Author Topic: What reactions we want to have?  (Read 5059 times)

Offline shvarz

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What reactions we want to have?
« on: March 20, 2005, 05:52:22 PM »
I am working on designing a metabolism for DBs.  I am going to stick my head out and guess that my make/break system together with Nums' enzyme systems will be accepted and coded into the next version, allowing all this metabolism to happen in DBs.  So I am asking here, what molecules do we want to have in metabolism at this point? (remember, the system will be open-ended and will allow to easily add more molecules later).

So far I have included steps for making the following molecules from energy

1. Fat (good energy-strage compound)
2. Carbs (good energy storage, but take up a lot of space)
3. Protein (cost a lot, poor energy recovery, but allow creation of muscles, enzymes, venom, poison, shell and slime)
4. Production of urea or "waste"

I am also planning to add the following things:

4. Photosynthesis reaction
5. Creation of muscles, enzymes, venom, poison shell and slime

I've heard suggestions to add lignin, cellulose, chitin.  I am not sure about the usefulness of that.  These are all analogous to "shell" in their properties and we already have "shell" molecule.  I see a possibility of making "shell" a property of molecules (instead of it being a molecule itself).  Some molecules would provide a lot of "shell" (chitin, lignin, cellulose), others - little or none at all (fat).  So the total "shell" amount is counted from all molecules that bot has and then is used to deter incoming shots.  Please don't discuss this in this thread, make a separate one.

I also know that many people want to have anaerobic energy-producing reactions.  I can add that, but please realize that these reactions are very inefficient.  For example, if you break down glucose in aerobic conditions - you get ~120 ATPs.  But if you break down glucose in anaerobic conditions, you only get 2 ATPs.  This means that all your anaerobic-style bots will be barely alive.
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Offline PurpleYouko

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What reactions we want to have?
« Reply #1 on: March 20, 2005, 06:28:54 PM »
Sounds good.

I say that we definitely have to differentiate between animal meat and vegetable tissue. Call it protein versus Cellulose or whatever but an important issue is that animals and veggies should not be digested with the same enzyme. That way we can get specialized plant eaters, carnivors and something in between

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Offline Zelos

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What reactions we want to have?
« Reply #2 on: March 21, 2005, 12:54:05 AM »
sounds good, but have you included all the other chemical reactions, like the Fe one, the sulfur photosytensis and stuff like that?
When I have the eclipse cannon under my control there is nothing that can stop me from ruling the world. And I wont stop there. I will never stop conquering worlds through the universe. All the worlds in the universe will belong to me. All the species in on them will be my slaves. THE ENIRE UNIVERSE WILL BELONG TO ME AND EVERYTHING IN IT :evil: AND THERE IS NOTHING ANYONE OF you CAN DO TO STOP ME. HAHAHAHAHAHAHAHA

Offline PurpleYouko

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What reactions we want to have?
« Reply #3 on: March 21, 2005, 09:09:06 AM »
That is a good point Zelos.

We really need these lesser used reactions like the Sulfer system so that we can model specific environmental niches like black smokers.

Another thing we are going to need at some point is temperature ranges for robots. They will need to be able to tell temp from the grid and decide if they can survive at that level. Temperature survivability is another feature that will need to be evolved somehow.

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Offline shvarz

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What reactions we want to have?
« Reply #4 on: March 21, 2005, 10:46:45 AM »
OK, I'll add the sulfur reaction.  But how can we model the sensitivity of that reaction to oxygen?  I will just assume that program will check if oxygen is around and "kill" the enzyme.  I'll label the oxygen-sensetive reactions as such.

About temerature adaptation.  We can always say that another two bits around the enzyme sequence would code for "temperature resistance".  The beauty of Nums system is that we can add more and more of these things if necessary :)
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Offline PurpleYouko

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What reactions we want to have?
« Reply #5 on: March 21, 2005, 10:56:15 AM »
So we just make it such that certain reactions (enzymes) are non-functional (or less functional) in different environmental conditions.

I am sure that some Sulfer reactions must be able to work with Oxygen present though. I don't think black smokers have zero oxygen around them. The heat must create convection currents that will bring in dissolved oxygen all the time, yet the creatures there manage to metabolize the sulfur quite happily.

I really like this bit pattern system that Num came up with.

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Offline shvarz

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What reactions we want to have?
« Reply #6 on: March 21, 2005, 11:02:52 AM »
That's why I thought that including gases was a problem...  Of course there is "some" oxygen around.  But there is very little and cells find ways to protect themselves.  Some build protective shells, others use up the oxygen as soon as it comes in.  When these organisms flourished, there was very little oxygen around.  Now they are marginalized.  And it is a matter of efficiency - some oxygen comes in, kills enzymes, but cells make more and so on.

