Author Topic: Genetic Metabolism  (Read 8449 times)

Offline PurpleYouko

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« Reply #15 on: March 19, 2005, 12:08:31 PM »
I have always thought that DB was too simple to allow decent mutations.

Here are some of my reasons why I think decent mutations are so rare
  • The environment is homogeneous. No niches, no reson to specialize!
  • Food is way too easy to find and all food is exactly the same Can't differentiate between veggies and meat as far as feeding is concerned.
  • the sim is too small. Robots are able to traverse great distances very cheaply. Again no reason to adapt to present surroundings when they are all the same.
  • Robots move too fast! For the same reason as above. Bit controversial maybe.
  • The most important one in my opinion is that The VB code that runs DarwinBots does not allow for enough variability More complexity has to be built in or we will never see speciation take place.
  • using .sexrepro, any robot can mate with any other robot. No possible speciation
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Offline Zelos

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« Reply #16 on: March 19, 2005, 03:28:50 PM »
well, ure right, there is no need for specializatoin, we need to make the bots unable to move across the entire board in matter of seconds, it shall cost alot. and it should take alot of time, like 5 min ti cross the board is more than 2 generations for them. and we need SEX (I mean in db), the sex shall only be capable whit bots who have most 5% different dna
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 Botsareus

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« Reply #17 on: March 19, 2005, 03:54:28 PM »
zelos just make larger maps in order for that to happen. Your problem is not really about the size of the board, but: Its about how mutch energy you want in your simulation. Another approch for you is to have very little energy on the map , try using F1 conditions.

Offline Anonomous Guest Person

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« Reply #18 on: March 19, 2005, 04:45:42 PM »
I like how sexrepro can work between different species.
Though I wish it were more random.

If the whole survival of the fittest thing starts working better, then bots that have sex with anything that move will hopefully mutate to only have sex when it'd produce an actual working offspring.

Offline PurpleYouko

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« Reply #19 on: March 19, 2005, 06:44:44 PM »
I think .sexrepro should be restricted to work on similar DNA a little like Zelos suggested.

I would also like to suggest that sexrepro should be completely overhauled in such a way that it actually requires both parents to be actively involved in combining their DNA in an offspring. A lone robot should not be able to use .sexrepro  the way it can now.

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Offline Zelos

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« Reply #20 on: March 20, 2005, 12:40:16 AM »
in reallity its only a few species who can get a child toghater, and that child is often sterile, but it happen its not. why that happen is coz the DNA in both the new chromosones dont match, its almost a miracle that the child was ever born. so it need to be specefied to bots that is simular whit a mariginal for evolution.
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 shvarz

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« Reply #21 on: March 20, 2005, 02:35:28 AM »
Actually, if you go by 5% difference in DNA criteria, then humans and chimps should be able to make kids together (we only have ~ 1 percent difference in genome).  I think most of cross-species restriction come from behavioural differences.  Our mating rituals are simply to different :)
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Offline Zelos

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« Reply #22 on: March 20, 2005, 03:56:59 AM »
the dna differense is important, but the most important is the amount of chromosones. a dog and a human cant get a child coz the genes which control vitial things are placed on different chromosones, if our lungs and heart are on our 3 chr (chromosone) it might be on the 5th and 9th chr on the dog. whit chromosones we could simply say, the same amount of chromosones -+ 0,5% or somethiung like that
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 #23 on: March 22, 2005, 03:50:32 AM »
I think when I work out chromosomes sex reproduction will fall in place almost as a natural consequence.

It's good to see everyone and their dog has an idea on how to make digestion work.  Here's the rules I've decided to stick to:

1.  No limit on enzyme length
2.  No limit on number of enzymes.

We can make any rules we want around these two, but the more I think about it, the more I realize this is how it needs to be.

Offline Zelos

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« Reply #24 on: March 22, 2005, 08:02:34 AM »
good whit many enzymes :D but it will cost more to have many right? maybe like in a formula E³ and some more things where E=amount of enzymes. will it?
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 PurpleYouko

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« Reply #25 on: March 22, 2005, 10:23:30 AM »
Just remember that you don't actually have to make all the enzymes in your arsenal.
What we are getting at here is that there are no limits to the possible enzymes that are able to evolve in a given robot.

Lets use an example.

