Author Topic: Darwinbots enzyme system  (Read 16411 times)

Offline Numsgil

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Darwinbots enzyme system
« Reply #30 on: March 17, 2005, 04:17:38 PM »
I really wanted to model deep sea trenches, with the tube worms and everything.  Call it a fetish.

I was originally against gases.  Now I have no feelings either way.
« Last Edit: March 17, 2005, 04:18:03 PM by Numsgil »

Offline Botsareus

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« Reply #31 on: March 17, 2005, 04:49:06 PM »
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 also feel we should just get Num's system coded and then release it to the public if people don't like somthing about it then we will change it later.

Offline PurpleYouko

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« Reply #32 on: March 17, 2005, 04:56:32 PM »
Quote
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.

What if you want aerobic and anaerobic in the same sim?

I always think of DB in terms of water so I would see the gasses as being dissolved in water at varying concentrations. They would be stored in various different levels of the e-grid.

I haven't really given that much thought to the mechanics of it yet.

 :D  PY  :D
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Offline Numsgil

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« Reply #33 on: March 17, 2005, 04:58:33 PM »
Problem is right now 'my system' is a handful of really silly reactions (zelos caught a duplicate even).

schvarz, I'm serious on this (or anyone else who wants to go through the work).

If you can come up with a list of reactions that represents the majority of single steps in:

1. terrestrial organisms
2. primitive organims (so we could have long running simulations of the evolution of biochemistry) (we could always just fake this by having a large amount of nrg actually available from the grid).
3. deep sea trenches.

And any other odd or unique reactions you can think of I'll adopt it in a minute.  I hate chemistry.  It does things to my mind... :bash: :pokey:

The only chemistry I can stand are the parts that overlap with physics (nuclear reactions and electron shell configurations) and biology (not the organic compound nomenclture though, I'm talking about things like the physical deformation of the molecular structure of enzymes).
« Last Edit: March 17, 2005, 04:59:01 PM by Numsgil »

Offline PurpleYouko

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« Reply #34 on: March 17, 2005, 04:59:20 PM »
Just had a thought.

Are some of these bit pattern "enzymes" going to make the robot alergic to certain things as well as giving them advantages with others.

Maybe a particular bit pattern might allow a robot to eat veggies real well but at the same time make it take a small amount of damage from sunlight. We could get nocturnal critters that hibernate in the sediment during the day time.  B)

 :D  PY  :D
There are 10 kinds of people in the world

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:D PY :D

Offline Numsgil

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« Reply #35 on: March 17, 2005, 05:03:39 PM »
How you would have anaerobic and aerobic in the same sim:

Imagine two worlds connected through a single small apeture.  This would be a non-toroidal sim with a wall running down the middle with only a single break in it.

Imagine this break is at the point where oxygen solubility is at the lowest in both worlds (this would be semideep water if you follow the oceanic model).

One world could exist as oxygen based, the other as anearobic.  At the threshold between the two organisms might learn to feed on the odd mixture of the two worlds.

Then the question becomes: will life forms at the threshold compensate for the power of diffusion?  Will the O2 world eventually poison the anearobic one?

Ooo, this is exciting!

Offline Numsgil

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« Reply #36 on: March 17, 2005, 05:07:55 PM »
I suppose some kind of 'allergy' system could be implemented in the enzyme engine.  It's really not technically infeasible.

Many anearobic processes are kind of 'allergic' to oxygen.  I'm not sure really.

I guess we could have something like:

X+Y - Z -> A
where - Z is the allrgen.

The most basic consequence is that it makes the reaction not work.  If we want more advanced consequences we'd have to work it out.

Offline PurpleYouko

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« Reply #37 on: March 17, 2005, 05:11:12 PM »
Quote
Ooo, this is exciting!

Oh yes!

It is rather isn't it old boy?

Another place where both exist is in everybodies fish tank (if it is a little sick anyway).

