridled zeal”, “excellent strategy”, “are concerned with”, “a chance to advance itself…it will not hesitate”. Sounds like (3) to me!

DAVID: Or the 'intelligence of cells' is the programmed information from God. 1,2, and 3 may all be the same.

dhw: I don’t know why you have to bring in the term “information”, when the alternatives are already perfectly clear. There is no way divine preprogramming (fixed beforehand), divine dabbling (fixed on the spot) and autonomous cooperation (fixed by the cells themselves) could possibly be the same.

DAVID: You have always resented the concept of information contained in DNA. Of course it is information. That is what codes contain, and 1,2 and 3 are an exchange or development of new information, instructions.

dhw: You are simply saying that if cellular intelligence (3) was in fact information provided by God (1) or (2), it would be the same as (1) or (2). You are juggling with the term “information” to blur the distinction between an autonomous mechanism that uses information and a mechanism which is preprogrammed with the information that enables it to use information according to an existing programme of information. This is a silly game. There is no way an autonomous mechanism can be the same as a preprogrammed mechanism or a mechanism that is directly dabbled with by the hand of your God.

My thought is I don't think God would permit your autonomous mechanism

2784 views

DAVID: You have always resented the concept of information contained in DNA. Of course it is information. That is what codes contain, and 1,2 and 3 are an exchange or development of new information, instructions.

dhw: You are simply saying that if cellular intelligence (3) was in fact information provided by God (1) or (2), it would be the same as (1) or (2). You are juggling with the term “information” to blur the distinction between an autonomous mechanism that uses information and a mechanism which is preprogrammed with the information that enables it to use information according to an existing programme of information. This is a silly game. There is no way an autonomous mechanism can be the same as a preprogrammed mechanism or a mechanism that is directly dabbled with by the hand of your God.

DAVID: My thought is I don't think God would permit your autonomous mechanism.

“Permit”? I am suggesting that if he exists, he would have invented it! I know you don’t think he would have invented it. You have a fixed belief that he preprogrammed or dabbled the Antarctic midge’s adaptation, not to mention every bacterial response to every situation throughout the history of life. But I’m glad you have now discarded your thought that preprogramming, dabbling and autonomous cellular design “may all be the same”.

DAVID: (Under "Antarctic midges") It is always amazing to see how tenacious life can be. […] dhw will want to know about God's role. I assume adaptive instructions were provided.

It certainly is amazing. You assume your God had to specially preprogramme this midge (= provide adaptive instructions for this particular situation) in order to keep life going so that he could eventually design H. sapiens. If he exists, I would be more inclined to believe that he equipped cells with the intelligence to find ways of adapting to all kinds of conditions. Not much point in inventing life if he didn’t give organisms the means of surviving! Even you have suggested that your God may have given cells the ability to make minor epigenetic changes to themselves, so I wonder where you draw the borderline between major and minor.

Hybridisation
DAVID: New findings suggest this may be a more rapid mechanism than chance mutations and natural selection:
https://www.quantamagazine.org/new-hybrid-species-remix-old-genes-creatively-20190910/

QUOTES: "The three authors’ views are shaped by their work on one of nature’s most explosive species radiations — that of African cichlid fish. In just 150,000 years, well over 700 species have radiated into a technicolor panoply of shapes, sizes and ecologies.”

"But Marques and his colleagues suggest that the accumulated genomic evidence warrants the introduction of “combinatorial speciation” as a new term to frame future research.

This is a cop-out. All the varieties of cichlid are still cichlid. The real mystery is how different species in the broader sense of the word can have evolved from common ancestors: how come there are insects, fish, animals, birds, all descended from the first single cells with which life began? “Combinatorial speciation” is no different from Margulis’s emphasis on cooperation. Even you agree that cell communities combine or cooperate autonomously to create minor changes, and the question is whether they can also do the same to create major changes. But you refuse to accept this possibility.

2797 views

DAVID: My thought is I don't think God would permit your autonomous mechanism.

dhw: “Permit”? I am suggesting that if he exists, he would have invented it! I know you don’t think he would have invented it. You have a fixed belief that he preprogrammed or dabbled the Antarctic midge’s adaptation, not to mention every bacterial response to every situation throughout the history of life. But I’m glad you have now discarded your thought that preprogramming, dabbling and autonomous cellular design “may all be the same”.

Autonomous under guidelines

DAVID: (Under "Antarctic midges") It is always amazing to see how tenacious life can be. […] dhw will want to know about God's role. I assume adaptive instructions were provided.

dhw: It certainly is amazing. You assume your God had to specially preprogramme this midge (= provide adaptive instructions for this particular situation) in order to keep life going so that he could eventually design H. sapiens. If he exists, I would be more inclined to believe that he equipped cells with the intelligence to find ways of adapting to all kinds of conditions. Not much point in inventing life if he didn’t give organisms the means of surviving! Even you have suggested that your God may have given cells the ability to make minor epigenetic changes to themselves, so I wonder where you draw the borderline between major and minor.

