Viruses nonliving?

Discussion in 'Biology & Genetics' started by unorthodox, Jun 20, 2012.

  1. Grumpy Curmudgeon of Lucidity Valued Senior Member

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    Billy T

    And with care, as I also took, it is possible to draw another, different line which is every bit as valid. That's what I mean about the boundary between living and non-living chemistry being arbitrary(IE subjective and fuzzy), based on the definition you give life, itself arbitrary. My point stands, there is no hard and clear demarcation line between chemistry and life.

    Grumpy

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  3. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    My definition, like ALL definitions, is arbitrary but that does not mean it (or others) are not designed to be useful. The most important characteristic of a well defined definition is that it clearly describes the object or field it is defining so that the borders are not vague. I think I achieved that and many definitions of life do not. You not may the result that prions and currently "printed objects" can not be alive. If not, offer your alternative definition of life.
     
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  5. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    What was your definition of life. I must have missed it.
     
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  7. Grumpy Curmudgeon of Lucidity Valued Senior Member

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    Billy T

    My definition is any molecule that can assemble copies of itself from it's environment. Prions qualify because they use elements in their environment to create copies of themselves(details are just details), crystals do not because they are forming structures not assembling molecules. The point is that there was no single point that can be called the point where life began. The traits that we call life accumulated, they did not come together at one time. And the chemical "evolution" that brought the first self replicating molecules together was a haphazard and chaotic complex chemistry all on it's own. The border between the two cannot be anything but fuzzy, despite any arbitrary border we mark.

    Grumpy

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  8. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    Is your definition of life???? Life is limited to molecules! I thought dogs were alive, etc. Please try again.
     
  9. FTLinmedium Registered Senior Member

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    Again, not all definitions are arbitrary. c, for example, is not arbitrary- there's nothing else like it. There's no fuzzy line possible there. Many concepts in mathematics and physics are non-arbitrary- the names we give them may be arbitrary (as language is), but the concepts themselves are not, and have clear meanings without any ambiguity. Likewise, in philosophy, there are many non-arbitrary concepts.

    The arbitrary nature of your definition naturally invalidates it as far as any philosophical relevance goes (and you were trying to argue not against a scientific point, but against a more philosophical one- a moot point, but still).

    ANY definition of 'life' is going to be arbitrary unless it is inclusive of the natural extremes and embodies a true conceptual whole- Grumpy's definition is much better, (I'm a little skeptical of the relevance of 'molecule'. I don't think life has to be molecular- but he achieves therein a full spectrum which encompasses all potential extremes rather than drawing subjective lines without justification).

    I think the concept boils down to self replication of an information system from its environment.

    Grumpy's definition being one of Molecular life (which I find acceptable for that qualification).


    Sure, but that doesn't make it philosophically useful. In order to be useful philosophically, it must also have the characteristic of not being arbitrary.

    That is something Grumpy Achieved (if we assume his is limited to "molecular" life).


    I'm not sure what you're saying. But Grumpy and I have both presented less arbitrary definitions.

    To demonstrate the importance of the definition being solid and non arbitrary, I will give you this.

    Following from your explanations of why Prions are not life:

    "Thus when it happens to be a prion that hits the existing protein molecule to trigger the refolding making another prion, I don´t consider that refolded molecule to be life. It could have been created by non-piron collisions too - no "reproduction.""

    The only conclusion, based on that, to be made is that life does not exist and can not exist. None of us are alive- because there are *possible* non-living mechanical means by which we could come into existence- and in fact, if we follow the chain back through generations, there are possible non-living mechanisms that must have originated our ancient ancestors (discounting time-travel).

    Invalidating the life of a prion because it could have been formed by a non-living process invalidates the life of everything that could have been formed by non-living processes- including the first life forms, whatever they were, which must have been so formed- thus invalidating the life of everything that came after (having been formed by something non-living).

    This may not be a problem with every day usage, but it's a gaping hole in your definition if you try to put it forwards in a philosophical context.
     
  10. Fraggle Rocker Staff Member

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    That covers growth and reproduction. Those are two of the phenomena on the list of seven. It's made clear that in order to qualify as "alive," a thing only needs to exhibit most of these phenomena, not all seven. But two out of seven does not quality as "most," in English or in logic. You have to have at least four. So you need two more, out of: homeostasis, organization, metabolism, adaptation and response to stimuli.

