Imagine a thunderstorm. Above the thunderstorm hot air is going up. It is hot because it rained. You are cold when you get out of the shower. This is like that, but backwards; latent heat is released so air is hot and it rises. That rising hot air is replaced with cool air dropping, because nature abhors a vacuum.
So the plane is flying horizontally through rising air in some places and falling air in others. Things shake when you hit the boundary.
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