Darwinbots Forum

General => Biology => Topic started by: viplex on March 08, 2007, 01:05:49 PM

Title: natural diversity VS simulated
Post by: viplex on March 08, 2007, 01:05:49 PM
What is the trick of nature, that allows genomes (species) appear at such diverseity at the same enviroment? Why are simulations so dull?
Title: natural diversity VS simulated
Post by: Jez on March 08, 2007, 02:14:13 PM
My guess would be time.
Title: natural diversity VS simulated
Post by: viplex on March 08, 2007, 03:52:45 PM
Quote from: Jez
My guess would be time.
But in the sim, why do all species but one extinct? Time doesnt help. On the contrary..
Title: natural diversity VS simulated
Post by: EricL on March 09, 2007, 12:39:10 AM
Nature is many many many orders of magnitude more complex than DB w.r.t. environment, genetic degrees of freedom, physics, etc.  and yes, nature has more time, not just in terms of linear time but in term of interactions per unit time at everything from the molecular to the organism level.  Nature is parallel.  DB is not.  

The short answer is that DB is so amazingly simplistic in comparsiom that it would be incredible if anything evolves at all (IMHO, we have yet to really see anything actually evolve beyond the most basic seiving response to enviromental constraints).  I could make a strong case that DB has yet to evolve anything.
Title: natural diversity VS simulated
Post by: viplex on March 09, 2007, 11:28:49 AM
Quote from: EricL
Nature is many many many orders of magnitude more complex than DB w.r.t. environment, genetic degrees of freedom, physics, etc.  and yes, nature has more time, not just in terms of linear time but in term of interactions per unit time at everything from the molecular to the organism level.  Nature is parallel.  DB is not.  

The short answer is that DB is so amazingly simplistic in comparsiom that it would be incredible if anything evolves at all (IMHO, we have yet to really see anything actually evolve beyond the most basic seiving response to enviromental constraints).  I could make a strong case that DB has yet to evolve anything.

In that case, I suppose, processor speed is completely irrelevant regarding evolution efficiency. Yes, I have already observed something: if nothing interesting evolves in five minutes, you maight run it for five days with no interesting result at all.  
Maybe those quantum computers will help us.
Title: natural diversity VS simulated
Post by: Numsgil on March 09, 2007, 03:46:59 PM
An interesting idea I have been toying with in my mind is that life is like the travelling salesperson problem.  It's possible to have something alive in computers, in the same way that a depth first traversal can solve the TSP.  Just don't go looking for the answer before the universe dies and protons start decaying
Title: natural diversity VS simulated
Post by: EricL on March 09, 2007, 07:51:25 PM
Quote from: viplex
In that case, I suppose, processor speed is completely irrelevant regarding evolution efficiency.
On the contrary, it's all about processor speed.  The more megaflops, the more physics that can be supportted, the more complex the interactions can be, the more bot-cycles per second per sim, etc.  I'm not saying DB will never evolve anything, only that with today's simplistic environment and cpu power, we have yet to see it.

Quote from: viplex
Yes, I have already observed something: if nothing interesting evolves in five minutes, you maight run it for five days with no interesting result at all.  
My zerbot sim is knocking on the door of 2000 hours of runtime with ~1500 bots and I've yet to see any conditional logic evolve even though I have tried to set up conditions to favor it.  I'll post it soon with some observations...
Title: natural diversity VS simulated
Post by: EricL on March 09, 2007, 08:05:20 PM
Quote from: Numsgil
An interesting idea I have been toying with in my mind is that life is like the travelling salesperson problem.  It's possible to have something alive in computers, in the same way that a depth first traversal can solve the TSP.  Just don't go looking for the answer before the universe dies and protons start decaying

"Alife is but a heuristic search through real world NP-completeness."   whoa.  Got to get me some ganja to fully grock that implications there...

I agree with you in the sense that serial time slicing of organisms whose possible interactions are limited to only those coded apriori into the simulator will always be a shadowy approximation of the completely parallel and messy real world.  That said however, I continue to beleive that something we would all call life is still possible in a digital environment.  BTW, this ties us back to the thread a month or two ago on simulator-less bots released into the Internet...
Title: natural diversity VS simulated
Post by: Numsgil on March 09, 2007, 11:14:23 PM
If you look at it, most of the things that life takes for granted, such as protein folding, are not things that computers can do particularly well.  They can do them, but you'll always be pushing.  It won't come naturally.

One could argue that life can be abstracted away from the particulars of protein folding, but until it's demonstrated the possibility that life is protein folding, et al, can't be ignored.
Title: natural diversity VS simulated
Post by: viplex on March 10, 2007, 11:32:27 AM
Quote from: Numsgil
If you look at it, most of the things that life takes for granted, such as protein folding, are not things that computers can do particularly well.  They can do them, but you'll always be pushing.  It won't come naturally.

