Author Topic: Darwinbots enzyme system  (Read 41098 times)

Offline Botsareus

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Darwinbots enzyme system
« Reply #45 on: March 17, 2005, 06:08:49 PM »
Thats why I sayed lets make one system already, and then Add or Remove from it later.

Offline shvarz

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« Reply #46 on: March 17, 2005, 06:28:31 PM »
I just had a crazy idea.  I did not have time to think about it, so it is totally out of the blue.  But here it is anyway:

We actually code in the molecules as strings of bits.  Then enzymes will be self-defined as their strings of bits will define which molecules they convert to what.

Carbon has four oxidated states as part of carbs and we define them through three-bit system:

CH2 --> 111
CHOH -->110
CO --> 101
COOH -->100

Then glucose would look like this (I'll separate carbon atoms by periods, but in the program we would not do that):

101.110.110.110.110.110

In this system 000 would serve as a "space" that separates different "molecule-words"
And we can even have designations for
CO2 - 011
H2O- 010
O2 - 001

As I said, crazy idea.  But fun...
"Never underestimate the power of stupid things in big numbers" - Serious Sam

Offline Botsareus

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« Reply #47 on: March 17, 2005, 06:31:41 PM »
SHVARTZ THE MORE WE "TALK ABOUT IT" THE LONGER THE "ACTUAL CODING" IS BEING DELAYED , I THINK ITS  TIME FOR US ALL TO BE QUITE LONG ENUGH FOR THEM TO ACTUALY CODE 3.0 AND RELEASE IT. THEN WE CAN TALK ABOUT IT FOR 3.1 OR SO.

Offline shvarz

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« Reply #48 on: March 17, 2005, 06:49:38 PM »
Nah, I don't see this coming out it V.3, so that should not be a problem.  The enzymes and metabolism are pretty far in the future.  This is all just throwing ideas out there for people to ponder on...

At least I thought that's how it is.  Right Nums?  We are just going to have proteins/carbs/fats system in 3.0, right?

Adding metabolism would be just another huge feature that would warrant the next shift in version number (to 4.0).
"Never underestimate the power of stupid things in big numbers" - Serious Sam

Offline Botsareus

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« Reply #49 on: March 17, 2005, 07:05:53 PM »
Quote
The idea is that robots feed on the e-grid before they figure out how to photosynthesize or hunt for food. Don't forget that.

I think only Metabolism is going to let us do that. right?

P.S.

I have to Appreciate shvartz lest post. It’s the Govt. man
« Last Edit: March 17, 2005, 07:09:20 PM by Botsareus »

Offline Zelos

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« Reply #50 on: March 18, 2005, 05:16:01 AM »
shvarz, as ive understand it the mebo (MEtaBOlism) system will be in 3,0. and ur system, I think ive came up whit a simulare things and said it to numsgil, not exacly the same but simular. when its about gravity, it doesnt effect the spread of something aslongest its not to heavy, and are liquid or gas. I like the idea of toxic, like a bot who uses the sulfur photosythensis, CO2 + H2S + Light, should be toxiced by oxygen. if om not misstagen the oxygen steals some electron or something like that which sabotage the entire reaction. while some using water photo uses the oxygen and arent toxiced by it :D . what I think is that we make the system you have came up whit numsgil, enzymes is a hexacode, some things are toxic to some reactions, you can have alimited amount of 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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« Reply #51 on: March 18, 2005, 05:48:42 AM »
The Mebo system is the last bit thing I want to include in 3.0.  After that is done, a few minor fixes, what PY's been working on in graphics, and we'll be done I think.

Don't worry about delaying the programming.  I'm taking a break from the DB source code for a few days to learn OpenGL.

Having the individual substances have their own bit patterns is a cool idea.

I was going to do something similar to it when reactions are read it.  If each reaction is an enzyme, you'll need a way of making and remaking the same unique activation site bit pattern every time the program is run.

That involves some kind of hash function.

The only drawback to what you've listed is that it increases the length of activation sites.  Which means it more closely models real life, along with the real length of enzymes (very long indeed).  Which means it may be harder to evolve new enzymes.
« Last Edit: March 18, 2005, 05:50:47 AM by Numsgil »

Offline Zelos

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« Reply #52 on: March 18, 2005, 06:32:41 AM »
:( numsgil, I sugjested something simular and you didnt liked it :(

I cant wait for 3,0 :D will be so awesome
« Last Edit: March 18, 2005, 06:33:57 AM 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 Numsgil

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« Reply #53 on: March 18, 2005, 06:50:19 AM »
Really?  I must have misunderstood.

