Author Topic: Genetic Metabolism  (Read 8435 times)

Offline PurpleYouko

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Genetic Metabolism
« Reply #30 on: March 22, 2005, 01:29:27 PM »
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we are going to have ~40-50 enzymes right now

I have a question here.
Are you
  • Specifying particular enzymes  that do one job?
  • Modeling multipe enzymes for each job, all with different efficiency rates?
  • Modelling a bit pattern for each enzyme and allowing the program to randomly try to match it through mutation?
  • Modelling mechanisms that Num and me (well Num mostly) have to figure out the best way to make a bit pattern system work with?
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Offline PurpleYouko

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« Reply #31 on: March 22, 2005, 01:35:27 PM »
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Also, I don't think the stomach should know which of the enzymes to use. If you have 10 fat digesting enzymes, each one can cleave n fat per cycle. The bot doesn't know which one does it better than others. Which one is used is random for each fat bit.

OK this is an interesting concept that I hadn't really thought of.

So are you saying that if the total bit pattern contains 50 sub patterns that are recognizable as enzymes by the program, that the bot will make all available enzymes in equal quantities?

If so then there will be a strong evolutionary drive to lose the ones that don't work too well in addition to getting better ones. It is obviously going to be more efficient to only make one good enzyme for a particular purpose (digesting fat) than to make one good one and a dozen cheesey ones that bairly work for the same purpose.

We should see robots with the bare minimum enzyme patterns with this method.

 :D  PY  :D
There are 10 kinds of people in the world

Those who understand binary.

and those who don't

:D PY :D

Offline Numsgil

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« Reply #32 on: March 22, 2005, 01:36:48 PM »
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I say we let 'em have as many as they want and if they can't afford them, tough! Evolutionary dead end!
That would be my thought.  Exactly how we charge for enzymes I'm still not sure on, but if you want to be an omnivore, and digest absolutely everything possible, it should be an option.  Remember that omnivores do actually exist in real life.  There are situations that call for it.

Offline Numsgil

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Genetic Metabolism
« Reply #33 on: March 22, 2005, 01:40:48 PM »
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...

We should see robots with the bare minimum enzyme patterns with this method.
That's the general idea I was after.  Reward minimalist bots.  The amount of reward is open to debate, but I would like to see a mechanism to prune inefficient patterns from the genome.  A spring cleaning incentive.

This of course only applies to activation sites on the same enzyme.  I may very well want to produce more of enzyme A than enyzme B.  But activation sites on an enzyme that cleve the same materials should be equally likely to work as each other.

Offline shvarz

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« Reply #34 on: March 22, 2005, 03:00:14 PM »
OK, I know this is open for discussion, so this is just my side of story:

   1. Specifying particular enzymes that do one job?

Right now I do one enzyme - one job.  The difference in efficiency will come from "3-bits on each end" idea of Num's, from enzyme complexes and from total amount of enzyme.

   2. Modeling multipe enzymes for each job, all with different efficiency rates?

No.  See above.

   3. Modelling a bit pattern for each enzyme and allowing the program to randomly try to match it through mutation?

No.  Enzyme function is hard-coded.  Again, see above.

   4. Modelling mechanisms that Num and me (well Num mostly) have to figure out the best way to make a bit pattern system work with?

Not sure what you mean.  As far as available enzymes, I just assume we'll have some kind of modification of Num's bit system.

P.S:  Jeez, I must do some work today.  But all these discussions make me wanna drop everything and present the metabolism I have to all of you.  But I don't want to rush it, cause if I explain it poorly, you all will hate it and all my work will go to waste :)
"Never underestimate the power of stupid things in big numbers" - Serious Sam

Offline Numsgil

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« Reply #35 on: March 22, 2005, 03:13:58 PM »
I'm not sure what your argument is.  Are you saying that one enzyme (meaning that string of bits.  What you call a complex) can't have multiple actiavtion sites for the same susbstance?

Offline PurpleYouko

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« Reply #36 on: March 22, 2005, 04:35:24 PM »
It's not an argument. I am simply trying to get to the point where we all understand exactly what the others are saying.

I have a strong suspicion that we are all thinking of more or less exactly the same thing but are describing it in different ways.

My questions today are mostly about descriptions rather than methods.

Shvarz answered the last few pretty well.
Quote
4. Modelling mechanisms that Num and me (well Num mostly) have to figure out the best way to make a bit pattern system work with?

Not sure what you mean. As far as available enzymes, I just assume we'll have some kind of modification of Num's bit system.

Not being sure actually answers the question effectively. It means that the concept has no clear idea of the bit pattern mechanism but just contains the metabolic mechanisms. That is just fine and I have no problem with that. It just means that it is now up to the programmers to fit the mechanisms into the game. It was Nums idea to use the bit pattern and I think I am coming to understand it pretty well now but it could still use a little explanation so here are a couple more questions/comments. (not arguments but clarifications)
  • How big is an activation site? Are we talking 4 bit (0000 through 1111 or 0 through 31 if you prefer decimal)? 5 bit? 1 more bit gives 64 combinations.
  • presumably the actual activation sites will be hard wired to specific bit patterns for specific functions and at birth, the whole pattern will be scanned and all sites found to match these patterns will be stored in an array such that multiple sites means higher efficiency. Right? or wrong?
    if 10101 represents the bit pattern of an activation site which cleaves fat then if this sequence is found 20 times in the pattern, that function will be 20 times more efficient?
  • I have been thinking in terms that what you are refering to as an activation site is an enzyme so the 10101 pattern would be the entire enzyme. In this scenario then I would most definitely be saying that an enzyme cannot contain more than one activation site since the whole thing is the activation site. Multiple enzymes with the same function sure. No problem there.
  • How will we define the start and end of each enzyme within the pattern if it contains many activation sites?
;)  PY  ;)
« Last Edit: March 22, 2005, 04:39:09 PM by PurpleYouko »
There are 10 kinds of people in the world

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and those who don't

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Offline Numsgil

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« Reply #37 on: March 22, 2005, 05:08:25 PM »
Okay, I'm going to try to answer what I can but we really need to use the same terms soon.  I'm willing to follow the concensus but as it is I think alot of cunfusion is arizing from terminology.

1.  I was imagining that activation sites are 8 to 11 bits long.  If we have 50 reactions, 8 bits means that roughly 1 of every 5 random bit patterns does soemthing, which is still really high in my opinion.  11 bits means 1 out of 40 actually does something, which is closer to the right direction.

Remeber that that's 1 out of 40 for any single 11 bit pattern.  Most enzymes (that long string of bits with ultiple activation sites) are probably like 50+ bits long.  In 50 bits you're bound to find some 11 bit long activation pattern.  I don't have time for a statistical test to find better numbers, but we can play around with it.

2.  Almost right.  Multiple sites don't mean that they are more efficient, just that there are more possible routes for any single substance to go through.

Say you have a 20%, 30% and 90%.  The efficiency of htat enzyme (or complex if you prefer) is the average, or 47%.  If something messes up the 20%, it will actually increaes the efficiency.  If something copies the 90% to another part of the enzyme, then it will increase the efficiency.  You get the idea.

4.  A pattern has no start or stop.  It's just a pattern.  101101 is an activation site, say.  Then whenever you can find 101101 in a bit pattern, that's an activation site.  If you have 101101101 as your pattern, you actually have two overlapping activation sites.