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Sexual Reproduction

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Welwordion:
Diploidity is useful, but not necessary as a bot does not need a backup Dna that is never used.
Also we should avoind making observation more difficult by introducing geno- and phenotype.
Shuffling the code which is quite similar is still the best solution.

Numsgil:
Clicky

That talks about the crossing-over technique.
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Don't you find it interesting that generally speaking sexual creatures have a lifestage where they're diploid, whereas asexual bacteria generally do not?

Diploidity and Sexual Reproduction happen, if I remember right, at the same time in history: the invention of Eukaryotic cells.

If we seperate the two are we sure we're not elimating the advantages of sex?  I think we can't be sure.  It's better to model it as closely as reasonably possible on real sex and hope we get everything that real organisms find useful.

Here's an article on Diploidy in Alife and GA.  It proposes that Diploidness is a way to remember past useful solutions in the population without necessarily expressing them.

I'm not sure if I believe that or not, but the fact remains that in nature Multi-Ploidness and sex are inextricably linked.  It would be naive to simulate one and not the other in some manner.

A side note, the paper also explores "non-stationary fitness functions".  I think that's why organisms become cannis even though canni species are less able to fight off other species.

The fitness landscape is always changing as you allow a species to mutate.

Numsgil:
Here's what I'm thinking to decide Dominance:

Each codule is passed through some sort of hash function, which assigns to each codule a weight.  Codules at the same location (ie: two or more codules at location 46 can be thought of as being polyploid at 46) each have a chance of being called when an organism calls that location with their goto command.

The chance is determined by the difference in the weights of the two codules such that:

chance is 50/50 if weights are equal
chance of executing codule A approaches 0 as codule A's weight << codule B's weight.

Probably a non linear function of the difference in weights.  An "s" curve probably Like this picture where the x axis is weight and the y axis is probability of being selected to be expressed per call.

The result is a system that allows for recessive, dominant, and co-dominant codules.

Greven:
Okay I just thought about something regarding "dominate" codules.
Instead of making new commands to like these, we could work it out similiar to nature (or nearly ):

Making the codule with most commands the dominate. Why?
Becuase in the real world, a genes expressiveness (word? now it is )
is determined by the amount of proteins or polypeptides or whatever it produces. If a genes produces more than another it is expressed, like brown eyes and blue eyes. Were brown eyes are dominate.

If a tie, the program could chose randomly each round, OR it could randomly choose one and use it all life, OR something else.

What do you think?

By the way micro & macro should both be available, in the end it will be much more exciting.

Numsgil:
Picking the patch of DNA that's longest isn't exactly biologically equivelant.  In biology, it's the gene that's pushing harder: ie: copying more proteins than the other recessive gene, that's produced.

I don't think it's a bad idea necessarily, but I'm not sure I want to be selecting for genome length.  Problems with viruses comes to mind.

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