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Computational Simulations of E.coli 51

Gearoid_Murphy writes, "BBC news has the story of a scientist who has been using computational models of bacteria to advance our understanding of actual bacteria — a step towards simulating fully fledged organisms in virtual environments and potentially an extraordinarily powerful tool for medical science."
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Computational Simulations of E.coli

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  • BBC news has the story of a scientist who has been using computational models of bacteria to advance our understanding of actual bacteria

    So the story is a simulation that actually simulates what it's simulating? (Isn't that what a simulation's suppose to do? Model and echo what happens in the real world)

    How stimulating.
    • I agree. It's basically saying, "Scientist is modeling something."


      Let me know when he gets *results*. Anyone can "make a model".
      • TFA (that is customary not to read) may be short on substance but it can also be said "I can pull results out of my arse", science = observations + models, you cannot judge any result without access to the observations and a basic understanding of the model.
    • Yeah, kind of. This type of big big model tells you that all of its pieces are essentially correct in modeling the bacteria behavior. My criticism of this type of modeling is that you don't learn much more. Simplified models are usually more revealing, in my opinion, because
      (1) You have to know which pieces you can simplify how, and doing so shows you what's important and what's just details.
      (2) You can actually analyze a simple model to see if it predicts things you didn't learn from dir
    • by Thusi02 ( 998416 )
      There isn't much news about this. The field of Bioinformatics has been around for quite sometime now. Where the analysis of genomes of bacteria such as the E.Coli or C.elegans has been done quite extensively. I believe every week a new species genome is published on the NCBI site. This can than be used to understand their homology between other species and than perhaps identify why humans can't fly yet or fight of disease or grow limbs back. Even though the field of Bioinformatics is rather developing rapid
    • Yes. The story is about the fact that these simulations are actually approaching being correct.

      Sort of like physics; every discovery in physics is always about how our understanding of the universe is approaching correctness.

      A lot of models don't work. A lot of simulations are broken either because they are wrong, too simple, or irrelevant.
      • by syousef ( 465911 )
        Gimme a break. With my background, I have lots of respect for scientists that spend their life computer modelling. It ain't slashdot front page news, and even if that were arguable, you wouldn't know from the submission that was so badly written it should never have been accepted.
    • In the world of intracellular biology, having a simulation that actually simulates what it is supposed to is a major accomplishment.

      Imagine if you didn't know how a computer was constructed, other than knowing it was composed of millions of transistors, resistors, capacitors, and other electronic components. Now imagine having simulated transistors, resistors, capacitors, and other electronic components. How difficult would it be (not knowing how a computer is constructed) to put together these simulated
    • by d2tu ( 589189 )
      While computer simulations are limited to what you program in to them, it's not always obvious what result you're going to get when you create a model and implement it. With as few as 3 chemical components you can create complex dynamics including chaos and other non linear behaviors that are not always predictable and rarely intuitive. Having read Dr. Bray's work, he was analyzing the effect of random fluctuations in the model and the model allowed him to figure out the mechanism that allowed a bacteria to
  • The Matrix! (Score:3, Insightful)

    by headkase ( 533448 ) on Monday November 06, 2006 @06:10PM (#16742811)
    We'll start with bacteria and move our way up to humans! ;)
    Hopefully this would eventually allow risky medial treatments to be simulated before they have to be performed with a scan of the patients physiology as a reference.
    • Re:The Matrix! (Score:4, Interesting)

      by jmp_nyc ( 895404 ) * on Monday November 06, 2006 @06:47PM (#16743503)
      We'll start with bacteria and move our way up to humans! ;)
      Hopefully this would eventually allow risky medial treatments to be simulated before they have to be performed with a scan of the patients physiology as a reference.

      The scientific community is already working on it, as you might well imagine. Take a look here [pathguide.org] for a list of published databases of protein interactions and metabolic pathways. The drug companies are throwing money at developing systems that can use this sort of data to (for example) predict negative drug interactions well before a new drug gets anywhere near clinical trials. They're also being used to better understand exactly how existing drugs work, trying to isolate causes of desired effects from those of side effects. This is an emerging field, applying well studied (in computer science) principles of graph theory to biological networks that are only now being mapped.
    • Which makes it quite likely that we're living in a simulation ourselves... [simulation-argument.com]
  • by Channard ( 693317 ) on Monday November 06, 2006 @06:14PM (#16742869) Journal
    ... a fully 3D representation of the work-counter of a kebab shop, where the E-Coli simulation starts?
  • .....avoid ingesting feces, unless there is something attractive about bleeding from ones be-hind.

    What next? Is some bored dude going to do a computer model on just what is it that makes Anna Nicole Smith stupid?

