Creating Digital dna that works just like its real counterpart

  1. Hello.
    Regards to all.
    I am working on an Organism Simulation Framework to simulate virtual organisms on low cost computers. I have already developed an alpha version of the project.
    To see the project, visit: www.sourceforge.net/projects/livmach

    Now I am in the phase where I require creating a digital equivalent of DNA. This 'Digital DNA' will work exactly like the real one in every way.
    I require help of someone specialised in genetics.
    i want to know the process(step-wise) in which dna commands cells,tissues and organs to grow and achieve a particular configuration.
    i require a step-wise explanation that will help me program it.

    I understand basic genetics and biochemistry...
     
  2. jcsd
  3. Ygggdrasil

    Ygggdrasil 1,518
    Science Advisor

    We still lack a detailed understanding of many of these processes, so I am not sure you will be able to find such information to be readily available. However, with some simplifications, researchers have been able to simulate a very simple bacterium (see https://www.physicsforums.com/showthread.php?t=622587). An organism with many different cells types and much more complicated gene regulatory programs would be much more difficult to simulate, however.
     
  4. Monique

    Monique 4,700
    Staff Emeritus
    Science Advisor
    Gold Member

    Every single intricate detail might not be known, that doesn't mean one cannot model the process. Just like how physicists can describe the world with relatively simple equations (Newton), only to get more details right the equations become more complex (Einstein).

    One can look up how DNA and development works in a text book, it will have hundreds of pages describing the processes in great detail. The amount of detail known is too complex to describe in a few sentences on physicsforums.

    One should rather say the amount of knowledge is too complex to model on a simple computer. The only way to achieve ones goal is to simplify the model into the building blocks. It would depend on what ones goal is.
     
    Last edited: Jun 14, 2013
  5. Ryan_m_b

    Staff: Mentor

    What you seek fills volumes of text books and is far from fully understood. I suggest investing in an introductory developmental biology book to get a glimpse of how complex the process is. Also you should note that DNA doesn't command anything, the interaction between DNA and cellular biochemistry (along with the micro-environment) creates the emergent properties of behaviour.
     

  6. Yes, but i still think that it is possible to simulate basic properties of DNA like replication on a simple PC using classes and functions and thats what I plan to do first. Then the next step would be to create specific proteins from this digital structure thus replicating at least partially the real process. This project is in its very initial stages. So as it progresses it can yield something useful.
    Thanks anyway for all the feedback.

    Regards to all
     
  7. I don’t know, but I think it possible that this video might help you:



    It is of a section of a lecture given by John Maynard Smith in which he discusses one theory of how the DNA code developed. The heart of it is about how certain amino acids became associated with particular RNA molecules, something which is entirely arbitrary. That is to say that there is nothing in the laws of physics that say one particular RNA molecule must associate with a particular amino acid, it just happens to have turned out the way it did. And it did so for a completely different reason, but having developed, it gave rise to the possibility of the development of a code to link together amino acids in a particular sequence to synthesise defined proteins.

    You might like to watch the whole lecture, and perhaps even to read the original piece by Eors Szathmary to which Maynard Smith refers. But I would not expect it to make particularly easy reading…
     
    Last edited by a moderator: Sep 25, 2014
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