Author Topic: Sexual Reproduction Focus Group  (Read 12098 times)

Offline PurpleYouko

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« Reply #15 on: August 09, 2006, 08:49:46 AM »
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If bots are inorganic, sexual reproduction has no analog and we're back to square one.
What would make you think that?
There is no reason why inorganic life shouldn't reproduce sexually.

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If we start departing too much, I think we're less likely to stumble on the correct combination that makes sexual reproduction more than a curiosity.
Agreed but I don't see any problem with using shots as sperm. It is completely analogous to many higher order aquatic organisms. If your only issue is one of scale of the shots then you are artificially injecting a problem that isn't really there by making assumptions about the nature/size of DarwinBots. By this reasoning we should probably scap viruses too.

The exact nature of the beasts has always been completely open so that they are whatever any one user wants them to be. And that's the way they should stay.
To me they are sometimes little machines and at other times they might be fish in a pond. DarwinBots are undefined so we can't really force them into non-existent niches by insisting on adherence to a reality that in many cases can't really apply.
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Offline Numsgil

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« Reply #16 on: August 09, 2006, 09:17:11 AM »
Quote from: PurpleYouko
What would make you think that?
There is no reason why inorganic life shouldn't reproduce sexually.

We don't know of any non-eukaryotic life that sexually reproduces (I don't even think bacteria are doing it), so we certainly don't have the template, the how, that is important in determining how we want to do sexual reproduction for artificial or alien life.

The only example we have is real life having real sex.

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Agreed but I don't see any problem with using shots as sperm. It is completely analogous to many higher order aquatic organisms. If your only issue is one of scale of the shots then you are artificially injecting a problem that isn't really there by making assumptions about the nature/size of DarwinBots. By this reasoning we should probably scap viruses too.

Sperm travel slowly in our frame of reference.  Shots travel quickly in the bots' frame of reference.  Sperm is incredibly fragile and dies easily, which makes long term transmission impossible.  Shots are incredibly impervious until they run out of energy, allowing them to cover great distances.  Sperm has to be placed in just the right spot, and mammals have even evolved an effective injection system (the penis).  Shots just have to touch a bot and their effects are felt.  In real life, the only effective strategy for macroscopic (specifically vertebrate) animals is to get up right close to the mate (or the eggs in the case of external fertilization, but eggs tend to be the same size as the animals, relatively speaking) and fertilize them.  More often than not this involves a coupling.  A coupling not dissimilar to the sort of coupling you get with ties.

Now, smaller critters do do a sort of mass release of sperm and egg, but this would be better modelled in terms of bots instead of shots, especially if we're imagining the more interesting creatures like the fungi.

It is for these reasons that I would support ties and only ties as the basal mechanism for transmitting large amounts of genetic information (such as the whole genome).

Viruses, since you bring it up, are miniscule compared to sperm.  Totally different orders of magnitude.  And while this fact does make fast moving shots somewhat unrealistic, viruses are also quite hardy, adept at surviving and spreading themselves around.

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The exact nature of the beasts has always been completely open so that they are whatever any one user wants them to be. And that's the way they should stay.

To me they are sometimes little machines and at other times they might be fish in a pond. DarwinBots are undefined so we can't really force them into non-existent niches by insisting on adherence to a reality that in many cases can't really apply.


I perfectly agree, but this undefined nature doesn't exist on all aspects, only when taken as a whole.  Shots have no natural analog really, you just have to accept them as a throwback to Darwinbots's idealogical predecessor: C Robots.  Ties sort of combine a variety of biological ideas into one mechanism, such as leech like sucking of resources, physical connecting proteins, the elongation of a cell during reproduction, etc.

Sex especially has no context when trying to seperate it from the organisms who participate in it.  Sex is a complex process.  Science is still wrestling with the basic question of "why?".  If we start reinventing how we want our sex to work, it's entirely probable we'll remove a key aspect that is imperitive for sex to become evolutionarily useful, and our efforts will be entirely wasted.

