Microwaves are a kind of radiation: their frequency is the same as the frequency that water molecules vibrate at. So when you turn it on any water in the microwave will vibrate and heat up. So when you are heating up some food you are really only heating up the water in the food.
Sometimes it can go wrong though: last year I had a case where a lady put a glass jug in the microwave and the glass melted. That is definitely not supposed to happen!!
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