141 thoughts on “Are viruses dead or alive?

  1. Allan Miller:

    CharlieM,

    He also mentions that all the ocean’s viruses if laid head to tail would reach over 100 million light years.

    Something to do while at a loose end, I suppose

    They like to do the conga just to rub our noses in it.

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  2. I think that one of the challenges here lies in understanding not just what viruses are but also what they are not.

    If one thinks about dynamic self-organization as an essential feature of cellular life and necessary for adaptive agency, then viruses fail to satisfy those conditions: they are not autopoietic, they lack agency, and they lack biological autonomy.

    So the question “are viruses alive?” could be rephrased as the question

    is it helpful or useful to use the term “alive” for things that replicate by disrupting and co-opting cellular replication, that evolve in response to how organisms adapt to them, but which fail to count as dynamically self-organizing autonomous agents?

    But to that question, I don’t think there’s any answer besides “it depends!”

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  3. Corneel: Who are you calling an “anti-reductionist”? If you really were a reductionist you would be writing shorter OPs.

    Ouch. Et tu, Brute? If the subject matter impacted something less than the bulk of eukaryote biology, and 50 years of puzzlement, I might find less to say about it!

    Anyway, given your purported appreciation of the wide interdependence of all players in organismal physiology, I do not understand why you insist on restricting the definition of life to the replication of nucleic acid polymers (which is what got this discussion started).

    Not restricting as such, it’s just that it seems to be to be a truth more fundamental than the rest.

    Why not include all features that characterize living things, even if you perceive some to be more significant than others?

    Because we have a derived state. It’s fine to look at that derived state; it allows neater dichotomy, just as elimination of transitional forms allows a neater dichotomy of taxonomies.

    But I’m interested in how far back we could go prior to LUCA to find the ‘first living thing’ that we would dignify with the term, and it seems that what we would strip away, as we ascend, are the ‘secretions’ of genomes: the products that enable cellular organisation, import, metabolism, homeostasis, export etc.

    On the ‘virus question’ itself, in CharlieM’s graphic I could go either way on any given day – Yes, No, Neither and Don’t Know. OK, that’s four ways. But the ‘replication question’ is more interesting, and (possibly) fundamental.

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  4. phoodoo: Right.I knew you never really believed in materialism.

    Have you ever met a materialist that acts that way? I guess I’m No True Materialist.

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  5. Allan Miller,

    Not really. Because materialists don’t really believe in materialism. I have maintained that is true all along. They say they do, but not in reality. There is no real reason for you to believe that your wife is anything more than a shell around DNA. Except you don’t, because you know life isn’t just material. There is magic. There is transcendence. There is a reality beyond the physical parts. Materialism accounts for none of this. No one believes in materialism.

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  6. Allan Miller: just as elimination of transitional forms allows a neater dichotomy of taxonomies.

    Wow, you want to go there? Some forms are transitional and some are permanent? How do we decide which are which?

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  7. phoodoo:
    Allan Miller,
    Not really.Because materialists don’t really believe in materialism.I have maintained that is true all along. They say they do,but not in reality.

    Like I say, you are peddling a No True Materialist fallacy. Whatever you call my position, I don’t possess the belief that my wife has a ‘soul’, or that there is a God sitting somewhere creating stuff or frowning at my actions. Call that what you like.

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  8. phoodoo: Wow,you want to go there?Some forms are transitional and some are permanent?How do we decide which are which?

    ‘Transitional’ does not mean what you think it means. I was talking to someone who grasps that.

    For dichotomous taxonomies from an evolutionary process, it is necessary that most lineages during divergence fall extinct. They would be deemed ‘transitional’ even though they are ancestral to neither surviving lineage.

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  9. Allan Miller: Not restricting as such, it’s just that it seems to be to be a truth more fundamental than the rest.

    Very well. So you’d gather that viruses are in fact living entities?

    Allan Miller: Because we have a derived state. It’s fine to look at that derived state; it allows neater dichotomy, just as elimination of transitional forms allows a neater dichotomy of taxonomies.

    All features of that derived state I’d include in my definition were established really early on.

    Allan Miller: But I’m interested in how far back we could go prior to LUCA to find the ‘first living thing’ that we would dignify with the term, and it seems that what we would strip away, as we ascend, are the ‘secretions’ of genomes: the products that enable cellular organisation, import, metabolism, homeostasis, export etc.

    What one calls life strongly depends on personal preference. With your definition, you just captured your preference that life started off with the first nucleic acid based replicators. That’s fine, but still arbitrary.