As before: minor is simple alterations, while major involves body design changes and/or complex physiological changes.

Hybridisation
DAVID: New findings suggest this may be a more rapid mechanism than chance mutations and natural selection:
https://www.quantamagazine.org/new-hybrid-species-remix-old-genes-creatively-20190910/

QUOTES: "The three authors’ views are shaped by their work on one of nature’s most explosive species radiations — that of African cichlid fish. In just 150,000 years, well over 700 species have radiated into a technicolor panoply of shapes, sizes and ecologies.”

"But Marques and his colleagues suggest that the accumulated genomic evidence warrants the introduction of “combinatorial speciation” as a new term to frame future research.

dhw: This is a cop-out. All the varieties of cichlid are still cichlid. The real mystery is how different species in the broader sense of the word can have evolved from common ancestors: how come there are insects, fish, animals, birds, all descended from the first single cells with which life began? “Combinatorial speciation” is no different from Margulis’s emphasis on cooperation. Even you agree that cell communities combine or cooperate autonomously to create minor changes, and the question is whether they can also do the same to create major changes. But you refuse to accept this possibility.

Because it involves the major use of mentally planned complex designs.

2784 views

dhw: It certainly is amazing. You assume your God had to specially preprogramme this midge (= provide adaptive instructions for this particular situation) in order to keep life going so that he could eventually design H. sapiens. If he exists, I would be more inclined to believe that he equipped cells with the intelligence to find ways of adapting to all kinds of conditions. Not much point in inventing life if he didn’t give organisms the means of surviving! Even you have suggested that your God may have given cells the ability to make minor epigenetic changes to themselves, so I wonder where you draw the borderline between major and minor.

DAVID: As before: minor is simple alterations, while major involves body design changes and/or complex physiological changes.

I’m just checking the extent to which you think your God did it, as opposed to the organism did it. Here we have him specially preprogramming the Antarctic midge (he provided “adaptive instructions”) to survive in extreme conditions so that it would provide food to keep life going until he could design the only thing he wanted to design, H. sapiens.

Dhw (under “Hybridisation”): This is a cop-out. All the varieties of cichlid are still cichlid. The real mystery is how different species in the broader sense of the word can have evolved from common ancestors: how come there are insects, fish, animals, birds, all descended from the first single cells with which life began? “Combinatorial speciation” is no different from Margulis’s emphasis on cooperation. Even you agree that cell communities combine or cooperate autonomously to create minor changes, and the question is whether they can also do the same to create major changes. But you refuse to accept this possibility.

DAVID: Because it involves the major use of mentally planned complex designs.

Yes, you refuse to accept the possibility that microorganisms are capable of mental activity. It’s not just major designs you discount. Your God has to preprogramme or dabble every bacterial response to every situation in the history of life past, present and future, and he even has to engineer midge adaptation. Billions of programmes and dabbles, all for the sole purpose of covering the time before he specially designed H. sapiens.

2787 views

dhw: It certainly is amazing. You assume your God had to specially preprogramme this midge (= provide adaptive instructions for this particular situation) in order to keep life going so that he could eventually design H. sapiens. If he exists, I would be more inclined to believe that he equipped cells with the intelligence to find ways of adapting to all kinds of conditions. Not much point in inventing life if he didn’t give organisms the means of surviving! Even you have suggested that your God may have given cells the ability to make minor epigenetic changes to themselves, so I wonder where you draw the borderline between major and minor.

DAVID: As before: minor is simple alterations, while major involves body design changes and/or complex physiological changes.

I’m just checking the extent to which you think your God did it, as opposed to the organism did it. Here we have him specially preprogramming the Antarctic midge (he provided “adaptive instructions”) to survive in extreme conditions so that it would provide food to keep life going until he could design the only thing he wanted to design, H. sapiens.

Dhw (under “Hybridisation”): This is a cop-out. All the varieties of cichlid are still cichlid. The real mystery is how different species in the broader sense of the word can have evolved from common ancestors: how come there are insects, fish, animals, birds, all descended from the first single cells with which life began? “Combinatorial speciation” is no different from Margulis’s emphasis on cooperation. Even you agree that cell communities combine or cooperate autonomously to create minor changes, and the question is whether they can also do the same to create major changes. But you refuse to accept this possibility.

DAVID: Because it involves the major use of mentally planned complex designs.

dhw: Yes, you refuse to accept the possibility that microorganisms are capable of mental activity. It’s not just major designs you discount. Your God has to preprogramme or dabble every bacterial response to every situation in the history of life past, present and future, and he even has to engineer midge adaptation. Billions of programmes and dabbles, all for the sole purpose of covering the time before he specially designed H. sapiens.

You are describing the wrong God. My God understood the time He would need to evolve humans He did not have the sole purpose of filling time. Have you forgotten evolution is a stepwise process? He proceeded step by step in a logical fashion. Pre-programming made his work easier.