    I think Billy is hitting on the same point from another angle. These molecules certainly perform tasks that help qualify the organism of which they're part as life, but they do not themselves so qualify.
    Well that's certainly a fair statement. If we want to go back into the primordial ooze and watch the various traits come into existence, it's going to be a purely semantic exercise to decide at what intermediate point there were enough of them to qualify the entire collection of molecules as "life."

    And no matter how carefully we do this, we're still completely mired in the physics and chemistry of this planet and its biosphere. In a few centuries we may discover things living in space, perhaps even in the vast empty space between galaxies, that are not comprised of molecules.
     
  11. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    Not why I say prion is not alive. It does not take energy or material from the environment and use it to reproduce. Or as Fraggle put it, it has no metabolism.
     
  12. FTLinmedium Registered Senior Member

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    Hi Fraggle Rocker,

    I think you might have missed a bit of the conversation. We're discussing a hypothetical new definition that is non-arbitrary (many of those classical qualities you mentioned are highly arbitrary).

    To evaluate them, though:
    It's easy to say such a molecule is organized for the task at hand- almost all molecules had an organization of a sort. Response to stimuli is also easy- it responds to the stimuli of having the necessary components to replicate itself by replicating itself. (these are at the extreme end, but it just serves as a point as to how arbitrary it is).

    For adaptation- it does so through evolution over multiple generations. Homeostasis is maintained in a single molecule by atomic forces (not so much active, since it doesn't really have an inside). Metabolism could be external- found in the molecule catalyzing energetically favorable reactions to do things (like engage in catalyzing those very reactions).

    Much of this is stretching, of course, but none of these have very clear delineations- and that is the point.


    A rough and subjectively applied definition may be fine for the day to day- but it is inadequate if we want to engage in serious philosophical discussion regarding what life is, whether it exists, and the importance of it to something.
     
  13. FTLinmedium Registered Senior Member

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    It was the explanation you gave, so I addressed that.
    Metabolism didn't seem to be part of your definition. But even so:

    The prion takes the non-prion protein and changes it into a prion protein. It does take from the environment, and give back. Its metabolism is external; it uses energetically favorable mechanics outside of itself rather than inside.
     
  14. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    Not by that name, but it is the now bold part of my definition:
    I only mentioned that this metabolism is used to reproduce, as that was the subject being discussed, but it is also used for maintaining homeostasis against the Second Law. (and that ends with death. Then their entropy increases as their order* is destroyed.) Prions don´t do either - they really can´t die. Pirons are not alive - they are just protein molecules folded in a particular way that differs from other folding of the same molecule.

    More crudely instead of the bold, I could have said: "eat food to make energy" (for various needs)

    *Fraggle called that "organization."

    I don´t know if during the process of refolding another identical chemical compound the prion folded version takes any energy from it or not, but it certainly does not take any material from it. So that alone places in as "non-life" by my definition. afaik, metabolism is ALWAYS an energy transforming process.
     
    Last edited by a moderator: Aug 2, 2012
  15. FTLinmedium Registered Senior Member

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    This new definition doesn't seem to pose any problem for prions being considered alive...

    It takes ALL the material from the environment. The entire protein- it takes it. Then it uses that old protein to make a new one which is folded differently- using potential and kinetic energy from the environment to do so.

    This is not a problem.
     
    Last edited: Aug 3, 2012
  16. Grumpy Curmudgeon of Lucidity Valued Senior Member

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    Fraggle Rocker

    We are talking here about how chemistry became life, not how we define complex life. The point I am making is that the first step where chemistry and life go separate ways is the point where the first self-replicating molecules came into existence. That would be the first real difference between just plain complex chemistry and simple life forms. By the way, all life is molecular, all other traits are developed by nature to support the chemical life(DNA)in your cells and to insure their reproduction. Richard Dawkins' "The Selfish Gene" is a good explanation of why this is true. Cells were far from being the first life, a definition that is based on the cell(and all it's processes)will never allow you to find first life(you wouldn't recognize it as life). Looking for simple life requires a simple definition, thus mine.