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  10. Corneel: That’s fine, but still arbitrary.

    Did you ever come across the ever-charming Upright Biped at TSZ or elsewhere? He believes he has a knock-down argument against OoL by pointing out metabolism is heavily dependent on proteins which are coded in DNA and thus there’s a classic chicken-and-egg conundrum.

    That RNA can both store genetic information and catalyse biochemical reactions is, for me, a strong hint for RNA world as a precursor to DNA/protein.

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  11. phoodoo: There is magic. There is transcendence. There is a reality beyond the physical parts. Materialism accounts for none of this. No one believes in materialism.

    Uri Geller.

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  12. OMagain,

    “Everything in that BBC expose is absolutely true. The things I’ve done for Israel I don’t speak about. I never made money out of my secret work, and many projects, tasks and missions I was given will probably stay top secret until the day I die.”

    A report from The Independent in July 2013 found Geller was also approached by British intelligence agencies in 2001 for a Ministry of Defence study into the use of psychic powers when searching for people or objects.

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  13. phoodoo: Not really. Because materialists don’t really believe in materialism. I have maintained that is true all along. They say they do, but not in reality.

    Ahh okay, cool story bro.

    phoodoo:There is no real reason for you to believe that your wife is anything more than a shell around DNA.

    I agree, there is no reason to believe that. We are all essentially shells for preserving and passing on heritable material.

    phoodoo:
    Except you don’t, because you know life isn’t just material.

    And by this you mean to imply he behaves in a way you take to be inconsistent with the belief that we are “just” material.

    Yet you could not advance a single coherent argument to support that any of his behaviors are inconsistent with the belief that life is “just” a materialistic phenomenon.

    phoodoo:There is magic. There is transcendence. There is a reality beyond the physical parts.

    And you believe that simply because believing that makes you feel good.

    You waste inordinate amounts of your time chasing down stories that leave you with a sense of confidence in these magical ideas, because deep down you actually don’t really believe them, which you essentially admitted above in your ironic Freudian slip that there’s no actual reason to believe anyone is more than just a packaging device for DNA.
    But you want to. So very much. So you go hunting for stories by people declaring they have amazing magical transcendent psychic powers they employed in secret work for the israeli government (Dude, I totes used to do magic for the KGB, but it’s classified), lives after death, invisible immortal friends that love them and will make them live forever in happiness etc. etc.

    If only you could truly believe it. But you can’t because assholes like us keep pointing out the obvious holes in your fairytales. So that’s why you’re here, endlessly infuriated that we can’t just let you wallow around in your delusions. If only all those “hot air skeptics” would just shut up and let you have your fantasies.

    phoodoo:Materialism accounts for none of this.

    Nothing is obliged to account for your comfortable fictions.

    phoodoo:No one believes in materialism.

    Prove it.

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  14. Rumraket: Yet you could not advance a single coherent argument to support that any of his behaviors are inconsistent with the belief that life is “just” a materialistic phenomenon.

    Except:

    I don’t talk to my wife as if she is a shell wrapped around her DNA

    Try to keep up Rummy.

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  15. Rumraket: He said it, you believe it, that settles it.

    phoodoo: A report from The Independent in July 2013 found Geller was also approached by British intelligence agencies in 2001 for a Ministry of Defence study into the use of psychic powers when searching for people or objects.

    Again, try your best to follow the conversation. That’s not HIM saying it.

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  16. Alan Fox: Did you ever come across the ever-charming Upright Biped at TSZ or elsewhere?

    I don’t believe I had the pleasure, but I saw his name here and there.

    Alan Fox: He believes he has a knock-down argument against OoL by pointing out metabolism is heavily dependent on proteins which are coded in DNA and thus there’s a classic chicken-and-egg conundrum.

    That’s a version of irreducible complexity, I guess. As you said, the catalytic properties of certain RNA molecules deep-six that argument.

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  17. It never ceases to amaze me how fervently anti-materialists cling to the false dichotomy “either it’s all just chemicals, matter in motion, or else there’s a transcendent immaterial”. It’s a striking legacy of Cartesian dualism that lingers unabated in these conversations — as if no critic of Cartesian dualism had ever lived or written.

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  18. phoodoo: Except:

    Try to keep up Rummy.

    How does that contradict what I said?

    My computer and a random rock outside on the ground are both material objects, yet I have vastly different interactions with them.

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  19. phoodoo: Again, try your best to follow the conversation. That’s not HIM saying it.

    “Everything in that BBC expose is absolutely true. The things I’ve done for Israel I don’t speak about. I never made money out of my secret work, and many projects, tasks and missions I was given will probably stay top secret until the day I die.”

