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Thank you for your post!

I've seen Pax-6 described both as a regulatory gene and a master control gene. This article calls it the eye gene, but perhaps more appropriately the eyeless gene. When it is expressed, it says to "make eyes."

Homologs of the eyeless gene found in Drosophila have also been found in a variety of vertebrates (including homo sapiens), insects, cephalopod, ascidians and nemerteans. The homolog of the eyeless gene of Drosophila is called the aniridia gene in humans and Pax-6 in mice. The genes all have much in common, including extensive sequence identity, the same three intron splice sites, and similar expression during development.
So what would happen if a mouse eye gene was introduced into a fruit fly genome? When the researchers induced expression of the mouse Pax-6 gene in the Drosophila fruit fly, additional (fly) eyes sprouted at the sites of the gene expression.
"The observation that mammals and insects, which have evolved separately for more than 500 million years, share the same master control gene for eye morphogenesis indicates that the genetic control mechanisms of development are much more universal than anticipated," note the researchers.

The eyeless gene appears to produce a protein that appears to be a transcription factor. The current hypothesis is that when expresses, this protein binds to a specific set of genes and basically says 'make eyes'. The discovery of this 'master control gene' will help researchers coordinate the extensive data they already have on some of the genes involved with the development of vision, and will also probably reveal the presence of many other vision-associated genes.

Below is an article on the Pax-6 protein which suggests the earliest role may not be related to eye development because the organism had no eyes. Seems to me that would work against the random mutation pillar since Pax-6 expressing eyes spans across the species.

Why would they overwhelming mutate, randomly, in the same way? Sounds more like "pre programmed adaptation capability" to me - more like the above article describes.

Distribution of Pax 6 Protein during Eye Development (pdf)

I've seen Pax-6 described both as a regulatory gene and a master control gene.

Master control genes are regulatory genes.

Why would they overwhelming mutate, randomly, in the same way?

That's a good question and open for exploration. It's a highly adaptive direction to mutate, and other mutations may be very deleterious, that is, evolutionary options may be limited. Some suggest horizontal gene transfer in the same way that bacteria share antibiotic resistance genes. We don't know yet, but there are quite a number of people doing research in this area.

Sounds more like "pre programmed adaptation capability" to me...

What sort of evidence is there for "pre programmed adapation capability"? This front-loading idea is a favorite of IDists, but what is a plausible scenario for it? How does it work at the molecular level?