Viruses nonliving?

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

  1. Captain Kremmen All aboard, me Hearties! Valued Senior Member

    What I say holds even with the opposite scenario for the earth.
    Say the earth at the end of the Universe becomes a nearly zero Kelvin lump of rock in space, with that coal we put on the fire unburned because we weren't there.
    Because that energy cannot be used to do work, there is still zero entropy.
    We made no difference.

    This is only an aside anyway.
    I don't want to divert the thread too long.
    Fraggle just mentioned something I had been pondering on.
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  3. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

    What I made bold in your text ("living") seem to be a very arbitrary concept of living, but you can hold the opinion that individual molecules are alive; however, I don´t think any molecule is "alive" as they fail to be able to do almost everything normally associated with life. (For example cannot do 6 of Fraggle´s seven characteristics of life.*) It is also strange & arbitrary that you exclude as "non-living" (assuming you do) other molecules that can also make copies of themselves from the environment:

    Or do you also say O2 molecules are alive? They can and do make more copies of themselves: Two oxygen molecules (O2) that pass thru the ozone stage can become three O2 molecule when two ozone molecules collide. Is O2, thus alive too?

    I.e. 2 O2 +2 O --> 2 O3 --> 3 O2. If O2 not is not also alive, why not? When Mp + M --> 2Mp you say is alive. (M is a particular protein molecule but not folded in shape Mp where the subscript "p" refers to the one of several possible folding of that chemically unchanged protein which we call a "prion.")

    I bet a good chemists can tell you of more than a dozen molecules that make copies of themselves from the environment. I am a physicist so only know of the O2 case and one other. Are you really wanting to say that any molecule which can be a catalysts making more copies of itself is "alive"? Again, as a physicist, I happen to know Fe2O3 is a "self catalyst" - I.e. when iron gets a little rust on it, O2 molecules are held on the surface longer making more Fe2O3 so with your (in my opinion, silly concept of life) Fe2O3 is alive too.

    * One of which was to "grow" or at least be able to grow. The least possible growth would be to add a single atom.
    Last edited by a moderator: Aug 9, 2012
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  5. Fraggle Rocker Staff Member

    Wikipedia says it's too close to call. 5B years from now, the sun will grow beyond 1 AU, but the weakening of its gravity as it sheds mass will allow Earth to move to a wider orbit. But on the other hand, tidal forces may draw it closer. The plus-or-minus delta will determine whether Earth survives as a distinct rock or becomes part of the sun.
    In any case, the sun will become hot enough that water will not be able to exist in a liquid state on Earth a mere 1B years from now. Based on these approximations it's anybody's guess how long it will be before the planet can no longer support life, but we probably have at least half a billion years to sort out our differences, learn to work together, learn more about cosmology and physics, invent amazing new technologies, and build a fleet of generation starships in which to search for new homes. That's about three thousand times as many years as our species has existed, and about one hundred thousand times as many years as civilization has existed. Considering what we've accomplished so quickly, we can probably do this.
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  7. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

    I´ll be quick as this is a detour: If even tiny fraction of sun´s mass gets more than 1 AU from sun, true sun´s gravity force on earth will be less, but there will be loss of kinetic energy as earth "plows thru" solar mass at 1 AU so "rock Earth" will spiral in towards the sun´s center until earth is just vapor.
  8. Grumpy Curmudgeon of Lucidity Valued Senior Member

    Billy T

    Ah, the light seems to have gone on above your head as you are realizing that there really is no difference between chemistry and life and any line you draw is purely arbitrary. While atoms simply following their natural properties is below the level of the first complex self replicators(hardly more sophisticated than prions are today)at it's simplest life itself is chemicals following their natural properties, WHEREVER you draw your arbitrary lines, and at it's most complex it is still all about the DNA molecules in your cells, still chemical, still molecular. The main reason I define life as a self-replicating molecule is that it is immediately subject to mutation and imperfection in replication and therefore subject to Natural Selection and Evolution. The only thing subject to NS and Evolution is life, by definition. Iron atoms are not subject to evolution, despite adding extra oxygen. They can either bind with two oxygen atoms or with 3, but they are the only two choices for those combinations, that is not true of proteins and amino acids.