2805 views

First example found:

https://www.nature.com/articles/d41586-021-00782-w

"The finding, reported today in Cell1, is the first known example of a natural gene transfer from a plant to an insect. It also explains one reason why the whitefly Bemisia tabaci is so adept at munching on crops: the gene that it swiped from plants enables it to neutralize a toxin that some plants produce to defend against insects.

***

"That some species of whitefly could owe part of their predatory prowess to genes from other organisms is not entirely surprising, because genetic thievery is common in the arms race between plants and their pests. Over millions of years, plants and insects alike have borrowed heavily from microbial genomes, sometimes using their newly acquired genes to develop defensive or offensive strategies.

"Some insects, such as the coffee berry borer (Hypothenemus hampei), have plundered microbial genes to extract more nutrition from hard-to-digest plant cell walls2, and a wild relative of wheat has pilfered a fungal gene to fight off a fungal disease called head blight3. But plants and insects were not known to steal from each other before now.

***

"study showed that the gene can transfer a chemical group on to defensive compounds called phenolic glucosides. Such compounds are made by many plants, including tomatoes, to ward off pests. But the modification caused by the whitefly gene rendered the compounds harmless.

***

"The results were surprising, but convincing, says Yannick Pauchet, a molecular entomologist also at the Max Planck Institute for Chemical Ecology. “According to the data they provide, horizontal gene transfer is the most parsimonious explanation,” he says.

"But how the whitefly managed to swipe a plant gene is unclear. One possibility, says Turlings, is that a virus served as an intermediate, shuttling genetic material from a plant into the whitefly genome.

"As researchers sequence more genomes, it’s possible that they’ll uncover more examples of gene transfer between plants and animals, says Gloss.

“'Insects taking the genes from the plants themselves is just that last bit of the arsenal that we hadn’t found yet,” he says. “In the battle between plants and their insect pests or pathogens, there are genes being drawn from all over the tree of life.'”

Comment: Undoubtedly more of this type of transfer will be found, and virus is the best guess as the agent. Horizontal gene transfer is shown again to be a driver of evolutionary change. This may be another answer/reason to why viruses are present at all?

2004 views

A new assertion:

https://www.quantamagazine.org/dna-jumps-between-animal-species-no-one-knows-how-often-...

"To survive in the frigid ocean waters around the Arctic and Antarctica, marine life evolved many defenses against the lethal cold. One common adaptation is the ability to make antifreezing proteins (AFPs) that prevent ice crystals from growing in blood, tissues and cells. It’s a solution that has evolved repeatedly and independently, not just in fish but in plants, fungi and bacteria.

"It isn’t surprising, then, that herrings and smelts, two groups of fish that commonly roam the northernmost reaches of the Atlantic and Pacific Oceans, both make AFPs. But it is very surprising, even weird, that both fish do so with the same AFP gene — particularly since their ancestors diverged more than 250 million years ago and the gene is absent from all the other fish species related to them.

"A March paper in Trends in Genetics holds the unorthodox explanation: The gene became part of the smelt genome through a direct horizontal transfer from a herring. It wasn’t through hybridization, because herring and smelt can’t crossbreed, as many failed attempts have shown. The herring gene made its way into the smelt genome outside the normal sexual channels.

***

"Nor are the smelt unique. Recent studies of a range of animals — other fish, reptiles, birds and mammals — point to a similar conclusion: The lateral inheritance of DNA, once thought to be exclusive to microbes, occurs on branches throughout the tree of life.

***

"...the smelt discovery and other recent examples all point to horizontal transfers playing an influential role in evolution."

Comment: The paper then covers many pages of research review om possible mechanism including parasite transfer. Nothing is conclusive but it certainly fits my notion of God dabbling.

1753 views

Latest study surprising:

https://www.sciencealert.com/there-are-a-bunch-of-bacteria-having-sex-in-your-gut-right...

"By forming a 'temporary union' with another bacterium in our gut, a microbe can therefore transfer its genes to another – it doesn't even have to be the same species.

"All the microbe has to do is stick out a tube, called a pilus, and attach itself to another cell, shooting off a transferable package of DNA called a mobile genetic element when it's ready.

"The discovery of bacterial sex was made over 70 years ago, when scientists realized this horizontal gene transfer was how microbes were sharing resistance genes for certain antibiotics, thereby spreading antibiotic resistance.

"More recently, it's become clear that bacterial sex doesn't just occur when microbes are under attack. It happens all the time, and it's probably part of what keeps our microbiome fit and healthy.

***

"'The big, long molecules from sweet potatoes, beans, whole grains, and vegetables would pass through our bodies entirely without these bacteria," explains microbiologist Patrick Degnan from the University of California Riverside.

"'They break those down so we can get energy from them."

"To colonize the human gut and help us break down carbohydrates, however, these microbes must compete for limited resources in the large intestine. Such resources include vitamin B12 and other related compounds, which help fuel the bacteria's metabolism and synthesis of proteins.

"Most microbes in the gut don't have the ability to synthesize these crucial compounds on their own, which means they have to soak up what they can from their environment.

"For this to be effective, it pays to have genes for an efficient vitamin B12 transport system at the ready.

