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First Digital Simulation of an Entire Life Form

An anonymous reader writes "LiveScience is reporting on what appears to be the first digital simulation of an entire life form. Researchers created more than a million digital atoms to reverse engineer the satellite tobacco mosaic virus, a relatively simple organism. But is it really a life form? From the article: 'Viruses are tiny bundles of protein and genetic material that straddle the line between life and non-life. Many scientists prefer to call them "particles" because even though they contain RNA or DNA like other lifeforms, they can only replicate inside other living cells.'"

15 of 271 comments (clear)

  1. Simulating intelligence? by 4D6963 · · Score: 5, Insightful

    If they can simulate something else than a virus (because I don't think viruses are intelligent) could they by this way obtain intelligence by simulating an intelligent animal?

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    1. Re:Simulating intelligence? by Paraplex · · Score: 3, Insightful

      I think the real difficulty here is that an intelligence (or any life form really) isn't really alive without input & output. You can't just simulate (based on any physical model) an isolated life form because it would just sit there. You need to simulate the environment it inhabits.

      The line between the organism and the environment is very blurred. I tried to write a cellular autonoma of a weather/ecology system at once stage and was overwhelmed with the sheer number of variables which would have to be included to make it complete. You essentially can't leave anything out.

      Don't mean to sound like a buddhist or anything, but everything is inextricably connected. You'd need to start by making a 500 million atom small environment or some such.

    2. Re:Simulating intelligence? by egomaniac · · Score: 5, Insightful

      If they can simulate something else than a virus (because I don't think viruses are intelligent) could they by this way obtain intelligence by simulating an intelligent animal?

      Of course. It would take an absolutely colossal amount of computing power, but given sufficient resources and a complete understanding of the basic physics and chemistry involved (neither of which we have yet) you could absolutely simulate a living creature, and the simulation would be intelligent. There have been many sci-fi stories that have used this basic concept. In fact I expect the first intelligent machine will attain its intelligence by simulating a living brain (although at a much higher level than individual atoms).

      If we assume that all physical processes can be simulated by a computer (given complete knowledge of the laws of physics), which seems to be a safe assumption, the question boils down to "is intelligence a physical process?" Everything we know about the brain's operation says that the answer is a resounding "yes" -- and if intelligence is merely a manifestation of the physical operation of the human brain, then there is nothing about it that can't, at least in theory, be simulated.

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      ZFS: because love is never having to say fsck
    3. Re:Simulating intelligence? by JesseL · · Score: 2, Insightful
      But to get back to more basic or philosophical considerations: Maybe we're simply not able to create structures more complex than ourselves...

      I read a quote somewhere related to that idea. It was somthing to the effect of "in that case Einsteins mother must have been one hell of a physicist".
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      "Prefiero morir de pie que vivir siempre arrodillado!"
    4. Re:Simulating intelligence? by 4D6963 · · Score: 2, Insightful
      Afterall the human brain is still by magnitudes more complex than any computer we can build nowadays

      Sure, but who talked about a human brain?

      Personally I'll content myself with a virtual genuinely intelligent simulated bug.

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      You just got troll'd!
    5. Re:Simulating intelligence? by iammaxus · · Score: 2, Insightful
      a complete understanding of the basic physics and chemistry involved (neither of which we have yet)

      I believe you are wrong and we already possess sufficient physical knowledge and have for years. As far as I understand it, the Schrödinger equation (and perhaps some other quantum mechanical theories) allows us to model the behavior of electrons completely. All the interactions involved in biochemistry are simply a result of electron behavior (nuclear reactions do not affect life significantly). This is not to say that there is not still work left to be done in the field as modelling at such a low level is probably impractical.

    6. Re:Simulating intelligence? by edremy · · Score: 2, Insightful

      As far as I understand it, the Schrödinger equation (and perhaps some other quantum mechanical theories) allows us to model the behavior of electrons completely

      IWAQC (I Was A Quantum Chemist), so I'll bite. In theory, this is true. All you have to do is solve the Schrodinger equation for the system and you're done. The problem is that we can only solve it exactly for a few systems, the most complex being the hydrogen atom. Even the He atom is beyond our abilities, at least in the realm of exactness.

      Now, you can get into any number of simulation methods- there's standard Hartree Fock, density functional theory, a bevy of semi-empirical methods and a host of others. The problem is that all of them are approximate, often wildly so. Even for the simplest system, they have a lot of trouble reproducing reality. Quick: which end of the CN- ion is negative? You'll get different answers with different basis sets in Gaussian, much less the changes you get from introducing correlation methods.

      Assume that you somehow manage to solve the equation "well enough". That's nice, but all of the above assumes only a single point in time. My grad work was in introducing time into the picture. Electrons move really fast. (Well, they don't really move in the way you and I think about motion, but still) You'll need to solve the above, nearly impossible set of equations every tenth of a femtosecond at the slowest if you want to have any hope of modling things accurately- really, you probably should be doing it every attosecond.

