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Software Science

Software Emulates Organism's Entire Lifespan 86

Posted by Soulskill from the sit-on-couch-and-eat-potato-chips,-increment dept.
An anonymous reader "Scientists have developed a software simulation, running on 128 computers, of an entire organism, a step toward carrying out full experiments without traditional instruments (abstract). 'For their computer simulation, the researchers had the advantage of extensive scientific literature on the bacterium. They were able to use data taken from more than 900 scientific papers to validate the accuracy of their software model. Still, they said that the model of the simplest biological system was pushing the limits of their computers. "Right now, running a simulation for a single cell to divide only one time takes around 10 hours and generates half a gigabyte of data," Dr. Covert wrote. "I find this fact completely fascinating, because I don’t know that anyone has ever asked how much data a living thing truly holds. We often think of the DNA as the storage medium, but clearly there is more to it than that." In designing their model, the scientists chose an approach that parallels the design of modern software systems, known as object-oriented programming. Software designers organize their programs in modules, which communicate with one another by passing data and instructions back and forth. Similarly, the simulated bacterium is a series of modules that mimic the different functions of the cell.'"
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Software Emulates Organism's Entire Lifespan More

Software Emulates Organism's Entire Lifespan

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  • Different viewpoints (Score:4, Insightful)

    by SmlFreshwaterBuffalo ( 608664 ) on Friday July 20, 2012 @05:34PM (#40719135)

    We often think of the DNA as the storage medium...

    You might, but I'm betting physicists think differently. It all depends on the information to which you're referring.

    • I think "we" meant "biologists" there, and "THE storage medium" as "that a cell uses."

      And that would be true, most biologists tend to assume that the nucleus is where the vast majority of the data of the cell is. We're aware that DNA is not the end all be all of the cell, but we often don't think about the other inputs into a cell's behavior as being as important. For instance, we often study isolated human cells isolated in a petri dish, and what changes when we turn off or on different genes. There'

    • Re: (Score:3)

      by nashv ( 1479253 )

      Biologists do not see DNA as merely a storage medium. This might be an issue of semantics, but when biologists say "DNA" , they mean the molecule. Just plain DNA.

      For it's 'non-storage-only' functions, DNA needs a bunch of proteins and RNA molecules. This entire functional and dynamic assemblage is referred to as 'chromatin'. This is why a bunch of other terms exist - exon, intron, promoter, enhancer, gene, telomere, tandem repeats, restriction site, nucleosome etc. Clearly, these are made up of DNA, but enc

  • OOP (Score:1, Funny)

    by Anonymous Coward

    I always figured OOP had some usefulness when used properly :)

    • It's a distributed processing system with interprocess (regardless of the node on which the process resides) message passing.

      While some, or even all, of he process modules MAY have been written in a object-oriented language AND style, this sort of processing predates all of the OOP languages and nearly all of the literature.

      If I wanted to get there quickly and scalably, I'd use the distributed systems created for weather or nuclear simulations as a starting point, since intracellular activity has no small a

      • Re: (Score:1)

        by Anonymous Coward

        There's no way this simulation was at an atomic or even molecular scale.

    • Organism Oriented Programming?

    • IMHO they should have used C; after all, it is the language of God and Root.

      • IMHO they should have used C; after all, it is the language of God and Root.

        But Melkor sought to improve it and add themes of his own making, and thus the cacophonous abomination known as C++ was born.

        I knew it!

      • Re:OOP (Score:5, Funny)

        by Celarent Darii ( 1561999 ) on Saturday July 21, 2012 @05:04AM (#40722411)
        No, no, no. Everyone knows God wrote the universe in LISP. He only had six days after all !

        For those too young to remember the song by Julia Eklar

        http://www.songworm.com/lyrics/songworm-parody/EternalFlame.html

        I was taught assembler in my second year of school.
        It's kinda like construction work -- with a toothpick for a tool.
        So when I made my senior year, I threw my code away,
        And learned the way to program that I still prefer today.

        Now, some folks on the Internet put their faith in C++.
        They swear that it's so powerful, it's what God used for us.
        And maybe it lets mortals dredge their objects from the C.
        But I think that explains why only God can make a tree.

