The 3-person rule for Nobel doesn't make sense at all.
Tough day to be Ed Boyden. Another casualty of the academic hierarchy.
Obviously Karl and Ed worked together, but it's pretty clear that the idea was Ed's. He came up with it 5 years before the Nature Neuroscience paper was eventually published!
"... in May 2000 I e-mailed the opsin pioneer Janos Lanyi, asking for a clone of the N. pharaonis halorhodopsin, for the purpose of actively controlling neurons with optogenetics. Janos kindly asked his collaborator Richard Needleman to send it to me. But the reality of graduate school was setting in: unfortunately, I had already left Stanford for the summer to take a neuroscience class at the Marine Biology Laboratory in Woods Hole. I asked Richard to send the clone to Karl."
Karl wanted to try a magnetic bead-based stimulation system, but Ed realised that optogenetics could be the way after Nagel et al. published their 2003 PNAS paper.
Ed was the one to propose the idea to Karl. Karl, being higher up the hierarchy than Ed, was the one to then email Nagel asking for the constructs.
Karl then optimised the expression of the constructs, but it was Ed who did the actual experiment showing optogenetics in neurons for the first time:
"Late at night, around 1 a.m. on August 4, 2004, I went into the lab, put a dish of cultured neurons expressing ChR2 into the microscope, patch-clamped a glowing neuron, and triggered the program that I had written to pulse blue light at the neurons. To my amazement, the very first neuron I patched fired precise action potentials in response to optogenetic stimulation with blue light."
Karl did a lot of the work pushing it to in vivo imaging, but what is the prize actually for? In my opinion, the prizes should go to actual discoverers: people who conceive of ideas.
This one could have gone to four people (at least), but if I had to drop one person, I'd probably drop Nagel and give it to Deisseroth, Boyden, and Hegemann. Hegemann had the radical hypothesis that a channel was directly gated by light—Nagel only got involved because Hegemann contacted him to use his tools/methods.
But yeah when the Nobel committee are weighing up a corresponding author (Deisseroth) and a PhD student first-author (Boyden), they're obviously going to go with the senior author. Sad!