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

    While all definitions are arbitrary, you seem to be reversing you prior position on prions being alive as they do NOT evolve, and do NOT mutate and are NOT subject to natural selection.

    If they refold to be one of the other forms that same chemical compound can take, then they cease to be the folded form called a prion, not an "evolved prion." If they are subject to a chemical change, a mutation, the same is true - the new chemical compound is no longer a prion. For example, if an -OH radical attaches to a prion, then they will at the very least no longer be a prior, never an "evolved or mutated prion" - Probably in most cases not even a single molecule, just two now separated new chemical compound molecules.

    When two molecules of a piece of Fe (iron) form new molecule from the environment (with atmospheric oxygen and iron atoms), Fe2O3, that new molecule can do everything a prion molecule can do - I.e. It helps more of the iron in its environment form additional Fe2O3 molecules. (Rust is self catalytic. - helps make more copies of itself from the environment just like a prion does.);however, unlike a prion helping form another there is a chemical change with chemical energy released. - I.e. Fe2O3 has another of Fraggle´s seven characteristic of life. - I.e. the process of replication of Fe2O3 includes a form of metabolism (Chemical change with energy release.) So I again ask why is a molecule exhibiting two characteristic of life not life while a molecule exhibiting only one characteristic of life is what you call a life form?

    Don´t misunderstand. I am not arguing that Fe2O3 is alive. No single molecule is alive IMHO, including the protein folded to have shape of a prion instead of one of the other shapes that same chemical compound can have. I just want your to explain why you reject / exclude Fe2O3 from the class of living molecules when it has twice as many characterist of life forms as the prion molecule does? - That seems to be a very inconsistent and arbitrary exclusion. Please try to justify it.
  10. FTLinmedium Registered Senior Member

    I don't agree with that. Like I said, prions grow by adding an entire molecule... and then they split in half when they reproduce. They're one molecule, then two molecule life... then two one molecule life forms.

    I love your example of O2. As I've said, I think life is more of a gradation of complexity in self replicating information systems. I don't see that which we commonly call "life" as fundamentally different, but rather more information being replicated. A larger clump of information- the smooth gradation down to very simple molecules like Oxygen is a perfect example of that- and it's what makes the notion eloquent and non-arbitrary.

    Oxygen being considered to have some very minimal living quality along that spectrum is not, to me, a problem. I consider it a mechanic of the universe that organized information can propagate in the environment, and higher order life is only a natural expression of that following from the logical consequences of evolution.

    I don't even need to see a molecular change to consider it a living quality; I'm happy with structural changes (like protein folding, or crystalline allotropes) too. I have no problem with that. I don't consider them to be *very* alive, but to have some of the very same quality. It's all about organized information propagating itself.

    Where's the distinction between a snack and a meal? There isn't one. It's a gradation. Same with life.

    You may consider it "silly", but it's non-arbitrary, and so it is philosophically relevant (unlike an arbitrary definition, which is only an opinion, and so irrelevant and incapable of carrying any philosophical weight). Philosophy deals with the extremes, and with the fundamental natures of things. Maybe you aren't a big fan of philosophy though, and that's your right.

    My criticism of your arbitrary definition was regarding your attempt to make use of it in a philosophical conversation. Outside of that context, I have no problem with it (as long as you recognize it as arbitrary, which it seems like you do). Your definition is fine for every day usage- and I wouldn't use the more extreme definition of fundamental quality in every day usage, because it would confuse people. But in a philosophical conversation, it's the only one that would be meaningful.

    Anyway, I think the argument you were having with that creationist is over now, right? So it's kind of moot.
  11. FTLinmedium Registered Senior Member

    Brilliantly put, Grumpy,

    I don't know if I agree with that though- what if a radical of Chlorine comes along in the environment and makes something new, which then catalyzes the production of more of itself?

    I think all molecules, due to the chaos of their environments, are potentially subject to evolutionary forces. The greater the complexity and interaction with the environment, the more forceful evolution will be- but I don't know if it's ever really gone (even at the subatomic level, down to its very limits at the quantum scale).
  12. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

    Why do you think that is how prions grow in number? Do you know of any link that suggest they are even very briefly one molecule of twice the mass? I find that both very hard to believe and a contradiction to what I have read about how the number of prions increases.

