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Thread: Is virus the primitive form of life in the ancient world?

  1. #1 Is virus the primitive form of life in the ancient world? 
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    According to the RNA world hypothesis, it proposes that self-replicating ribonucleic acid (RNA) molecules were precursors to current life, which is based on deoxyribonucleic acid (DNA), RNA and proteins. (wiki)

    "Most evolutionists agree to consider that our present RNA/DNA/protein world has originated from a simpler world in which RNA played both the role of catalyst and genetic material.
    Recent findings from structural studies and comparative genomics now allow to get a clearer picture of this transition.
    These data suggest that evolution occurred in several steps, first from an RNA to an RNA/protein world (defining two ages of the RNA world) and finally to the present world based on DNA."

    The two ages of the RNA world, and the tra... [Biochimie. 2005 Sep-Oct] - PubMed - NCBI

    However, it seems that there is a problem for the replication of virus in ancient world. As viruses are a kind of thing similar to parasite which require hosts for its replication,
    in ancient world there were not mature living organism which can be suitable host for virus. So, the ancient world was not a good environment for the continuity of virus.
    ​Is virus the primitive form of life in the ancient world?


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    Moderator Moderator Cogito Ergo Sum's Avatar
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    Quote Originally Posted by a283ta9 View Post
    However, it seems that there is a problem for the replication of virus in ancient world. As viruses are a kind of thing similar to parasite which require hosts for its replication, in ancient world there were not mature living organism which can be suitable host for virus. So, the ancient world was not a good environment for the continuity of virus.
    ​Is virus the primitive form of life in the ancient world?

    No, as I do not regard viruses as forms of life.
    Second, the "ancient" world (I prefer the term "prebiotic") was actually an environment that could support the existence of viruses.

    Patrick Forterre explains this in the paper you provided:
    In both ages of the RNA world, a variety of organisms should have coexisted with preys and predators, free-living cells and cellular parasites. As a consequence, it is very likely that cells and virus-like organisms already coexisted and fought each other (or cohabited in various ways) in the RNA world. Since all present-day viruses contain proteins, the first viruses most likely originated as RNA viruses in the second age of the RNA world. I suggested some time ago that viruses evolved by parasitic reduction from ancient cellular lineages that were out-competed in the Darwinian selection process before LUCA, and thus could only survive as parasites in the winner of this competition. In this model, RNA viruses originated from RNA cells.

    In the end, viruses are thought to have had major roles to play in the early evolution of life; for example viruses may have evolved DNA before cellular life (cells may have been RNA cells initially), and the eukaryotic nucleus may be the remnant of a large DNA virus, just to mention two ideas. Yet, it is all hypothesis building.


    PS: Thanks to member Zwirko for his helpful PM.


    "The only safe rule is to dispute only with those of your acquaintance of whom you know that they possess sufficient intelligence and self-respect not to advance absurdities; to appeal to reason and not to authority, and to listen to reason and yield to it; and, finally, to be willing to accept reason even from an opponent, and to be just enough to bear being proved to be in the wrong."

    ~ Arthur Schopenhauer, The Art of Being Right: 38 Ways to Win an Argument (1831), Stratagem XXXVIII.
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    Viruses need hosts only to replicate and not to exist. Therefore although there weren't any other life forms that could be used by viruses for replication, this does not mean that the viruses could not simply exist. We are assuming that the virus is not a living organism and thus it cannot "die" of age, hunger etc as it does not perform these processes and therefore it may have existed but could not replicate until living organisms as we know them started to develop. What could have happened then was that the virus adapted in such a way to use these organisms for replication and thus became the parasite as it is still known today.
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    Quote Originally Posted by Cogito Ergo Sum View Post
    No, as I do not regard viruses as forms of life.
    some people, including myself, would disagree with that assessment
    i consider anything that exhibits "descent with modification" as a characteristic to be a form of life
    that makes viruses a form of life

    on the other hand, to call them primitive ignores the fact that viruses depend for their replication on a host, which implies that viruses have secondarily simplified their make-up from what was once a autonomously replicating unit
    "Reality is that which, when you stop believing in it, doesn't go away." (Philip K. Dick)
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    Quote Originally Posted by marnixR View Post
    Quote Originally Posted by Cogito Ergo Sum View Post
    No, as I do not regard viruses as forms of life.
    some people, including myself, would disagree with that assessment
    i consider anything that exhibits "descent with modification" as a characteristic to be a form of life
    that makes viruses a form of life

    Yes, but virions are metabolically inert, they cannot generate energy nor carry out biosynthesis. They must rely on host cells to provide energy and materials needed for replication and protein synthesis. I do not regard objects that lack these fundamental characteristics of life as 'alive'.

