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Royce Riggan Jr., a biological consultant in San Diego for 25 years, was driving back to his office at RBRiggan and Associates one Sunday afternoon in January. His route, from the west end of Miramar Road to his workplace in the heart of Mira Mesa, took him down Trade Place through the Miralani Business Park, where for a mile or more one long warehouse abuts another. The route also took him past a lone, fenced wetland habitat, alien in such a locale, on Arjons Drive. It was a habitat he knew well. Riggan, who describes himself as “one of the gray-haired guys” in environmental consulting, had helped designate this 8.7-acre parcel above Carroll Canyon in 1977 as a preserve, for it was home, at the time, to three threatened species — the San Diego fairy shrimp (a crustacean), the button celery (also called coyote thistle), and the San Diego mesa mint — each of which has become federal-listed endangered species. (The plants are also state-listed.) These species germinate and live out their brief lives when their shallow basin homes inundate with spring rains, becoming vernal pools. Suddenly Riggan stopped, parked the car, and hustled to the fence. He was furious at what he saw: One-quarter of the site had been “scraped of vegetation”; only “naked dirt and some sandbags” remained. It looked as though dozers were readying the parcel for development. His first thought was, Who could have done this? For a quarter century this site had (supposedly) been protected land and that fact was known, Riggan said, “to me and a large number of people.”

Riggan peered through the hoary 23-year-old chain-link fence and observed that the bulldozers had torn up what he describes as a chaparral ecosystem — a mound-and-basin topography made up of dense thickets of scrub oak, chamise, and small depressions that collect rain. In these basins the endangered fairy shrimp hatch from cysts, while the celery and mint sprout from seed each spring. If it’s a wet year. In dry years, cysts and seeds wait it out. Biologists estimate cysts — the hulled embryo is dormant — can wait for decades.

Checking his maps later, Riggan determined that in the two-acre scraping about “20 vernal pools had been severely damaged or destroyed.” He described to me what Square One had wrought. “They went onto the property with small bulldozers. They ripped the vegetation. Most of these shrubs have underground lignotubers or burls, for fire adaptation: If a fire swept through, in a week or two, they’d start sprouting back from these underground woody burls. Most of the burls had been ripped out of the ground. You can see individual burls lying on the surface here and there where they weren’t cleaned up. There has been surface movement of the dirt in several locations such that there may be vernal pools buried under fill.”

To restore the pools, Riggan continued, a biologist would have to draw a “micro-scale topographic map” to identify the mounds that were cut down and the basins that were filled in. This would guide the restorer to convert the mounds and the basins to their original forms. He emphasized any reclamation is as much science as art and estimated the cost to be “way out in six figures.”

Riggan’s anger — and that of other biologists who, in subsequent days, observed the grading — rose red-hot because nowadays these wetland habitats are rare in San Diego County. In fact, according to Dr. Ellen T. Bauder, professor of biology at San Diego State University, expert on our endemic soil systems and restorer of damaged vernal pool complexes at Miramar Marine Corps Air Station, 97 percent of all vernal pools in the county have been destroyed. Covered in asphalt and concrete. Tilled for gardens and tomato fields. Graded for golf courses and soccer fields. The largest and best-tended vernal pool complexes are on the Miramar Air Station land, Del Mar Mesa, Lopez Ridge, and Otay Mesa. State and federal law protects these pools because of the endangered species they contain, regardless of whether they are publicly or privately held. To list a plant or animal on state and federal ledgers means, if the law is enforced, any removal (or “take,” a surprisingly direct term conservationists and bureaucrats also use) can result in fines and jail time.

Knowingly grading a protected vernal pool site is a violation of the state Endangered Species Act as well as a violation of the federal Endangered Species Act and the federal Clean Water Act. Under the latter acts, one can be fined up to $25,000 per violation. Under the state act, the fine is $5000. The state liability for “take” of an endangered species is $25,000 for each species “taken,” in this case the mesa mint and the button celery. Imprisonment can run to one year. Civil penalties may also be levied. The heaviest fine comes under the Clean Water Act, where a violator can be assessed up to $25,000 for each day there is unauthorized fill of any kind in a vernal pool complex. On this charge alone, 100 days since early December when the project was halted adds up through mid-April to $2,500,000.

The immediate bulldozing culprit is clear: Square One Development of La Jolla, co-owned by Mickey Cafagna, the mayor of Poway. At 57, a former Poway City Council member, and the mayor since 1998, Cafagna has spoken very little about the bulldozing. He has said (in a voice-mail message) “nothing’s been destroyed” at the Arjons site. “I don’t know if we even have a story here. There really isn’t a story.” Square One, the owner of the site, however, did receive a permit from the City of San Diego to begin grading. Square One bulldozed for a week or two last December, then stopped when the city discovered its “error” and told Cafagna to “cease and desist.”

In March, in response to the wrongly issued grading permit, the U.S. Fish and Wildlife Service and the California Department of Fish and Game coauthored a letter charging the City of San Diego with violating state and federal regulations as well as the city’s municipal code for handing out permits. The agencies have not, at this date, brought Cafagna up on any charge, although the city attorney’s office is investigating both the permitting office and Square One. Fish and Wildlife and Fish and Game are “requesting” “remedial action” or else they will revoke the city’s right to issue “take” permits, which authorize the destruction of protected lands.

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