PaperProphet said:
Do you have any thoughts on whether or not molecules at the top of a gas filled tube would be cooler than molecules near the bottom?
This isn't a matter of "thoughts", it's a matter of physics, and the answer can be worked out from physical principles. That is what the other posters in this thread have been trying to get you to do.
Here are the key physical principles involved. We are assuming that the system is in equilibrium, i.e., nothing is changing with time.
(1) There must be no net heat flow anywhere in the gas. That implies, as you have assumed, that there cannot be any variation of temperature anywhere in the tube; the entire tube must be at the same temperature. The question then is, how does this relate to the effects of gravity? So the next thing we need to look at is, what are the effects of gravity?
(2) The effect of gravity is that the gas inside the tube must be in
hydrostatic equilibrium. That means, if we consider a small parcel of gas at a given height ##h## in the tube, with a small thickness ##dh##, there must be a pressure difference from the bottom to the top of the parcel, and this pressure difference must be just sufficient to balance the weight of the gas above the small parcel we are looking at. If we work out what this means, taking the limit as the thickness ##dh## goes to zero, we get the equation
$$
\frac{dP}{dh} = - \rho g
$$
where ##dp / dh## is the rate of change of pressure with height, ##\rho## is the density of the gas, and ##g## is the acceleration due to gravity (we assume this is constant everywhere in the tube). The fact that ##dp / dh## is negative means that pressure decreases with height.
(3) Also, it is important to realize that the pressure, density, and temperature of the gas are not independent; they are related by an equation of state. For this case, we can assume that the equation of state is that of an ideal gas, which is
$$
P = \rho R T
$$
where ##P## is the pressure, ##\rho## is the density, ##R## is a physical constant called the "gas constant", which will depend on the chemical constitution of the gas, and ##T## is the temperature.
If we assume that ##T## is constant, the above equations tell you that ##P## and ##\rho## will vary with height in the tube. Can you see how they will vary? And can you see how that explains how the temperature can be constant in the presence of gravity?