        For God wrote in Lisp code
        When he filled the leaves with green.
        The fractal flowers and recursive roots:
        The most lovely hack I've seen.
        And when I ponder snowflakes, never finding two the same,
        I know God likes a language with its own four-letter name.

        Now, I've used a SUN under Unix, so I've seen what C can hold.
        I've surfed for Perls, found what Fortran's for,
        Got that Java stuff down cold.
        Though the chance that I'd write COBOL code
        is a SNOBOL's chance in Hell.
        And I basically hate hieroglyphs, so I won't use APL.

        Now, God must know all these languages, and a few I haven't named.
        But the Lord made sure, when each sparrow falls,
        that its flesh will be reclaimed.
        And the Lord could not count grains of sand with a 32-bit word.
        Who knows where we would go to if Lisp weren't what he preferred?

        And God wrote in Lisp code
        Every creature great and small.
        Don't search the disk drive for man.c,
        When the listing's on the wall.
        And when I watch the lightning
        Burn unbelievers to a crisp,
        I know God had six days to work,
        So he wrote it all in Lisp.

        Yes, God had a deadline.
        So he wrote it all in Lisp.
  • So how much extra data do we need for a parrot?

    • Re: (Score:2)

      by keeboo ( 724305 )
      I guess that depends on how long are the silly songs you wish to be part of the parrot's repertory.

  • Obligatory... (Score:2)

    by Anonymous Coward

    Well I, for one, welcome our uploaded lobster simulations, and the following Vile Offspring overlords :)

    • Mod parent up! My first reaction was "F@#*( -- Charles Stross was right!" For the uninitiated, here's a summary [wikipedia.org] and here's the full text of the mind bending novel Accelerando [jus.uio.no].

      • Re: (Score:2)

        by HiThere ( 15173 )

        The interesting part is that at the time that he wrote it, someone at the University of California (in southern California, but I don't remember which campus) was doing a simulation of a lobster neural net. Don't know how detailed. And I don't know if he knew about it, but naturally one suspects that he did.

  • Comment removed (Score:4, Funny)

    by account_deleted ( 4530225 ) on Friday July 20, 2012 @05:44PM (#40719227)
    Comment removed based on user account deletion

  • OO vs real life (Score:4, Interesting)

    by robi5 ( 1261542 ) on Friday July 20, 2012 @05:50PM (#40719299)

    I wonder how naturally an object oriented design worked out, given that molecular pathways are extremely complex and there are causal links between almost any pairs of phenomena. While OO is OK for CAD and man-made things, nature was much less restrained about high cohesion, low coupling, encapsulation and other heuristics. So the details would be interesting about inheritance, state representation, graph complexity, time-varying behavior etc.

    • My guess is they didn't completely emulate an organism, they simulated it roughly, but simulated it with enough detail to make it useful for testing drugs , theories, etc.

      I don't understand biology well enough to verify this in this case, but I do know it has been true of recent high-profile brain simulations.

      • Re: (Score:2)

        by HiThere ( 15173 )

        I certain you are correct ... for a given value of roughly. They certainly didn't specify the position of each atom. And I really doubt that the simulated the positions of water molecules, though they possibly simulated hydration levels by subdivision of the cell.

        The thing is, you need to decide which details are significant, and simulate those. If you pick the right selection, then specifying more carefully doesn't buy you much. E.g., you might gain by having a thermostat in each room, and possibly by

        • Re: (Score:3)

          by garaged ( 579941 )

          And neglecting atomic level interactions invalidates the method for most phamaceutic studies.

    • Re:OO vs real life (Score:5, Informative)

      by macklin01 ( 760841 ) on Friday July 20, 2012 @06:24PM (#40719609) Homepage

      Simplified answer:

      These models tend to be object-oriented in the sense that a genetics "module" interacts with a protein signaling module, etc. In each module, you'd have the member data (say, a list of all proteins) and member functions (say, a model of the reaction network that discretizes the massive system of ODEs).

      The objects then interact. You have well-defined interfaces between these modules to codify currently known (or hypothesized!) biology. For example, members of the proteins module activate certain genes in the genetics module to (eventually) drive synthesis of more proteins.

