Author Topic: Darwinbots enzyme system  (Read 16537 times)

Offline Numsgil

  • Administrator
  • Bot God
  • *****
  • Posts: 7715
    • View Profile
Darwinbots enzyme system
« Reply #15 on: March 16, 2005, 11:00:12 PM »
I want complexity!

Chemistry was never my thing.  I understand it in theory, but I always get muddled in the details.

I'd like the terrestrial variety and whatever they're using in the deep sea black smokers.

Oh, and I should say please.  Don't forget the magic word ;)
« Last Edit: March 17, 2005, 10:33:20 AM by Numsgil »

Offline Botsareus

  • Society makes it all backwards - there is a good reason for that
  • Bot God
  • *****
  • Posts: 4483
    • View Profile
    • DJ Paul Kononov
Darwinbots enzyme system
« Reply #16 on: March 17, 2005, 10:42:05 AM »
Why? Is Shvartz trying to simplify things again? It's still all crazy to me so...

Offline shvarz

  • Bot God
  • *****
  • Posts: 1341
    • View Profile
Darwinbots enzyme system
« Reply #17 on: March 17, 2005, 11:14:07 AM »
If I understand correctly, the system is going to be quite open, so we can start with basics now and add more reactions later.  Thing with metabolism is that everything depends on everything and complexity increases exponentially (maybe even steeper).  

I thought some more about this enzyme system.  I'm with PY thinking that this system actually much better represents my "mutation accumulation" theory than your "pleiotropic effect" theory.  Imagine a basic enzyme that has only 14 bits, with middle 8 bits representing the "enzyme" and three on each side to define its efficiency.  Given enough slective pressure such enzyme would mutate pretty quickly to gain maximum possible efficiency, as there are no disadvantages to that.  It is going to be very cheap and very good.  So the optimal set of enzymes would reduce to a set of short enzymes that are very good.  The best organism will be the one that has enzymes to eat pretty much any type of food available in the system.  And it would not even pay that much for them (enzymes are very short).

The balancing effects that you describe come from overlapping enzymes, but there is little incentive for bots to keep them overlapped.  We can make the incentive bigger if we make all enzymes to be in a single line of bits.  Then non-overlapping enzymes will make the line too long and bots will be forced to have overlapping sequences.  Say we have total of 20 enzymes available and we design costs of enzyme production to be unreasonably expensive for a string over 140 bits.  This will make impossible for bots to have more than 10 non-overlapping enzymes and hopefully will force them to start overlap enzyme sequences.
"Never underestimate the power of stupid things in big numbers" - Serious Sam

Offline Botsareus

  • Society makes it all backwards - there is a good reason for that
  • Bot God
  • *****
  • Posts: 4483
    • View Profile
    • DJ Paul Kononov
Darwinbots enzyme system
« Reply #18 on: March 17, 2005, 11:23:51 AM »
Quote
Given enough slective pressure such enzyme would mutate pretty quickly to gain maximum possible efficiency, as there are no disadvantages to that. It is going to be very cheap and very good. So the optimal set of enzymes would reduce to a set of short enzymes that are very good. The best organism will be the one that has enzymes to eat pretty much any type of food available in the system. And it would not even pay that much for them (enzymes are very short).

I think thats a Perfict system Shvartz! Why dont you think so?

I love very cheap and very good , because the robots still have to win agenst each other right? They are not figting you shvartz right? I mean all you do is make up cheat codes , but you not even fighting them.
« Last Edit: March 17, 2005, 11:26:30 AM by Botsareus »

Offline Numsgil

  • Administrator
  • Bot God
  • *****
  • Posts: 7715
    • View Profile
Darwinbots enzyme system
« Reply #19 on: March 17, 2005, 11:31:04 AM »
Okay, so we're basically in agreement to limit the total number of enzymes a bot can have?  I'm not sure how enzyme length and cost should correlate.  Either linearly or exponentially, or maybe some other system.

20 may be too many enzyme slots.  I'm really not sure.  I really have no idea how natural selection would affect them.  Having a single enzyme that can be infinitely long is an interesting idea.  I would say something like 7-13 enzyme slots would be about right, depending on how in depth and detailed we make digestion.

Offline Botsareus

  • Society makes it all backwards - there is a good reason for that
  • Bot God
  • *****
  • Posts: 4483
    • View Profile
    • DJ Paul Kononov
Darwinbots enzyme system
« Reply #20 on: March 17, 2005, 11:32:44 AM »
How may enzime slots do real organisms have?

Offline shvarz

  • Bot God
  • *****
  • Posts: 1341
    • View Profile
Darwinbots enzyme system
« Reply #21 on: March 17, 2005, 11:35:49 AM »
Yeah, limiting the number of slots is another way to approach this.  I agree.

P.S:  In some thread someone asked if any scientists are interested in DBs.  I am a scientist, so there you go :)  As I said, as soon as new version comes out I'll advertise it to my buddies.  Would be nice to update the web-site too (I could do that if no one else wants, but I'll need to get access).  Is Carlo still around?
"Never underestimate the power of stupid things in big numbers" - Serious Sam

Offline Botsareus

  • Society makes it all backwards - there is a good reason for that
  • Bot God
  • *****
  • Posts: 4483
    • View Profile
    • DJ Paul Kononov
Darwinbots enzyme system
« Reply #22 on: March 17, 2005, 11:39:25 AM »
Quote: "It's still all crazy to me so... "

I did try to asking some qustions to figure it out, but it looks like they are ignoring me through the whole forum tuday not only in this thread.

