The original idea of using zoning codes to separate residential from industrial uses was fear that people would want to put factories into residential neighborhoods whose residents deserved protection from the pollution and such that would result. But over time as zoning codes have grown stricter and the structure of the American economy has shifted, we've found ourselves with a lot of the reverse phenomenon—areas where developers would like to put housing and office buildings but that's specially zoned for industrial uses. This is an odd sort of roundabout subsidy for locating manufacturing facilities on urban land that's probably not very appropriate to it.
Here's a paper from a couple of years ago by Roderick Hills and David Schleicher that makes the case against this practice, which reduces housing supply and is costly to cities' economic development.
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