      You write the rules based upon our current state-of-the-art in understanding cell biology, simulate, and see what happens. To the extent that it quantitatively matches experiments, we can assess the underlying hypotheses, refine them, or toss them out.

      In this work, it looks like they pulled information from 900 papers on this species of bacterium to simulate 525 genes, God knows how many proteins (genes can encode multiple proteins), and 28 processes.

      Notably, there is no spatial component (e.g., transport of proteins, RNAs, cell volume changes, cell mechanics, etc.), but it's an incredible set of work. And to be able to predict phenotype solely based upon the emergent behavior of this network is pretty incredible.

      • Re: (Score:1)

        by robi5 ( 1261542 )

        Thank you for the answer! Not having access to the body of the article, it is informative.
        I bumped into this cool video: http://www.youtube.com/watch?v=au4sl9CjKFU [youtube.com]

        How useful OO is interesting, because it is possibly one of the first uses of OO as applied to modeling wetware behavior, and there must be some lessons learned.

        Calling it OO may be something to do with a superficial aspect of the realization, but at its core, it looks like a giant filter [wikipedia.org] where the external signals to be processed are the time ser

    • I wonder how naturally an object oriented design worked out

      I don't know the details, but if they really did replicate the results from a diverse range of 900 or so studies, then that to me says their simulation is pretty good.

      • Re: (Score:1)

        by rmstar ( 114746 )

        I don't know the details either. But if they as much as claim that they could replicate the results of 900 or so studies, then I would start from the assumption that they are full of it.

        Perhaps I should read the paper. But as someone who knows how how the information in "studies" gets there (you choose the nicest picture), and how much it is worth (the result will be mostly OK, but the data will have, ah, simmered a little bit in hot water), I can tell you that replicating the results of 900 or so studies i

    • "Right now, running a simulation for a single cell to divide only one time takes around 10 hours and generates half a gigabyte of data," Dr. Covert wrote.

      life's too short for java. http://farm4.staticflickr.com/3245/2652438835_4f0f3b366b.jpg [staticflickr.com]

    • Re: (Score:2)

      by tbird81 ( 946205 )

      I understand because it was OO, it was difficult (but not impossible) to write in C.

  • Software Emulates Orgasms in Japan

    • Software Emulates Orgasms in Japan

      We all know how much the Japanese love their gadgets, I doubt anyone considers a reciprocating function news (or surprising, anyway).

    • In Japan of all places, I'm pretty certain that software doesn't emulate orgasms, but rather actually experiences them.

  • Stupid question (Score:1)

    by Anonymous Coward

    How are they calculating protien conformations? I can't believe this is being calculated in realtime on only 128 processors.

  • It's just a model of gene-expression and metabolism. Not exactly what I would call emulation. They haven't generated any hypotheses with it which have been found to be true, so of course, there is no reason to think it has anything to do with anything.

    Some colleagues of mine did just this thing on a smaller scale in a different system last year, it didn't go too well and generated absurd predictions which were so assumption heavy as to be interesting only as a theoretical exercise.

    It's not like they can t

  • Really so complex? (Score:3, Funny)

    by chrism238 ( 657741 ) on Friday July 20, 2012 @06:09PM (#40719455)
    What? You mean the dividing cell doesn't just call fork() ?

    • Re: (Score:2)

      by dargaud ( 518470 )

      What? You mean the dividing cell doesn't just call fork() ?

      That's only the top API...

      More seriously I wonder why simulations are not used more commonly in biology/medicine. One example is endocrinology. If you go to an endocrinologist for hormonal balance (for instance because you have a missing thyroid), over time (s)he adjusts the dosage of your medicine 'out of thin air' (and a lot of experience, Okay), but there are so many retro-actions that I'm sure they'd do it much faster if they just punched in the numbers (your past and current analyses and your curren

      • For most of biology, we haven't yet been able to create numerical models. There are a huge number of variables, interactions, and feedback loops, and frankly we don't even fully understand how many biological processes work, so creating mathematical models is very difficult. But this is sure to be a productive area of research so any young computer geeks with an appetite for the squishy science should take note!

