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First Digital Simulation of an Entire Life Form

Posted by Zonk on Mon Mar 27, 2006 04:42 PM
from the who-doesn't-love-alife dept.
Science
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.'"
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  • Story is a dupe...original story can be found here [slashdot.org].

  • Life is not a binary distinction (Score:5, Interesting)

    by wsherman (154283) * on Monday March 27 2006, @04:46PM (#15006239)
    But is it really a life form?

    Language is digital (as opposed to analog) in the sense that you either use a word in a sentence or you don't. 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). This creates (willful?) confusion in the minds of people who are very focused on a literal interprtation of language based laws and moral codes that "life" is a binary distinction.

    The reality, however, is that the word "life" refers to a whole variety of concepts. There are all different ways of being alive and there are all different levels of being alive. Certainly we can find examples of things that are very "alive" just as we can find examples of colors that are very "blue" - but that doesn't mean every color is either pure blue not blue at all and it doesn't mean that something is either completely alive or not alive at all.

    Going way off topic, the whole "life begins at conception" is what we in the sciences refer to as "not even wrong". After all, it's kind of hard for dead people to have children. If you really want to talk about when life began it would be at the big bang when matter developed the properties that cause it to form into complex self-replicating patterns over very long time scales.

    • Re:Life is not a binary distinction (Score:5, Insightful)

      by Red Flayer (890720) on Monday March 27 2006, @05:01PM (#15006361) Journal
      "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.
      [ Parent ]
      • 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.

        My definition of science would be that it is an attempt to organize and summarize mutually agreed upon fact

      • 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).

        Curse those platypus...

    • Language is digital (as opposed to analog) in the sense that you either use a word in a sentence or you don't. 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 a
    • "but you can't use a fraction of the word"

      you've obviously never heard one of bush's speeches ;-)

  • Simulating intelligence? (Score:5, Insightful)

    by 4D6963 (933028) on Monday March 27 2006, @04:50PM (#15006268) Homepage Journal
    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?
    • 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 simul

    • Re:Simulating intelligence? (Score:5, Insightful)

      by egomaniac (105476) on Monday March 27 2006, @05:02PM (#15006379) Homepage
      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.
      [ Parent ]

      • 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?"
        I believe that we should worry

        • Re:Simulating intelligence? (Score:2, Insightful)

          by JesseL (107722)

          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 m
          • This just made my day. Thanks a lot.

            • Re:Simulating intelligence? (Score:3, Informative)

              by JesseL (107722)
              You're welcome. Here's the correct quotes with attributions (from a fortune file circa 1989):

              "Anything created must necessarily be inferior to the essence of the creator."
              -- Claude Shouse (shouse@macomw.ARPA)

              "Einstein's mother must have been one he

        • Re:Simulating intelligence? (Score:2, Insightful)

          by 4D6963 (933028)
          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.

      • 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 [wikipedia.org] (

        • Re:Simulating intelligence? (Score:3, Insightful)

          by edremy (36408)

          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 t

      • Re:Simulating intelligence? (Score:3, Informative)

        by fnurb (310028)
        As Kurzweil and many others have pointed out, we don't need to simulate every single neuron and synapse, let alone every single neurotransmitter molecule, in order to simulate the operations of an intelligent brain. Rather, research now focuses on simulati

      • Re:Simulating intelligence? (Score:5, Funny)

        by binarybum (468664) on Monday March 27 2006, @06:45PM (#15007191) Homepage
        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).

              Dude, this is going to blow your mind. [tamagotchi.com]
        [ Parent ]
    • 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?

      Would you consider a bacterium intelligent? I bacterium is several orders of ma
    • Intelligent animals are orders of magnitude more complex than viruses. In some theories, if there was a supercomputer powerful enough to simulate all the atoms in your body, it would be conscious. Others invoke quantum uncertainty to explain consciousness,
    • The equations that govern the behaviour of nuclei and electrons are extremely complex and have currently only been solved for a handful of atoms interacting with each other. For this reason, the simulation mentioned in the article can only be an approxima

    • 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?

