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Biodiesel emissions are significantly lower than the emissions from an engine burning normal diesel.
Biodiesel contains oxygen and this is one of the reasons that it burns more completely. Carbon Monoxide, Particulate Matter, Hydrocarbons and all the other air pollutants except for Nitrous Oxide are reduced. Interestingly Carbon Monoxide and Particulates are a sign of incomplete combustion in an engine. Carbon Dioxide is also reduced but this is not categorized as a pollutant by the EPA. It is however one of the biggest green house gasses contributing to global warming. So a reduction in CO2 is a good thing.
The carbon that is being released when burning biodiesel does not contribute to an increase in green house gasses and Global Warming. To illustrate this imagine a field where a sunflower is growing. As it grows it gets bigger and absorbs carbon from the air in the form of CO2. When the sunflower is harvested and the seeds are pressed the carbon forms part of the oil. When the oil is burnt the carbon goes back into the air and is ready to become part of another plant. When fossil diesel is burnt the carbon which has been buried underground for millions of years is added to the air, and increases the overall amount of carbon in the atmosphere,.
The only biodiesel emissions that increase are Nitrous Oxide (NOX). Nitrous Oxide is also known as Laughing Gas and it is used as an anesthetic especially by dentists. It is the only one of biodiesel's emissions that increases compared to fossil diesel. NOX is formed in an engine's cylinders when nitrogen from the air comes into contact with oxygen at a high temperature. NOX is also used as a booster fuel for drag racers and rockets.
High NOX can cause smog and ozone both of which are harmful especially in cities. For this reason NOX emissions are regulated and there are government bodies that frown upon biodiesel for this reason.