Code center > Specialization, Metabolism, Digestions and Env Grid
Built-in Enzyme Regulation
shvarz:
I like this idea. It provides another benefit for keeping enzymes that work in the same chain in a single complex. And it encourages moving non-related enzymes away from each other (you don't want to stop protein degradation simply because there is too much fat-CoA...
What I don't like is the fact that more precise regulation will favor disassembling of complexes into single-standing enzymes (because then you can fine-tune each enzyme individually). But I guess we can live with it...
I would still prefer to keep enzymes sorted by molecules they work on. In cases where its A+B>C, we can just pick one of the substrates. Or we can have two versions.
P.S: I don't see a need for 32000 threshhold value, since it is maximal amount anyway, this just means there is no regulation. Is 12-bit molecule code long enough?
Zelos:
soudsn good to me
Numsgil:
--- Quote ---What I don't like is the fact that more precise regulation will favor disassembling of complexes into single-standing enzymes (because then you can fine-tune each enzyme individually). But I guess we can live with it...
--- End quote ---
We can offset this by rewarding reactions that take place on the same complex, as you suggested earlier. Then it's a balancing act.
Oooo, should make for some interesting enzymes.
--- Quote ---P.S: I don't see a need for 32000 threshhold value, since it is maximal amount anyway, this just means there is no regulation. Is 12-bit molecule code long enough?
--- End quote ---
32000 just seemed a logical point, but you're right, that's the same as no regulation.
So maybe we make 32000 no regulation and 0 always off.
I'm not sure how long everything needs to be. Too short and you have 17 regualation sites on the same complex that's only 20 bits long. Too long and you never develop them.
Keep in mind that 4 bits is a hexedecimal letter. So 12 bits sounds like alot, but it's only 3 digits in hex. I think we're underestimating what the length needs to be. Real complexes are very long. I don't want to go quite that long for obvious reasions, but there is certainly reason enough not to have the bare minimum.
PurpleYouko:
Here's a thought.
Why leave it in hex.
We could use the entire alphabet, even differentiate between cases.
I have a code system in one of my sample log spreadsheets that uses base 36 but that was just limited because people were unable to right it accurately if I went to base 64 or even higher.
If you want complete incomprehensibility to programmers then use a super condensed number base system.
Instead of 0 through 9 then A through f, we could have 0 - 9, a-z, A-Z for base 62. Add a period or a comma or some other symbols to round it up to base 64 and you can quickly and easily convert back and forth to binary.
Means much shorter words in the DNA too.
In this system
z=35
Z=63
ZZ=4095 or 111111111111 in binary (a 12 bit word)
(This is FFF in Hex)
whereas in Hex, the biggest you can get with two characters is
FF = 255 or 11111111 in binary (an 8 bit word)
Just a thought. Kind of interesting and extremely (deliberately) confusing as hell to programmers.
:D PY :D
Numsgil:
If we really want to ahve fun we could pick a non power of 2 base. Then the resultant bit string doesn't divide right into the storage letters.
Base 12 was popular because it was divisible by 2,3,4 and 6. Base 60 was really fun because it's divisible by 2,3,4,5,6,12,15, and alot of other numbers (this was back when people hated fractions and decimals weren't invented yet).
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