Code center > Specialization, Metabolism, Digestions and Env Grid
Darwinbots enzyme system
Mathonwy:
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.
shvarz:
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).
Carlo:
--- 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).
--- End quote ---
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".
Greven:
I must agree on Carlo here. DB needs to selforganize the things it self ;) No fun in already knowing what the outcome would be.
Numsgil:
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?
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