    Yet, I can understand why people would disagree with my point of view.
    "The only safe rule is to dispute only with those of your acquaintance of whom you know that they possess sufficient intelligence and self-respect not to advance absurdities; to appeal to reason and not to authority, and to listen to reason and yield to it; and, finally, to be willing to accept reason even from an opponent, and to be just enough to bear being proved to be in the wrong."

    ~ Arthur Schopenhauer, The Art of Being Right: 38 Ways to Win an Argument (1831), Stratagem XXXVIII.
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    Quote Originally Posted by a283ta9 View Post


    However, it seems that there is a problem for the replication of virus in ancient world. As viruses are a kind of thing similar to parasite which require hosts for its replication,
    in ancient world there were not mature living organism which can be suitable host for virus. So, the ancient world was not a good environment for the continuity of virus.
    ​Is virus the primitive form of life in the ancient world?
    Viruses are incredibly diverse, so it's probably a mistake to assume that they all appeared by the same process. Large DNA viruses and small RNA viruses, for example, likely have very different origins.

    It's also possible that some viruses appeared before cells were around. There's one hypothesis that suggests that early life consisted of metabolic reactions taking place within microscopic cavities within rocks. Based on this idea, it's been suggested that some viruses may have evolved at this time and could "infect" such cavities. Viruses could perhaps thus be truly ancient, pre-dating cells. True cells and viruses have perhaps been duking it out since always.
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    Quote Originally Posted by marnixR View Post

    some people, including myself, would disagree with that assessment
    i consider anything that exhibits "descent with modification" as a characteristic to be a form of life
    that makes viruses a form of life

    Over the years I've moved in to the "non-life" camp. For me, the ability to capture, store and utilise free-energy is an essential characteristic of life. Viruses can't do this, so... Non-living biological entity is where I'm at, (I think). While they exhibit descent with modification, it bothers me that they can't reproduce. It might be more correct to say that they are replicated (dare I say, manufactured?) by cells.
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    The articles mentioned above made me think of an old question i once had.

    Especially the comment by Zwirko, that cells probably made viruses to reproduce. To implement their own DNA/RNA in other cells. This was so effective it split from the original species and even became an individual.

    How cool it would be to be able to reconstruct the original creator of viruses, by the remains of DNA or RNA in the capsule that has no apparent function.

    Would this even be possible, due to the obvious mutagenic properties of the virus itself?
    Growing up, i marveled at star-trek's science, and ignored the perfect society. Now, i try to ignore their science, and marvel at the society.

    Imagine, being able to create matter out of thin air, and not coming up with using drones for boarding hostile ships. Or using drones to defend your own ship. Heck, using drones to block energy attacks, counterattack or for surveillance. Unless, of course, they are nano-machines in your blood, which is a billion times more complex..
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    Making a disitnction between life and non-life is a digital decision, reflecting the tendency of humans to classify things. Life however blends imperceptibly to non-life and vice versa in an analogue fashion. Less satisfying for category prone humans, but then the universe doesn't care about our foibles.
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    In that case, I'd ask the question: are viruses part of the spectrum of life? Have they fallen off the edge, or were they ever on it?

    Going non-digital still means we can say whether something is alive or not. A barrel of whisky is non-living, for example. Deciding whether or not some parasitic bacteria are alive or not is already quite tricky and definitely a grey area. It's my view that viruses are too far removed from the sticky zone to be considered as living or nearly-living. For me, they are fundamentally different from living systems in too many ways. Because they are biological entities they have, by default, features in common with living systems. I'm not sure that this necessarily puts them on a continuum with living agents like cells though. A continuum of life would still end in a non-life zone. Perhaps that is where viruses reside?