Offline Numsgil

  • Administrator
  • Bot God
  • *****
  • Posts: 7715
    • View Profile
Darwinbots enzyme system
« Reply #23 on: March 17, 2005, 11:51:13 AM »
It's because you keep asking questions we've already discussed at length...

1.  Schvarz is not trying to simplify things necessarily, he's just hashing out how the system would work.  There are still a few fine points that need to be reviewed.

2.  Real organisms have, it seems, infinite enzyme slots.  Schvarz posted two very good links on two different theories on eating digestion and specialization not more than a day or two ago.  I'm too lazy to find the exact posting...

3.  'It's still so crazy to me'.  I hate it when people ask general questions.  'I don't get it.'  'Huh?' 'That doesn't make any sense'.  "Can you explain it again."

I'll answer all those general questions for you here with my own general answers:

1. It's not crazy.
2. Tough
3. No, I can't explain it again.

If you want a better answer, ask a specific question.

like:

"Gee Numsgil, I don't understand how the program interprets the enzymes.  Is it possible for activaton sites to overlap?"

-or-

"I don't understand what you mean by a string of bits.  Sounds like some kind of candy necklace to me.  Mmm... candy."

Then I can answer you and address your concerns.
« Last Edit: March 17, 2005, 11:51:39 AM by Numsgil »

Offline Botsareus

  • Society makes it all backwards - there is a good reason for that
  • Bot God
  • *****
  • Posts: 4483
    • View Profile
    • DJ Paul Kononov
Darwinbots enzyme system
« Reply #24 on: March 17, 2005, 11:54:41 AM »
Hmm \\ I was only asking how many enzimes real organisms have

'well then I gess each slot must be really simple in real organisms and in our system we make it more complex if we want to have only 7 slots
« Last Edit: March 17, 2005, 11:55:19 AM by Botsareus »

Offline shvarz

  • Bot God
  • *****
  • Posts: 1341
    • View Profile
Darwinbots enzyme system
« Reply #25 on: March 17, 2005, 11:55:17 AM »
Bots, if we wanted, it would be extremely easy for us to make perfect bots.  Take alga minimalis, throw it in the sim alone and give it plenty of food - it will conquer the world.  The point is not to create bots that are very good in environment that we give them, but bots that represent real life with all its imperfections, balances and tradeoffs.  The system that we have right now allows creationf of "cheap and good" bots, but no one is absolutely happy with it.  It's the other way around - everyone (including me) wants to make life more difficult and complicated for bots, because harsh and complex conditions lead to appearance of specilized and complex bots.  Does it make sense?
"Never underestimate the power of stupid things in big numbers" - Serious Sam

Offline Botsareus

  • Society makes it all backwards - there is a good reason for that
  • Bot God
  • *****
  • Posts: 4483
    • View Profile
    • DJ Paul Kononov
Darwinbots enzyme system
« Reply #26 on: March 17, 2005, 11:57:29 AM »
ok , teaches me not to talk were people are talking about stuff I dont understand. Don't reply , I still have a problem in "Advanced Randomness Generation Thread" we need to sort out.

Offline Zelos

  • Bot Overlord
  • ****
  • Posts: 707
    • View Profile
Darwinbots enzyme system
« Reply #27 on: March 17, 2005, 03:22:13 PM »
I like the system numsgil have came whit, cant see any problems whit it. If it cost to have many enzymes active and have big enzymes the bots wont allways create as many possible. but still there shall be a limit, I think less than 10, feels best. thats a amount which I think would force them to specialize. buts numsgil, why do you have 2 reactions whit H2S + CO2? sounds kinda stupid unless the 1 whit light gives 2 carbs. how about this list:
Light + CO2 + H20 -> 3 carbs + O2
Light + CO2 + H2S -> 2 carbs + H20 + S (poisoned by O2)
S + H20 + O2 -> 2 SO4 + nrg
H2S + CO2 -> S + H20 + carbs (or nrg)
FeS + H2S -> FeS2 + nrg
NH3 + 3O2 -> NO2 + H20 + nrg
NO2 + O2 -> NO3
carbs + O2 -> 5 nrg
carbs -> nrg (lifge can break down glycose by it self to get energy, not much but some)
digesting fats -> fats
digesting nrg -> nrg
digesting carbs -> carbs
metablozing poison
digesting muscles -> proteins
digesting proteins -> proteins
digesting limestone(calcium) to use in shell
digesting silicate to use in shells
digesting slime -> carbs
digesting protiens -> NH3 + CO2 + nrg + aminoacids
NO3 + carbs + aminoacids-> proteins
protein + nrg -> muscle
amino acids -> nrg

how about it?
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

  • Administrator
  • Bot God
  • *****
  • Posts: 7715
    • View Profile
Darwinbots enzyme system
« Reply #28 on: March 17, 2005, 04:05:21 PM »
We can figure out the reactions as we go along.  Ideally the enzyme sytem will exist independantly of the reactions.  (If that just blew your mind, get off crack :P)

Offline shvarz

  • Bot God
  • *****
  • Posts: 1341
    • View Profile
Darwinbots enzyme system
« Reply #29 on: March 17, 2005, 04:15:40 PM »
I am still not covinced about the benefits of having O2, CO2 and H20.  The change in atmosphere took millions of years, we are not even approaching this level of modeling.  

Are you thinking about having these in env.grid?  With what values (how much per location)?  CO2 does not exist in form of gas in the water, how are you going to approach that?  

I think we should just assume that there is enough of each in the sim, so that bots don't have to worry about that.  Maybe have "aerobic/anaerobic" checkmark in options.

And why are people so hot on oxidizing sulpher/iron?
"Never underestimate the power of stupid things in big numbers" - Serious Sam