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Why is that when you scuff with your shoes on, charges move (since electrometer moves back and forth), but if you don't have your shoes on, the electrometer doesn't move.

Here's the corresponding video detailing the event.

It is at about 47 min of video from beginning. I don't get the logic behind it.

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In the linked video he is demonstrating that there is always some conductivity through any matter. He uses the well known phenomenon that when rubbing what is nonconducting material, charges separate from the surface atoms, and some stay on the mat and the opposing ones are seen on the electroscope. The fact that the electroscope stops showing charge when he stops scuffing means that the neutral balance is regained easily even though there is a large resistance to ground through his body and shoes. The small conductivity is enough to drain the charge back to ground, ground being 0 charges.

Without shoes the resistance to ground level is smaller and the rubbing does not build up charge measurable by the electroscope because it is immediately dispersed back to ground.

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