"In both petri dishes and in living mouse models, researchers have now identified B12 transporters that are shared via bacterial sex.

***

"'The horizontal gene exchange among microbes is likely used for anything that increases their ability to survive, including sharing [genes for the transport of] vitamin B12."

"When two gut microbes were placed on a dish in the lab, researchers noticed the bacterium that couldn't synthesize B12 transport systems connected up with the bacterium that could. Once the sex pilus bridged the gap between the two, the 'receiving' bacterium could unpack its precious cargo.

"After the experiment, researchers examined the genome of the receiving bacterium, which was still alive, and found it had incorporated an extra band of DNA from the donor.

"Among living mice, something similar appears to happen. When researchers administered two forms of Bacteroidetes to a mouse – one that possessed the genes for transferring B12, and another that didn't – they found the genes of the former had 'jumped' to the latter after five to nine days."

Comment: a well-recognized process now shown to happen in very short times. Luckily for us the gut bacteria like to work for us and process veggies we cannot on our own.

1153 views

QUOTES: "By forming a 'temporary union' with another bacterium in our gut, a microbe can therefore transfer its genes to another – it doesn't even have to be the same species.

"All the microbe has to do is stick out a tube, called a pilus, and attach itself to another cell, shooting off a transferable package of DNA called a mobile genetic element when it's ready."

"The discovery of bacterial sex was made over 70 years ago, when scientists realized this horizontal gene transfer was how microbes were sharing resistance genes for certain antibiotics, thereby spreading antibiotic resistance.”

Wow! This is a real eye-opener for me, though obviously not for people in the field. I’ve always thought that sexual reproduction was an astonishing leap forward in evolution, but the basic principle was already established by bacteria through horizontal gene transfer! For me, this provides a crucial link in the chain of common descent. Many thanks to David for this “revelation”!

QUOTE: “The horizontal gene exchange among microbes is likely used for anything that increases their ability to survive.”

Yes indeed, all these steps in life’s history are likely to be motivated by the quest to improve chances of survival.

1151 views

QUOTES: "By forming a 'temporary union' with another bacterium in our gut, a microbe can therefore transfer its genes to another – it doesn't even have to be the same species.

"All the microbe has to do is stick out a tube, called a pilus, and attach itself to another cell, shooting off a transferable package of DNA called a mobile genetic element when it's ready."

"The discovery of bacterial sex was made over 70 years ago, when scientists realized this horizontal gene transfer was how microbes were sharing resistance genes for certain antibiotics, thereby spreading antibiotic resistance.”

dhw: Wow! This is a real eye-opener for me, though obviously not for people in the field. I’ve always thought that sexual reproduction was an astonishing leap forward in evolution, but the basic principle was already established by bacteria through horizontal gene transfer! For me, this provides a crucial link in the chain of common descent. Many thanks to David for this “revelation”!

QUOTE: “The horizontal gene exchange among microbes is likely used for anything that increases their ability to survive.”

dhw: Yes indeed, all these steps in life’s history are likely to be motivated by the quest to improve chances of survival.

Yes, organisms must survive long enough for the next stage of evolution to develop.

1165 views

More research, more transfers found:

https://www.the-scientist.com/features/horizontal-gene-transfer-happens-more-often-than...

"Horizontal Gene Transfer Happens More Often Than Anyone Thought
DNA passed to and from all kinds of organisms, even across kingdoms, has helped shape the tree of life, to a large and undisputed degree in microbes and also unexpectedly in multicellular fungi, plants, and animals.

"...whatever the delivery vehicle, one thing is clear: in contrast to the simplicity of evolution from a common ancestor as commonly depicted, the branches of the tree of life appear to be inextricably tangled, and scientists are only just beginning to understand the extent of this complexity.

“'As our sampling increases, so does our power to detect horizontal gene transfers,” says Rokas. “So as we sequence more and more and more diverse lineages, I think we’re going to find more and more cases.”

***

"Still, when the first studies hinting at the possibility of HGT in eukaryotic organisms came out in the 2000s, researchers were hesitant to trust the results, citing numerous barriers that seemed insurmountable. For example, while foreign DNA can easily access bacterial genomes free-floating in the cytoplasm, in eukaryotes it would have to cross through highly regulated nuclear pores to enter the genome’s nuclear home. Also, because eukaryotic genomes are organized into pairs of homologous chromosomes that need to line up properly during meiosis, some researchers argued that large insertions would simply be too physically disruptive and would impede gamete production.

"To this day, the evidence for eukaryotic HGT is far sparser than that for bacterial HGT, and some scientists remain skeptical of its prevalence or importance in the evolution of diverse taxa. But Andrew Roger, a comparative genomicist at Dalhousie University in Nova Scotia, says that those who work with single-celled eukaryotes have readily embraced the idea. Genomic data—particularly long-read sequencing data, which establishes the genomic context for putatively foreign genes—has been unequivocal, he says. “The more genomes you get, the more you realize: here’s this chunk of chromosome from this organism in this one over here. And it’s just clearly a transfer.” In his mind, he adds, there’s little doubt that horizontal gene transfer has played a large role in the evolution of protists.

