The act of defecating or passing stool; also used informally to mean becoming very tired ('I'm pooped').
From imitative Middle English 'popen' (to break wind), derived from onomatopoeia. The word's origins are intentionally unflattering, which is why it's considered informal or childish in most contexts.
The word 'poop' as a ship term (the deck at the back) comes from a completely different French root, so English accidentally created a homophone that sounds silly—a linguistic coincidence that's hilarious.
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