    It's all a sticky mess: Some viruses are so simple that they'd make a chunk of a human chromosome look like a divine being.
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    Quote Originally Posted by Zwirko View Post
    It's also possible that some viruses appeared before cells were around. There's one hypothesis that suggests that early life consisted of metabolic reactions taking place within microscopic cavities within rocks. Based on this idea, it's been suggested that some viruses may have evolved at this time and could "infect" such cavities. Viruses could perhaps thus be truly ancient, pre-dating cells. True cells and viruses have perhaps been duking it out since always.

    Do you have a source for this hypothesis? I would like to read more about it.

    Quote Originally Posted by Zwolver View Post
    How cool it would be to be able to reconstruct the original creator of viruses, by the remains of DNA or RNA in the capsule that has no apparent function.
    Would this even be possible, due to the obvious mutagenic properties of the virus itself?

    I'll get my lab coat.
    "The only safe rule is to dispute only with those of your acquaintance of whom you know that they possess sufficient intelligence and self-respect not to advance absurdities; to appeal to reason and not to authority, and to listen to reason and yield to it; and, finally, to be willing to accept reason even from an opponent, and to be just enough to bear being proved to be in the wrong."

    ~ Arthur Schopenhauer, The Art of Being Right: 38 Ways to Win an Argument (1831), Stratagem XXXVIII.
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    Quote Originally Posted by Cogito Ergo Sum View Post


    Do you have a source for this hypothesis? I would like to read more about it.
    It was the same guy as mentioned in the OP: Patrick Forterre. I recall reading about it in the Desk Encyclopedia of General Virology. I don't know what page - I'm sure it was mentioned in drive-by fashion though, not a full article on the topic.

    EDIT:

    The encyclopedia doesn't cite references (a bit weird). It does, however, have a "Further Reading" section. The only relevant article I could see in that list was this one:


    Eugene V. Koonin and William Martin
    On the origin of genomes and cells within inorganic compartments
    TRENDS in Genetics Vol.21 No.12 December 2005


    I haven't read it all, but it does seem to be along the correct line in places. Worth downloading just for the amazing diagram it contains.
    Last edited by Zwirko; December 18th, 2013 at 02:27 PM.
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  14. #13  
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    i prefer the theory that both us and viruses evolved together. just makes a lot more sense imo.
    also i can't agree with zwolvers statement.

    are there any virologists around?
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    Quote Originally Posted by bio View Post
    i prefer the theory that both us and viruses evolved together. just makes a lot more sense imo.
    also i can't agree with zwolvers statement.

    What statement are you referring to?
    "The only safe rule is to dispute only with those of your acquaintance of whom you know that they possess sufficient intelligence and self-respect not to advance absurdities; to appeal to reason and not to authority, and to listen to reason and yield to it; and, finally, to be willing to accept reason even from an opponent, and to be just enough to bear being proved to be in the wrong."

    ~ Arthur Schopenhauer, The Art of Being Right: 38 Ways to Win an Argument (1831), Stratagem XXXVIII.
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    Quote Originally Posted by Zwirko View Post
    In that case, I'd ask the question: are viruses part of the spectrum of life? Have they fallen off the edge, or were they ever on it?
    The scientists in this article refer to viruses as living things and fast-evolving. In fact their entire research, experimentation and claim appear to require a living virus. Not sure if the story helps anyone but I thought what the scientists did was kind of cool if anything.
    All that belongs to human understanding, in this deep ignorance and obscurity, is to be skeptical, or at least cautious; and not to admit of any hypothesis, whatsoever; much less, of any which is supported by no appearance of probability...Hume
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    Quote Originally Posted by zinjanthropos View Post

    The scientists in this article refer to viruses as living things and fast-evolving. In fact their entire research, experimentation and claim appear to require a living virus. Not sure if the story helps anyone but I thought what the scientists did was kind of cool if anything.
    I think the interviewee is using that phraseology to highlight that they are actually doing a real biological experiment rather than just messing about with mathematical models, as has been done for decades when exploring such topics. It doesn't mean that they think viruses are alive (even though they may or may not hold that view). That'd be my interpretation.
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    Quote Originally Posted by Zwirko View Post
    Quote Originally Posted by zinjanthropos View Post

    The scientists in this article refer to viruses as living things and fast-evolving. In fact their entire research, experimentation and claim appear to require a living virus. Not sure if the story helps anyone but I thought what the scientists did was kind of cool if anything.
    I think the interviewee is using that phraseology to highlight that they are actually doing a real biological experiment rather than just messing about with mathematical models, as has been done for decades when exploring such topics. It doesn't mean that they think viruses are alive (even though they may or may not hold that view). That'd be my interpretation.