***

"Now, Rokas says, he thinks that DNA is not only moving around the tree of life, but it’s moving a lot more frequently than anyone had imagined, and the cases of HGT that have been identified are just a small sample of the total transfers that have taken place over evolutionary time. “My sense is there is orders of magnitude more integration than retention,” Rokas says. “So there is a lot more DNA coming into fungal genomes, and only a tiny fraction of that DNA is adaptive or selected enough to be maintained.”

***

“'We have the tools and the data now that allow us to quantify these transfers and quantify the impact they’ve had on evolution of eukaryotic genomes,” he adds. “I think the [whitefly] study that we did prompts us and prompts many others to start conducting such systematic analyses now. And we may come to realize that these transfers are not that not as rare as we thought they were.”

"Even if transfers in multicellular organisms are indeed less common than in microbes, Gilbert notes that evolutionary importance is not just a numbers game. “We want to think not [just] in terms of number, but also in terms of impacts. Perhaps just one transfer may have had a huge impact on the viability of some species.”

"Moran agrees. “In many cases, [horizontally transferred DNA] seems really central to the ecology or lifestyle of that particular group. Even if it’s only a tiny part of the genome, it can still be a major influence.'”

Comment: an enormous review article filled with research examples. I've pulled out the researcher's conclusions. HGT is a major evolutionary mechanism and as I view God's controls, a way He can step in for a 'dabble'.

1065 views

A new review:

https://www.quantamagazine.org/how-genes-can-leap-from-snakes-to-frogs-20221027/

"Perched on a leaf in the rainforest, the tiny golden mantella frog harbors a secret. It shares that secret with the fork-tongued frog, the reed frog and myriad other frogs in the hills and forests of the island nation of Madagascar, as well as with the boas and other snakes that prey on them. On this island, many of whose animal species occur nowhere else, geneticists recently made a surprising discovery: Sprinkled through the genomes of the frogs is a gene, BovB, that seemingly came from snakes.

"After poring over genomes from frog and snake species around the world, the scientists reported in April in a paper in Molecular Biology and Evolution that this gene has somehow traveled from snakes to frogs at least 50 times all over the planet. But in Madagascar it has inserted itself into frogs with startling promiscuity: 91% of the frog species sampled there have it. Something seems to make Madagascar an exceptionally conducive place for the gene to get mobile.

***

"...this new paper, which shows that the horizontal transfer of genes may be more likely in some places than others, complicates the story even more. It suggests that when seeking explanations for horizontal transfers, researchers may need to look beyond simple genetic mechanisms to the ecological contexts in which species live. Genomicists are still struggling to understand how common or rare horizontal transfers are in complex organisms, but some places, like Madagascar, may be hot spots for them.

***

"The cells of eukaryotic organisms like humans, frogs and snakes, however, are different [than bacteria] Their cell nucleus usually seems like a fortress for protecting the genome. The DNA is carefully coiled up and stored in that citadel’s library, with enzymes calling forth only the genes they need to examine at any given time. The cell is loaded with fail-safes to prevent damage to its DNA and to repair wear and tear. If the genome is like a priceless illuminated manuscript, its librarians carry swords.

***

"As strange as it might seem for eukaryotes to pick up genes from bacteria, stranger still is the fact that examples of horizontal gene transfer in the other direction are vastly rarer. For some reason, bacteria don’t want our genes. Eukaryotic genes have structural features that make them less than perfect material for bacteria, but there may be other contributing factors as well.

***

"Findings like these have persuaded some biologists that at least some horizontal gene transfers may be facilitated by viruses. If viruses can pick up genes from their hosts, and if they can leave behind pieces of their genomes, it seems possible that they could also sometimes ferry over genes from the last host they infected, or even one from generations ago, and give them to a new host.

***

"The involvement of viruses could also help to solve another puzzle about horizontal transfers in eukaryotes. For the transfers to occur, the traveling genes need to clear an entire series of hurdles. First they must get from the donor species to the new host species. Then they must get into the nucleus and ensconce themselves in the host genome. But getting into the genome of just any cell won’t do: In multicellular creatures like frogs and herrings, a gene won’t be passed down to the animal’s offspring unless it can sneak into a germline cell — a sperm or an egg.

***

"Is there something about the environment of Madagascar that makes it a hot spot for gene transfers?

***

"But the abundance of parasites on the island might also be a contributing factor. For example, “in Madagascar, there are lots of leeches,”

***

"Unfortunately, it isn’t easy to prove or disprove scenarios describing how such horizontal transfers might have occurred. Without selection to preserve DNA sequences, they tend to mutate and get scrambled over long stretches of time, erasing the molecular evidence of a transfer. And if a virus is involved in the transfer, it may leave very little evidence in the first place, Graham said. Researchers might therefore almost need to catch a genetic jump in the act to know how it is happening."