      Ten years ago I managed a crappy simulation of a few lithium and hydrogen atoms undergoing a few tens of femtoseconds of a reaction. Computers are faster, yes, but Moore's law is never going to solve this issue.

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      "Seven Deadly Sins? I thought it was a to-do list!"
  2. Re:Life is not a binary distinction by Red+Flayer · · Score: 5, Insightful

    "You can either use the word "life" in a sentence or not but you can't use a fraction of the word ("li" or "fe" don't mean fractional life - or anything at all for that matter)."

    Oh, without capital letters, they mean nothing -- but I know quite a few chemists who'd dispute that Li and Fe are meaningless. :)

    To get on-topic, I think that humans constantly categorize and assign labels to things as either a member of a group or outside it, which IS binary.

    That creature is a fish|not a fish. That creature is a mammal; or it lays eggs and has a bill, so it is a bird (ummm, bad example, on second thought). That rock is igneous; or it is not. That tree is deciduous|not deciduous.

    What is the point of defining something if the definition does not allow us to use it to categorize? Things like this virus, and viruses in general, raise the debate over what is life|not life. And that debate can stimulate greater knowledge, and greater understanding, by challenging our assumptions and our definitions... so I'm all for making distinctions when we can.

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    "Trolls they were, but filled with the evil will of their master: a fell race..." -- J.R.R. Tolkien on Olog-hai
  3. Re:I don't get it by shawb · · Score: 3, Insightful

    I personally just put viruses firmly in the "gray area between living and not living" because those are arbitrary distinctions: nature always finds a way to find exceptions to the niches that man creates. Not to say that our classifications are pointless, we just have to realize that there are always going to be things in that gray area. This can be shown more dramatically in other biological definitions as well: when is a fetus "alive?" What is the exact point where two diverging groups are no longer the same species? All questions that have legal ramifications which essentially require a precise definition in order to make decisions as impartial as possible, but some things will straddle the line no matter how precise you try to make your definitions.

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    I'll never make that mistake again, reading the experts' opinions. - Feynman
  4. Re:I don't get it by shaitand · · Score: 5, Insightful

    Perhaps the better solution to this dillema is to realize the debate can not be settled because "life" is not a thing. It is a label. Humans invented the label and since it is an artificial construction its scope is equally artificial.

    There is no such thing as "life" we invented a classification without defining it and therefore we have a debate. The only reason we even find it to be important is that we are still trying to come up with excuses to think of ourselves as something more than a random cluster of protein soup.

  5. Re:I don't get it by Wizardry+Dragon · · Score: 2, Insightful

    That's possibly the most intelligent post I've read on Slashdot. I salute you!

  6. Re:Oh yes, now I get it! by shaitand · · Score: 2, Insightful

    "water" is also a noun. Water, is however a label for something real. "Life" is a label for a concept that does not exist, we made up the concept itself and not merely the label. It is not even a classification like a mammal, there is a valid definition of mammal, there has never been an agreed upon definition of life.

    There is a very substantial difference there.

  7. Re:Oh yes, now I get it! by tsm_sf · · Score: 1, Insightful

    "Life" is a label for a concept that does not exist, we made up the concept itself and not merely the label.

    Wow. You should set that as your sig so people know what kind of an intellect they're dealing with.

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    Literalism isn't a form of humor, it's you being irritating.
  8. Life = Non-life by foxxo · · Score: 3, Insightful

    "Life" and "non-life" are useful, but ultimately meaningless ontological distinctions that really have no purpose at the sub-microscopic level. Any sensible person can see that ultimately there is no difference between what we deem living and what we call non-living, as the quick and the dead are still naught but particles in relationship to one another. The notion of self-identical objects larger than the fundamental particles is useful, but when dealing on such a tiny scale it's best to forget about such pointless ontological nonsense.

  9. Re:Oh yes, now I get it! by nickco3 · · Score: 2, Insightful

    Life obviously exist since we're having this debate - I doubt we could have it if we weren't alive.

    You're confusing concepts with their labels.

    He's not saying there's no such thing as life, which is easily falsified. He's saying the concept "life" is arbitrary, and that the boundaries of that concept are arbitrary: there are seven specific conditions you need to meet to be officially alive. Why those particular 7? What if we changed the list to 6 or 8?

    Having dreamt up a classification called "alive" it's easy to demonstrate there are things that meet it. But don't fall into the trap of thinking that the classification exists outside our collective heads. Because we dreamt it up it.

    Let's say we change the definition of "life", adding requirement number 8 "wings". Things that are "alive" have "wings". Therefore, you and I are not "alive" because we no longer meet the definition. BUT (this is where you got confused) we carry on exactly as we were, still reading Slashdot, still eating, moving around, excreting, etc, because we're only talking about labels, and not reality.

    See Zen and the Art of Motorcycle Maintenance if you're struggling. It took me ages to get it.

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    -- Nick "Hallo this is Beel Gates, und I pronounce weendows as ... WEENdows"