    Even if the authors of the original study hold the view that viruses are 'alive',
    I wonder where viruses should be put in the Tree of Life (i.e. what is the taxonomy of viruses) according to them.
    "The only safe rule is to dispute only with those of your acquaintance of whom you know that they possess sufficient intelligence and self-respect not to advance absurdities; to appeal to reason and not to authority, and to listen to reason and yield to it; and, finally, to be willing to accept reason even from an opponent, and to be just enough to bear being proved to be in the wrong."

    ~ Arthur Schopenhauer, The Art of Being Right: 38 Ways to Win an Argument (1831), Stratagem XXXVIII.
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    I remember a few years ago there were some papers that tried to put nucleocytoplasmic large DNA viruses (NCLDV's) in to a fourth domain of life. I don't know whether that idea has been abandoned or not - I have a vague memory of some controversy about the idea. Or that could be my imagination. Or not.


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    Quote Originally Posted by Zwirko View Post
    I remember a few years ago there were some papers that tried to put nucleocytoplasmic large DNA viruses (NCLDV's) in to a fourth domain of life. I don't know whether that idea has been abandoned or not - I have a vague memory of some controversy about the idea. Or that could be my imagination. Or not.

    Well, I guess that the discussion about whether viruses are alive or not, is not yet settled in the scientific community.
    Thank you for the illustration, but may I ask you what those numbers indicate?
    "The only safe rule is to dispute only with those of your acquaintance of whom you know that they possess sufficient intelligence and self-respect not to advance absurdities; to appeal to reason and not to authority, and to listen to reason and yield to it; and, finally, to be willing to accept reason even from an opponent, and to be just enough to bear being proved to be in the wrong."

    ~ Arthur Schopenhauer, The Art of Being Right: 38 Ways to Win an Argument (1831), Stratagem XXXVIII.
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    The text below figure says: "The tree is unrooted, and values near branches are SH-like local supports computed by the FastTree program and are used as confidence values of tree branches". The paper is here. I think it's probably speculative at best. I don't think such trees indicate that viruses are necessarily alive though, because after all the tree is just illustrating the evolutionary history of genes. Ironically, you can have non-living things on a tree of life.

    For me the root of the whole "are they or are they not" problem is due to a poor understanding of what it means to be alive. If the very definition of life itself is problematical then viruses end up being stuck in limbo. Under some definitions of life viruses are alive, under others they are not, so you can change the definition of life to include or exclude viruses. I am guilty of this myself by insisting that life must have one particular characteristic. "marnixR" used a different criterion and concluded that they are alive. "John Galt" put them on a continuum.

    I don't know what the resolution to the dilemma is. I suppose you can either give up, pick one and stick to your guns, float in the middle or chop and change your mind. All I really know for certain is that they are a part of the web of life. It's a fun topic.
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    WYSIWYG Moderator marnixR's Avatar
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    i can see a good headline coming up : "Does the Tree of Life have a dead branch ?"
    "Reality is that which, when you stop believing in it, doesn't go away." (Philip K. Dick)
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    Quote Originally Posted by Cogito Ergo Sum View Post
    Quote Originally Posted by bio View Post
    i prefer the theory that both us and viruses evolved together. just makes a lot more sense imo.
    also i can't agree with zwolvers statement.

    What statement are you referring to?
    Probably my statement that a micro organism used to use viruses or virus like particles to reproduce. These reproduction mechanisms obviously began leading a life of its own when they infected the wrong organism.
    Growing up, i marveled at star-trek's science, and ignored the perfect society. Now, i try to ignore their science, and marvel at the society.

    Imagine, being able to create matter out of thin air, and not coming up with using drones for boarding hostile ships. Or using drones to defend your own ship. Heck, using drones to block energy attacks, counterattack or for surveillance. Unless, of course, they are nano-machines in your blood, which is a billion times more complex..
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