    "Hard to believe" as prions are large 3D structures and can not "fit together" with exactly the same protein when it is folded in a different 3D configuration. These molecules have several possible foldings, as most proteins do, and it is the shape, not the chemical compounds making that shape, which is mainly important in many biological processes with "receptor sites" that do not change the chemistry. - For example neurotransmitters are proteins that fit "lock and key" like into their receptor sites. They are released and then taken up again for re use by the pre-synaptic nerve ending. (No chemical change, only the shape is important and many neural drugs have a good approximation of that same shape, but are made with entirely different chemicals.) Why many different chemicals with the same shape taste sweet to you, etc.

    As I understand a prion making another one, it simply collides with the same natural chemical compound (a particular protein but in a different folding). The collision has enough kintetic energy, KE, to allow / to excite / the "hit" non-prion, normal folded same protein molecule, so that it may settled down into the prion´s folding (which may be a slightly lower energy folding)

    I.e. the KE of the collision is the "activation energy" that many chemical reactions need before they can go to a lower energy form. For example, a room temperature mix of twice as many H2 molecules as O2 molecules does not explode to form H2O despite that being a much lower energy formation for the mix as there is an "activation energy" barrier to the formation of H2O. (Before H2O can form, these diatomic molecules must be split. As I recall, to split H2 requires several eV (5 eV ?) and room temperature KE is on average less than 0.03 eV.) Likewise to refold a protein from the shape it was built in requires supplying an "activation energy".

    I forget the name of the molecular factories found in living cells that read the DNA code and construct the particular protein that the DNA is telling that factory to make. Because proteins are built a little bit at a time by that factory, they all come out with one particular shape (for that protein). Later, with some collisions supplying "activation energy" especially, if in a different pH environment, they make take some different folding than their "birth fold."

    One of us, has a very false idea about how the number of prions increases. You think somehow two of these complex 3D proteins with very different shapes merge into a one united molecule with double the mass and then that double mass molecule soon splits into two identically shaped molecules we call "two prions."

    I think that is essentially impossible -the two very different 3D shapes will not fit together. I think that with a collision supplying the needed "activation energy," the "hit" protein can end up in a slightly lower energy configuration - a different folding than the one it was born with at the cellular factory running under DNA code to build this protein in the shape specified by the DNA instructions.

    That is why I am asking for a link that suggests your concept is even possible.
    Last edited by a moderator: Aug 11, 2012
  13. FTLinmedium Registered Senior Member

    No... because they don't do that, and that's not what I said...

    I'm not sure why you thought I said that.
  14. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

    Because you said: "They're one molecule, then two molecule life... then two one molecule life forms. ..." the middle step sure sounds like to me you have them joined. If not joined into one unit how are they "two molecule life" - they have entirely different 3D shapes - how could they fit together?

    Do you agree with my description of how a new prion is formed? I.e. the necessary "activation energy" to change the folded shape from the healthy non-prion version to the prion version is given by the Kinetic Energy of a collision with a prion (usually). If yes that means the prion does NOT grow, does NOT evolve, does NOT have any metabolism.

    If you don´t agree, then how is the new prion made?
  15. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

    I have a huge amount of information I can recall from memory, especially for one my age, but it is not always without corruption, so I decided to check what I said about how prions increase in number (There are no errors in what I said from memory). This recent text is quite good description of prions:

    Prions: Not alive but they can evolve - News: Cell Biology December 31, 2009

    "... Prions are mostly protein. Although protein is a fundamental component of living cell material, prions are not alive. They behave something like viruses, without DNA or RNA yet able to reproduce by forcing living cells to do the reproduction for them. Prions were hypothesized in the 1960’s (Alper and Griffith) but not discovered until 1982 by Stanley Prusiner (for which he received the Nobel Prize in 1997). Like the role of proteins in epigenetics (adaptation or change in gene expression not caused by DNA), the more molecular biologists dig into proteins the more versatile and important they become. New research shows that includes the ability of prions to evolve.*

