Author Topic: Metabolism  (Read 6206 times)

Offline Endy

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Metabolism
« Reply #15 on: September 21, 2005, 05:54:12 PM »
I was thinking that the reactions for plants and animals could produce different types of waste this way they couldn't feed from their own waste. We could probably just include waste types, as enzymes specified by the enzymes used initially to feed. Should make many more niches possible for the system as a whole.
« Last Edit: September 21, 2005, 05:54:52 PM by Endy »

Offline Numsgil

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Metabolism
« Reply #16 on: September 21, 2005, 06:33:21 PM »
The way the system described in the paper worked, there were many metabolites that were excreted as waste.  With a little tweaking I'm sure we could create a stable cycle between autotrophs and heterotrophs.

Offline d-EVO

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« Reply #17 on: December 07, 2008, 04:13:08 PM »
just an idea

maby add anothere factore like mineral and salt deposits.
plants will grow on them and depending on how much contact they make with the diposit and how much sunlight they recieve. they produce energy.
this will encorage plants to make "roots" in the soil and branches above for both minerals and sunlight.
as well as creating a more dinamic environment encoraging complex behavior to evolve. eg. tuneling ant bots.

plants cant make energy from sun alone. it simple stores the suns energy into molicules "nrg" which can be accesed by the plant or eaten by herbivores.
« Last Edit: December 07, 2008, 04:13:42 PM by d-EVO »
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Offline ikke

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Metabolism
« Reply #18 on: December 08, 2008, 03:19:50 AM »
Great minds think alike. Some time ago in a discussion on the simplicity of DB ecology I launched the idea of shapes having their own physics. Basically cost, movement type etc , mutation rate are a parameter of the shapes in the sim, not of the sim itself. Yesterday I was thinking that with this construct ion you can also expand the difference between plants and animals. If a shape has a concentration of nutrients and if the defining characteristic of plants is they can convert nutrients and energy into body by means of surface exposure to nutrients and energy we can do all sorts of fun stuff.
Water: shape with nutrients & energy both available. Plants possible
Soil: shape with nutrients only, high density / movement cost, no energy. No plantgrowth
Air: shape with low density / movement cost, no nutrients, energy only. No plantgrowth
Border between soil & air: plant possible bottom half of the plant gets nutrients, top half gets  energy, the plant converts it into body.
If energy is further defined as having a direction (pond and / or shading) there is a reason to develop MB veggies with roots and leaves
Animals are defined as having the ability to convert body into energy (-6  shots, strbody )or to steal energy (-1 shots), and by doing so forsake the ability to convert nutrients & energy into body

Offline Numsgil

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« Reply #19 on: December 08, 2008, 04:22:37 AM »
My ambitions are more temperate from 3 years ago, but I'm still playing around conceptually with this stuff.  It's tempting to implement some sort of photosynthesis metabolic pathway, and other metabolic pathways for animals, etc., but I'm also wary of making it complicated for the sake of complication.  I definitely like the idea of tunneling through shapes.  For antbots if nothing else.  Right not the bot-bot interactions are pretty rich but the bot-environment interactions are pretty weak.

Tunneling will probably work through ingestion, so I'm going to have to invent a new substance to represent what shapes are made out of.  I'm also tempted to allow for liquid shapes: essentially ponds I suppose.  The physics would be pretty cool if the bottom of the sim is liquid, and bots use buoyancy to rise and fall, and the top of the sim is more like what we have now, and bots have to fight gravity.  I'm still working through how the physics would work for a bot floating on the top of a liquid, but I think it's doable.  Anyway, those two could cover water and soil.

It's the last step that I'm hung up on.  I don't know that I like the idea of requiring water or soil or something like that for plants to photosynthesize.  It puts a real limit on the sort of sims that people can run.  And having those substances provide some sort of bonus (+25% photosynthesis) seems especially silly.  On the other hand, cycles are important for the healthy functioning of an ecosystem.  Carbon cycle, water cycle, etc.  So another idea is to require substances in addition to light to photosynthesize, and just have them ordinarily be omnipresent.

So I dunno, it's an interesting problem I'm still thinking about.