A robot evolves a particular enzyme bit pattern (for the sake of arguement 512 bits long). Inside this bit chain we may be able to locate 25 different enzymes. Some overlapping, some not.
Of these 25, 10 may be specifically suited to digest fat but they all work at different efficiency rates. We have no way to tell which is best but the program will search for the best one when it needs to digest fat from the stomach. (or to put in a -6 shot maybe)
The robot will then create the best enzyme in its arsenal and will be charged energy proportional to the length and efficiency of that enzyme. The other 9 are simply ignored. Maybe later mutations of the enzyme bit pattern could make them better but for now we don't want them. They are simply patterns for possible future use.

Another robot may have 70 or 80 overlapping enzymes in his bit pattern but they could all be crappy and inefficient. That robot probably won't survive to pass on his genes.

The point is that at birth the bit pattern will be searched and the best enzyme for each type of reaction will be identified by the program and stored in the robots (hidden) enzyme array. This will save on processor time later since it is quite intensive to search the bit pattern on every cycle.

Some robots may not have any enzymes for a certain substance so that slot will remain empty.

Total enzyme slots available will be dynamic but will in effect be determined by the amount of enzyme reactions that we intend to model. This will most likely change as we add more processes with successive version releases.

Questions anybody?

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Offline shvarz

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« Reply #26 on: March 22, 2005, 10:55:46 AM »
I'm going throw back your own argument at you PY:  What's stopping the bots from being omnivores?  They'll just bloat up their enzyme sequences to have all possible digestion routes.
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Offline Numsgil

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« Reply #27 on: March 22, 2005, 11:08:16 AM »
I agree with schvarz on this one.  I don't see a mechanism, either programmed in or implied, stopping bots from digesting everything and anything.

Also, I don't think the stomach should know which of the enzymes to use.  If you have 10 fat digesting enzymes, each one can cleave n fat per cycle.  The bot doesn't know which one does it better than others.  Which one is used is random for each fat bit.

Also, I think having multiple activation sites of the same substance on the same enzyme should have a slightly deleterious effect.  It can only cleave what fat comes to it through osmosis.  So each enzyme gets n fat per cycle and then an activation site is randomly chosen.

The idea is that each enzymes is a self regulated machine.  Each activation site on the enzyme is encapsulated, and has no knowledge of the other sites.

My personal goal is to make the bots as object oriented in philosophy as possible.  By that I mean that the right hand doesn't know what the left hand is doing unless they specifically interact.
« Last Edit: March 22, 2005, 11:10:14 AM by Numsgil »

Offline shvarz

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« Reply #28 on: March 22, 2005, 11:22:09 AM »
Here is the system I think would work fine:
We have several slots for enzyme complexes.  "Complex" is a string of bits.  The length of the string is not limited.  The longer the string the more we charge.
If enzymes that work in sequencial reactions are located in the same complex, then they do their work more efficiently.

We will adjust the number of slots allowed and the charge per enzyme with time:  when metabolism will start getting more complicated we'll allow more slots/cheaper enzymes.  This way the potential number of enzymes will not be limited, but at any given times bots will have to make a choice between all available enzymes.

I am almost done with metabolism and it looks like we are going to have ~40-50 enzymes right now (don't get scared, the system is very simple).  So we should force the bots to choose ~20-30 enzymes from this variety.  I'd say to let them have 8 complexes and charge at the rate that makes it almost impossible to have more than 5 enzymes per complex (there are no sequencial reactions longer than 5 steps anyway).
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Offline PurpleYouko

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« Reply #29 on: March 22, 2005, 01:24:00 PM »
Quote
I'm going throw back your own argument at you PY:  What's stopping the bots from being omnivores?  They'll just bloat up their enzyme sequences to have all possible digestion routes.
Yes they could but the cost of doing so would be prohibitive as they would have to pay to make all those different types of enzymes. This would make them a whole lot less efficient than a specialist feeder.

Why spend all that energy making useless fat digesting enzymes when the only available food is cellulose.

Bots with all the possible enzymes in full production would soon die out.
Evolution will see to that.

Quote
I am almost done with metabolism and it looks like we are going to have ~40-50 enzymes right now (don't get scared, the system is very simple). So we should force the bots to choose ~20-30 enzymes from this variety. I'd say to let them have 8 complexes and charge at the rate that makes it almost impossible to have more than 5 enzymes per complex (there are no sequencial reactions longer than 5 steps anyway).

Looks like you are pretty much in agreement with me in this later post. Only difference is that I say we let 'em have as many as they want and if they can't afford them, tough! Evolutionary dead end!

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

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