Carlos:
Also, what Francis mentioned, junk DNA could perform "internal control" over expressing genes. However, I believe that only a small part of junk DNA would be like this, otherwise any mutation would cause changes in phenotype...
Part of my proposed hypothesis was that there would be a large redundancy in "internal regulation" DNA, as many repeated strings would code for variable amounts of "control RNA". A mutation in one of the many repeat sequences would merely reduce the amount with one unit, which is equivalent to a neural net in which one of the connections would become slightly weaker so that it would produce slightly less activation. Neural nets are robust under such changes (and under even more radical changes, such as cutting several connections at once). What's more, they need such "noise" to adapt and learn efficiently. So, I wouldn't expect any catastrophic changes in genotypes because of a mutation in "regulatory DNA".
You need also to explain where would new genes come from. Since not all combinations of adenine, cytosine, guanine, and thymine will produce useful genes (via proteins or other genes), you would expect that there will be several "non useful" chunks of DNA.
"Silent" DNA would merely represent reduced activation. Another mutation may "reawaken" the DNA, and increase activation, although possibly in another node (other RNA type) of the genetic network.
In the workshop of a sculptor, you don't see ONLY finished works, do you? (especially if the sculptor likes to work on several works in parallel)
It's the same in a neural net. Babies start out with immensely more neurons and synapses than they will later use. Most of those are pruned or 'sculpted away' during cognitive development, and this sculpting continues throughout life.
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Francis Heylighen Evolution, Complexity and Cognition group Free University of Brussels http://pespmc1.vub.ac.be/HEYL.html