    I dont know about you, but when do we get the computer models showing exactly why Guinness tastes better than Budweiser, so someone can share that data in time to save me some damn money?

    • You don't need to know *WHY* Guinness tastes better than Budweiser, all you need to know is that Guinness *DOES* taste better than Budweiser. Thus you can spend your money on quality beer right from the outset.
    • As soon as some beverage company decides to model human taste buds in order to determine how they can modify their beverage to make it more appealing to consumers without actually modifying the process by which they brew their beverage, brewing a new batch, and conducting taste trials. Simulations are likely to cost less than actually making and testing the modifications to their recipes or processes.
      • Simulations are likely to cost less than actually making and testing the modifications to their recipes or processes.

        If the simulation framework would already exist, you would be right, but in the particular case you mention you're probably not: you'd have to first find out which receptors in the tastebuds are responsible and what their structure is. To be honest, computer simulation is still far away from such amazingly complex tasks.

        Furthermore changing a beverage can be done fairly cheaply, you just

  • by QuantumG ( 50515 ) <qg@biodome.org> on Monday November 06, 2006 @06:20PM (#16743007) Homepage Journal
    Hence, discrepancies between what the scientists see in biological experiments and what they see in the simulations allows them to test the models. If there is a mismatch it suggests the model is incorrect and needs to be refined.

    Wow, that kinda sounds like.. umm, what's the word I'm after here, umm, science, yes, that's it.
  • by gardyloo ( 512791 ) on Monday November 06, 2006 @06:23PM (#16743085)
    That article pretty much sucks for communicating anything that the scientist is doing. I won't remedy that, but I'll say this: I audited a biophysics class two semesters ago, and the astounding complications of what goes on in cells was a real eye-opener. Of course, I'd learned about chemical pathways, and mitochondria, etc., before, but the class showed how damned complicated and *fast* everything is at the cellular scale.
          The professor used this analogy: think of filling a football/soccer (your choice) stadium with ping-pong balls, and paint just two of those balls orange. Then hire some bulldozers to push the balls around randomly and continuously for several decades. How often will the orange balls collide with each other? Once a week? Once a month? Once a year? Maybe only once in a decade? Now envision the stadium scaled down to the size of a cell, with the ping-pong balls now being your average-sized molecule important for some process (chunks of amino acids, say). These will be moving around randomly due to Brownian motion, chemical gradients, etc. How often will two given molecules interact? Probably several times per second. THAT's how amazingly extreme cellular processes are.

            It's that sort of analogy (sorry it wasn't about cars, but we could probably work those in somehow) that the article should have had. This stuff is complicated, and requires VERY efficient computation. Kudos to the researchers, and pfft! to the author of the article.
  • LOL (Score:3, Interesting)

    by SilentOneNCW ( 943611 ) <silentdragon@gm[ ].com ['ail' in gap]> on Monday November 06, 2006 @06:52PM (#16743623) Homepage
    Wow, figures. I actually used TFA for my Cambridge application -- nice to see it appearing on /. albeit slightly later than I expected. Really though, Cambridges Computer Science Lab (funded by our friend Bill Gates, among others) is doing some amazing things. Check out their website at http://www.cl.cam.ac.uk/ [cam.ac.uk].
  • I've had E.Coli before, but I'm not quite sure what a computational simulation of severe diarrhea would look like; maybe Microsoft code?
  • I dont know what they modelled but I know why they modelled it. So that the California Spinach farmers can claim, "No E Coli was actually harmed in filming this commercial".
  • They had articles like this ten years ago, that some grad student somewhere simulated an "actual bacterium" on a PC. The topic is useful primarily as a graduate student's thesis topic, along with "robotic simulations".
  • a step towards simulating fully fledged organisms in virtual environments..

    Yeah but it's like, a really small step isn't it? You couldn't do anything useful with it except maybe simulate Dubya's cerebral activity, and that's not very useful at all.

    And besides, didn't you hear: Virtual Environments/Machines are going to be banned on Vista!
  • I don't know this research, and the article doesn't really say anything at all, but as a grad student who has done a lot of cell modeling research, I like his approach of limiting the model to something very simple and easy to verify. We are a long, long way off from "simulating fully fledged organisms in virtual environments". Probably not in our lifetimes. You just have no idea how complex even E. coli is until you study it, and if you have, you'll understand how primitive and limited our models are.

    • I do, I work within the field of bacterial chemotaxis and have spoken with Dr. Bray. You're right, chemotaxis was an excellent modeling choice due to wealth of knowledge available (20-30 years of prior experimental research).
  • Reminds me of this book (I think I got the right name, read it a couple of years ago.)
    Hard-scifi, check it out!

A bug in the code is worth two in the documentation.