Code center > Suggestions
Recombination mechanism
shvarz:
Yes, it is a mutation, but it is such a good, nice mutation that it was the direct cause of many-many-many cool things evolving. Like most of our immune system, or taste and smell receptors and so on... And that's just in eukaryotes.
The problem with counting from centromere is the same as counting from the beginning of DNA - it does not solve anything. A single insertion or deletion and bots can't recombine anymore. Besides, you are still thinking in recombining genes, but my method allows recombination to occur anywhere, and it almost always will produce meaningful working bot. In addition, it will allow repair mutations using second strand as a template if we decide to go diploidal.
Numsgil:
--- Quote ---A single insertion or deletion and bots can't recombine anymore. Besides, you are still thinking in recombining genes, but my method allows recombination to occur anywhere, and it almost always will produce meaningful working bot. In addition, it will allow repair mutations using second strand as a template if we decide to go diploidal.
--- End quote ---
I'm thinking in terms of breaking off whole areas of the chromosome and reattaching them elsewhere, quite irregardless of genes at all.
As you insert a new condition in one chromsome, then the strands become unequal and an unequal crossover occurs ipso facto. The centromere, no matter where it is spatially at first, will eventually become more or less in the middle since the DNA is shuffled around it.
If nothing else, the centromere system solves other problems as well as recombination, and it's older. From a few simple rules I can construct most of the rules of eukaryotes.
Centromeres allow chromosomes to be paired within the genome. Centromeres can be developed naturally from repetitive sequences. Centromeres allow chromosome pairing to be epigenetic. Centromeres ensure incentive for similar chromosomes to become paired since that way they'll for sure move to opposite ends during mitosis. And they allow crossing over to occur by simple breaking of both strands and swapping pieces.
ie:
chromo1:
1-1-1-1-1-1-1
chromo2:
2-2-2-2-2-2-2
after one crossing over event:
1-1-1-2-2-2-2
2-2-2-1-1-1-1
It doesn't even have to occur at a gene break point. It can occur anywhere. If they're unequal lengths:
1-1-1-1-1-1-1-1
2-2-2-2-2-2-2
after one crossing over event:
2-2-2-2-1-1-1-1
1-1-1-1-2-2-2
Numsgil:
If I can add to my last post:
I was going to model crossing over on the Holliday Model.
shvarz:
Centromeres is a nice idea. And it can work together with my UID (unique ID) system in parallel.
I still think UID system is a lot more powerful, because for recombination it allows all that your system does and then some more.
Imagine that two people start evolving the same bot, then share through internet. By that time genomes changed a lot, new genes were introduced, mutations accumulated, some commands got deleted. Your system of simply counting off a certain number of commands and switching will produce only non-viable bots. My system will allow them to recombine and almost always create a viable bot.
Another example:
imagine a series of sequencial commands:
a-b-c-d-e-f-g
Say one of the bots got an insertion (I) that really increases its fitness
A-B-I-C-D-E-F-G
Bots are reproducing sexually, so that this bot must mate with an old-style bot. Your system creates a number of different bots with this insertion, with general types like this:
a-B-I-C-D-E-F-G (alive)
A-B-I-d-e-f-g (dead)
A-B-I-C-D-f-g (dead)
Basically, the only survivable bots are those that crossed over before the insertion. Any time after - and the whole gene is messed up. Unless cross-over happens in junk DNA.
My system will always make a viable bot, because it aligns the DNA correctly. It does not introduce any additional insertions/deletions during reproduction, so that the chances for off-spring to be viable are much-much higher!
P.S: Holliday model assumes you have aligned the DNA first.
Numsgil:
Okay, correct me if I'm wrong, but:
--- Quote ---a-B-I-C-D-E-F-G (alive)
--- End quote ---
simple insertion of new instruction, and trading of chromosome arms.
--- Quote ---A-B-I-d-e-f-g (dead)
--- End quote ---
small deletion and trading of chromosome arms (remember that for DNA missing a letter is disaterous because it makes all words downstream meaningless. But for us each DNA instruction is atomic, so in our system such an event would be like DNA losing the coding for a single amino acid).
--- Quote ---A-B-I-C-D-f-g (dead)
--- End quote ---
insertion of new instruction and deletion of E/e.
Neither deletions nor insertions are automatically lethal, unless they're in a gene that codes for important behavior. And then you shouldn't be mutating it anyway.
That said, some mechanism like polymerase that zips up two paired chromosomes for crossing over could be useful. How does real DNA pair up the chromosome? How do polymerases do it? Maybe we can do something similar.
Mind you I'm not against an ID system, I just want to understand the problem and solutions possible before picking one.
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