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Da steh’ ich nun, ich armer Thor! Und bin so klug als wie zuvor.
I take it you didn't read the whole article then?

But while losing your life is in question, you would most definitely lose the hand.

That’s what it says but that conclusion doesn’t feel any more solid to me than all those in the video.
Thus confirming that it's actually quiet a difficult problem, important given that quiet a few in the comments on the video suggested they should have definitely knew thing kind of thing off the cuff.
No need for theories when sadly there is real-world data:

http://en.wikipedia.org/wiki/Anatoli_Bugorski#Particle_accel...

The U-70 did, iirc, 70 GeV. A bit under a hundred times less energy per proton, and with an unknown number number of total protons. (Technical data is a bit light on the ground for a 50 year old Soviet particle accelerator.)
That's incredible, poor guy. It doesn't sound like he got a great deal of compensation, either - I'd be fairly hacked off if my face was half-melted off because of someone else's / a machine's incompetence.
He doesn't look very happy in those pictures. A reminder that all sorts of weird stuff can go wrong in life :-(
He is able to function perfectly well, except for the fact that he has occasional complex partial seizures and rare tonic-clonic seizures.

How the hell is that perfectly well!? Sounds like something out of a Monty Python sketch ... oh just some small seizures, but he's fine really. It's perfectly safe to stick your head in a proton beam kids. Perfectly safe.

Really interesting though, I was under the impression the beams needed a very strong magnetic field to remain stable. How come he was able to stick his head in one?

It says "except". Except when he's having his occasional or rare seisures, he's functioning perfectly well.

Which is pretty good, since the initial medical reaction was to watch him die.

Right. This is on par with Phineas Gage - considering that they both had something ridiculous pierce their brain, and shouldn't have expected to survive, they both did pretty okay.
The question is somewhat complicated by the fact that to reach the beam, you have to be in vacuum...