I’ve just completed a disturbing article for BusinessWeek.com about Doug Kirkpatrick, a Michigan farmer who is committed to raising natural beef, pork, and poultry, and selling directly to consumers.

He ran into a problem nearly a year-and-a-half ago when several of his cattle tested positive for bovine TB, a serious disease that cows can get from wild animals like deer. I report on the difficulties he’s encountered dealing with regulators from the Michigan Department of Agriculture (MDA) and the U.S. Department of Agriculture (USDA).

Doug is a very intelligent and conscientious farmer—someone who is completely upfront with his customers and everyone else he deals with–who’s been nearly forced out of business because the regulators won’t allow him to resume raising cattle and hogs. He’s also very brave in going public with his tale of frustration; most farmers in his situation are so intimidated by the regulators that no one hears about their experiences–which is exactly how the regulators want it. Doug has taken a significant risk in sharing the details of his ordeal, since he is still at the mercy of MDA and USDA.

What does his experience say about the National Animal Identification System (NAIS)? If you read (and believe) the USDA’s rhetoric about NAIS, you’ll see that the system is designed first and foremost to be “a modern, streamlined information system that helps producers and animal health officials respond quickly and effectively to animal disease events in the United States.”

Knowing what Doug has gone through, I’d say the key word in that stated goal is “respond.” If Doug’s case is typical of what farmers can expect for a response, then they have every reason to be afraid of NAIS.

“Dealing with the USDA and the MDA has been awful,” Doug told me. “They take over. You can’t do anything without getting their approval,” including re-launching the main farming operation.

Would the regulators be the same with NAIS in place? No one knows for sure, but I for one would expect them to be even more aggressive, more “creative.” With ID tags and records on each animal, they could go off on all kinds of tangents—i.e. “Gee, Doug, we see you bought your diseased animals from Farmer Jones a mile down the road, so I guess we’re going to have to quarantine his farm as well…and, oh yeah, we see a dozen of your turkeys came from a farm we just shut down last month, so unfortunately we’re going to have to condemn those 1,000 turkeys we thought were okay. Gee, we’re really sorry…And with so many farms being quarantined, we’re backed up the you-know-what with paperwork. Looks like it’s going to take us two years instead of one year to get your herd plan straightened away so you can resume farming.”

What Doug has discovered is that the regulators care primarily about doing everything possible to cover their rear ends; they care little about small farms, which are in fragile financial condition and which tend not to be a source of major disease. NAIS creates an entirely new paper trail that the regulators will likely conclude they can ignore only at their own peril.