A ‘baker’s dozen’ is where a baker slips a gratis 13th bun into a customer’s order. (Also known as a long dozen, the phrase dates from 1599, but may refer to a much older practice of adding something to a batch to seem generous.) The banker’s dozen, by contrast, is much more recent. It can mean literally one less than the full dozen, ie 11 items instead of the expected 12: sometimes it just means a short measure of any kind.
More technically, the phrase may refer to a method of lending where interest or penalties are deducted before the loan is transferred, so the debtor borrows ten pounds but receives only nine. This topical reference to financiers’ avarice is probably the inspiration for a trader’s dozen which, in City of London slang, means a dozen drinks in quick succession on a Friday lunchtime (per person, that is), typically charged covertly to a client or employer.
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