Offline PurpleYouko

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« Reply #17 on: August 09, 2006, 12:17:48 PM »
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We don't know of any non-eukaryotic life that sexually reproduces
We don't know of any non-organic life form period.
Who knows how they will reproduce if we ever discover them?

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The only example we have is real life having real sex.
Ha! limiting ourselves to real life is boring.  
I want to go way beyond what real life can do. I want to explore fantasy worlds as well as real ones.

Certainly sperms (real life ones) are slow and fragile when they move under their own power but they can be packaged up and ejected with considerable force over a short distance. Shots do the same thing. They die too if they don't hit something within a reasonable time frame.

Besides, if my DarwinBots are inorganic, electrical lifeforms then a shot containing a digital code is totally in-keeping with the reality of the sim. It lives as long as it has enough electrical power to maintain it and if it hits a taget during its limited lifespan then it transfers its pattern to whatever it hits.

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Shots have no natural analog really, you just have to accept them as a throwback to Darwinbots's idealogical predecessor
I have been pointing that out for years. There are a bunch of things in DB that have no natural analog. Pretty much all the eye based sensory inputs (apart from distance) would fall into that catagory too.

I don't think we should really concern ourselves with making DBs match real life except where that gives us the best chance of something working right. My philosophy is to give them as many avenues as possible to do whatever they need do and let them choose how to do it themselves. Realistic? Not realistic? Doesn't make a lot of difference to me.


Incidentally, some pretty weird stuff happens in real life too.
In some fish such, as guppys and a few other live bearers, the female can carry a package of sperm for a couple of years and use it to fertilise mamy many batches of young. How do they keep the fragile sperm alive? I have no idea. I expect somebody does though. I just never bothered to look for the info.  
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Offline Numsgil

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« Reply #18 on: August 09, 2006, 02:23:05 PM »
Quote from: PurpleYouko
We don't know of any non-organic life form period.
Who knows how they will reproduce if we ever discover them?

Exactly.  We don't know how they'd reproduce.  Not only that, we aren't even qualified to guess.  Biologists still don't understand why sex exists in the first place.  What could possibly be so powerful as to entirely overwhelm The two-fold cost of sex.  There are theories, but few of them have much experimental data to back them up.

With some very real drawbacks to sex, we have to be very careful setting up our DB sex.  We know that real life sex is successful, we just don't know why.  It would seem relatively easy for a group of humans to invent something like sex (say, in an ALife program), miss the point entirely, and create a deleterious method of reproduction.  I would strongly recommend following the only existing and proven method of sexual reproduction as closely as possible.

IMO we need to follow the actual process of actual sex as clearly and perfectly as we possibly can in the hopes that be sheer dumb luck our version of sex can overcome the two-fold cost of sex as well.

Since our organisms are all haploid, we're already facing a rather significant difference with real life.  Given that we may have already taken too great of liberties in this one single regard, we need to proceed very carefully.

If we create a method of sex that does indeed seem to outweigh that two-fold cost for sex, then we could proceed abstracting the process, seeing how far it can be stretched before it breaks.

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Ha! limiting ourselves to real life is boring.

While most of life is boring, surely you're not implying that sex is boring!

Offline Carlo

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« Reply #19 on: August 09, 2006, 07:35:50 PM »
Nums, it seems to me that you're taking things from the wrong side. The first thing one should ask himself, before doing anything, is: why do I want sex reproduction? A few good reasons to introduce sex reproduction in DB have been formulated in the (helas) past years (I'll list them later); but we can just say that introducing it would change the rules of the simulation and give rise to some desirable effect. What's important with in this plan is that it takes the new feature as a starting point for some (foreseeable and desired) effect.
Now, you're taking things the other way. You say, well, sex repro exists in nature, and it is obviously advantageous (because so many organisms adopt it), though I don't know why. So if I want to introduce it, I have to copy it as accurately as possible from nature, so that I'm sure not to leave out something important.
There's something not convincing me in this argument. If you don't know what's the advantage of reproducing sexually, then you may want to investigate about it; to do so with an artificial life simulator, you should take as a starting point a very general set of rules - flexible enough to allow many different types of reproduction - and observe the outcome of natural selection. The result may consist in organisms with, say, one, two, n chromosomes; or no chromosome at all, but just exchanging floating dna or single genes. In any case, you're interested in the result, whatever it is. You want to explain sexual reproduction, but you don't actually need it. It is your goal, not your starting point; hence you should not code it directly in the simulation.
At the same time, you say you want to hard code sexual reproduction in the simulation - just as a rule that you need for new complexity. This would make sexual reproduction a starting point, not a goal, and you should be able to list the benefits of introducing it.

