The Center for Biological Diversity and its allies weren’t the only ones who found serious problems with the San Diego Multiple Species Conservation Program. Inside the Fish and Wildlife Service, two biologists, who have since left the agency, harbored private doubts.

Jacalyn Fleming spent two years at the service’s Carlsbad office north of San Diego, writing a biological opinion for the habitat plan. “Innately skeptical” at the start, she says, she grew more disenchanted with the plan as time passed, and left her job for personal reasons soon after the plan was approved by the San Diego City Council. Today, she works as a lawyer on Long Island, practicing zoning and other land-use law.

“I did and do believe that a large-scale approach to habitat conservation, based on preserving interconnected areas, is the proper approach based on sound biological principles,” she wrote in an e-mailed interview. But all the habitat on the county’s west end was already extremely fragmented, she said, and there was no political will to put together a plan that would prevent, much less erase, development. The core areas that were supposed to be connected were already largely isolated and fairly fragmented, and little more than half of the planning area’s remaining land would be conserved.

The limits of the program’s science were openly discussed by everyone at the agency, she said: “It was acknowledged that for many of the species of concern, there was inadequate understanding of their natural history, genetics or numbers.” But when she raised concerns with her superiors, Fleming said, they responded that the plan required “adaptive management.” In her words, “preserve management would be tweaked to save any floundering species or populations.”

One of Fleming’s former supervisors, Sherry Barrett, says the service was working with the best information available. “You have to take some sort of risk,” says Barrett, today the agency’s southern Arizona field supervisor in Tucson. “If you didn’t, it was all going to go away very quickly. If we had waited five or 10 years for more information, the options for preserve design would have been significantly diminished.”

But the service was in such a hurry that it often failed to make use of the science it had, says former agency biologist Fred Roberts. He left the service in 1999; today, he is a private consultant and board member for a leading critic of the program, the California Native Plant Society.

Roberts singles out the willowy monardella, a perennial herb in the mint family with lance-shaped leaves and pale white to rose-colored flowers, which thrives in sandy washes and floodplains. There are only about 6,000 of the spearmint-scented plants left in the United States. The service listed it as endangered in 1998, a year after the conservation program promised to protect it.

But after the plan was approved, Roberts and other agency officials noticed something peculiar. One population of about 200 to 300 plants, growing at the bottom of a steep bank in Carroll Canyon, had been shown on earlier maps as being within the preserve. The final maps, however, left the plants outside the preserve boundaries — in an area where the City of San Diego has approved building a business park.

Exactly how this happened remains a matter of debate. Roberts believes the service intended to protect the Carroll population, and that the maps weren’t properly drawn. But Patrick Mock, a biologist who helped shape the original plan while working for a private consulting firm, asserts that it was never a “core” population, and was never intended to be preserved.

The Fish and Wildlife Service has since allowed the plants to be removed, but no plans are in place for replanting them. According to Cindy Burrascano of the California Native Plant Society, all previous attempts to transplant willowy monardella have failed.

The native plant society is now pressing a lawsuit charging violation of the Endangered Species Act, after losing a suit based on California law.