One could argue that life can be abstracted away from the particulars of protein folding, but until it's demonstrated the possibility that life is protein folding, et al, can't be ignored.

Maybe its chemistry and all... and if we can make some abstraction and create some lifelike thing without chemistry, there is still a possibility that we will understand nothing of what is happening. If you know tierra or avida, with their "chemistry" being assembly, you can imagine what I'm speaking of: its hard to figure out how the simplest self-reproductor code works.
Though Darwinbots is very didactical, comprehensible to us, that exactly may be its weakness, since its language is too artificial (high level?)
Title: natural diversity VS simulated
Post by: viplex on March 10, 2007, 11:52:58 AM
Quote from: EricL
On the contrary, it's all about processor speed.  The more megaflops, the more physics that can be supportted, the more complex the interactions can be, the more bot-cycles per second per sim, etc.

you are right, but my point is...
if you have nothing interesting evolved in half an hour in your sim, processor time will not solve the problem, just like waiting for some hours more wont solve it. This late being an experience of mine.
So okay, this "completely irrelevant" is a bit exagerrated
Title: natural diversity VS simulated
Post by: Endy on March 11, 2007, 01:50:41 AM
EricL, what kinds of settings are you using. I've found making the enviroment more complicated, yields substantial benefits in terms of more relativly complex life evolving. Oh yeah, what species is the zero bot? For plants they tend towards evolving pacifistic/defensive forms, rather than agressive ones.

I've found starting with a highly developed bot will work wonders. While evolution may take a long time to evolve things, it's easy for it to modify them to fit the enviroment.

Your choice of plants can also have a huge impact. An evolving continually reproducing plant, will adapt to your animals' feeding methods making them adapt in turn.
Title: natural diversity VS simulated
Post by: Jez on March 11, 2007, 12:05:32 PM
I chose time originally over space because of the length of time that evolution has been around, the excessive time it took for life to mutate beyond a unicellular point and because there are small enclosed areas, such as caves, that do hold a variety of life, albeit a limited variety.

Watching a bit of 'State of the Planet - David Attenborough - UKTV History' today did make me reconsider this point though. He referred to an effect that mankind is having on biodiversity known as 'islandisation'.  Basically; the detrimental affect that something as simple as a road through a jungle can have by dividing the natural environment into smaller parcels.
For instance there is a little bird that steals insects from army ants, the army ants need a large amount of jungle to survive, when the army ants run out of insects in their bit of jungle they are quite happy to cross the road to find more insects but the bird, never having had a lesson on road safety, won't.
All along these man made boundaries both the plant and animal diversity is lessened.

Weigh this against an animal heavyweight such as the crocodile, a reptile that stopped evolving a long time ago because it had reached an apex for its environment.

If your bot has stopped evolving I would suggest a quick game of 'Darwin’s Finches'. Change the environment, if it has stopped mutating then it probably (having reached the ‘crocodile point’) doesn't need to any more.

I am changing my original answer from time, (although important in its own right) to space, environment and genetic pool.

PS
In Africa, many of the original game reserves are now considered too small, the solution they are now thinking about is joining many of these game reserves using ‘corridors’, much like the affect hedgerows used to have on biodiversity here in England and the reason that we now have laws about the removal of hedgerows.
This reminds me of the internet sharing idea that has never been fully implemented, diverse environments joined by an internet pipeline.
Title: natural diversity VS simulated
Post by: viplex on March 11, 2007, 04:21:38 PM
Quote from: Jez
This reminds me of the internet sharing idea that has never been fully implemented, diverse environments joined by an internet pipeline.

That's an interesting idea, but
There is an evo software the name of which I dont remember, with rotating, stiff-body bots called "biots". Internet sharing works fot it. I evolved some cool biots and connected to other enviroments (to 4 directions, via borders of the screen). What do you think happened? There came some tens of thousands generations old terminators and quickly eliminated my whole population.
But if there was some way to standardize enviromental parameters, and then defining some kind of fitness for the creatures involved in the multiPC sim, then screens with close average fitness could be put next to each other, thus creating a great world of adjoining screens. That should elongate stability.
Title: natural diversity VS simulated
Post by: viplex on March 11, 2007, 04:29:42 PM
Quote from: Endy
Your choice of plants can also have a huge impact. An evolving continually reproducing plant, will adapt to your animals' feeding methods making them adapt in turn.

