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I'm a computer programmer deeply interested in Biology.

I wish to write a computer simulation for cell differentiation. I understand there will be seemingly impossible challenges in doing this. But first I am looking for answers to some basic questions.

  1. I've learned that a zygote turns into 'embryonic stem cells' which results in the organism. How does the zygote turn into embryonic cells ?
  2. What are the factors that determine the specialization of embryonic stem cells into more specialized types of cells and how does this transformation take place physically ?
  3. Where is the data stored which acts as the "guide" for all these processes ? Is it stored in the DNA ? If it's stored in the DNA , is it known how the cells interpret the information in the DNA?
  4. What are some textbooks I should be referring for this project ?

PS : Pardon my ignorance if these questions sound stupid, but I'm willing to commit time for learning anything needed to do this. Also , I understand all these questions cannot be answered in a few lines. Please provide references/pointers . Thanks !

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Basically to answer this question, people are devoting entire careers towards this goal. Even a simplified simulation can quickly become a PhD thesis if you so choose. I will assume you want a simulation which takes into account some level of biochemistry since the simple calculation of dividing cells is trivial. What you should decide on up front is to what depth of information do you want to simulate (eg, can you make some simplifications to make your model less realistic but more manageable)? –  leonardo Jan 2 '13 at 16:59
    
There is plenty of literature that shows information is stored in at least 3 major places. DNA is the lowest level of information (raw 'bits' of storage), then you have epigenetic modifications which can modulate the level of DNA accessibility and expresion (which are still not fully understood how these are inherited). The last important information encoding is at the level of protein and can be as trivial as a protein switched on/off, or embodied in the behaviour of a whole network of protein interactions. We are just starting to grasp the latter. –  leonardo Jan 2 '13 at 17:02
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3 Answers

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Trying to answer this question in a few lines is a tedious task. Mostly I'm not sure that as of today we know all there is to know about it.

I'll try to give you some hints though.

  1. The process is called embryogenesis. The zygote (or ovum) undergoes rapid mitotic divisions with no significant size growth which will lead to the development of an embryo. This process is called cleavage. Blastomeres are created during this process. On the third day - time may vary but not significantly - cleavage reaches the state of 16 cells. Cell divisions always occurs by parallel division (1 -> 2, 2 -> 4, 4 -> 8, 8 -> 16). Study the links I gave you and come back with more specific questions.

  2. Again that's kind of impossible question to answer without explaining the entire process from fertilization to fetal development, because creation of tissues (cells) and organs happens along the way, not at once. However, it's documented.

  3. Not sure.

  4. Start with the wikipedia links and try to come back with more specific questions. I have a couple of text-books but I'm afraid they are not as detailed as you would want :-)

Good luck!

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The answers to most of your questions are under active research and there are many unknowns. Understanding this process is one of the main goals of developmental biology. So, try to set reasonable goals for your project, mainly by seeing where you have sufficient data to work with.

I would start with reading some basic textbook on developmental biology.

Regarding the flow of information: Remember that starting from the zygote and onwards to the whole organism, the DNA sequence is generally the same between all cells. As a computer scientist it might help you to think about it this way:

Think of the DNA as a very complicated mathematical function $f()$ acting on cellular states. The current cellular state $S_i$ will be the total molecular components of the cell and will yield the biological function of the cell. So, you start with an initial cell state $S_0$ (could be a vector, for example) and then the daughter cells will be: $S_1=f(S_0)$, their daughter cells will be $S_2=f(S_1)$. This is not a perfect representation of the process (since at time point 2 you may actually have both $S_0$ and $S_1$ cells), but it emphasizes the point that although the DNA sequence "computes" the next step it is in fact constant, and the point that each cellular state dictates the next state. Seems to me like a Markov chain could be appropriate. Of course you can also try more sophisticated models - but it is better to start simple.

Also, I would suggest starting with C. elegans as your modeled species. This is because the full differentiation fate of each of its 1031 somatic cells is known - a remarkable achievement and something you will not have in other species.

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I would start with Developmental Biology, 9th Ed. It's not up to the absolute cutting edge, as it was published in 2010, but it has a lot of good stuff in it. Wikipedia is a decent resource to get very brief overviews on certain subjects, but a lot of the life science articles I've read tend to be lacking, as opposed to the physics and math articles, for example.

As for question 3, yes, the "data" is stored in DNA. For a thorough guide, one of my favorite books is Molecular Biology of the Cell, 5th Ed.. It's a little dated now (published in 2007), but if you want to understand how DNA, RNA, and proteins work, it's a great overview text.

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Note that the data is actually stored not only genetically (in the DNA sequence) but also epigenetically (e.g. modified chromatin). –  Bitwise Jan 2 '13 at 15:25
    
@Bitwise - yes, I know, but I figured a short, direct answer was the best here, as the questioner is obviously very new to this field. I could spend a long time talking about DNA sequences vs. DNA modifications, the contributions of histones and their post-translational modifications, and the overall structure and organization of the chromatin in general if you'd like :) –  MattDMo Jan 2 '13 at 20:15
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