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There are a number of theories about the origin of loon as it refers to a crazy person, its most common current meaning. One is that it comes from loony, meaning "crazy." But based on currently available evidence, loony is a late 19th-century alteration of lunatic that didn't come into use until decades after the meaning of loon in question. (It's still possible that loony influenced the development and spread of this meaning of loon.) Another guess is that this loon is from the avian loon, inspired either by the bird's maniacal cry or its displays to distract predators, such as skittering over water with its neck crooked.

This is certainly possible, and is the origin story favored by some. But the story our dictionaries favor is a bit more quotidian: the current use of loon developed from earlier uses, primarily in Scottish and other northern dialects of British English, of loon to refer to a lout (an awkward, brutish person) or idler (someone who is idle, lazy, or inactive). While that loon, which is from Middle English loun, never spread to British English more broadly, immigrants from the regions where it was used had a significant influence on American English, and it's not far-fetched to posit that their loon developed into the distinctly American use of the word to refer to daffy people.