Comment: lots of evidence but still no answers as to how horizontal transfer occurs in eukaryotes.

882 views

As the oldest branch of life, this new finding is no surprise:

https://www.the-scientist.com/news-opinion/archaea-sport-structures-that-shuttle-genes-...

"Studies show that members of different domains can traffic genes back and forth, potentially fast-tracking evolution. How they do so remains unknown, but a study published today (November 16) in Science Advances provides a possible clue with the first report that archaea have integrons—gene exchange machinery previously thought only to exist in bacteria. This may allow microbes from the two domains to swap information and instantly acquire new functions. (my bold)

***

"It was unknown if archaea have integrons, partly because they’re hard to study, says Ghaly, as they live in a variety of difficult-to-access environments, from our guts to muddy, sulfuric hot springs. But recent advances in genomic sequencing, in particular a technique called metagenome-assembled genomes (MAG), have allowed researchers to piece together archaea genomes from environmental samples.

***

"Bacteria swap genes in the form of a gene cassette that consists of a single gene and a gene recombination site called AttC. When they encounter stressful circumstances, bacteria exchange these cassettes like mixtapes, plugging them into and taking them out of their genomes.

"To begin the DNA transfer process, bacteria use integron integrase (IntI), a protein in the tyrosine kinase family. Intl induces recombination between the gene cassette’s AttC site and a region on the bacterium’s genome called an integron attachment site, or AttI. Bacteria end up with a long string of gene cassettes, strung together by AttC sites, in their genomes.

"On the bacterial genome, integrons consist of a gene for an IntI protein, Int, followed by a series of integrated gene cassettes. In the new study, the researchers screened all publicly available genomes of archaea, 95 percent of which were MAGs. They searched for AttC-like sequences and for sequences coding for IntI-like proteins. The researchers say they haven’t found a way to predict AttI sequences, and thus didn’t look for them.

"In the nearly 6,700 archeal genomes they scanned, the researchers found 75, spanning nine phyla, that had evidence of integrons. All of the archaeal integrons had the same structure and components as bacterial integrons. (my bold)

Comment: it is widely accepted Archaea were the first life, so it is no surprise transferring integrons were there. Note my bolds. They are a way to fast-track evolution. It is a tool for a designing God to use.

842 views

Nothing really new:

https://www.the-scientist.com/news-opinion/archaea-sport-structures-that-shuttle-genes-...

“'We’ve known for a while that there are a lot of genes that bacteria and archaea exchange,” says Olga Zhaxybayeva, an evolutionary biologist at Dartmouth College who was not involved in the study. If integrons turn out to be widespread in archaea, “it could be another mechanism for microbes to exchange the traits they need.”

"Gene exchange can help bacteria survive in new, harsh environments, or strengthen their symbiotic relationships with plants. Study coauthor Timothy Ghaly, a microbiologist at Macquarie University in Sydney, says that he and his team had always been interested in how integrons allow bacteria to take on novel, sometimes incredibly useful traits such as antibiotic resistance.

"It was unknown if archaea have integrons, partly because they’re hard to study, says Ghaly, as they live in a variety of difficult-to-access environments, from our guts to muddy, sulfuric hot springs. But recent advances in genomic sequencing, in particular a technique used to generate what are known as metagenome-assembled genomes (MAG), have allowed researchers to piece together archaea genomes from environmental samples.

***

"Bacteria swap genes in the form of a gene cassette that consists of a single gene and a gene recombination site called AttC. When they encounter stressful circumstances, bacteria exchange these cassettes like mixtapes, plugging them into and taking them out of their genomes.

***

"In the nearly 6,700 archeal genomes they scanned, the researchers found 75, spanning nine phyla, that had evidence of integrons. All of the archaeal integrons had the same structure and components as bacterial integrons.

"Based on the sequences they found, the researchers then synthesized archaeal AttC-containing cassettes and found that, when exposed, E. coli bacteria incorporated these cassettes into their genomes.

“"It’s always interesting to find [horizontal gene transfer] in new organisms,” says Zhaxybayeva. She adds that, in the future, it would be useful to have a complete genome of a cultured archaea, as opposed to a constructed MAG as the team used in this study, and begin to piece together the mechanism behind the gene transfer. She’s particularly interested in whether archaea in the human gut have integrons, “and whether they participate in the exchange around antibiotic resistance.'”

Comment: not surprising that all bacteria use the same mechanisms of gene transfer.

782 views

Looking at ease of transfer:

https://phys.org/news/2023-06-complexity-barrier-horizontal-gene.html

"This process is a major contributor to microbial evolution, accounting for 10–20% of the protein-coding genes in most bacterial genomes, while HGT is less prevalent among eukaryotes. Through HGT, bacteria and archaea can acquire new traits, ranging from antibiotic resistance to metabolic capabilities, which enhances their ability to adapt to changing environments.

"In a new study from Genome Biology and Evolution titled "Empirical evidence that complexity limits horizontal gene transfer," researchers from the University of North Carolina, led by Christina Burch and Corbin Jones, investigated the factors that influence the ability of individual genes to be transferred into a new recipient bacterial strain via HGT.

