As an adjective, it describes something that is higher in position, level, or rank. As a noun, it can mean the top part of a shoe or an informal term for a stimulant drug.
From 'up' + the comparative suffix '-er', used since Middle English. It mirrors pairs like 'high'/'higher' to express relative position.
Upper is literally 'more up', the comparative form of 'up' even though we rarely think of it that way. The shoe sense is neat: the 'upper' is just the 'up' part of the shoe above the sole.
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