    FTLinmedium

    Precisely. Not only did first life live in a medium which contained themselves, but also contained other, competing molecules that could be subjugated for another purpose, disassembled for spare parts or even replicated symbiotically(one molecule assembling a different molecule that then assembled the first molecule(kind of reminds you of the DNA molecules series of bases, one base always determining what it's matching base will be), maybe moving into a single fat globule and becoming one creature, as RNA and proteins moved in with DNA at a later stage, or Mitochondria was eaten but not digested, eventually becoming an organelle). When looking for first life(the study of Abiogenesis)your standard definition of life does not apply(does not yet exist), you must break it down to little baby steps that chemicals accomplished to become the first life with all those traits. The first of these steps is self-replication from materials and energies in it's environment.

    Billy T

    First life was limited to molecules, was it not? DNA is just a particularly complex set of molecules. And a dog is a support system for the reproduction of that dog's DNA. All it's traits were tested(naturally selected)by just one thing, survival to reproduce. Yes, all life is molecular, from the smallest self-replicating molecule to mankind the only subjective purpose of any lifeform is the reproduction of it's DNA molecules(actually, the reproduction of half of it's DNA in the gametes in sexual creatures), all else is just detail.

    Grumpy

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  17. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    Grumpy said: "My definition is any molecule that can assemble copies of itself from its environment." Which got this overly generous reply:
    No prions DON`T grow, not even one atom is added. They collide with the same protein and help it reform its shape - that is all they do.*

    * except this new shape can be quite harmful to the organism it is in by binding to critical shape specific sites of cells.
     
  18. Captain Kremmen All aboard, me Hearties! Valued Senior Member

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    I've had that thought myself, but on further reflection I think it is wrong.
    That humans, or their other world equivalents, increase the rate of entropy by their actions, is undoubtedly true.
    When we feel a bit cold, we will put coal on a fire instead of putting on a coat.
    We heat the whole room so that the room heats us.

    But surely this increased entropy is only loaned, and will have to be paid back at some point.
    In our case, if the earth is engulfed by the sun, there will be less coal to burn off then because we used it now.
     
  19. Grumpy Curmudgeon of Lucidity Valued Senior Member

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    Captain Kremmen

    The "entropy costs" have already been paid because coal is a result of previous lifeforms(swamps, peat, etc.)that increased net entropy when they were alive. We shouldn't even be looking at life like this because the Second Law of Thermodynamics never is applicable to open systems. The sun pays huge entropy costs for the minor decreases of local entropy that life represents, there is always a net increase in entropy in the solar system even if the Earth becomes a fuzzy green ball of rampant Kudzu thousands of miles thick.

    Grumpy

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  20. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    No. What is possible in economics (pay back a loan) is IMPOSSIBLE in thermodynamics - Entropy (its total) can only increase (or in principle, but not in practice, remain constant if all things done are 100% reversible.)
     
  21. Captain Kremmen All aboard, me Hearties! Valued Senior Member

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    What I mean is that the rate of increase of total entropy in the future, when the earth is burned up by the sun,
    will be slower than it would have been had we not stoked up our fires now.
    The energy in that coal has already been dissipated, and cannot be burned in the future.
    Thus it balances out.
     
  22. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    That is better but still not fully correct, I think as Earth is not expected to melt when when the sun becomes a red giant - Mercury and Venus will become vapors but the expansion of the sun is not likely to give it a 1 AU radius. It will be from Earth´s POV just a big dull red circle perhaps less than 80 degrees wide in the sky (now on 0.5 degrees wide) Probably giving Earth enough heat to boil the oceans into space so you should plan on moving somewhere else before 3 million years or so.

    Most of the life forms now found in the ocean floor thermal vents will die, but a few may be able to adapt and survive in the hot dry earth for a few million years more, but if they don´t want to eventually freeze, they had better evolve, build some space ships and leave too.
     
  23. FTLinmedium Registered Senior Member

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    No living molecules really "grow" in that sense (except by mutation). Either they are, or aren't, what they are. Requiring that atoms be added to a molecule is a rather arbitrary qualification, and doesn't define growth.

    Prions reproduce wholesale, creating like prions from their environments- they just don't happen to need to add atoms, because all of the needed atoms are there.

    We could also easily call the coupling of a prion and non-prion precursor protein growth (preceding division). There's no perfect distinction between growth and reproduction- it all depends on where you draw the line of individualism, and that is highly subjective.


    It's easy to draw the imaginary line between life and non-life in any arbitrary way, defined by any one person's opinions; but that doesn't make it meaningful. It's all a gradation- and it is that degree to which something is alive that is meaningful.

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