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Metabolism v.1.0

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shvarz:
8.  It would be VERY easy for me to include all glycolisis steps.  Question is whether we actually want it.  Let's make a poll to find out.  One diffuclty that I see is that since glycolisis will consist of multiple steps, it will require multiple enzymes.  Therefore it will be more costly to keep glycolisis - we shift the balance to other pathways.  The level of detail and complexity should increase proportionally in all pathways.  

9.  Certainly can be one of ways to do that.  Among others.

Numsgil:
We need a better word than A-CoA for acetyl coenzyme A.  I vote CoASH, since that's another way to write CoA, it sounds cool, is actually pronouncable, and 0easy to remember.

Numsgil:
8.

I'd vote to make the pathways as realistic as possible.  Organisms should favor whichever pathways give the most nrg.  If we do it right, we should see a very realistic evolution of organisms into the groups they're in now.

If we keep the details entirely hidden from the DNA, no one has to know how complex all this stuff is.  The enzymes will deal with it all automatically, allowing complex evolution without making it hard on the DNA programmers.

shvarz:
CoASH - it is actually not accurate.  Look at structures more.  Coenzyme A is CoA-SH, then it joins to acetyl and becomes CoA-S-Ac.  Wanna call it CoASAC?  I don't really care....

8.  As realistic as possible...  What a concept....  This will need a whole new sim program, cause those are crazily complicated.  I don't have enough competence to design stuff like this - it would involve chemistry, physics, advanced biochemisty, etc..  We need to chose a level at which we stop.

BTW, when you are coding the metabolism, you should make it possible to run metabolism simulations separately from the complete sim.  Basically like having an indivdual bot under a microscope with a command line.  You say "give 20 glucose" and watch the bot to go through hooplas with it.  It will achieve at least two goals:
1. debugging metabolism will be much easier
2. understanding metabolism will be much easier

Numsgil:

--- Quote ---CoASH - it is actually not accurate.  Look at structures more.  Coenzyme A is CoA-SH, then it joins to acetyl and becomes CoA-S-Ac.  Wanna call it CoASAC?  I don't really care....
--- End quote ---

I no CoASH isn't entirely acurate, since it doesn't involve the acteyl group, but I don't think we have another instance of Coenzyme A except as A-CoA, so why not call it CoASH?


--- Quote ---8.  As realistic as possible...  What a concept....  This will need a whole new sim program, cause those are crazily complicated.  I don't have enough competence to design stuff like this - it would involve chemistry, physics, advanced biochemisty, etc..  We need to chose a level at which we stop.
--- End quote ---

I just mean we have all the steps of the chemical reactions.  Basically just increasing the resoltuon of what you already have.  I think there are like 9 reactions in the Krebs Cycle.  We wouldn't need to go more in depth than that.

I don't imagine doing anything more than a freshman biologist would understand.


--- Quote ---It will achieve at least two goals:
1. debugging metabolism will be much easier
2. understanding metabolism will be much easier
--- End quote ---

Great Idea, I love it.

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