FORTUNE -- There's much more to New York's trash than meets the eye. Just ask John Doherty, commissioner of the city's Department of Sanitation. He knows more about keeping the city clean than probably anyone else alive, having risen through the ranks within the department since starting as a sanitation worker in 1960. Now, he's in charge of its nearly 8,000 uniformed workers and thousands of vehicles including collection trucks, street sweepers and salt spreaders. The city has changed considerably since the 60s, and so has its refuse. There's much less paper, Doherty says, with the popularity of e-readers and email, and you can't ship garbage on a barge to Staten Island anymore. He talks to Fortune about jumping rats and how to keep employees motivated after a particularly daunting snowstorm.