      It is theoreticaly possible (although it would be many orders of magnitude mor
    • The simple answer to your question is no. In the field of Molecular Modeling, we have a pretty good idea of how to simulate a system at the atomistic level. As the article states, we are pushing the limits of computational resources and time to complete

  • I Hope... (Score:4, Funny)

    by eno2001 (527078) on Monday March 27 2006, @04:50PM (#15006278) Homepage Journal
    ...Symantec/Norton, McAfee, CommandPoint, Crudpuppy, ClamAV, Grisoft and the rest are all preparing signatures, otherwise if this thing gets in the wild it will turn your data into nothing but pond scum... ;P (Aren't there ANY moderators with quirky senses of humor anymore?)

  • Move along, nothing to see here... (Score:5, Funny)

    by PoprocksCk (756380) <poprocks@gmail.org> on Monday March 27 2006, @04:51PM (#15006285) Homepage Journal
    ...We've been able to have viruses on computers for many years now.

  • Life vs. Non-life (Score:2, Redundant)

    by Absolut187 (816431)
    This is one of those areas where any attempt to draw a line is subjective.


    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.'

    Ok, so does that
    • >> Ok, so does that mean that cuckoos and cowbirds are not "lifeforms"?

      No, Cuckoos and cowbirds have all the needed apparatus for procreation. Viruses on the other hand generally require the transcriptional "machinery" of a host cell in order to rep
    • Cuckoos and cowbirds can, in a pinch, replicate without parasitizing another birds nest. Viruses are snippets of RNA in a protein coating that, simply put, do nothing outside of a cell. Vast difference here.

      • Re:Life vs. Non-life (Score:4, Interesting)

        by pomo monster (873962) on Monday March 27 2006, @06:45PM (#15007189)
        Human beings do nothing outside a very specific environment tailored to their needs, where temperature, pressure, oxygen content of air, gravity, radiation, &c., all lie within specific bounds. How is this different from a virus needing an environment that includes cellular structures in order to replicate?

        Me, I subscribe to structuralism.
        [ Parent ]

  • Duplicate; here's a link to the research anyway. (Score:3, Informative)

    by tskirvin (125859) on Monday March 27 2006, @04:58PM (#15006344) Homepage
    The main research page [uiuc.edu] may interest some of you. And for those that it doesn't help, perhaps you want to look at our Linux clusters [uiuc.edu] instead?

  • I doubt it. Might be the first simulation that isn't forced to take any shortcuts to simulate the behavior of a life form (highly unlikely, because there's too much left regarding genes which we don't fully understand)
    But even if this is a complete simulat
    • Is it really that interesting to watch such a simulation if it doesn't interact with other models of the same quality?

      Sure. Being able to take the together the basic building blocks (atoms), arrange them into molecules (amino acid residues), which then ca

  • Its awesome (Score:3, Interesting)

    by mnmn (145599) on Monday March 27 2006, @05:08PM (#15006424) Homepage
    Simulating life is awesome. Now the next step is to simulate something like an Amoeba in water... let its DNA drive it to 'eat' a food particle, and see how accurate the digestion (and binary replication) is with the input being only the DNA and initial conditions. I wonder what kind of computers are required to simulate all that, in how much time? I'd more gladly donate cpu cycles to this than to SETI.

    Next I wonder if the computer can be used to run regression tests to create the ideal bacteria or virii for a given situation. Virii can be built to repair human DNA in various ways... a particularly disadvantageous gene can be switched off throughout the body once infected with the virus.

    Of course this only allows Cybernet to have more destroying power once it 'wakes up'.

  • Simulation of an entire lifeform, my ass! (Score:5, Informative)

    by Expert Determination (950523) on Monday March 27 2006, @05:09PM (#15006431)
    This is such a misleading headline. It's a simulation of the dynamics of the proteins forming the outer case of the virus to understand how it maintains its structure. It's purely about studying the structure - like an engineer's finite element simulation of a bridge. It's great work from this point of view. But it's not a simulation of any kind of biological process because the time scale is something like nanoseconds. So yes, it's a simulation, but it's not a simulation of a lifeform qua a lifeform.

    And that word 'lifeform' - it brings the quality of the reporting down to the level of Star Trek psychobabble. Try 'organsim', or even 'virus', next time.

  • You are not a life form, then? (Score:3, Interesting)

    by Roadkills-R-Us (122219) on Monday March 27 2006, @05:19PM (#15006525) Homepage
    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.'"