    That sounds to me like someone talking in the 1st person. The fact that he managed to hoodwink some people into contacting him does nothing to establish that he has magical powers. I can find no shortage of people lopping praise at Orange Man, and yet he has done nothing to merit it. This is not an unusual situation.

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  20. Corneel: Very well. So you’d gather that viruses are in fact living entities?

    Yes, no, maybe and don’t know. One perspective might be provided by origins – if they are extremely reduced former cells, they somehow lost the designation ‘living’ during that transition, when they lost their metabolism. If, on the other hand, they are escaped transposons, they never really had it. I actually favour the latter origin, so I’m talking myself out of it!

    All features of that derived state I’d include in my definition were established really early on.

    I dare say. It’s all relative though. What’s a few tens of millions of years?

    What one calls life strongly depends on personal preference.

    I don’t think I’ve argued otherwise.

    With your definition, you just captured your preference that life started off with the first nucleic acid based replicators. That’s fine, but still arbitrary.

    It’s all relative. Commencing with the most fundamental of the features of organisms would seem to be less arbitrary than insisting that they have to have one or several of the later features to qualify.

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  21. Allan Miller: Yes, no, maybe and don’t know. One perspective might be provided by origins – if they are extremely reduced former cells, they somehow lost the designation ‘living’ during that transition, when they lost their metabolism. If, on the other hand, they are escaped transposons, they never really had it. I actually favour the latter origin, so I’m talking myself out of it!

    What’s this?!? You argued at length that nucleic acid replication is the fundamental process that characterizes life and that metabolism and cellular organization were secondary. If that is your position, you should stick to your guns and call viruses living beings, regardless of their origin.

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  22. Corneel: What’s this?!? You argued at length that nucleic acid replication is the fundamental process that characterizes life and that metabolism and cellular organization were secondary. If that is your position, you should stick to your guns and call viruses living beings, regardless of their origin.

    Nope – if I wouldn’t call transposons living, it would be inconsistent to give that designation to an escapee. That suddenly, having hijacked the replication of a different organism, it becomes ‘alive’. Whereas the reduced genome hypothesis requires simply that extraneous activity be dropped, being supplied by the host, as happens with many a parasite.

    Since I’m basing my approach on copying series, the designation ‘living’, once acquired by a lineage, is not lost on reduction. On the other hand, if a fragment of a genome discovers a means to be copied outside of its ‘parent’ cell, I feel less secure in declaring it to be separately ‘alive’. An anticipated objection, ‘what about haploid genomes in eukaryotes?’, is addressed by recognising that the true relationship starts with haploidy.

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  23. Allan Miller: Since I’m basing my approach on copying series, the designation ‘living’, once acquired by a lineage, is not lost on reduction. On the other hand, if a fragment of a genome discovers a means to be copied outside of its ‘parent’ cell, I feel less secure in declaring it to be separately ‘alive’.

    So you cannot resolve whether viruses are alive until we have learned their origin, even though your preferred definition does not even call for that?
    You are not one for making life easy for yourself, are you?

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  24. Corneel: So you cannot resolve whether viruses are alive until we have learned their origin, even though your preferred definition does not even call for that?
    You are not one for making life easy for yourself, are you?

    It would seem eccentric to argue that a copying series can suddenly become ‘not-alive’ at the point it dispenses with a particular feature its ancestors possessed, as a result of parasitism, so I’m prepared to take my lumps. It seems no worse than arguing that pre-LUCA lineages were not alive if they lacked certain features possessed by her descendants. That’s chauvinism!

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  25. phoodoo:
    OMagain,

    phoodoo: A report from The Independent in July 2013 found Geller was also approached by British intelligence agencies in 2001 for a Ministry of Defence study into the use of psychic powers when searching for people or objects.

    UK Ministry of Defense also pursued the use of psychic powers, namely remote viewing. In 2002 the Ministry of Defense carried out a program designed to test the validity of using such abilities to sense hidden objects such as bombs. During the research, blindfolded psychics were presented with brown envelopes that contained various images such as a knife, Mother Teresa and an “Asian individual.” However, while 28% of the participants were able to correctly guess the contents to within a startling range of detail, in most cases the volunteers were not even close, and the project was scrapped.

    A Ministry of Defense spokesperson would say of the project:
    The remote viewing study was conducted to assess claims made in some academic circles and to validate research carried out by other nations on psychic ability. The study concluded that remote viewing theories had little value to the MoD and was taken no further.

