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Messages - ikke

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286
Simulation Emporium / my first evo sim
« on: June 08, 2008, 03:51:35 AM »
Quote from: ikke
2) once on a while the number of subspecies collapses. Population of predators noramally ranges beteen 180 and 220, so I don't see mass extinction as the cause. I think it is a more adapted subspecies taking over at the expense of population diversity.
Now I think the driver here can also be local extinction. In one area food prey is no longer available so the subspecies living there go extinct while other areas with abundance keep the total population relatively constant

287
Simulation Emporium / my first evo sim
« on: June 06, 2008, 02:50:35 AM »
Quote from: Numsgil
Oh, that's really, really cool.  They learned how to body feed instead of nrg feed.
What is the advantage there?

288
Simulation Emporium / my first evo sim
« on: June 06, 2008, 02:27:45 AM »
A major shift occurred last night: average costX increased from 6 to 12. What happened? Purple shots, not red? Predator genome:
[div class=\'codetop\']CODE[div class=\'codemain\' style=\'height:200px;white-space:pre;overflow:auto\']'''''''''''''''''''''''  Gene:  1 Begins at position  1  '''''''''''''''''''''''
 cond
 *.eye5 6 !~=
 *181 -565 sgn 9 dist *.refeye *.myeye !=
 start
 *.refveldx 4 54 *.refvelup pow floor store
 .up inc
 stop
''''''''''''''''''''''''  Gene:  1 Ends at position  23  '''''''''''''''''''''''

''''''''''''''''''''''''  Gene:  2 Begins at position  24  '''''''''''''''''''''''
 cond
 *.refypos *.eye5 44 >
 pyth *.refeye *.myeye !=
 start
 %=
 dup inc
 pow dist xor
 312 -6 .shoot store
 *.shflav 385 -52 !=
 *.refvelup .up store
 dec
 pow -206 * or

''''''''''''''''''''''''  Gene:  2 Ends at position  55  '''''''''''''''''''''''
''''''''''''''''''''''''  Gene:  3 Begins at position  56  '''''''''''''''''''''''
 cond
 *.eye5 0 =
 start
 *.myeye div 1099 .aimright store

''''''''''''''''''''''''  Gene:  3 Ends at position  65  '''''''''''''''''''''''
''''''''''''''''''''''''  Gene:  4 Begins at position  66  '''''''''''''''''''''''
 cond
 *.nrg 25075 >
 start
 .repro store
 xor
''''''''''''''''''''''''  Gene:  4 Ends at position  73  '''''''''''''''''''''''

289
Simulation Emporium / my first evo sim
« on: June 05, 2008, 12:07:34 PM »
Quote from: EricL
Cool sim.  The above is especially interesting to me.  As you describe, one would expect to see a reduction in diversity following fixation of a new adaptation.  Fixation perhaps isn't the right word for an asexually reproducing species, but the diversity dropping is key.  Would love to see the graph.   I'll try to get the genetic distance graph working right soon so we can see that as well.
here you are
Quote from: EricL
FYI, I'm not sure how the subspecies graph handles sexual reproduction.  It may become meaningless for a sexually reproducing species.
Ultimately, with enough gene combinations possible, it should show each individual is unique. You'd have to track gene diversity (how much variants are there of a given gene) within the species.[attachment=953:diversity.bmp]

290
Simulation Emporium / my first evo sim
« on: June 05, 2008, 08:39:10 AM »
Just wanted to share some of my first experiences with the community, so here it goes.

My intention was to get an evo sim going with predator and prey coevolving in a predator prey cycle without external interference like constant energy (day night) or polulation caps (max veggies, costX). I started with just a veggie (runaways) and set the physics and cost. I adjusted the nrg influx so that the veggie population barely survived the first reproduction cycle, figuring that if the veggies would get more than that they swould have conquered the world already. Next I added the predator(animalis minimalis) in a 1:10 ratio. The sim busted for several repeatedly for several reasons:
1) no variance in population:  predators and all prey each started all having the same parameter values: age, energy and body of each individual in the population were the same. This meant that every so much cycles the prey would reproduce all at once, peaking its population. I tried to solve this by adding some randomness to the prey reproductive gene, but that wouldn't help me at start up. Secondly the predator would reproduce sucessfully but its offspring would not survive food competition. The original predator population grew old and died without leaving sustainable offspring. A decent age build up would have prevented that
2) predator and prey were both dumped with in an environment. They hadn't coevolved with each other in this environment. Basically I dumped an alligator and a penguin in the desert and was waiting for predator prey cycle. What are the chances of that happening?