Now, it's been a long time since we first thought about introducing sex in DB. There are a few reasons for this:
1) many of the organisms we're most familiar with (expecially those showing complex behaviour) reproduce sexually. It is not to say that then reproducing sexually is good; but, as DB should show a parallelism with the real world, it is good for DB to reproduce some major traits of the world, sometimes even directly coding them;
2) sex should enhance evolution, by letting the result of good mutations which may have taken place in different branches of the evolution tree mix together;
3) sex, requiring compatible DNAs to mix, gives rise to real species and speciation, which always lacked in DB. The very concept of species is blurry without sex;
4) sexual selection becomes possible, though still hard. The criteria generally used in the choice of the partner influence evolution.

Now, given these points (2,3,4), it is possible to have an idea of what this kind of sexual reproduction in DB should look like. For 2), sex repro should be able to mix dnas of two (or more) individuals, transferring some genes from one to another, or mixing the genes in a new individual; 3) is the consequence of a reproduction mechanism which requires the source dnas to be similar enough to produce a well-formed destination dna; 4) requires robots to be able to make some kind of choice of the partner(s).

These requirements seem to be not too distant from what the actual .sexrepro command does. The least fulfilled is 4): .sexrepro is very weak in that, partially because it is maybe a too simple mechanism, but also because of intrinsical limitations of DB: things in it simply go too fast and good communication between robots which aren't tied is too difficult. Which should be the elements for a good partner's choice?
Also the algorithm which mixes the two dnas is probably too simple - though working, and not too difficult to improve. Has anybody tried to run extensive simulations making use of (and exclusively of) sexrepro?

Anyway, my point is simply that, before thinking of adding features to DB, one should know exactly what he needs.

Bye,
Carlo
« Last Edit: August 09, 2006, 07:43:11 PM by Carlo »

Offline Numsgil

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« Reply #20 on: August 09, 2006, 09:41:35 PM »
I would say my primary motive for desiring sexual reproduction is that others desire it.  It is quite common for people to want to run a simulation experimenting with sex.  I've seen several users come and go for this reason.

Allowing the sexual reproduction to be created from more basic commands has a problem with backwards compatibility.  Not impossible to resolve, but still quite noteworthy.  .repro is a perfect reproduction method, as opposed to Avida where the entire genome is concerned with reproduction.  If sexrepro is  orders of magnitude more complex than .repro, we have a problem of a slanted fitness landscape where sex is concerned.

To resolve it, should we wish, we could generate a sequence of very basic commands to operate on the DNA, and have .repro act as a modifiable macro, perhaps using codules or some such.

I am of the strong opinion that we need to move as much of the program away from the gene as a fundamental unit.  DNA should be treated more as a long strip of magnetic tape and less like a collection of pearls on a necklace, if that makes sense.  Especially since modern gene structure can be quite peculiar and convoluted.

Offline Carlo

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« Reply #21 on: August 10, 2006, 06:44:08 AM »
Quote from: Numsgil
I would say my primary motive for desiring sexual reproduction is that others desire it.  It is quite common for people to want to run a simulation experimenting with sex.  I've seen several users come and go for this reason.

Well, if you don't know your goal, no surprise you don't have clear ideas on how to reach it.