I always use auto-repopulation for plants because genetic reproduction never works for me somehow: the population is wildly oscillating (when reaches max pop treshold, too many vegs reproduce at the same time) and many other issues I can't recall now. How do you set up a stabile veggy pop? Do the plants learn to move and shoot and things?
Title: natural diversity VS simulated
Post by: Carlo on March 12, 2007, 01:57:06 PM
Quote from: viplex
But in the sim, why do all species but one extinct? Time doesnt help. On the contrary..

It's an old problem. My opinion is that the enviornment DB offers is way too small and homogeneous to allow the existence of more than one species at a time. Simply, there isn't any reason for different species to share the same environment in a simulation; a few thousand cycles are always enough for evolution to tell the best one and make the others go extinct.
Real world is different because of specialization to different environments or different niches in the same environment. The complexity of real chemistry and physics allows numberless different niches to coexist in the same physical space. Spatial segregation, due to distances or natural barriers, is another source of diversity.

We discussed for a long time the opportunity to add complexity to the environment by superimposing to the field a so-called "environment grid". But there were different opinions about which properties of the field had had to be specified by the grid and nothing was done in the end.
Title: natural diversity VS simulated
Post by: Numsgil on March 12, 2007, 03:54:41 PM
I find that features like the env grid are hard to program because you never feel that the discussion is "done".  You keep reinventing it, and eventually it just gets put on the backburner.  Probably a downside of design by comittee
Title: natural diversity VS simulated
Post by: rsucoop on January 19, 2008, 10:52:19 PM
The biggest contributor to the precission lost in the simulation is the fact that sexual reproduction is impossible. It appears that the best way to create a stronger dna strand is not to copy the same one over and over with mistakes and hope it works, but to splice the genes and mix up the commands/values resulting in a mutant of the two parents. This splicing is not 50% exactly even in reality, and is 100% random everytime. So things like more complex multi-organisms from two seperate organisms would be possibly in nature, but not necessairly in the simulation. Until sexual reproduction is properly used, the simulation will never truely match the evolutionary process of the Earth.
Title: natural diversity VS simulated
Post by: Peter on January 20, 2008, 03:40:20 AM
On earth species have evolved long enough without any sexual reproduction. Is not necesarily needed for evolution.
It would be nice to have sexual reproduction but it isn't there.

And what do you mean?

Quote
This splicing is not 50% exactly even in reality, and is 100% random everytime.
The splicing is 100% exact in reality, or do you mean things like crossover that change every side somewhat.
Title: natural diversity VS simulated
Post by: rsucoop on January 20, 2008, 10:03:31 AM
I refer to the selection of genes. Everytime this happens in life, it is 100% random and independent of the result of the previous gene that was copied. When I say 50% exact, I mean a perfect cross between parents resulting in a perfect 50% child. That's not always thre case, a black family with the correct recesive genes could potentially produce a red headed light skin child; not necessairly a mutation, but a very new type of person from the parents dominant/recesive genes.
Title: natural diversity VS simulated
Post by: Peter on January 20, 2008, 11:53:07 AM
Quote from: rsucoop
I refer to the selection of genes. Everytime this happens in life, it is 100% random and independent of the result of the previous gene that was copied. When I say 50% exact, I mean a perfect cross between parents resulting in a perfect 50% child. That's not always thre case, a black family with the correct recesive genes could potentially produce a red headed light skin child; not necessairly a mutation, but a very new type of person from the parents dominant/recesive genes.
Ok, I thought you where speaking of chromosomes.
The selection of the chromosomes is in many cases not 100% random, and maybe even dependable of the earlier gene, with the splitting of chromosomes and the crossover of genes an really 50% exact cross between the parents seems hard too. Making a exact selection of the genes of 50% each and randomness for every gene possible, pretty plausible, everything is dependable of eachother. Genes aren't for nothing together in desame chromosome.

And the last sentance, that's not a case of genotype but of fenotype. It is true two cows with a hetero-zygote black gene could have a brown cow, chance is 25% roughly.

The whole dna-story in a whole is pretty complicated. But simply said there is nothing that is 100% random. If there are certain genes you took from your father you can predict that some others are too if they are in desame chromosome. I heard some genes even try to cheat to get in the dna.

The good point of sexual reproduction is indeed the mix of genes that didn't knew eachother before and they really work working together, you're right there.
What really is better then the 'normal' reproduction that depents for a big part on trial and error, altrough bacteria seem to exange eachothers genes too.

It has been stated before, but the reason DB hasn't got a complicated ecosystem and nature does. Is becouse nature is just a 'little' more complicated then DB.
I heard they tried to simulate a very small virus in a water drip, some time ago wih a supercomputer. That took some weeks to simulate it for a few seconds. The computer simulated literaly everything from every molecule. And nature can do it in real-time, and also then look how long it took to come this far.