What were the origins of that turbulence?
The cause last night was vertical wind shear, a large change in wind speed/direction with height. We were not flying in clouds or storms, and the turbulence was not connected with any terrain feature.
Take a look at the vertical sounding at Medford, Oregon, at about the half-way mark of my bumpy trip (see graphic). The pennants give you the winds-both the direction and speed (big solid lines are ten knots, triangles are 50 kts.) The height in pressure (millibars) and meters are shown on the left. The plane was flying around 36000 ft, 11ooo meters, for most the time. (This is around 250 mb). Between 250 and 300 mb
there was strong flow from the north (more than 100 knots), with the winds weakening rapidly below and above that level. The northerly flow slowed the plane down considerably, making the flight take longer by roughly 10-15 minutes. On the flanks of this wind maximum, above and below, there was large wind shear. At 5500 meters (500 mb) the winds were westerly at 15 knots, with weak winds below.
Wind shown by pennants (all I talk about). Solid lines are temperature and dewpoint (left one). Slanting lines you dry and moist adiabats and mixing ratio.
So why do we care about wind shear? Because if it is large enough, the atmosphere can breakdown into turbulent eddies. The fancy name for this breakdown is Kelvin-Helmholtz instability. And smaller scale turbulence can develop within these eddies. Sometimes you can even see this instability expressed in the clouds, as in the picture shown below. Looks like waves breaking at a beach...and like those waves there is lots of turbulence and sloshing around. Your plane enters an area with such shear-induced turbulence and it gets bumpy. Sometimes VERY bumpy.
I always pick a window seat when I fly (for obvious reasons!) and occasionally I see such clouds ahead. Last time I did told the person next to me to buckle up and they gave me a strange look. I told him I was a meteorologist and he smirked (the kind of smirk that says...sure...you guys can really predict ANYTHING). A few minutes later the plane was jerking all over the place and the seat belt sign was on. I bet he didn't joke about weather folks after that!
The thing about shear turbulence is that it is often limited in vertical extent and taking the plane up or down a few thousand feet can make a huge difference. That is why during uncomfortable rides pilots often chat with other planes and air traffic control to see how the "ride" is at different elevations and then alter their flight level if possible. "Testing" altitudes for better rides is not unusual. Interestingly, I know someone who flew the same root a half-hour earlier but at 41,000 ft and experienced virtually no turbulence.
Shear turbulence is probably the most important one for modern high-altitude jet travel, but there are others...mountain wave turbulence, convective turbulence from cumulus and thunderstorms, wake turbulence behind other planes (see picture at the top), and a few others. Fortunately, modern aircraft can handle the worst of it (except thunderstorms), but understanding what is going on certainly makes it more tolerable. And having your seatbelt on is essential...nearly all the injuries to passengers are to those unbelted.
The best web site for getting turbulence information is:
http://aviationweather.gov/adds/turbulence/
There you will find both current and forecast turbulence levels over the U.S.