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The answer is the reigning racial discrimination doctrine used from about 1890 until the 1950’s that enabled segregation.
"Separate but Equal" was the notion that blacks and whites should use separate facilities, but that each of those facilities would remain "equal" in quality. This idea allowed segregation - or, the institutionalized separation of black and white people - to persist until the Civil Rights movement of the 1950's-1960's.
The actual phrase derives from an 1890 Louisiana law which required "all railway companies carrying passengers on their trains in this state, to provide equal but separate accommodations for the white and colored races."
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