"Their study reveals that a gene's transferability is affected by several factors, including its sequence divergence from the recipient and how many interaction partners the resulting protein has (i.e., its connectivity). Moreover, a gene's divergence and connectivity interact to further influence its transferability.

"While previous studies have observed a relationship between gene transferability and protein connectivity, scientists have puzzled over the mechanism underlying this link. Two potential hypotheses have been suggested: the Balance Hypothesis and the Complexity Hypothesis.

"The Balance Hypothesis suggests that newly transferred genes may result in gene dysregulation by upsetting the balance between expressed proteins, while the Complexity Hypothesis proposes that newly transferred genes may fail to engage in normal protein-protein interactions. Importantly, while the divergence between the donor and recipient strains should not affect the former process, it is expected to impact the latter, as more divergent proteins are more likely to experience protein-protein interaction failure.

***

"After correcting for biases related to bacterial physiology (i.e., frequent initiation of replication in actively growing cells), the authors investigated the relationship between gene transferability (as estimated by sequencing coverage) and several factors that may affect HGT, including gene function, protein connectivity, the divergence between the donor species and E. coli, and the expression level of the native gene in E. coli.

"Importantly, they found a significant interaction between divergence and connectivity, supporting the Complexity Hypothesis and suggesting that the ability of a transferred gene to engage in normal protein-protein interactions plays a key role in the success or failure of HGT.

"In addition to these findings, an important contribution of this study was the development of a statistical test capable of evaluating the Complexity Hypothesis. Burch notes, "Prior to this work, the Complexity Hypothesis had been described only using verbal arguments. I think it was an important step forward to translate the hypothesis into a specific statistical test. The fact that we could then conduct the statistical test on existing genomic data was icing on the cake. We are grateful to the Sorek team for leading the way."

"One caveat of this analysis is that all the genes studied were on the plasmids (i.e., extrachromosomal DNA) used to transfer them into the recipient cell. Different dynamics may be observed when genes are transferred directly onto bacterial or archaeal chromosomes.

"Ultimately, we would like to understand better the consequences of incorporating transferred genes into recipient genomes," says Burch. "Modern genome sequencing technology makes it possible to investigate that question using microbial evolution experiments, and a few have been done, but a lot more data are needed."

"Moreover, the current analysis was necessarily limited to genes that were already present in the E. coli genome. "We would also like to understand better the horizontal transfer of new or accessory genes that are not already present in recipient cells," continues Burch. "Those genes are not relevant to the Complexity Hypothesis, so that investigation remains for future work.."

Comment: it is not surprising that complexity limits horizontal gene transfer. As organisms become very complex through evolution the process disappears. In humans viral infections have added to our DNA without making us something different. It is not a significant event.

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The role of virus-like transposons:

https://www.sciencemagazinedigital.org/sciencemagazine/library/item/30_june_2023/411231...

"While studying the evolutionary origin of a selfish element in the nematode Caenorhabditis briggsae, we discovered that Mavericks, ancient virus-like transposons related to giant viruses and virophages, are one of the long-sought vectors of horizontal gene transfer. We found that Mavericks gained a novel herpesvirus-like fusogen in nematodes, leading to the widespread exchange of cargo genes between extremely divergent species, bypassing sexual and genetic barriers spanning hundreds of millions of years. Our results show how the union between viruses and transposons causes horizontal gene transfer and ultimately genetic incompatibilities in natural populations.

***

"...transfer of genes between eukaryotes is thought to be rare, especially in metazoans, because it requires a chain of unlikely events: DNA must find its way out of the donor species, come in close contact with the germline of a second species, and finally integrate itself in the genome of the new host. Nonetheless, from antiparasitic toxins in butterflies to antifreeze proteins in fish, a growing body of evidence indicates that HGT between eukaryotes is far more common than was previously thought and could be an important evolutionary force.

***

"Here, by studying the evolutionary origin of a selfish toxin-antidote (TA) element in the nematode Caenorhabditis briggsae, we found that Mavericks, ancient eukaryotic viruslike transposons, are widespread vectors of HGT between nematodes. Further, we showhowHGT fueled the evolution of genetic incompatibilities in natural populations.

***

"Overall, our results indicate that two novel nematode protein families, WOSP proteases and KRMA kinases, are preferentially associated with Mavericks. These genes likely correspond to cargo sequences that were originally “captured” by Mavericks from nematode genomes during transposition and, as a result, broadly exchanged between species that have been reproductively isolated for tens or even hundreds of millions of years. In support of this view, we found that the GC content of wosp and krma genes largely matched that of host genes but differed significantly from that of Maverick core genes.

***

"In this study, we provide evidence for widespread Maverick-mediated horizontal gene transfer across extremely divergent nematode species that drove the evolution of a novelMULE-associated selfish TA element. The TA found in C. briggsae is capable of both spreading in nature by poisoning individuals homozygous for the susceptible allele and changing its position in the genome through transposition.

