The new diesels that this article doesn't mention are many times cleaner than any gasoline engine from a few years ago, and that's by the EPA's own gas-biased pollution scale which doesn't even take into account CO2 emissions. Check it out here:
www.fueleconomy.gov

The fact is, how recently an engine was made makes a much bigger difference in pollution than whether it's a gas or diesel.

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2004 VW Jetta TDI (manual)

Past MB's: '96 E300D, '83 240D, '82 300D, '87 300D, '87 420SEL