You could make "junk DNA" a fitness criterion, and kill off entities that have lot of it that way. Natural selection doesn't really penalize that, because it ha

You could make "junk DNA" a fitness criterion, and kill off entities that have lot of it that way. Natural selection doesn't really penalize that, because it has no effect on survivability. However, it might have a long-term advantage, because of evolution's randomness; if you eliminated the junk DNA you'd also have a much more directed walk through the genome's expression space, which means that you might miss a lot of very good solutions.