Way down there in the gravel where little Nitrobacter chugs away on that Ammonia, tirelessly making Nitrites. Sometimes he gets a little clogged up and can't find enough Oxygen for the redox reaction so he starts to go the other way and makes stinky sulfides instead.

Ever noticed on a beach if you dig down you often get a smelly layer of grey or even black sand? That is the work of our little Nitrobacter and his pal Nitrosomonas when they run out of Oxygen.

You already added a "sediment depth" function so all we have to do is to dramatically reduce the diffusion rate below the sediment floor.

I like your idea too  B)

 :D  PY  :D
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Offline Numsgil

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« Reply #38 on: March 17, 2005, 05:22:11 PM »
We need a realli advanced tool for editing the environment grid.

It would need to have ways of quickly editing the whole field, setting up gradients that follow a f(x) type function, setting up sinks and sources, etc.

Something between a simple paint program and something like a RTS map editor.  More complex scripting abilities would tie into this.

Daunting.  Look for it after 3.0  :P

Offline Numsgil

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« Reply #39 on: March 17, 2005, 05:25:01 PM »
If we want organisms to be able to perform anearobic reactions underneath soil we need a way to get them under the soil.  I'm still not sure how things like sand and limestone (and walls, which I guess are like bedrock) would work.  Alot of ideas, just no idea how to implement them.

Like what is the carrying capacity of a single env grid square?  If you have lots of heavy stuff on top does gravity increase the carrying capacity as it squishes stuff together?  Speaking of gravity, how does it affect diffusion?

Offline Botsareus

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« Reply #40 on: March 17, 2005, 05:32:36 PM »
Quote
We need a realli advanced tool for editing the environment grid.

It would need to have ways of quickly editing the whole field, setting up gradients that follow a f(x) type function, setting up sinks and sources, etc.

Something between a simple paint program and something like a RTS map editor. More complex scripting abilities would tie into this.

Daunting. Look for it after 3.0

Wow slow down there , I think the program should randomly engineer the environment (things must randomly be plased/configured) and the environment should change over time.

Look how it works now:
lets say you set the range of plants across the whole screen:

The program randomly creates patches of plants , and the patches move , appear or disappear over time.
« Last Edit: March 17, 2005, 05:34:16 PM by Botsareus »

Offline shvarz

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« Reply #41 on: March 17, 2005, 05:36:05 PM »
Please don't use the term "allergy".  What you are talking about is plain toxicity.

Nums, about your

One thing I just realized is that
Quote
If you can come up with a list of reactions that represents the majority of single steps in: blah-blah


I can do it, but this is a lot of work.  

About primitive metabolisms - does it matter where the energy to organism is coming from?  For some it comes from light, for others - from chemical compounds, but in the end it is just a way to grab some energy from environment - the further steps are quite similar.  I am too lazy to figure all that stuff out.

How about this - I make up a set of rules for basic plants and higher animals.  If other people want, they can always add to that.

P.S: I'll include the CO2, O2, H2O, but...  you know...
"Never underestimate the power of stupid things in big numbers" - Serious Sam

Offline Numsgil

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« Reply #42 on: March 17, 2005, 05:37:21 PM »
Random settings are fine if you don't have a particular scenario in mind, but let's say you're a researcher using DB for an experiment.  You'll want to be able to set some very specific parameters.  That's what I'm talking about.

Offline Botsareus

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« Reply #43 on: March 17, 2005, 05:37:45 PM »
The order of posts is messed up;

Ok Num , thx for including that.
« Last Edit: March 17, 2005, 06:07:14 PM by Botsareus »

Offline Numsgil

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« Reply #44 on: March 17, 2005, 05:41:28 PM »
Whatever you're willing to do schvarz.  Seriously, thinking up all the reactions gives me a headache.  Every source I consult has a different way of representing it.  I don't have the training to make a single, all-encompasing system.
« Last Edit: March 17, 2005, 05:41:47 PM by Numsgil »