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  26. Corneel: So you cannot resolve whether viruses are alive until we have learned their origin

    Whether viruses are stripped-down parasitic descendants of free-living ancestors seems a more interesting question than assigning them to a “living or not” category.

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  27. Allan Miller: It would seem eccentric to argue that a copying series can suddenly become ‘not-alive’ at the point it dispenses with a particular feature its ancestors possessed, as a result of parasitism, so I’m prepared to take my lumps.

    What’s so important about the word “alive” that you are reluctant to apply your preferred definition correctly?

    Also, I like eccentric 😉

    Alan Fox: Whether viruses are stripped-down parasitic descendants of free-living ancestors seems a more interesting question than assigning them to a “living or not” category.

    Both questions are intriguing. However, there seem to be people around here who think living things merit special attention*.

    Speaking of which, where is our graceful original poster?

    *biologists

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  28. Corneel: Both questions are intriguing.

    I dunno. The “living” question depends on definitions. Decide on your preferred definition and you answer the question. The origin of viruses might be answered by research or observation but it seems clear to me that as viruses depend on another organism to be able to replicate, they cannot be further back on the path to LUCA than lifeforms that can self-sustain and self-replicate.

    Incidentally, I mentioned the conundrum to someone (we maintained social distancing) and they said, well, what about seeds?

    Contents of this vault? Alive or dead?

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  29. Corneel: What’s so important about the word “alive” that you are reluctant to apply your preferred definition correctly?

    I’m just using j-mac’s word; I have no particular attachment to it. But, I have an issue with a continuous lineage becoming less [that] than its ancestors were, given that replication is somewhat central to the whole shebang.

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  30. Alan Fox:
    Incidentally, I mentioned the conundrum to someone (we maintained social distancing) and they said, well, what about seeds?

    Or pollen, spores or sperm.

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  31. Alan Fox: Decide on your preferred definition and you answer the question.

    I suspect that most people take the reverse approach: They decide what needs to be included in the category and try to come up with a definition that encompasses that.

    I’m guilty of that as well, BTW.

    Alan Fox: well, what about seeds?

    Given that seeds are dormant stages of organisms that fit my definition, I think I can talk my way out of that. 😄

    Allan Miller: pollen, spores or sperm

    That’s tricky, for sure.

    Allan Miller: I have an issue with a continuous lineage becoming less [that] than its ancestors were, given that replication is somewhat central to the whole shebang.

    Issue? Do you want to talk about it? 🤓
    Lineages experience regressive evolution, become maladapted or just plain go extinct. Why is becoming “less than your ancestors” an issue?

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  32. Alan Fox: Plant life in general!

    Plants have cellular organisation, metabolism, growth, reproduction, maintain homeostasis, respond to external stimuli and evolve.
    That’s a mark with every criterium: they are clearly alive in my book.

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  33. Corneel:Lineages experience regressive evolution, become maladapted or just plain go extinct. Why is becoming “less than your ancestors” an issue?

    If they keep on replicatin’, they keep on livin’!

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  34. Corneel: So viruses are alive by your definition. Where’s the issue?

    Ancestry. If we have a lineage possessed of the capacity of independent replication (oh, did I not mention independence? 🤣), then subcontracting that function does not appear to be a compelling reason to deem it having ‘passed over’. On the other hand, transposons never had that capacity – they were part of an independently-replicating genome that merely migrated to another part of that genome, and now migrate to other genomes.

    What about haploids, anyway? In my view, they were independently-replicating entities that started to – and continue to – form diploid unions. Gradually, some lineages stopped replicating at all in the haploid state; the haploid became reduced and often possessed of little in the way of metabolism, consumption, excretion etc. With Charlieesque chauvinism, only the diploid phase is truly ‘alive’. Whereas on the ‘independent replicator’ view, both phases are, being descended from a long line of (independent) replicators that now happen to do their replicatin’ in pairs.

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  35. Allan Miller: subcontracting that function does not appear to be a compelling reason to deem it having ‘passed over’

    Clear. So if we change your definition to “having autonomous nucleic acid based replication”, would that about cover it?

    Allan Miller: What about haploids, anyway?

    Yes, I have been thinking about your “pollen, spores or sperm”. First, I’ll note that there are organisms that have a prominent or even dominant haploid phase (bryophytes!). The problem are the lineages where the haploid phase became reduced. You are correct that, since they cease to be individual organisms, they are not strictly living entities. We can salvage that situation by recognizing that they are part of the haploid-diploid cycle of a lineage of living things, but I’ll grant that my proffered definition is a bit fuzzy at this point.

    ETA: correction

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