STOCKTON – Bill Jones has left government. But as a businessman pushing the most popular – and perhaps the most controversial – alternative to petroleum, he seems more enmeshed in politics than ever.

Jones, a former California secretary of state and a candidate for governor just six years ago, is chairman of Pacific Ethanol, a fast-rising company that opened the state's largest ethanol plant here earlier this month.

It is a gleaming facility that stands out in the otherwise grimy Port of Stockton, sitting at the end of a long, curving ribbon of jet-black asphalt paralleled by a shiny new railroad spur. Both are getting plenty of use as 100-car freight trains deliver Midwestern corn and trucks rumble from nearby fields or head out filled with fuel.

The plant itself is state of the art, controlled by two employees at a time sitting at computer terminals. A few dozen other employees putter around in shifts doing maintenance and other minor tasks that can't be automated.

Whether the corn arrives by road or rail, the kernels are quickly dumped through metal grates onto an underground conveyor belt, then combined with enzymes and yeast, heated to 90 degrees and fermented.

The fermented product is piped to a massive still and boiled so that the ethanol steam can be separated from the liquid, then cooled and trucked to Northern California oil refineries, which blend it with their gasoline to create a cleaner-burning fuel. Most of the water that remains behind is recaptured and reused. The corn mush, once it gives up its sugars to make the ethanol, is dropped from another belt into two huge piles inside a cavernous building.

That mush – known as wet distiller's grain – will be one of the secrets to the plant's success if all goes according to plan. The grain is packed with protein and some fat, a power meal for the cows at nearby dairies. Because of that proximity, Pacific Ethanol can sell the stuff as feed and deliver it fresh, instead of having to dry it for long-distance shipping. That means the plant can forgo a drying process that, in a typical Midwestern ethanol refinery, accounts for 30 percent of the energy use.

Jones and his business partners are hoping that their design and strategy will allow them to sell all the fuel they can produce into a California market that currently imports 80 percent of its ethanol from the Midwest. But questions remain about just how large that market will become.

Corn-based ethanol burns cleaner than gasoline, but it has always been dogged by questions, never more than now. The industry emerged thanks to massive federal subsidies, and even today, the government gives the oil companies 45 cents for every gallon of ethanol they blend with gasoline.

At the same time, the government mandates that every gallon of gasoline include at least 6 percent ethanol, a standard that, in California, will soon rise to 10 percent.

Critics point out that ethanol, because it is not as dense a fuel, does not produce the same fuel efficiency as gasoline unless cars are modified to run on either product. And because corn must be heated to ferment and distill it, some say ethanol actually provides no advantage over the fossil fuel it replaces.

But the real debate that will shape the industry's future is just beginning, as California and the nation grapple with global warming by looking for ways to reduce the emission of greenhouse gases, especially carbon dioxide. Reliable studies, including one by the Argonne National Laboratory, have concluded that ethanol produces 30 percent to 40 percent fewer emissions than gasoline, even when the entire process, from the farm to the tailpipe, is included.

The one factor that comparison does not include, however, is the indirect effect of moving land from pasture, forest or other types of farming into growing corn for ethanol. If corn yields remain constant and demand for other corn-based products doesn't decline, this theory goes, then every acre of corn used for ethanol will have to be replaced with an acre of corn to take its place in the food supply. If the land used for ethanol is taken out of other crops, then that food will have to be replaced as well, increasing carbon emissions as forests or grasslands are turned into farmland.

The California Air Resources Board is currently studying whether to count the effects of those indirect land shifts against ethanol as it tallies up the carbon content of alternative fuels. Depending on which numbers the regulators use, ethanol's value as a greenhouse-gas fighter might be considered nil, bringing the growth of the industry to a screeching halt just as it is gaining a foothold as viable alternative to petroleum.

"That doesn't make any sense from a public policy standpoint," Jones said. "This idea of indirect land-use impacts is not based on science. It's based on economic modeling that is hypothetical and unproven." Jones, his company and his entire industry will soon be mounting a full-court press to persuade regulators not to count those hypotheticals.

For this former state official, it seems, his new business is every bit as political as his old one.

Call The Bee's Daniel Weintraub, (916) 321-1914.