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Simoltaneous DNA execution

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Numsgil:
Manually.  The two systems just don't mesh.  And anyway, the promise of more interesting mutations and natural development lies along this path, so why would you want to mutate old top bots and mutated bots anyway when you can get more interesting results elsewhere.

shvarz:
Cool idea.  Here are ways to solve some of the problems mentioned:
1. Chromosomes should be defined by DNA commands.

chromostart
blah-blah
chromoend

Within a single chromosome the stack is used as before - allows inter-gene communication.  Each new chromosome resets the stack.  To make your old files run in new version, simply add chromostart in the beginning and chromoend at the end - most of the bots should be just fine this way.

2. Allow single-chromosome genomes.  After all, not all genomes are diploid.  Poliploidy is not necessary, it does not add much anyway.

3. All pairing up that is needed is just to place paired chromosomes one after another.  During sexual reproduction, take odd chromosomes from mother, even from father (just like sexrepro works now).  This actually makes tetraploidy possible (or any other even-number-ploidies).

Comment:
Nums, organisms don't go through meiosis just because it is faster :)  There are always better reasons :)  But we can make meiosis possible, should not be hard.

Numsgil:
We could allow stack manipulations to pass along the same chromosome I guess...  but the store commands would have to be at the same time.

Ideally the program wouldn't have a 'diploid mechanism', it'd just set up the basic mechanisms that allowed it to develop in the first eukaryotes.  I think a 'double strand DNA break' mutation would prompt this kind of action (that's why real organisms became diploid).  So single strand chromosomes are really the default.

How do we know which chromosomes to associate with one another though?  How do real cells know which chromosomes to stick together during mitosis?  I've heard some plant species can interbeed with others, then double their chromosome number to become a proper diploid creature.  Something like that should be possible too, I think.

Basically, I think we should have sub commands, like crossing over and chromosome reproduction that can be macroed with a simple meiosis command.

I read that thing about meiosis being faster somewhere on the internet.  After looking it up it's actually much slower since their are 4 cells at the end instead of 2.  Shows you that you can't always trust info online.

shvarz:
The chromosomes are linked in pairs.  Same will be here.  Just like this:
1a
1b
2a
2b
3a
3b

and so on.  If the order gets mixed up - the off-spring will also get severely mixed up and die.


--- Quote ---So single strand chromosomes are really the default.
--- End quote ---

What do you mean?


--- Quote ---I've heard some plant species can interbeed with others, then double their chromosome number to become a proper diploid creature. Something like that should be possible too, I think.
--- End quote ---

It is possble, but not that important.  Don't bother.


--- Quote ---Basically, I think we should have sub commands, like crossing over and chromosome reproduction that can be macroed with a simple meiosis command.
--- End quote ---

You mean actual commands for cross-over?  That would say "crossover here"?  But cross-overs are random.  Anyway, recombination is a whole other matter.  Simple re-assortment of mother's and father's chromosomes will add a lot of power already.

Numsgil:
Here's what I'd like to see.

Imagine a system where a single chromosome bot learns to associate two identical copies of the same chromosome together to fix DNA damage, or split up chromsomes randomly, or whatever.  Maybe two haploid identical copies of a cell combine to form a diploid individual.

If we have the right rules in place, we should see things like sexual reproduction and diploid-ness arise naturally.

That's what I'm talking about.  Then chromosomes learn for themselves how to associate similar chromosomes together.  As long as we can figure out some kind of mechanism for them to use, we're set.

Unfortunately, the process that real chromosomes use is somewhat epigenetic, which probably wouldn't work well.  Any ideas?

And recombination is only a part of the advantage of meiotic reproduction.    Crossing over helps keep chromsomes more or less consistant with one another.  It wouldn't be alot of extra work to figure it out.

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