“Yes, there are some large organizations that make up a portion of the board, but they’re not at all a majority,” says Will Daniels, senior vice president for operations and organic integrity at Earthbound Farms Organic, one of the country’s largest organic produce processors. “Four of the 15 board members could be considered from a corporate structure, a number that means they don’t have power to do much of anything.”

Those four are Earthbound, Driscoll Strawberry Associates, Whole Foods and the Zirkle Fruit Company. Only one of them, Earthbound, has a fully organic business.

Critics say the system has never truly operated as intended. “It’s been neutered,” says Mark Kastel, director of the Cornucopia Institute, an advocacy group.

Cornucopia began taking a harder look at the history of the addition of carrageenan and other substances to the accepted organic list after a bruising battle last December over the addition of docosahexaenoic acid algae oil, or DHA, and arachidonic acid single cell oil, or ARA. Its research led to a paper titled “The Organic Watergate.”

“After DHA got onto the list, we decided to go back and look at all of the ingredients on the list,” Mr. Kastel says. “The average consumer has no idea that all these additives are going into the organic products they’re buying.”

Mr. Potter of Eden Foods was initially supportive of the government’s efforts to certify organic products. But he quickly became disenchanted. He has never sought a board appointment, for himself or anyone at Eden. “I bought into the swaddling clothes wrapped around it,” he said. “I had high hopes the law and the board would be good things because we needed standards.”

By 1996, he realized that the National Organic Program was heading in a direction he did not like. He said as much at a National Organic Standards Board meeting in Indianapolis that year, earning the permanent opprobrium of the broader organic industry. “They think I’m liberal, immature, a radical,” Mr. Potter says. “But I’m not the one debating whether organics should use genetically modified additives or nanotechnology, which is what I’d call radical.”