Very cool :) One small nitpick though, is the use of map in void context. Specifically (in Individual->get_code):

my $code = "";
map { $code .= $_} (@{$self->{GENES}});
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could be:

my $code = join('', @{$self->{GENES}});
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Also, if your Individual->create() method returned $self at the end, you could change this (in Population->new):

for my $i (0 .. $self->{SIZE}) {
      my $individual = Individual->new();
      $individual->create();
      push (@{$self->{INDIVIDUALS}}, $individual); 
}
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To this:

push (@{$self->{INDIVIDUALS}}, Individual->new->create) for 0..$self->
+{SIZE};
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Or maybe even this:

$self->{INDIVIDUALS} = [ map {Individual->new->create} 0..$self->{SIZE
+} ];
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But now I'm probably being too nit-picky :) </code>