    Prions are chains of proteins (polymers) that exist in many cells in a native harmless form. There are also infectious prions, from which the name is derived (proteinaceous infection). The infectious prions force normal prions to assume a misfolded shape, thereby reproducing the infection. In the misfolded shape, called an amyloid beta sheet, prions are very stable. The stability lets them accumulate in infected tissue, eventually causing tissue damage and cell death. This is the basis of some very nasty illnesses such as bovine spongiform encephalopathy (mad-cow disease) and Creutzfeldt-Jakob disease in humans. All known prion diseases are incurable and fatal. ..." From:

    Read more of this text to see why they say prion, although not alive can adapt (or evolve) to a changed environment. This adaptation is not any change in stored information - the prion has none - no DNA etc. The adaption is more like isolated water molecules at low temperature, joining together as the temperature is lowered and eventually forming a solid or a liquid.

    I.e. an ordinary water molecule, H2O, is polar with both protons (Hs) on the same side of the negative -O- (With angle of 105 degrees between the two Hs). As water is cooled, polymer chains develop. I.e. water at 4 C or lower is nH2O molecules where "n" is some small integer and n = 1 becomes increasingly rare as 0 C is approached.

    I´ll represent the polar isolated H2O molecule by (+2H,-O-). As the temperature cools, you get electrostatically bound chains like:
    (+2H,-O-)(+2H,-O-)(+2H,-O-)(+2H,-O-) ... (+2H,-O-)(+2H,-O-)
    These chains have some flexibility - are not linear as I illustrated, but sort of like a bowl full of half cooked spaghetti with voids between the tangle of chains. As temperature drops below 4C, which is the densest state of water, the typical value of n increase, i.e. the typical chain grows longer, and the void volume steadily increases.

    Thus, in the same sense as this article does, one can say: "Water is not alive, but does evolve" (with changing environment).

    * This "evolution" or joining together of individual prion molecules to form even more stable units is well illustrated in this short video: animations/prions_characteristics.html

    It is important to note that this "evolution" of both water and prions is NOT any change in the information they contain - A million years from now prions and water will be exactly like they are today - doing the exactly same joining together ("adaptation" or "evolving") as the environment changes they do today - no new creature will ever evolve from either water or prions. They do not do that Darwinian type of "evolution" that life forms do.

    If you want to say "prions are alive," then you must say that about water too. The article, in the title even, clearly states prions are NOT alive.

    My main** criticism of these articles is they fail to point out, as I did, that the non-prion folding of the same molecule MUST first be given a little energy (the activation energy) to at least partially unfold it before it can refold into the prion shape. I.e. If the environment is cold, the prion can not change the shape of the non-prion molecule to the shape of a prion, as the collision between it and a prion lacks the "activation energy." Article I read some years ago, noted this fact.

    ** I also don´t like the articles´s occasional calling of the non-infectious folding of the same chemical compound a "normal prion" - IMHO, it is better, less likely to confuse, to reserve "Prion" only for the infectious foldings and just call the other foldings of the same chemical compound just that; or more completely: "non-infectious foldings of the same protein, a particular chemical compound, as the infectious prion folding is." (But I can see why only two words were used instead.)

    In contrast to prions, virus are very definitely alive. They do contain information that can "Darwinian evolve" under natural selection. - If you don´t believe that, just stop taking your anti-biotic immediately when your sickness is over. ToE applies to viruses but not to prions. Although Darwin did not know it, ToE is all about AND ONLY ABOUT, how stored information in a group of living creatures changes with time. No individual molecule stores any information so ToE, a theory about how stored information change in living forms, does apply to prions.
    Last edited by a moderator: Aug 11, 2012
  16. FTLinmedium Registered Senior Member

    See emphasis. Not as one molecule. That's why I said two molecule life.

    Prion A, let's call him Bob, grows by assimilating another molecule into his existence. Bob is now two molecules (not one). He's not two molecules for very long- only for the duration of contact- the end of which is Bob's reproduction cycle, where Bob splits in half to form Bob1 and Bob2.

    How are you multicellular life?

    The boundary between what is and is not 'you' is highly arbitrary- just as is the boundary between what is and is not Bob.

    I say Bob eats, grows, and reproduces. And Bob's use of kinetic energy, if that is the case, is a metabolism of Kinetisynthesis just as plants Photosynthesize- or in the more likely case that the refolding is simply energetically favorable in that situation, then that would be the form of metabolism.