Offline ikke

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« Reply #20 on: December 08, 2008, 05:14:47 AM »
Quote from: Numsgil
Tunneling will probably work through ingestion, so I'm going to have to invent a new substance to represent what shapes are made out of.  I'm also tempted to allow for liquid shapes: essentially ponds I suppose.  The physics would be pretty cool if the bottom of the sim is liquid, and bots use buoyancy to rise and fall, and the top of the sim is more like what we have now, and bots have to fight gravity.  I'm still working through how the physics would work for a bot floating on the top of a liquid, but I think it's doable.  Anyway, those two could cover water and soil.
I haven’t looked at the pysics part of the code, to do for tonight. Is there any part I would need to look at in particular if I want to see what you already have?
Quote from: Numsgil
It's the last step that I'm hung up on.  I don't know that I like the idea of requiring water or soil or something like that for plants to photosynthesize.  It puts a real limit on the sort of sims that people can run.  ()  So another idea is to require substances in addition to light to photosynthesize, and just have them ordinarily be omnipresent.
To me this would be what I defined as a water shape; pretty much the current environment. So I don't see your comment with respect to complexity. As for the physics of metabolism: I'd leave it at nutrients (isn't this really an expanded version of waste?) and energy. Define a level of presence in the environment for each, and a ratio of consumption when transforming into body by veggies. I don’t know if I created a wrong impression, but to me water was a medium, like soil and air, not a part of metabolism.
I'd not go for modeling the integral ATP ADP cycle. If this was the original idea I do see your point about complexity.

Offline Numsgil

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« Reply #21 on: December 08, 2008, 08:21:44 AM »
Quote from: ikke
I haven't looked at the pysics part of the code, to do for tonight. Is there any part I would need to look at in particular if I want to see what you already have?

Nothing much in the code right now.  I have a C++ version I was playing with, that I'm slowly copying from to fill out the C# version.

Quote
To me this would be what I defined as a water shape; pretty much the current environment. So I don't see your comment with respect to complexity. As for the physics of metabolism: I'd leave it at nutrients (isn't this really an expanded version of waste?) and energy. Define a level of presence in the environment for each, and a ratio of consumption when transforming into body by veggies. I don't know if I created a wrong impression, but to me water was a medium, like soil and air, not a part of metabolism.
I'd not go for modeling the integral ATP ADP cycle. If this was the original idea I do see your point about complexity.

Yeah, the original idea was to model some complex metabolic cycles analogous to the critic acid cycle.  But I'm not going down that route anymore.

The bot environment right now, under default settings, is more like air or even vacuum.  There's very little reactive forces.  The idea I'm playing with is for the users to be able to define specific shapes with some custom parameters.  They could make them solid, like they are now, or play with some other settings.  Making them a dense liquid would let bots use buoyancy to float and sink, etc.  I'm playing with the idea that bots could gather abiotic resources from shapes when they dig into them, and use those as raw materials for various things.  The other option is for the user to specify how saturated shapes are in various resources when they set up the custom parameters.

I want to shy away from hard defined things like "this is a water zone, therefore it has properties X Y Z", because I think it's too artificial.  I much prefer lots of tweakable parameters and a few defaults to set them to.  So you could create a shape, set it to some default (loose soil, water, granite, etc.), then tweak parameters as desired.

I'll probably end up creating 1-3 abiotic resources, and incorporate them into the manufacturing process for various components and photosynthesis.  Like maybe you need dirt/rock/soil/whatever to make shell with, or you can make shell without it but you have to manufacture some extra components first, or something like that.  On the other hand, by default I don't want sims to have issues with bots being unable to create shell because every single shape has been mined by other bots already (though it might be a fun custom sim).

Then, with those 1-3 abiotic resources, we need a process whereby bots can extract the resources.  For a solid shape, they could just ingest some of the shape (useful for tunnelling, too), digest the good bits, and poop out the waste.  For a fluid shape they'd do something similar but maybe there's diffusion to deal with, so a bot would have a hard time (diminishing returns) extracting all the useful raw materials from a fluid  shape.  The trick is to decide if the useful resources are the shape, or if they're embedded in the shape and most of the shape is just junk.

Ah, I'm rambling.  Just consider it a brain dump of what I'm thinking right now.

Offline d-EVO

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« Reply #22 on: December 08, 2008, 09:11:56 AM »
That is exactly what I had In mind
Will make a small diagram to illistrate it to others
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Offline ikke

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« Reply #23 on: December 08, 2008, 09:45:17 AM »
Quote from: Numsgil
Nothing much in the code right now. I have a C++ version I was playing with, that I'm slowly copying from to fill out the C# version..

Four letter word starting with an F. I'll have to wait and have a look at that next time I'm able to use SVN (which is at home).
Quote from: Numsgil
I want to shy away from hard defined things like "this is a water zone, therefore it has properties X Y Z", because I think it's too artificial.  I much prefer lots of tweakable parameters and a few defaults to set them to.  So you could create a shape, set it to some default (loose soil, water, granite, etc.), then tweak parameters as desired.

