Transforming a business to be more in harmony with nature can be tough going, especially when nature is woven into the fabric of a company’s products. It’s even more difficult when many of the unnatural systems -- government, the supply chain, and the marketplace -- work against you.

That’s the takeaway from my recent day-long field trip into California’s Central Valley, part of an annual pilgrimage by the Sustainable Cotton Project (SCP), a nonprofit group that helps cotton farmers switch to less-toxic farming methods and encourages major cotton buyers to purchase these farmers’ crops.

First, some background. Cotton is among the most toxic of crops. Its soft, fuzzy image belies the fact that it is tough to grow, due to its susceptibility to pests. In the U.S., a fourth of all pesticides are applied to cotton. It takes about a third of a pound of synthetic fertilizers and pesticides to grow enough fiber for just one T-shirt. Some of these chemicals end up downstream of cotton fields, in the air breathed by farmworkers and their families, and in the edible crops grown nearby.

The U.S. is the second-largest cotton producer in the world (after China) and California the second-largest cotton-growing state (after Texas). California’s cotton come from the Central Valley, the same fertile region that produces much of the nation’s food.

SCP has helped more than two dozen local farmers switch to integrated pest management (IPM) -- a method that relies on beneficial bugs and cover crops, with pesticides as a last resort -- and to organic farming, which shuns all chemical pesticides and fertilizers. Though most farmers are reluctant to change, many are drawn to the cost savings that come from cutting chemical use, and the potential profit of selling organic crops at a premium.

It’s not that simple, of course. Consider Claude and Linda Sheppard, who switched to IPM farming 13 years ago over concern about their children’s health, then moved to organic. Claude himself had gotten sick from applying the pesticide aldicarb, a toxic compound similar to a deadly chemical accidently released in 1985 at a chemical plant in West Virginia.

The Sheppards are a cheery, 50-something couple who treated a busload of SCP visitors (mostly from Nike and Patagonia, plus some students and a journalist) to a homemade Mexican lunch on the Chowchilla, Calif., farm once owned by Claude’s grandparents. They told their story and showed off their operation.

It’s no walk in the park. Farming organically is a labor-intensive effort. Harsh chemical defoliants traditionally used to force open cotton bolls so they can be harvested are replaced by milder, citrus-based ones that aren’t as effective. That means the Sheppards’ cotton-picking machines must comb fields twice to grab the harvestable crop, and some cotton is lost. When pests invade, organic remedies can take weeks to work, unlike the instant results from aerial-sprayed chemicals.

That’s just the beginning. To be certified organic by third-party firms -- a prerequisite for buyers like Nike and Patagonia -- the Sheppards must pay for ginning facilities to be thoroughly cleansed of conventional cotton and for a bale or more of organic cotton to be sacrificed to flush the system. Those sacrificial bales must be sold as conventional cotton at much lower prices.

There’s more. Organic certification requires that the Sheppards pay fees and taxes conventional farmers needn’t pay. It also requires extensive, time-consuming recordkeeping.

Most frustrating of all is the demand for organic cotton, which has softened in recent years. Early pioneers -- Gap, Levis, and Esprit -- have severely cut back or curtailed organic cotton buys. (Nike, for one, has pledged to increase its purchases.) As a result, organic cotton farming in the Central Valley has dropped from 11,000 acres a few years ago to only about 1,000, though IPM farming is on the rise.

The Sheppards, who once saved enough money by cutting chemicals to build their house, have lost money the past three years and are hard-pressed to make loan payments. But they remain steadfast in their belief that organic is the better way. Their commitment is inspiring, to say the least.

"I hate the thought of going back to chemicals," says Linda, a mother of five. "I want my grandchildren to be able to play in the dirt. When you’ve lost that, you’ve lost a lot of things."

Amen to that.

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Joel Makower is editor of The Green Business Letter and producer of GreenBiz.com.