Author Topic: Metabolism  (Read 14374 times)

Offline Old Henk

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« Reply #15 on: October 28, 2005, 12:07:32 PM »
Quote
Part 9: Control from DNA

As a rule we are not going to encourage and even allow control of enzymatic functions from DNA.  After all, if I could willfully tell my enzymes to create muscle from beer that I drink, I'd be one tough guy :)
Would a bot (in the proposed system) have the ability to know it's own
  • Chemicals (amounts of)
  • Enzymes
through DNA commands?
« Last Edit: October 28, 2005, 12:07:55 PM by Henk »

Offline Numsgil

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« Reply #16 on: October 28, 2005, 12:11:00 PM »
I'm thinking not.  Better to have the DNA only vaguely aware of what's going on under the hood, and build a seperate control mechanism for what's under the hood.

More likely the bot could determine how slimey, shell-y, etc. it is instead of the amounts of each substance, etc.

Offline shvarz

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« Reply #17 on: October 28, 2005, 01:49:58 PM »
I agree.  It should be possible for a bot to tell its general energy state, but not exact amounts of chemicals.
"Never underestimate the power of stupid things in big numbers" - Serious Sam

Offline Numsgil

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« Reply #18 on: October 28, 2005, 03:41:02 PM »
Technical note:

Suposse substances are 3 bits (for clarity, but it applies to all numbers of bits).

000 and 001 can't react.  Why?  Because they can only form each other.

000 + 001 = either 001 + 000 or 000 + 001

which are identical as far as the bots are concerned.

Which means either we accept that there'll be a large number of reactions that can't happen, we set up reactions to involve more than two reactants (so 000 + 001 + 011 can react, say), or we allow more than one group to be transfered at once.

Unless you mean that all reactions are mono-substrate...  (that is, just one single substance is converted into one other substance).
« Last Edit: October 28, 2005, 03:42:44 PM by Numsgil »

Offline shvarz

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« Reply #19 on: October 28, 2005, 04:06:34 PM »
Yes, yes, yes!!! They are all monosubstrate.  They are all either gaining or losing 1 in one of the positions.

000 can turn into 001, 010 or 100  No need for second substrate.

The whole 0 and 1 concept is there just to facilitate the understaning of an N-dimentional cube with all the possible lines connecting 256 vortices of this cube.  The numbers themselves don't represent anything specific.
"Never underestimate the power of stupid things in big numbers" - Serious Sam

Offline Numsgil

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« Reply #20 on: October 28, 2005, 04:08:04 PM »
Ah, I see.  The article you showed me didn't do it like that, and well...

Makes sense now ;)

Offline Numsgil

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« Reply #21 on: October 31, 2005, 08:23:18 PM »
I played around with this on paper some during math class today.  I think it'll work, I just have to figure out some minor things...  Should be really interesting.  I'll probably make a working stand-alone version first.  That way we can play around with it and be sure it works jsut like we want before we add it into Darwinbots.

Offline shvarz

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« Reply #22 on: November 01, 2005, 12:34:55 AM »
Sounds so good, I don't know what emoticon to insert....

Have to go back to same old:  Mmmm, stand-alone version...   :drool:
"Never underestimate the power of stupid things in big numbers" - Serious Sam

Offline Numsgil

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« Reply #23 on: November 05, 2005, 05:35:32 PM »
Do we want the system to equilibriumilize (yep, that's a word now) in a single cycle or over multiple cycles?

Offline shvarz

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« Reply #24 on: November 05, 2005, 10:02:00 PM »
The whole system - definetly over multiple cycles.  In fact, the whole system is supposed to never reachequilibrium, as that would be a state where no energy canbe extracted and bot would die.  

Individual reactions come to equilibrium depending on their "enzyme amount", which is basically a rate constant.  If it is high enough, then reactions can come to equilibrium in a single cycle.
« Last Edit: November 05, 2005, 10:03:12 PM by shvarz »
"Never underestimate the power of stupid things in big numbers" - Serious Sam

Offline Numsgil

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« Reply #25 on: November 05, 2005, 10:51:32 PM »
Awesome, this just becamse a whole lot easier.

I bet I'll have a sample demo for this by the end of the week at the latest, depending on when I can find some time to get started.
« Last Edit: November 05, 2005, 10:52:02 PM by Numsgil »

Offline Numsgil

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« Reply #26 on: November 20, 2005, 02:54:01 AM »
Haven't forgotten about this...

Anyway, found these interesting articles on how the Creatures series handles metabolism:

First one.

Second one.

Obviously they're attempting it from the top down, and there seems to be a push in Darwnibots more for from the ground up...

Offline shvarz

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« Reply #27 on: November 20, 2005, 04:13:59 AM »
Yes Nums, as you certainly can notice thier approach is very close to what I proposed at first.  They introduce a number of chemicals with known properties and known effects of conversion of one molecule into another.  Then it's all about optimization of an existing system.

It's funny, looking at their system right now I can see just how far away I was from the system that DB really needs.  That system was definately not satisfactory for our purposes.

But for the purposes of a computer game it is perfectly fine, because the main goal of computer games is to entertain player, not to create some sort of of perfect imitation of life.  Perhaps the best explanation of this concept comes from Gabe Newell, creator of "Half-Life", who said someting along the lines of: "we tried to create AI that would look convincing to the player."  And their approach certainly succeded - the opponents felt quite human, even though their programming was very basic.  On the other side of the spectrum is "Black and White", which attempted to build AI from bottom up.  The aatempt was impressive, but resulted in a very poor gameplay.

Just different goals.  I suspect the new system will introduce so much complexity that newbies are just going to be blown away.  Just like real life, life in DB will suddenly become very fragile.  It is exciting and troubling at the same time.  Well, we can only tell ourselves that we are atetmpting something that's never been attempted before and enjoy that as much as we can...
« Last Edit: November 20, 2005, 04:15:41 AM by shvarz »
"Never underestimate the power of stupid things in big numbers" - Serious Sam

Offline Numsgil

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« Reply #28 on: November 20, 2005, 05:27:55 PM »
Was rereading that one article you posted a while ago that this is based on...

I'm curious as to what made you decide to chose monosubstrate reactions instead of whatever 2 half reaction reactions they were using.

They experimented with monosubstance reactions and concluded that the resulting graph is less complex...

Offline Numsgil

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« Reply #29 on: November 22, 2005, 04:27:21 PM »
I'm going through that article again with a fine tooth comb.  It makes more sense on the 10th read :P