Of course, Otherwise you’d need specific rules for every variation.
Quote from: Numsgil
I'll probably end up creating 1-3 abiotic resources, and incorporate them into the manufacturing process for various components and photosynthesis.  Like maybe you need dirt/rock/soil/whatever to make shell with, or you can make shell without it but you have to manufacture some extra components first, or something like that.  On the other hand, by default I don't want sims to have issues with bots being unable to create shell because every single shape has been mined by other bots already (though it might be a fun custom sim).

I was thinking the other way around: not a shape with a predefined amount, but with a contant concentration (infinite supply). Combining the two: initial amount and replenishment rate gives all the freedom. Complexity increasing…
Quote from: Numsgil
Then, with those 1-3 abiotic resources, we need a process whereby bots can extract the resources.  For a solid shape, they could just ingest some of the shape (useful for tunnelling, too), digest the good bits, and poop out the waste.  For a fluid shape they'd do something similar but maybe there's diffusion to deal with, so a bot would have a hard time (diminishing returns) extracting all the useful raw materials from a fluid  shape.  The trick is to decide if the useful resources are the shape, or if they're embedded in the shape and most of the shape is just junk.

Ah, I'm rambling.  Just consider it a brain dump of what I'm thinking right now.

Complexity increasing even further…. Simple rules complex behaviour, not the other way around. Don’t know where we are on the scale at this point
« Last Edit: December 08, 2008, 09:48:57 AM by ikke »

Offline d-EVO

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« Reply #24 on: December 08, 2008, 10:56:06 AM »
Ok here it is

tunnels will be difficult with db2 which is 2d. no factor like tunnel wall to hold up roof
3d would be easier.

Nutrients from the soil must be prescent in the leaves to photosynthisize
watar must be prescent in soil to form solution that can be absorbed by the plants.
surface area will be a top priority like in real life.
single cells are capable of being auto trophes but wont be very efficient. like alge.
will encourage complexity because of the need to transport nutrients into differt parts of the organism.

roots will be very vunerable to attack encouraging bots to tunnel into the soil.
wery small cells will be capable of remaining airborn.

will at least make it theoreticaly possable to evolve life like we have on earth

note. the green cells contain chloryphyll (photosynthesis). brown cells collect nutrients, and the lime cells transport nutrients
« Last Edit: December 08, 2008, 10:58:11 AM by d-EVO »
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Offline SlyStalker

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Re: Metabolism
« Reply #25 on: March 10, 2013, 01:08:08 AM »
I agree with this model but we should still have a 'pond mode' because it will be very complex to have MBs that can coordinate well with the added pressures of gravity :/
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Offline Botsareus

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Re: Metabolism
« Reply #26 on: November 29, 2014, 07:17:22 PM »
This will be cool for db3.

Offline Botsareus

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Re: Metabolism
« Reply #27 on: November 29, 2014, 07:54:09 PM »
More constructively, if you add it to db3 it is going to blow db2 chemical algorithms out of the water. Chloroplasts and all.

Note that I got db2 chloroplasts reasonably balanced out.

Offline Numsgil

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Re: Metabolism
« Reply #28 on: December 04, 2014, 07:16:23 PM »
This will be cool for db3.

This has been on my mind since 2005.  Thinking about it all this time, I've come to the conclusion that I think it's outside the scope of Darwinbots.  Here's why: in the real world, metabolism is highly conserved.  The way we break down or build up sugars and proteins and fats is pretty much the same way that a yeast does.  That is, metabolic pathways evolved once, billions of years ago, and ever since it's been the base level on to which everything else is built.  In a certain sense, it's like the OS life is written for.

Darwinbots is more about behavior than ability.  That is, the DNA scripts we write are concerned with when to shoot, or reproduce, or spin, or move, and not how.  Evolving metabolism is fundamentally a question of how.  Once you know how, that is, once the metabolite graph has been mapped and you know the most efficient ways to get from A to Z, anything outside that pathway is "wrong".  So bot authors would know the "correct" solution and always use it.  Evolved bots would have to figure it out, but it's just an arbitrary hoop to jump through before you can get to the far more interesting questions of strategy and how to compete against other bots.

Not to say that I don't think this sort of thing is interesting.  It is.  But it's not interesting in a gameplay sense.  It's interesting in a computer science sense.  There's an arbitrary directed graph and you want to find the most efficient nodes to do certain things, and the best ways between them.  That's a problem, and there's a specific solution, and finding the solution is non trivial.  But once you have it, you have it and it's done and solved.  Contrast that with deciding when to reproduce.  There's no "right" solution.  Each choice of when to reproduce carries with it different strategies and implications, and it works to create an gameplay decisions for bot writers, and an interesting landscape for bots to evolve on.

Offline Botsareus

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Re: Metabolism
« Reply #29 on: December 04, 2014, 07:40:33 PM »
Good one. Later.