  • "Right now, running a simulation for a single cell to divide only one time takes around 10 hours and generates half a gigabyte of data," Dr. Covert wrote. "I find this fact completely fascinating, because I don’t know that anyone has ever asked how much data a living thing truly holds.

    Wrong paradigm.. I can create a 100k program that generates that much data. DNA is storage and instructions, but it creates more than it holds from that small data set.

  • At what level are they simulating the organism? Is it at a gross molecular level, or are they simulating each individual electron transport path through the Krebs Cycle, or somewhere in between?

  • Is this some ploy by the united front of Object-Oriented Programmers to convince the world that multiple inheritance isn't as bad as everyone thinks it is? I'm sure the global union of Object-Oriented Programmers is already planning a seminar on how Interfaces are appropriate subsitutes for multiple inheritance.

  • Was already done.... (Score:2, Insightful)

    by ArcadeNut ( 85398 )

    Long time ago :)

    http://www.bitstorm.org/gameoflife/ [bitstorm.org]

    Ok, so maybe it's not as sophisticated as this version...

  • Don't get me wrong (I think that's really cool and stuff)...

    But I wonder what will take to simulate a few amoebas in a petri dish, what is not exactly the apex of biological complexity.
    Obviously multicellular organisms are out of question for some time still.

  • From the summary:

    In designing their model, the scientists chose an approach that parallels the design of modern software systems, known as object-oriented programming.

    No wonder the program is enormous!

  • and I thought "Damn, that must be a pretty short program.

  • "I find this fact completely fascinating, because I don’t know that anyone has ever asked how much data a living thing truly holds." To posit that information came from ignorance (vacuum, nothing) is astonishing. To posit that it arose with a mere 13,700,000,000 years boggles the mind at the imagination of some people.

  • This is cool, but as I read it here (and someone correct me if I'm wrong), it's no substitute for doing a real experiment. I'm going to launch into a long explanatory diatribe - models like this one can be VERY useful for hypothesis generation, or to try and understand seemingly disconnected results that (very often) arise in a biological experiment. They are especially useful when you have some hypothesis/theory of how a complex system is governed and you need to generate some prediction which you can e

    • Re: (Score:2)

      by Rich0 ( 548339 )

      I don't think anybody is suggesting that this is a substitute for in-vivo studies.

      However, I suspect we could learn quite a bit through simulations and modelling just the same, as you basically start out.

      I think some challenges are going to be spacial partitioning and kinetics. If you just model your cell as a uniform box that makes the math a lot easier, but it completely ignores the fact that cells actively manage their micro-environment (especially as you scale up to eukaryotes). The concentration of s

  • fraud (Score:1)

    by Anonymous Coward

    These so-called constraint flux based analysis (FBA) models are a big fraud. Perhaps most people in this field do not even realize this, but I think such models are of little direct biological value.

    Some time ago, I switched from experimental physiology/mol biology to computational biology. As part of my job, I was overseeing two students starting on such FBA models. What these models generally do is ask a genome or expression database for a list of all expressed genes. Then filter out things that have a bi

  • So far it is more of an assembler, but it includes all the "header files" for basic life functions like cell_wall.h, DNA_replication.h, ribosome.h, etc. Each of the header files describes the DNA code for all the needed proteins with all the switches needed.

    It is called YADA.jar (Yet Another DNA Assembler)

    Right now, the "printer" to get a real organism is cumbersome, but you can run the whole life form as a simulation. If you are Google, you may even grow real humans, and give them all kinds of fun function

  • Maxis SimLife

  • The idea of imitating a simple bacterial organism as a piece of software came through my mind a couple of times in the past. Although, it's really interesting, I think there is a fundamental problem with it. How deep the simulation has to go? To properly simulate a living organism, you would have to simulate more fundamental ideas laying inside, like chemistry behind substances involved or physics on a molecular level. As far as I know, there are still parts of these matters that have not been explored / di

    • Re: (Score:2)

      by Hentes ( 2461350 )

      Yes, emulation is a huge overstatement, this project basically simulated only the DNA and the metabolism of the cell.

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