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What biodiesel enthusiasts did not realize before they began trading in their gasoline powered cars for diesel powered ones is that, although the EPA is happy to replace the diesel burned in buses and heavy transport trucks with a cleaner fuel (biodiesel), it would not want to see everyone trade in their gasoline cars (with their three stage catalytic converters) for diesel cars even if they burn soy-based biodiesel because of the increase in pollutants. It is one thing for industrial trucks to use biodiesel. They have to use diesel engines for their higher torque, and with the exception of NOx and hydrocarbons, biodiesel is cleaner than regular diesel, but thanks to air-pollution controls (that cannot be applied to diesel yet) soy-based biodiesel is not cleaner than gasoline-powered cars at this time. Half of the cars in Europe run on diesel and they are a major source of air pollution there. That is why the EPA would like to restrict their usage here.

The question isn't whether biodiesel is cleaner than diesel, it is. The question is, do people who opt to buy a diesel car to burn biodiesel know that it will have a worse EPA pollution rating than an equivalent gasoline car (source1, source2)? They can buy cars with a higher score if they are concerned about that issue. Most think that a biodiesel burning car is the cleanest machine available and it isn't, not by a long shot. It has benefits and downsides like all energy sources. One must weigh the benefits and the downsides (once they are known) to make a decision. Some people care not a wit about anything but cost. Some people make biodiesel out of free waste oil because it is cheap and want nothing to do with the tree huggers. Most people will buy the cheapest fuel available, regardless of environment downsides. Some people won't buy it because it supports environmentally damaging industrial agriculture, others because it is already beginning to destroy rainforests in South East Asia, Africa, and South America, while yet others are concerned that if the food crop source gets too dominant, it will drive up food prices, which is also already starting to happen.

If you buy a new Jetta, Golf, or Beetle diesel today and burn 100% biodiesel, you will also produce 30 times more  NOx (at the tail pipe) than the equivalent gasoline powered car. Note here that a car with a score of 9.5 (a gasoline Golf) is allowed to emit up to 0.02 grams of NOx per mile. A car with a score of 1 (a diesel Golf) can emit up to 0.6 grams per mile (the 2006 Jetta emits 0.55). That is 30 times more NOx per mile. Since a diesel Golf emits about 30 times more NOx than a gasoline powered Golf, one must conclude that a biodiesel Golf would be at least as bad in this respect since biodiesel emits 10% more NOx than even diesel. And once again, you will find diesel enthusiasts arguing that NOx emissions are not important, again at odds with the EPA which has worked for decades to reduce that pollutant. Massachusetts, Vermont, New York, Maine and California do not allow the sale of new diesel cars just for that reason. The Texas Commission of Environmental Quality is trying to get B-20 banned because it exceeds NOx limits. Volkswagen will not sell the diesel versions of the Jetta, Golf and Beetle models from its US line-up for the 2007 model year due to their inability to meet the new, incoming stricter emissions standards nationwide.

According to an EPA study of biodiesel emissions, biodiesel emits half as much particulate matter as conventional diesel. But, this still means that a Golf running on 100% biodiesel emits four times  more particulate matter than the equivalent gasoline Golf. Particulate matter (sooty particles) are a major health concern and are also a potential concern for global warming. You will find some diesel enthusiasts arguing that soot is also not a big health concern, which puts them at odds with the EPA.

Hydrocarbon emissions are also a point of contention in the issue of diesel, biodiesel, and gasoline. Diesel and soy-based biodiesel are essentially equal in hydrocarbon emissions because, although soy biodiesel produces about 35% less at the tail pipe, the production of that biodiesel produces about 35% more hydrocarbons than the production of conventional diesel. The HC issue boils down to evaporative losses (no pun intended). When one accounts for the higher volatility of gasoline you find that HC is being released into the atmosphere away from the tail pipe, in the loading and unloading of gas by tankers at the gas pump nozzle. The EPA works to control these emissions and apparently does not go so far as to promote diesel cars as a solution to the problem (as diesel enthusiats would like to see).

In conclusion, you get to pick your poison but at least now you have heard  information that is missing or hard to find so you can make an informed decision. The chemical properties of biodiesel are in my opinion less of a concern than its already demonstrated capacity at this early stage to destroy biodiversity and carbon sinks. If you don't buy that agurment or care about those things, then your decision will be shaped by other considerations. Making decisions without hearing all sides to an agument is just not optimal. One way to have your cake and eat it too is to only use biodiesel made from waste.

Ultra low sulfur diesel fuels will start making their way into the market in the next few years. This will allow some diesel engine manufacturers to put improved pollution controls on diesel engines making them almost as clean as gasoline cars are today. In other words, you will get low emissions from diesel engines without using soy-based biodiesel. Soy-based biodiesel will lose that advantage while maintaining its disadvantages: the consumption of 10 football fields (14 acres) of soy oil per car annually, as well as vast quantities of water, pesticides, fertilizer, all with massive government subsidization. What is true today won't be true tomorrow. Hopefully diesel cars will get much cleaner and hopefully the continuous destruction of our carbon sinks and biodiversity won't be exacerbated by biofuels.

One last  thing to keep in mind is that this discussion is about emissions regulated by the EPA for their short term health risks. CO2 is a non-toxic, non-regulated gas. In my opinion, the price already starting to be paid by destroyed carbon sinks, lost rainforests, dead zones in the Gulf of Mexico caused by agricultural runoff easily outweigh the benefits of using food crops to reduce CO2 in the US by a fraction of a percent.

From a biodiesel friendly article by the Union of Concerned Scientists:

"In a full lifecycle assessment, smog forming HC [hydrocarbon] emissions were 35% higher than conventional diesel."