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Allowing the sexual reproduction to be created from more basic commands has a problem with backwards compatibility.  Not impossible to resolve, but still quite noteworthy.  .repro is a perfect reproduction method, as opposed to Avida where the entire genome is concerned with reproduction.  If sexrepro is  orders of magnitude more complex than .repro, we have a problem of a slanted fitness landscape where sex is concerned.

I don't see why sexual and asexual reproduction, or even complex/new style repro and old simple .repro, should cohabit in the same simulation. Sex seems to be per se not competitive with asexual reproduction, at least in the DB world. (This don't necessarily means that there's something wrong with DB: maybe sex just needs huge and complex environments to develop and be advantageous). So I would simply allow to run simulations with sexual repro, without worrying about its complexity or competitivity. Later, but much later, one can think of creating a more AVIDA-like control over genetic material to allow, through the same mechanisms, both asexual and sexual repro.

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To resolve it, should we wish, we could generate a sequence of very basic commands to operate on the DNA, and have .repro act as a modifiable macro, perhaps using codules or some such.

As I just said, it would be a completely different project. The problems to address now are (at least) those four points I listed in my previous post.

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I am of the strong opinion that we need to move as much of the program away from the gene as a fundamental unit.  DNA should be treated more as a long strip of magnetic tape and less like a collection of pearls on a necklace, if that makes sense.  Especially since modern gene structure can be quite peculiar and convoluted.

That's again another project, which has almost nothing to do with sex.

Bye,
Carlo

Offline Carlo

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« Reply #22 on: August 10, 2006, 09:27:50 AM »
By the way, could anybody tell me what's so wrong with .sexrepro?
Thanks

Offline PurpleYouko

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« Reply #23 on: August 11, 2006, 09:17:59 AM »
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By the way, could anybody tell me what's so wrong with .sexrepro?
Nothing really (in concept) It just doesn't seem to work.  
Also it does not give either parent a real choice in the who the other one will be as it takes the DNA of the nearest bot in physical space to combine with its own.
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Offline Elite

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« Reply #24 on: August 11, 2006, 10:32:55 AM »
Actually, after some experimentation in 2.37.6 with a .sexrepro-using Animal Minimalis, it doesn't seem that bad at first glance. Slightly buggy in some areas (ie. no reproduction collision detection) but not that bad

My first worry was that the sexreproing bot would combine with a veg or an entirely different bot, but the code seems to prohibit sexual reproduction if the genomes are two dissimilar

My only concern is that, as PY said, there's no way to choose your 'mate' - you just get your DNA yanked out of you if you're nearest

How about having .sexrepro fire a tie forward, which, on hiting another bot, takes that bot's DNA and mixes it with the original bot in a manner similar to the original .sexrepro

That way you can choose your mate by hunting round, say for a bot with more than a certain energy or kills (ie. allows for sexual selection), and then aquiring it's DNA through a sex-tie

Offline Carlo

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« Reply #25 on: August 11, 2006, 11:48:17 AM »
Quote from: Elite
Actually, after some experimentation in 2.37.6 with a .sexrepro-using Animal Minimalis, it doesn't seem that bad at first glance. Slightly buggy in some areas (ie. no reproduction collision detection) but not that bad

What do you mean precisely with "reproduction collision"?

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My first worry was that the sexreproing bot would combine with a veg or an entirely different bot, but the code seems to prohibit sexual reproduction if the genomes are two dissimilar

Hm, no. The code shoudn't prohibit nothing but, as one would expect, if the dnas are too different the reproduction fails - the child isn't able to do anything and dies rapidly.

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My only concern is that, as PY said, there's no way to choose your 'mate' - you just get your DNA yanked out of you if you're nearest

Well, ideally the bots should activate their .sexrepro locations just when they've found a good partner and are in contact with it. Activating it and then keeping roaming waiting for a random collision is just the simplest way to reproduce - not the best one. Also, if I'm not wrong, the procedure requires both the bots have their .sexrepro activated, so the collision should be with one who is also willing to reproduce.

