I don't know how to operate a train. Does pushing a throttle up or down count as a "manoeuvre"? What's "tricky" about this? Am I missing something, or is the author embellishing here?
edit: grammar
1) The range of acceleration and deceleration rates available to a train engineer is much, much smaller than you would think. There is simply limited traction and power available and the weight of the full consist is really enormous. This requires planning everything well ahead, which can be difficult in busy areas where you must both anticipate signals and mind an often large number of temporary orders. Train operations tend to sort of happen in slow motion, it's not about fast responses simply because by the time you try to make a fast response the situation is already unrecoverable.
2) Depending on the exact systems in use, speeding up and especially slowing down a train is more complicated than doing so in a vehicle. You have multiple brake systems available (primarily the dynamic and train air brakes), and the most powerful brake system, the air brakes, comes with a lot of tricky caveats as to how strongly you can apply it (mostly related to applying and releasing it too frequently, which can drain the air reserves). There's a lot of great info on this from a former engineer here: http://www.alkrug.vcn.com/rrfacts/brakes.htm
Certainly the author has decided to dramatize the situation. For these reasons, train speeds are established with a wide margin for error (of course not one of an additional 100%+ as in this incident).
You can see what the engineer's station look like in the type of train discussed in the article here:
http://www.eweek.com/mobile/slideshows/amtraks-new-siemens-l...
Looks like there is a combined throttle/braking control on the left side, then (multiple?) brakes on the right.
Also FYI, maneuver isn't an error, it's the American English spelling.
Above the dynamic control on the left you see a small rotary lever - if I'm not mistaken this is the reverser, which simply selects between forward, neutral, and reverse. As a fun fact, this lever pops out and is used as the "key" for the train. For safety reasons, the engineer removes it when they leave the cab so that it's difficult to get it out of neutral.
The big red button left of the dynamic control is the alerter acknowledge. This is the dead-man protection on locomotives and I suspect may factor into the conclusion on this investigation. When an alarm sounds, the operator has to press that button. The alarm becomes very jarring so it might have brought a confused or unconscious operator back to attention.
I'd expect that trainee engineers are trained on specific routes. Whereas a car or truck driver would be expected to operate safely on roads they've never encountered before, this should not be the case for a passenger train engineer. So the difficulty would be doubly embellished.
It appears to me that the most difficult part about driving a train is remaining alert and sober, absorbing and executing the restrictions on the track, and doing so confidently well in advance of turns or restrictions. The theory presented in the article, that he was injured as a result of a rock throw and lost control of the train, seems like as good a conclusion as any. Especially given how unusually dedicated the purported evidence shows him to be.