The theory is that the carbon-based fuel acquired its carbon from the atmosphere recently during creation of said fuel, was burned, and returned the same carbon back to the atmosphere. Free CO2 is absorbed into a plant, plant is converted to biodiesel, biodiesel is burned, emissions consists of same carbon atoms absorbed not long before. Net atmospheric carbon change: zero.
Whats the carbon footprint from building the thing?
But then again, I'm an engineer. And a skeptic. And a global warming denier. However, IMHO the jury is still out on whether AlGore is a shrewd con man, or a blithering idiot.
:-)