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How about having .sexrepro fire a tie forward, which, on hiting another bot, takes that bot's DNA and mixes it with the original bot in a manner similar to the original .sexrepro

(Original sexrepro? What sexrepro are we talking about?) . Anyway, the tie isn't a bad idea. By the way, maybe glue would be even better. Has anybody thought of a glue which makes robots stick together without being actually tied, that is, something that just keeps two robots attached until a slight force divides them?

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That way you can choose your mate by hunting round, say for a bot with more than a certain energy or kills (ie. allows for sexual selection), and then aquiring it's DNA through a sex-tie

I'd like better a simmetric process, in which both bots are willing to mate and the offspring just belongs in the same way to both partners.

Offline Griz

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« Reply #26 on: August 11, 2006, 12:06:35 PM »
why does a bot have to choose?
isn't the fact they, and their 'mate' ...
have survived in a given enviornment enough?
shoudn't the ablity to survive be the determining factor?
any 'choice' should be based upon that, eh?
can we please keep this sort of anthropomorphism ...
the attribution of human/animal motivation, characteristics,
and behavior to the bots to a minimum?

they don't have to look like or behave or conform
to our expectations and ideas of what it should be.
keep it simple:
what works continues ...
what doesn't ends.
that's evolution.

unless one prefers intelligent design.
as far as I know ...
we ain't in kansas anymore toto.
不知
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Offline Carlo

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« Reply #27 on: August 11, 2006, 12:32:10 PM »
Quote from: Griz
why does a bot have to choose?
Because one of the most important mechanisms of natural selection is called sexual selection. Animals tend to evolve features which can increase the probability of being chosen by a partner for reproduction, even if those features are useless or noxious in everyday's life. The usual example of the results of sexual selection is the peacock's tail, but the examples are countless. It is common opinion that sexual selection may have played a major role in the evolution of the human brain itself, favouring language and other kinds of abilities (musical, for example) much beyond the real needs of the species.

A great artificial life simulator designed to play with sexual selection is Ventrella's Darwin Pond.
http://www.ventrella.com/Darwin/darwin.html

(though I'm sure that everybody here knows it already    )

Offline Elite

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« Reply #28 on: August 11, 2006, 01:43:10 PM »
Quote from: Carlo
What do you mean precisely with "reproduction collision"?
It's a very minor issue. The bots reproduce whether there's space in front of them or not, while 'normally' bots can only reproduce if there is sufficient space for the offspring.

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Hm, no. The code shoudn't prohibit nothing but, as one would expect, if the dnas are too different the reproduction fails - the child isn't able to do anything and dies rapidly.

Well, ideally the bots should activate their .sexrepro locations just when they've found a good partner and are in contact with it. Activating it and then keeping roaming waiting for a random collision is just the simplest way to reproduce - not the best one. Also, if I'm not wrong, the procedure requires both the bots have their .sexrepro activated, so the collision should be with one who is also willing to reproduce.
Ah, that must be the reason. I was wondering why the bots weren't just grabbing veg and nearby bot DNA, but both bots must be sexreproing at the same time, that explains it

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(Original sexrepro? What sexrepro are we talking about?)
The one we have now, that you coded

Offline Elite

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« Reply #29 on: August 11, 2006, 02:17:49 PM »
Here's a thread from the old DB forum about sexual reproduction
There's some very interesting ideas there to think over

I've had a think, and IMO we need a simple system that doesn't try to model real life too closely, that does the absulute minimum to combine the DNA of two bots, and leave the complicated stuff to evolution and bot-programmers. As Carlo said, sexual reproduction should be a starting point, rather than a result.

You could make a reproduction system that modeled nature exactly, but the only thing you would be able to do with such a system is reproduce in a certain, predetermined way, which may stifle creativity. A simple back-to-basics system that does the bare minimum will undoubtedly have great potential for interesting things which we may not have thought of, for example, as mentioned in the above thread, using .sexrepro as a weapon. Perhaps a bot could use such a system to incorporate the DNA of other species into into it's own, creating deadly hybrids that 'learn' new tricks from other bots.

Responses?
« Last Edit: August 11, 2006, 02:30:27 PM by Elite »