Re: Does the upper atmosphere rotate with the earth?

Winds on earth are caused by differences in temperature across the planet. 
In the troposphere, the lowest 30000 to 50000 feet or so (depending on the 
latitude and the season), the difference in temperature between the poles 
and equator results in a global circulation pattern.   In the northern 
hemisphere, this causes weather systems in the tropics to move from east to 
west while weather systems in the middle latitudes (roughly 30 degrees 
north to 60 degrees north) move from west to east.  North of 60 degrees 
north, weather systems tend to move from east to west again.  While the 
wind at any one location on the planet may periodically reflect the 
prevailing global flow, the wind at any location more often reflects 
weather systems moving through the area or local differences in 
temperature.  Warm fronts, cold fronts, areas of high pressure, areas of 
low pressure, and thunderstorms (or thunderstorm complexes) are examples of 
weather features that will affect local winds.  Sea breezes and variable 
winds in mountainous areas are examples of winds that result from local 
temperature differences.

As differences in temperature across the planet, hemisphere, country, 
state, and county can drive the wind on various scales of motion (global, 
hemispheric, etc on down to the local level) the result is that all of the 
atmosphere does not move at the same speed.  Even upper levels of the 
atmosphere have temperature differences across different scales so that the 
wind at 70000 feet over Chicago wont be blowing the same as the wind at 
70000 feet over Miami.  As a result, it would not be possible to dye a spot 
in the atmosphere red since it would be scattered by the wind.  

This discussion of winds has been purposefully general as wind and weather 
is a very complicated subject.  For further information consult weather 
guides readily available in bookstores or libraries.  For more detailed 
information about upper levels of the atmosphere, consult the following 
meteorology texts:

Middle Atmosphere Dynamics by D.G. Andrews, J.R. Holton and C.B. Leovy
The Dynamic Meteorology of the Stratosphere and Mesosphere by J.R. Holton