But from April 1999 through August 2000, the turtles and 98 other rare, threatened and endangered species were all but defenseless because the best tool for their protection -- the Pennsylvania Natural Diversity Inventory -- was broken.

The Pennsylvania Natural Diversity Inventory, or PNDI, is a computerized data bank that keeps track of where "at-risk" species live.. County, state and federal agencies use it to determine if proposed shopping centers, factories, highways and smaller development projects that move dirt, cross water or otherwise leave a footprint on nature will squash rare species or their habitats.

However, a software programming error that went undetected by the state Department of Conservation and Natural Resources for 16 months caused almost all of the more than 13,000 computer searches of the PNDI database made during that period to return "all clear" responses for those 99 species even when they should have identified potential conflicts.

Four months after the problem was finally fixed, state officials still don't how many permits were approved for projects that dug up, filled in or paved over the habitats of those species.

But the bog turtles' situation gives some hint of what was missed.

Only 36 potential conflicts were identified for bog turtles during the 16 months the software problem existed. By comparison, in the two months after the computer problem was fixed in September, 153 inquiries resulted in potential conflicts with bog turtles.

More than 750 potential conflicts, also known as "hits," were probably missed on the bog turtle because of the computer problem, according to the U.S. Fish and Wildlife Service.

The computer problem occurred after the Fish and Wildlife Service and the Pennsylvania Fish and Boat Commission asked the conservation department to increase the size of buffer zones around known rare species habitats to provide greater protections.

But when a PNDI data manager tried to make the changes in the spring of 1999, he mistakenly entered negative values for the buffer zones.

Rather than making the buffer zones larger, the error made the buffer zones disappear. So whenever anyone checked to see if a project would come in conflict with an at-risk species, the database could not find any potential problems.

"During that period of more than a year, no conflict letters, or very few, were generated," said Robert Hill, section chief for ecological services in the state's Department of Environmental Protection.

Stopping water lines

"The bog turtle is just one of the 99 species affected. There were a lot of potential conflicts missed," said Carole Copeyon, an endangered species specialist at the Fish and Wildlife Service field office in State College. "And some of those no doubt resulted in actual conflicts of projects and the threatened species or its habitat."

One such conflict occurred near Downingtown, Chester County, just west of Philadelphia, where the Philadelphia Suburban Water Co. sought permits this summer to build pipelines through the Brandywine watershed. The area is a known bog turtle habitat, according to consultants for the Downingtown Water Authority, which was fighting the private water company's expansion plans.

The state Department of Environmental Protection planned to issue the required permits because the database showed no conflicts. Luckily for the turtles, the project ran into a conflict of another sort -- with local political powers -- and was stopped before the lines were dug.

How did this software glitch go undetected for so long?

"I don't think anyone knows," said Gretchen Leslie, a conservation department spokeswoman. "I do know that the Pennsylvania inventory is one of the most sophisticated in the country and it has done a good job in protecting our at-risk species."

But people familiar with the species inventory system say the breakdown went unnoticed because the data bank has not had its own data manager since April 1999, has received little money or attention from the Ridge administration and remains a low priority within state government. As such, the problem was symptomatic of a larger institutional problem, they contend.

"There's no reason to believe the problem was the result of foul play, but the failure to establish the PNDI as a priority and provide adequate staffing increased the chance of something going wrong," said Michael McCarthy, who reviews index conflicts for the Fish and Wildlife Service.

"If there're not enough people assigned to the program, given the amount of inquiries, it creates a situation that's ripe for problems."

Rechecks will be done

The conservation department has characterized the index problem as a "computer glitch," not an institutional failure. John Oliver, department secretary, portrayed the risk it posed to endangered species as "minimal."

But because the problem took so long to fix, permits were approved for hundreds of projects -- housing developments, sewer projects, timber cuts, stream crossings -- where hits were missed and no review occurred, and thus no protective action was required.

In addition to the bog turtle, the list of at-risk species in the state includes the bald eagle, shortnose sturgeon, eastern massasauga rattlesnake, Indiana bat, coastal plain leopard frog and the pink heelsplitter mussel.

The state's 65 County Conservation Districts, which have been delegated responsibility by DEP for handling permits that involve diversity checks, still haven't been informed that there was any problem. The Western Pennsylvania Conservancy, which gets state grant money to help with the diversity database, was similarly unaware until just this week.

"I thought this was just about bog turtles." said Charles Bier, the conservancy's Natural Heritage Program director. "The conservancy strongly urges that all the inquiries in that 16-month time frame be re-run as quickly as possible to see what was missed and what may need to be corrected."

Federal officials from the Fish and Wildlife Service also asked that the missing months of index checks be re-run, but at first, the conservation department resisted, saying it didn't have the time or personnel to do the work.

However, two weeks ago, following questions by the Pittsburgh Post-Gazette, the state belatedly agreed to re-run those inquiries.

"Checking to make sure proposed projects that we permit do not impact our most sensitive plants and animals is an important part of our technical review process, and PNDI is the best resource we have to do these checks," DEP Secretary James Seif said last week. "Although we believe the chance of missing something was small, we think it's important to find out for sure."