    I don't think you can make the absolutist claim that prions can not evolve. If you believe it, that's OK... but I don't think you know it. As your belief, that's all it is, unless you have proof.

    You might benefit from reading about Amyloids. Sorts of growing colonies of symbiotic prions that form structures not terribly unlike corals.
  17. Crunchy Cat F-in' *meow* baby!!! Valued Senior Member

    Because they fail to meet the criteria humans have made for distinguishing between life from non-life. An example is that viruses don't respond to stimulus. You can poke them, tickle them, make them hotter, make them cooler, etc. and there will be no response. The best they have is glue on their protective coatings which gets stuck to cells and dissolves a hole in them. From here, viral content leaks into the cell and floats around until the cell's replication machinery gets a hold of it; after which, this machinery will typically replicate the virus until the cell is so full that it explodes. The process then starts all over again, glue sticks to a cell->makes hole in cell->virus content floats into cell->cell replicates the virus. No stimulus involved.
  18. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

    Orthodox read post 72, especially the last paragraph. Don´t believe anyone telling you viruses are not alive - they are.
    Yes there is a stimulus and response to it -the one you not very accurately described. Put a virus into contact with a cell (change its environment to stimulate it) and it goes thru a complex response which it needs to do - contracts its skin to inject its RNA into the cell. Process is much like when the "stinger cell" of jelly fish contracts to inject a toxin into its target.

    There are lots of energy fluxes in the environment that you do not respond to. For example EM waves* and E-fields, but other creatures do. Quite a few bottom feeding fish sense the very weak changing E-field from the heart of a buried smaller fish (or worm). The duck-billed platipus usually lives in water muddy water and then his primitive eyes are useless but inside the "duck bill" is a very advanced electric field sensor. Point being virus need not respond to same stimulus you do; but to environmental stimulus that are important to it, it responds very well, thank you.

    * There are a few human exceptions - some people with a slightly oxidized tooth filling can listen to radio waves.
  19. KilljoyKlown Whatever Valued Senior Member

    So what you are saying is that life is determined by how we define it?

    But viruses do have a way to reproduce and they do have (life cycles) that allow them to become successful parasites of larger lifeforms. So they do have some life like characteristics. So maybe it's also not right to call then not life either? How about primitive or quasi-life?
  20. Crunchy Cat F-in' *meow* baby!!! Valued Senior Member

    Quite correct.

    I am not sure what the best approach would be. Trying to subjectively come up with objective criteria for delineating life from non-life is a bit of a mind-fuck.
  21. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

    Many non-living things grow by addition of matter from the environment like NaCl does. Some even make mutations in the process: For example quartz crystals have two different forms. I have seen several with the main part in one form and sticking out of it is a smaller piece, which does not extend into the center of the larger piece, of the other form. I own a very pretty half geode (which I cut in half myself with a powered diamond saw in the physic shop)* with a complete colony of little bluish crystal all joined together - it is not alive.

    * They were very cheap, uncut. I picked up many from the basket and bought the lowest density one in the basket for only 1 dollar as I recall.
  22. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

    Not so hard. I did it and so has Grumpy:
    In other words: life is the things the ToE applies to. (and ToE is the about how stored information in life forms changes with changes in the living form´s environment.)*

    * leaving out spontaneous mutation is not really an error. If the environment did not change for a very long time, then that life form is already optimum for that environment and the mutation is not - it will soon die out of the gene pool.
    Last edited by a moderator: Aug 11, 2012
  23. Crunchy Cat F-in' *meow* baby!!! Valued Senior Member

    My current understanding is that the International Committee on Taxonomy of Viruses currently considers viruses as non-living entities. I cannot objectively say nor agree if viruses are alive or not-alive; however, I do understand why you would consider them to be alive. Yes, I did present an analogy to a virual life cycle (and anologies of complex processes inherently lack accuracy), but I wouldn't know how to communicate it otherwise to a kid over a forum. Your example of viral entry by injection is interesting and I do understand your argument for it being a stimulus reaction.

    I was treating a stimulus response as a sensory / motor nerve reflex and I suspect you are treating a stimulus response as something more general... something akin to work performed in response to change. Does that sound about right?

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