So I gave up and added caps: CostX for the predator, constant system energy for the prey. A minimum veggie population above the starting population increasing by 1 every cycle, to get a more even prey population build up, adding predators manually for the same reason. CostX screwed up my minimal energy balance of prey, so I upped the nrg/turn. This resulted in the working sim attached

The first muation to catch on was collision avoidance: dont up the speed for distance <6, which makes sense in the elastic collision sim. At first I thought the gene was degrading, so I reran with both the original and the mutation. The mutation would replace the original every time. Another was conditional rotation: rotate small angles with targets in sight, otherwise large. A third was to travel if no food was available as opposed to waiting and starving. All clear energy aquiring or saving mechanisms. I have to admit after that the genes have become too obscure for me to identify improvements beyond that.
One mutation I was expecting but which did not appear for considerable amount of time was higher survival of offspring. Amimalis give 10% to offspring, which leads to high infant mortality (8-9 average offspring) in the environment. A mutation on this point could take over quick.

I have observed a number of things in the sim:
1) Since animalis genes are all functional neutral or positive mutations usually start within randomness or at the end of a gene. A future experiment of mine is to duplicate all genes and re-run. Is the species with all genes double stronger (better resiliance when mutating) or weaker (killer breakdowns occur more often)?
2) once on a while the number of subspecies collapses. Population of predators noramally ranges beteen 180 and 220, so I don't see mass extinction as the cause. I think it is a more adapted subspecies taking over at the expense of population diversity. I wonder what impact sexual reproduction would have on stability of species diversity.
3) best mutations don't occur first. Open door of course, since mutations are random, but I was waiting for infant mortality to come down by an improvement in the reproduction gene, and all kinds of things happened, but not that.

291
Biology / Crows are pretty damn smart
« on: May 25, 2008, 01:13:13 PM »
Quote from: shvarz
Have you seen the famous video of the crow that makes (sic!) a tool to reach a piece of food?  Now, that is amazing!
Upd: Here it is http://www.youtube.com/watch?v=TtmLVP0HvDg...feature=related  and more on related videos
Didn't know this one. I saw a similar one about one of them making a barb on a twig to catch grubs.

292
Bug reports / db recording generates error
« on: May 20, 2008, 11:18:52 PM »
file error 52 bad file name pops up when enabling database recording.  Used various names &paths. Didn't matter

293
Thanks.

294
I have a hard time interpreting subspecies distance and species diversity. I am running an evo sim. Species diversity is 20 and subspecies distance is 771 for the (evolved version) of the animalis minimalis bot I am running now. What do these parpetes mean?

295
Bugs and fixes / CostX not reset when starting a new sim
« on: May 18, 2008, 09:02:21 AM »
when using dynamic cost adjustment costXis not reset when starting a new sim

296
Suggestions / gimmic for zerobot evolution
« on: May 16, 2008, 02:08:11 PM »
Quote from: shvarz
BTW, you can treat each bot at that stage as a puddle of water that is full of pre-biotic material. In that case the evolved replicator (a particular set of DNA commands within that pe-biotic material) does indeed replicate all other stuff along with itself.  So it's not self-contained. The abstract nature of bots can be interpreted in many different ways
Nice abstraction. However, I would say it is contained by the puddle.
Quote from: shvarz
It's a good point and there is nothing we can do about this - DB is based on the concept of bots.
I don't see the concept of bots needs to be broken to implement this. All that is needed is a set of rules to define gene behaviour in uncontainend conditions and defining when the condition applies. As an inprovement to the original suggestion to a new ''close'' command a body could be said to exist when  body, slime or shell have been increase by the genome. No new command needed.
Quote from: shvarz
It never was specifically design to ask the question of emergence of life - from the beginning it was always about evolution of existing life. The "zerobot" approach is relatively new here. It was brought in just as a fun challenge.
I'm not judging the work done. I like the concept of zerobot evolution and I think this may be a nice extension. I for one am curious about the interaction between containment and replication. Outside that it has no purpose. A gimmick, as the title says

297
Suggestions / gimmic for zerobot evolution
« on: May 16, 2008, 04:55:32 AM »
I was thinking about the way DB behaves around zerobot evolution an the emergence and propagation of replication. It occurred to me that the zerobot as it currently has been defined already has a fundamental characteristic of life that greatly impacts propagation of replicating genes: self containment. Two randomly evolved genes cannot bond head to tail when in physical contact, nor can a gene split up in two autonomous parts. Imagine a zerobot developing some sort of replicating mechanism without this auto containment: it would pass on replication to whatever other bots it would come into contact with. Inversely, the population could grow without replication. In DB this could be modelled by introducing a few items: a close to represent the boundaries of the selfcontainment, and the rule that bonding or breaking cannot occur before the first close. Combined with probabilities of bonding and breaking this should push back the start of DB simulation back further ito the aminoacid soup

298
Newbie / Hi
« on: May 15, 2008, 06:44:35 AM »
Hi everybody,
A couple of days ago I came across the site, program and forum. I have a longstanding love for simulations and A (actually I came across from c-evo, a civilisation clone where you can program your own AI module) and some programming experience. I just wanted to complement everyone on the relaxed and cooperative atmosphere on the board, and make myself known before posting anything else.

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