The state said re-running the more than 13,000 inquiries will be done by the end of the month. Any potential conflicts will be sent to the U.S. Fish and Wildlife Service and the Pennsylvania Fish and Boat Commission for further review. If the projects haven't started, the permit holder could be required to make changes.

State and federal environmental employees who use the index estimate that about 25 percent, or 3,275 of the site inquiries made during the 16 months in question, could have registered a "hit," and half of those -- about 1,600 -- might have resulted in an actual "conflict" with an at-risk species.

"If someone that received an 'all clear' from PNDI proceeded and the project is done there's not much we can do," Fish and Wildlife's Copeyon said. "We're most interested in cases where they haven't done any earth disturbance and there's a chance we can still avoid any damage."

How it came to light

The problem didn't come to light until the index's supervisors began to get reports from field officers in the Game and Fish and Boat commissions that endangered species were being stepped on by permitted activities.

"When we found out about it, we felt sick to our stomachs," said Andrew Shiels, the state Fish and Boat Commission's non-game and endangered species coordinator. "When I think about all the troubled projects I've seen over the last year and a half, it's a concern. There very well could have been some very good places that were impacted."

In one case, the Game Commission hired a private logging firm to cut more than 200 acres of timber on State Game Land No. 166 in Blair County after an index inquiry resulted in a "no conflict" determination. The trees were already marked for cutting when a game officer saw them and noted that the area was near the largest Indiana bat hibernating area in the state.

The timber sale contract had to be re-negotiated and the cutting limited to winter months when the bats would not be roosting in the area. Still, important bat habitat will be destroyed.

Another case, in Monroe County in the eastern part of the state, involved two separate index inquiries for a road project and a utility line project crossing Marshalls Creek . They got "no conflict" responses despite the presence in the creek of two threatened species of fish known as shiners.

How the state compares

The index, a partnership between the state, the Western Pennsylvania Conservancy and The Nature Conservancy, was established in 1981 to identify, describe and keep track of the commonwealth's rarest and most significant ecological features, including plant and animal species of special concern, rare natural communities and outstanding geological features.

The listing is regularly updated as new data become available and includes about 500 endangered, rare and threatened mammals, birds, reptiles, fishes, mollusks and amphibians, and more than 600 plant species. It also includes 150 natural communities and geological features.

The index program, part of the Bureau of Forestry within the Department of Conservation and Natural Resources, is used to help make state planning decisions and land acquisitions. Since 1988, it also has been routinely used in environmental assessments to help guide development.

If an inquiry identifies a potential conflict, conservation agencies conduct more in-depth reviews to determine if there is an actual conflict that warrants an adjustment to the proposed project.

Similar biological inventories, also known as "heritage programs," exist in each of the 50 states, seven Canadian provinces and 14 Latin American nations, and almost all of those were started by, or done in cooperation with, The Nature Conservancy.

Pennsylvania and a handful of other states -- New York, Delaware, West Virginia, Alabama and Florida -- continue to operate their natural diversity indexes as partnerships. But most states have committed the money and staffing to absorb the heritage programs into state government or, if politics is a concern, moved them under the supervision of universities, as in Michigan, or into the state library system, as in Montana.

"I can't help but believe that much of this could have been avoided if the state had a more coordinated natural heritage program," Copeyon said. "In Pennsylvania it's really a partnership of the private organizations with very few state employees."

Virginia's Heritage Program was jump-started by the Nature Conservancy in 1986 and is now run out of the state Department of Conservation and Recreation with a full-time staff of 46 and eight seasonal workers.

Conservation department spokeswoman Leslie said the state Bureau of Forestry has one employee working full-time on the index, plus one college intern and three supervisors who devote part of their time to overseeing the program. In addition, the state gives grant money to the Nature Conservancy and the Western Pennsylvania Conservancy, which is used to pay their employees to work on the database.

Anthony Davis of The Nature Conservancy said the state's commitment to the program has increased substantially over the last five years. State grant money pays for 13 conservancy employees, including Davis, who work on the index.

"The PNDI is really middle of the road compared to other states. It's not the best or the worst," Davis said.

The Bureau of Forestry budget for the index program, including all salaries, is $340,000 a year, Leslie said. That's less than the $500,000 each that Forestry spends on its off-road vehicle program and snowmobile program.

Hill said the state has recently agreed to spend up to $1.2 million for a computer upgrade of the PNDI that would link the database to a geographic information system so it will be easier to use, but that won't be in place for two or three years.

Seif said he isn't convinced that making the PNDI a part of state government is the way to go, and actually favors expanding the partnerships with the conservancies.

"Biodiversity is a huge asset to the Commonwealth," he said. "If the state is doing things that put that at risk, and I don't know that we are, then we should change the system."

Last month, the conservation department's own Citizens' Advisory Council sent a scathing letter to department secretary Oliver. It said the department was failing to address the state's biodiversity issues and has "displayed no apparent urgency" to do so.

The letter, signed by chairwoman Paulette Johnson, recommended that the department perform an administrative review of its handling of biodiversity issues and implement an aggressive new strategy to improve the process.

"Basically we're urging the department to get its act together," said Kurt Leitholf, the Advisory Council's executive director. "The problem experienced by PNDI might be a symptom of a larger problem in coordination of the biodiversity program."

Post-Gazette

-- Anonymous, December 21, 2000