    The same could be same for most species of animals; they ``contain RNA or DNA like other lifeforms, they can only replicate inside other living organisms''.

  • Cigar Store Indian (Score:5, Funny)

    by Doc Ruby (173196) on Monday March 27 2006, @05:27PM (#15006589) Homepage Journal
    "satellite tobacco mosaic virus"

    That sounds like the greatest hits of American products, all in one convenient album.

  • "life" is a lousy line to draw (Score:3, Interesting)

    by smellsofbikes (890263) on Monday March 27 2006, @06:10PM (#15006947) Journal
    I think we can agree that bacteria are alive. But there are types of bacteria, the ones that cause leprosy and chlamydia, frinstance, that cannot reproduce outside of a living cell. (They, unlike most bacteria, invade and live inside cells.) It's fairly difficult to draw a hard line between them and some viruses that have lipid bilayers full of receptors on their outsides. Even prions self-amplify, so where do you draw the lines on what's alive?

  • Life and the living (Score:3, Funny)

    by jandersen (462034) on Tuesday March 28 2006, @04:11AM (#15009247)
    I think we have to distinguish between 'life' as a concept and 'living organisms'. Life is an abstraction - it is the 'quality' that is common to all life processes, ie the processes that we know from living organisms.

    The only thing that is reasonably clearly defined is 'living orgnism'; and as several posts have already pointed out, viruses can't quite be called living organisms; not because the don't display life, but because they are too simply to qualify as organisms. However, they do have life proceses - eg. they reproduce.

    How can one define the concept 'life'? It is a difficult one - there are many that feel it would be too narrow to define it simply as the set of chemical processes that we know from biology; among other things, there is no sharp boundary between simple non-organic chemistry and 'life-chemistry'. There are some that define life as chemical evolution (http://en.wikipedia.org/wiki/Chemical_evolution [wikipedia.org]) - this theory has the advantage that it can be generalised; all that is needed is a good generalisation of 'chemistry'.

  • Life = Non-life (Score:3, Insightful)

    by foxxo (262627) on Tuesday March 28 2006, @06:23AM (#15009563) Homepage
    "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.

    • Why virii are not alive (Score:5, Informative)

      by chrisjbuck (950790) on Monday March 27 2006, @07:57PM (#15007654)
      A (biological) virus does not eat or photosynthesize or have any metabolism at all. That's why they are virus particles, other than the slow degradation of all complex molecules if you have a tube full of virii they will just sit in the tube forever. Doing nothing. If you add sugar, protein, complex carbohydrates and sunlight to the tube of virii they will... sit there. Doing nothing. Not eating. Not metabolizing. Not replicating. Living things would either die, metabolize, or replicate, the virii do not. The virii does contain genetic information, if inserted into a cell the information is used to hijack the cell into making more copies of the virus. The virus may only encode a handful of proteins, but it uses the ribosomes and other protein building apparatus of the infected cell to make the viral proteins, and more copies of the viral genetic info (DNA or RNA) which is packaged and released from the cell (sometimes killing the cell in the process, sometimes not). Does this mean the virus is alive? All the protein synthesis, and packaging of the virus is done by the infected cell, the virus does not technically replicate itself, which is part of what we define as "life as we know it". They are not dead they just exist as a glitch. A primordial cell probably had a mutation that produced lots of particles that happened to be capable of causing the same glitch in other cells they encountered, virii are perhaps analagous to a "goto" loop that somehow copies itself to other programs, more than to actual computer viruses which imitate their biological namesake only to a certain degree. Maybe when the sony robot dogs start giving each other roborabies via bluetooth the analogy will be closer... IAABC - I am a biochemist - but genetic coding is still trickier than php scripting :P
      [ Parent ]

      • Re:I don't get it (Score:4, Insightful)

        by shawb (16347) on Monday March 27 2006, @06:35PM (#15007123) Journal
        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.
        [ Parent ]

          • Re:I don't get it (Score:5, Insightful)

            by shaitand (626655) on Monday March 27 2006, @07:49PM (#15007617) Homepage Journal
            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.
            [ Parent ]

              • Re:Oh yes, now I get it! (Score:3, Insightful)

                by shaitand (626655)
                "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

                  • Re:Oh yes, now I get it! (Score:3, Insightful)

                    by nickco3 (220146) *
                    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 arbit
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