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Indeed, the issue is that we used to think eyes were the result of convergent evolution but now, because of the Pax 6 master regulatory gene, understand that all eyes have a common ancestor.

No, the Pax-6 gene is seperate from the genes that code for the eye. DNA evidence (as I posted above) indicate that those genes arose independently.

Amazing to me is that the gene is conserved across phyla. Between human and mouse, it is 100% identical and between human and drosophilia 94%.

It makes a lot of sense when you understand the phylogenetic relationship between organisms. Humans and mouse are much more closely related than humans and flies.

We also know that eyes form whereever they are expressed, i.e. ectopic (eyes on a wing, etc.) Mouse Pax-6 in drosophilia leads to fully formed ectopic eyes – and vice versa!

Yes. The genes for eye development are present in all tissues and Pax-6 (highly conserved) is able to activate the developmental pathway in several other tissues.

The assertion was that the Pax-6 in the common ancestor was a factor in survival. I challenged that assertion per se because at that level, the organism had no eyes – thus nothing manifest physically as a factor for survival.

I guess it didn't occur to you that transcription factors can be used for regulation of other genes. Recruitment of genes for different purposes is a common theme in evolution.

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)