Basically, I think "Green" the anonymous undergrad from a University in the UK, raised a few valid issues that are worth thinking about. A lot of the evolutionists, while I agree with their points on general terms, are not addressing the concern of "Green" directly.
Her main point is (from the comments at Panda's Thumb):
“Co-option may not be the de novo formation of genes, but it still requires mutations (such as, for example, the gain of a cis regulatory region). My whole point was that simultaneous mutations are required for the evolution of the phototransduction cascade. Correct me if I’m wrong, …”
This is in part true, and raises the point that we should be discussing EXAPTATION and not co-option, to most clearly convey the point.
Green is stating that even if all the components of phototransduction are present an ancestral genome that lacks phototransduction, multiple mutations would be required to assemble all those components into a phototransduction cascade. So, multiple co-option events would be required, and this is what she is having a problem with.
HOWEVER, what is false is the requirement for all these mutations to occur simultaneously. Instead, the components could be assembled one by one in a graduated, step-wise (Darwinian) fashion.
Instead of focusing on co-option, Green should focus on "exaptation". Exaptation is the idea (roughly) that features can arise for one function, and then change function later on. In the case of phototransduction, much of the phototransduction cascade originated for another purpose - sensing some signal from outside the cell to elicit changes inside the cell. (And just because a yeast pheromone cascade isn't THE phototransduction precursor, doesn't mean there wasn't one). One response to a signal evolves, changing the signal that is detected (to light) seems pretty surmountable. In fact, this has happened independently in the lineage leading to C. elegans (see my post here).
For another example of exaptation, we've found that many components used in synapses predate synapses themselves. See these posts in pharyngula, Newsweek. The open access paper and other news sites (including radio interview) are here.