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The cloud starts of with a lot of protons and electrons. Soon enough, the electrons start to get pulled down in the cloud because of the protons on Earth. Also, it is electrons and not protons that get pulled down because protons are harder to move because they are in the center of the nuclei in an atom. In other words, the protons on Earth cause charge separation in clouds because opposites attract, and the protons on the ground pull the electrons down.

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Q: What causes a charge separation in clouds?
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