***

"We show in unprecedented detail how cooperation between parasitic genetic elements can lead to the evolution of new biological function and ultimately affect gene flow between populations. However, several intriguing aspects of the TA evolution are still unknown. For instance, it is not clear whether msft-1 became a toxin before or after its capture by the MULE transposon and if msft-1 has nonselfish roles that could also have contributed to the evolution of the TA.

"Our work reveals Mavericks as one of the long sought-after vectors of HGT. Because of their unique biology, which shares features of both transposons and viruses, Mavericks are responsible for the widespread transfer of genes across extremely divergent species...We hypothesize that Mavericks, like E. coli λ phage and human herpesvirus, integrate into the genome of their host and passively replicate until an environmental factor triggers the formation of infective particles (Fig. 6B). In support of this model, maviruses, virophages evolutionary related to Mavericks, are not constitutively expressed when integrated in protozoan genomes, but they are specifically transcribed after superinfection by the giant virus CrV."

Comment: wow!!! viruses and transposon-like viruses acting like bandits in the night, attacking genomes indiscriminately. A hidden mechanism for evolution?

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A special plasmid pathway grows and moves slowly:

https://phys.org/news/2023-09-scientists-uncover-ways-bacteria-antibiotic-resistant.html

"Plasmids, found in bacteria and some other microorganisms, are physically separate from chromosomal DNA and can replicate on their own. Bacteria can acquire plasmids from other bacterial cells or from viruses, and as plasmids build up, they give bacteria antibiotic resistance.

"But some plasmids are easier for bacteria to acquire than others. What makes these plasmids spread more easily?

"While common sense might suggest that plasmids that spread the easiest are the ones that allow bacteria to grow the fastest, a new study in Nature Communications, led by Allison Lopatkin, an assistant professor of chemical engineering at the University of Rochester, outlines the surprising evolutionary tradeoff between lag time and growth rate.

***

"Lopatkin and her team studied the growth rates of single colonies of bacteria immediately following plasmid acquisition. Across nearly 60 conditions covering diverse plasmids, selection environments, and clinical strains, they found that intermediate-cost plasmids outcompete both their low and high-cost counterparts.

"The research shows plasmid costs are more complex than previously believed and is a step toward better understanding why certain types of pathogens are better at acquiring plasmids than others. If scientists can understand what controls the costs of acquiring a plasmid, they can potentially use that information to limit the spread of antibiotic-resistant genes.

"'We see horizontal gene transfer as an engineering tool to control how genes can spread and help bacterial communities interact," says Lopatkin. "By understanding the individual parts, we hope not only to be able to fight things like antibiotic resistance, but also to use plasmids to deliver genes that can help natural bacteria degrade oil from oil spills. There are many applications microbiomes can be useful for.'"

Comment: more evidence that at the single-cell-level, a bacterium is the most complicated form of a cell. The original animal at the start of life and through all of evolution an integral part of all developments. Now performing as useful microbiomes. They can extensively edit their own DNA. Other single cells as part of multicellular organisms have specific consigned duties to perform, actively manufacturing proteins and other molecules or monitoring levels of oxygen in the hypothalamus or sodium in the kidney. They do not edit their own DNA.

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Now dust is a problem, finding plasmids which bacteria use to transfer DNA is there:

https://www.newscientist.com/article/2231210-antibiotic-resistance-genes-can-be-passed-...

"Genes that make bacteria resistant to antibiotics have been found in dust in buildings in a form that could be passed to disease-causing microbes.

"The finding suggests that people in households where people frequently take antibiotics could be at higher risk of getting infected with antibiotic resistant “superbugs” – although it isn’t known if this is actually happening.

"Antibiotic resistance is seen as one of the biggest global threats to public health, as growing numbers of dangerous bacteria have evolved the ability to withstand antibiotic treatment.

"To try to slow the spread of resistance, we are supposed to limit our use of antibiotics, for example by not taking them for coughs or colds, which are usually caused by viruses.
However, it is unclear how useful it is for individuals to take such steps when resistant bacteria are common in the environment, such as in hospitals and perhaps our homes and workplaces too.

"Previously, resistant bacteria have been found in dust – but it is unclear how dangerous this is, as most bacteria that can survive the dry conditions of dust are harmless to people.

"Erica Hartmann at Northwestern University in Illinois and her colleagues wondered whether the antibiotic resistance genes in the bacteria in dust could get passed to more dangerous microbes. Bacteria often share genes with each other by swapping small sections of DNA called plasmids.

"The researchers looked at dust samples from 43 public buildings. Over a quarter of the resistance genes they found were on plasmids or other transferrable forms of DNA.

"It raises the possibility that if a home were contaminated with a bacterium such as the food poisoning microbe Salmonella, the microorganism could become more dangerous, says Hartmann. “It’s possible that something that would make you sick could pick up an antibiotic resistance gene.'”

Comment: Should we now wear masks in public. Considering the Chinese corona pneumonia virus running around the world, perhaps we should.

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