You know, using sulfur sounds cool, but in essense it is exactly the same reaction as regular photosynthesis, only with different electron acceptors.
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Offline Zelos

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What reactions we want to have?
« Reply #7 on: March 21, 2005, 01:57:46 PM »
wanna hear a funny things guys? ive allready sugjested temperature to numsgil by msn :D and I think he said he liked it. but if we want the enzymes to be sensetive to things, we can add pH also.

and shvarz, they used sulfur in the begining, why I dont know. but when they started using water they got something much better, O2 which could be used to get even more energy from glucose.

anyway, back to sensetivity. if you want reactions to be sensetive to things, you can add a "periodic table" whit all the elements and some stats.

like "thingy" (thingy just poppeed up in my head) where O can have 5 and S 3, so when O is present the sulfur reactions have problems but isnt completly helpless, if there is 5 S reactions and there is only 2 O there would still be 3 capable of working. and so on, in that way you can make reactions not work perfect whit certain elements, you can add more stuff if you want.

 and when it comes to temperature. we would need a temperature scale, celsius (ever played ToS?) or something we make up. could simply call the thing we make up for DB, man its 50┬░DB here :P . and then use some bits in the enzyme that tells the maximum and minimum temperature, and the closer thje temperature is to the value beetween max and min, the better it worx.

 if there is a big glap between max and min the enzyme cost alot, whit a little glap cost much less. And if we want pH, we could do the same, but there we dont need the same amount of bits. the original pH scale goes from -2 to 16, but to remove the - we can make it 0-18, or even if we want 0-10 to make it even easier (why am I simplefieng when I hate it?).

 whit all this we come whit that the sensetivity of chemicals is decieded by a periodic table, the sensitivity of pH and Tmp (temperature) is decieded by the code. if you guys want I can come up whit the tmp system and the pH to, I would love doing it.

 plz let me do it, my brain have had nothing challenging to do for a weekend. how about this system?

Numsgil inserted paragraph breaks. whit out zelos knowing anything :angry:
« Last Edit: March 22, 2005, 02:59:41 PM by zelos »
When I have the eclipse cannon under my control there is nothing that can stop me from ruling the world. And I wont stop there. I will never stop conquering worlds through the universe. All the worlds in the universe will belong to me. All the species in on them will be my slaves. THE ENIRE UNIVERSE WILL BELONG TO ME AND EVERYTHING IN IT :evil: AND THERE IS NOTHING ANYONE OF you CAN DO TO STOP ME. HAHAHAHAHAHAHAHA

Offline Zelos

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What reactions we want to have?
« Reply #8 on: March 22, 2005, 02:29:52 PM »
take a look here and read
When I have the eclipse cannon under my control there is nothing that can stop me from ruling the world. And I wont stop there. I will never stop conquering worlds through the universe. All the worlds in the universe will belong to me. All the species in on them will be my slaves. THE ENIRE UNIVERSE WILL BELONG TO ME AND EVERYTHING IN IT :evil: AND THERE IS NOTHING ANYONE OF you CAN DO TO STOP ME. HAHAHAHAHAHAHAHA

Offline Botsareus

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What reactions we want to have?
« Reply #9 on: March 22, 2005, 02:31:02 PM »
I did , but I think they are taking time to comprehand it....

Offline Numsgil

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What reactions we want to have?
« Reply #10 on: March 22, 2005, 02:54:31 PM »
I've been for temerature since the old forum where we discussed cold and warm blooded animals.

pH is pointless, IMO, but then I'm no chemist.

I imagine that the sensitivy of a pathway is defined not by the enzyme but by the environment.

Offline Zelos

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What reactions we want to have?
« Reply #11 on: March 22, 2005, 02:56:08 PM »
it is very important that its the right pH for enzymes
When I have the eclipse cannon under my control there is nothing that can stop me from ruling the world. And I wont stop there. I will never stop conquering worlds through the universe. All the worlds in the universe will belong to me. All the species in on them will be my slaves. THE ENIRE UNIVERSE WILL BELONG TO ME AND EVERYTHING IN IT :evil: AND THERE IS NOTHING ANYONE OF you CAN DO TO STOP ME. HAHAHAHAHAHAHAHA

Offline Numsgil

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What reactions we want to have?
« Reply #12 on: March 22, 2005, 02:57:22 PM »
in real life yes, but what will adding pH add to the simulation?

Offline Zelos

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What reactions we want to have?
« Reply #13 on: March 22, 2005, 03:01:15 PM »
more specialization :D now we got that bot who likes that tmp and that pH and we got anbother bot whit the same tmp but different pH, they cant live toghaterm either to acid or basic for one or another
When I have the eclipse cannon under my control there is nothing that can stop me from ruling the world. And I wont stop there. I will never stop conquering worlds through the universe. All the worlds in the universe will belong to me. All the species in on them will be my slaves. THE ENIRE UNIVERSE WILL BELONG TO ME AND EVERYTHING IN IT :evil: AND THERE IS NOTHING ANYONE OF you CAN DO TO STOP ME. HAHAHAHAHAHAHAHA

Offline Botsareus

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What reactions we want to have?
« Reply #14 on: March 22, 2005, 03:02:04 PM »
I think its one of these cases....

Earlyer zelos sayed
Quote
well, right now I got no problem exept im bored which result in that I argue for things I either dont care about or something I dont like, in this case, something I dont care about