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I have seen time Gravitational time dilation experiments measured using atomic clocks on airplanes, such as the Hafele–Keating experiment. The clocks aboard the airplanes were slightly faster than clocks on the ground. This is measured from the point of view of the clock on the ground.

Is it possible, that the time dilation you see in this experiment is due to the distant between the 2 clocks and not gravitational effect? Perhaps the time difference observed is due to the time it takes for what ever time is to travel between the 2 clocks.

Have there ever been an experiment where they take two clocks ON THE PLANE, then take one to the ground for some time, then take it back to the plane so the observation is from the starting point of the plane?

Just wondering as if gravitational time dilation is true then if you reversed the experiment you would still see the same results.

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Is it possible, that the time dilation you see in this experiment is due to the distant between the 2 clocks and not gravitational effect? Perhaps the time difference observed is due to the time it takes for what ever time is to travel between the 2 clocks.

No, the clocks were compared at the end when they were all physically together. So the distance was negligible as was the light travel time.

Have there ever been an experiment where they take two clocks ON THE PLANE, then take one to the ground for some time, then take it back to the plane so the observation is from the starting point of the plane?

As far as I know this experiment has never been done. There is also no theory that I know of which predicts anything different for this scenario than what was actually measured.

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