Past tense of flail; to move your arms or legs wildly and without control, or to beat something with a flail.
From Old French 'flael' and Latin 'flagellum' (whip). Originally meant to beat grain with a tool, evolved to mean any wild, uncontrolled movement.
When someone flails, they're literally doing what medieval farmers did to separate grain—but panic has replaced purpose, and the tool became the body itself!
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