Offline Zelos

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« Reply #54 on: March 18, 2005, 12:16:07 PM »
yeah, but there I said for the atoms, like
S=001
H=101
then H2S would have 101,101,001 (,=to show its different atoms)
buts its basacly the same, instant of have to come up whit a bit code for each new reaction (I assume it will come more) you simply add them and then the program calculate what the bit code for it is, right now you would need 6 code, H,S,Fe,O,C,N is all the atomtypes ive seen, but for like carbs, fat and so it would need a customed code, but I think you get the idea. but if we use carbs to be like glucose it would have a long code. if we dont make it possible to tell the number after the type. glucose have the formula C6H12O6, if we say H=100, C=110 and O=101, the first 1 would represent its a element. and numbers would have the usual bit number, + a 0 in the front to tell its a number, like 1=01 2=010, you get the idea, so the bit number for glucose would be (once again ,=just to show its different things), 110,0110,100,01100,101,0110 its a long code but shorter than keep making c after c codes, this is just an idea, how you numsgil fix it whit programing I have no idea. think it could be hard making it seperate numbers from elements, unless it constanty check the list. that was my idea from the begining or something like that
« Last Edit: March 18, 2005, 02:24:49 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 Mathonwy

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« Reply #55 on: June 30, 2005, 12:34:34 PM »
Wow, interesting, and I'll have to admit I not sure I understand it all (in fact I'm pretty sure I don't). This suggestion seems to be progressing towards the idea of modeling the chemistry and reactions down to an atomic level, I might be wrong but doesn't that then introduce a whole set of rules to be added to cover what reactions are possible what atoms will form stable molecules, and if you start modeling that then would you need to introduce to the model the atomic structure of atoms, because the structure changes the properties ? For example Carbon; Diamond, Coal, Buckminster Fullerenes (carbon 60  - The surface is made from hexagons and pentagons and is an example of a semiregular solid called a truncated icosahedron) anything trying to use carbon will have to check it's current form and see if it has the energy to break that form, a headache waiting to happen I'm sure.

I'm sure the chemists amongst us could say far better than I if the rules governing such behaviour are simple enough to reproduce for modeling, however the question remains, is this level of detail required for what is being modeled ?

Thanks for reading,
Math.

Offline shvarz

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« Reply #56 on: June 30, 2005, 03:05:08 PM »
There are (at least) two possible approaches to model biochemistry in DBs:
1. Take real biochemistry as an example, copy reactions and allow bots to do only those reactions that we introduce.  This is a fairly easy approach and I think we managed to come up with a system, which would be open-ended - we can start with a small subset of reactions and slowly introduce new steps/pathways in a way that is backwards compatible.
2. The second approach is not to rely on real chemistry at all, but instead invent our own set of molecules and rules through which these molecules can interact.  Then allow bots figure out the biochemistry on their own.

Right now we are almsot set on the first approach, although I do like the second one too ( I am sure Carlo would go with the second approach as well, if that matters to anyone).
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Offline Carlo

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« Reply #57 on: July 01, 2005, 06:15:54 AM »
Quote
There are (at least) two possible approaches to model biochemistry in DBs:
1. Take real biochemistry as an example, copy reactions and allow bots to do only those reactions that we introduce.  This is a fairly easy approach and I think we managed to come up with a system, which would be open-ended - we can start with a small subset of reactions and slowly introduce new steps/pathways in a way that is backwards compatible.
2. The second approach is not to rely on real chemistry at all, but instead invent our own set of molecules and rules through which these molecules can interact.  Then allow bots figure out the biochemistry on their own.

Right now we are almsot set on the first approach, although I do like the second one too ( I am sure Carlo would go with the second approach as well, if that matters to anyone).

That's not what "open ended" means. Open ended means that you expect robot to figure out their own way to use molecules and even build new molecules that you never thought of. The approach of defining each single molecule in the world, and then describing all the possible reactions between them, with all the energetic balances, and so on, is used in simulations of biological processes. There it makes sense. In darwinbots it makes no sense at all. Why should we define sugars, water, carbon dioxide, and so on, when our organisms have a DNA written in reverse polish notation, their genes don't produce proteins or enzymes but values in a memory array? What's the meaning of "sugar" with respect to a computer program like db's DNA? Simply, no meaning at all.
I think that DB should be a good metaphor of nature, not bad copy. I mean, we should not copy from the real world things like sugar, carbon dioxide, etc. If we want to have something that recalls a chemistry in DB, then

a) it must be because we understand that some of the complexity lacking in DB comes in the real world from the existence of a chemistry - and not because we want to mock up nature
b) we should create something that makes sense in the universe of db, and can give the complexity we're looking for. It has not necessarily to have to do with sugar and oxygen and ATP; it must only give the desiderd complexity, in the context of the db general rules and principles
c) if - I say if- there will be a parallelism between the system created for DB and real chemistry, it has to come from DB, and not from nature. I mean, you should not put sugar in DB because in nature you have sugar; but you may _discover_ an element of the DB system that seems a good metaphor of sugar, and nickname it "sugar".
« Last Edit: July 01, 2005, 06:19:01 AM by Carlo »

Offline Greven

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« Reply #58 on: July 01, 2005, 06:42:36 AM »
I must agree on Carlo here. DB needs to selforganize the things it self ;) No fun in already knowing what the outcome would be.
10010011000001110111110100111011001101100100000110110111000011101011110010110000
011000011000001100010110010111101001110100110010111100101000001000001111001011101
001101001110011011010011100011110100111000011101100100000100110011010011100110110
010110000011100111101001110110111101011101100110000111101001101001110111111011101
01100100000111010011010001100001110111010000010001001000010100001

Offline Numsgil

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« Reply #59 on: July 01, 2005, 01:08:59 PM »
As far as I know, the environment isn't supposed to be self adapting.  The bots are.

The bots don't get to know what does what before hand.  So if we just assign a bunch of random substances and relationships, or carefully model every real reaction in the universe, the bots won't be able to tell the difference.

So I'm not sure I see your point.  Perhaps you didn't read through the document in the first post?