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BROCKTON, Mass. — Now that it has cleared a major environmental review, opponents of a controversial plan to put a commuter rail line through the Hockomock Swamp are focusing their efforts on questioning the choice of that route over another, less-damaging, alternative, according to the Brockton Enterprise.

On Friday, Secretary of Environmental Affairs Robert Durand issued the project a certificate under the Massachusetts Environmental Protection Act, signifying that the rail plan protected the environment enough to proceed. A key assumption underlying Durand’s finding is that the route chosen by the Massachusetts Bay Transportation Authority is the only practical route for the rail line.

But unless the MBTA can succeed in showing that the so-called Stoughton alternative is really the only viable route the entire $669 million rail project will be at least delayed for years, if not scuttled altogether.

Rail opponents say that politics, rather than practicality, drove the MBTA to select the Stoughton route as its preferred alternative and assert that it was the only viable route. Durand accepted the MBTA’s argument that there was only one viable route and allowed the MBTA’s Environmental Impact Report to consider that route only as it went through the MEPA process.

But at least two of the agencies that will eventually have to issue permits for the project recently warned that they may want to revisit the route selection decision before they grant a permit.

The federal Environmental Protection Agency and the state Natural Heritage and Endangered Species Program separately indicated that the issue of the route was not closed as far as they were concerned.

The three towns affected by the proposed route – Easton, Raynham and Stoughton – have been working closely with an organization that supports environmental whistle-blowers to raise questions about the route.

The tri-town alliance commissioned a transportation consultant whose report is highly critical of the MBTA’s route selection, while Public Employees for Environmental Responsibility released a scathing white paper that blasts the MBTA. PEER has said that it’s involved in the fight because public employees involved in developing the rail plan are upset that politics has trumped science and legal requirements in their view.

All roads lead to Taunton – at least if you’re talking about the railroad. All of the proposed routes to extend Boston commuter rail service to Fall River and New Bedford meet in Taunton.

The primary choices considered by the MBTA were the so-called Attleboro, Middleboro and Stoughton alternatives.

The Middleboro alternative has won little support because of low ridership projections and track capacity limits in the Braintree area. That line would use existing commuter rail lines to Lakeville and then a connecting line to existing freight rail lines to Taunton, Fall River and New Bedford that would be upgraded. The MBTA does not consider it a viable route and rail plan foes have generally agreed.

The Attleboro alternative uses existing commuter rail lines to Attleboro. A two-mile line would connect to existing freight rail lines that lead to Taunton and then on to Fall River and New Bedford.

The Stoughton alternative uses existing commuter rail lines to Stoughton and then runs about 14 miles along an abandoned railroad right of way to Taunton, where it also joins the existing freight lines. This route runs through the Hockomock Swamp, a state-designated Area of Critical Environmental Concern. The swamp earns that status in part because it is home to a number of rare species of plants and animals.

Rail line foes were given more ammunition this week when researcher Michael Clemmons of the Wildlife Conservation Society determined that two female blue spotted salamanders were a rare purebred species. Kyla Bennett, New England director of PEER, said that information will prompt her group to petition the Natural Heritage and Endangered Species program to upgrade the salamanders two levels from “special concern” to “endangered.”

Even before the salamander findings were announced Natural Heritage informed the MBTA that it would have to meet a high standard in order to win a permit because of its negative impact on the habitat. In its comment on the MBTA’s Final EIR the agency warned “changes in the assessment with respect to no viable alternative could alter our ability to issue a Conservation Permit … .”

The federal EPA was even more blunt in its warning to the MBTA that it had questions about its claim that Stoughton is the only viable route.

“Based on the information provided to date, the MBTA has not overcome the presumption that a less environmentally damaging practicable alternative to the Stoughton alignment exists. The Attleboro alignment appears to be both practicable and less damaging to the aquatic environment,” the EPA’s comment letter on the FEIR said.

The MBTA admits that there will be an impact on the environment, said state Department of Transportation spokesman John Carlisle, but he said the MBTA’s plan minimizes the damage as much as possible.

The MBTA argues that the Stoughton route is the only one that can meet its Standards of Service policy by providing three inbound and three outbound trips during the morning and evening rush hours from each terminal in New Bedford and Fall River.

In addition the MBTA said that the Stoughton route has the highest ridership and the shortest transit time of the alternatives among other, lesser benefits. The problem with the Attleboro route, according to the MBTA, is that it competes with other rail traffic on the congested Northeast Corridor used by Amtrak for its New York to Boston trains. According to the MBTA the Amtrak trains get the first two time slots available per hour, which reduces its schedule flexibility.

Using computer simulations the MBTA’s analysis shows that only one trip to and from New Bedford could be scheduled during the peak commuting times of 7-8:59 a.m. and 4-5:59 p.m. and only two to Fall River during the morning and one in the evening peak. This level of service would not make the project worth doing, the MBTA said.

The MBTA also predicts that trains will often be delayed because of traffic. If trains are scheduled too closely together an unexpected delay for one train can cascade into major delays for the whole route in a domino effect, the MBTA said.

The Stoughton route allows three inbound and outbound trips to each terminal city during the peak times, according to the MBTA analysis. It also has the advantage of only adding a total of four more trains to the incoming load at South Station because it uses much of the existing Stoughton rail schedule and just extends the runs. Currently 30 trips per day go back and forth between Stoughton and Boston, the MBTA said.

In contrast the Attleboro route adds 28 new trips per day, the MBTA said, straining the system’s capacity.

The MBTA says that the Stoughton alternative will be quicker for commuters, saving seven minutes per trip from New Bedford over the Attleboro route’s one hour and 27 minutes. The time saving from Fall River will be negligible, with Stoughton just a minute quicker at one hour and 18 minutes. The MBTA projects far higher ridership using the Stoughton route at 4,280 compared to 2,470 for Attleboro.

According to the MBTA analysis the Stoughton route is the only one that can supply the level of service needed to justify building the line.

An transportation consultant hired by Easton, Raynham and Stoughton to evaluate the MBTA’s analysis says he has found flaws in that analysis and charges the MBTA with falsifying some of the data.

If the critic’s charges hold up, the entire basis of the MBTA’s argument is endangered because the environmental impacts are so profound the MBTA would have to choose any other route that is also practical, said Easton Assistant Town Administrator Martha White, who has become the lead official for the three-town coalition against the plan.

“The route is a key point in this fight,” she said. Michael Nelson, the transportation consultant hired by the towns, raised a number of technical questions about the MBTA’s analysis in two reports on April 19 and Aug. 21.

Among many technical faults Nelson says that the MBTA’s analysis understates the capacity of the Northeast corridor and created delays in its simulation model by introducing a train trip which does not actually exist.

Nelson said that the MBTA’s simulation report asserts that the line can only handle five trains per hour, which means 12 minutes between trains, but in reality the line already handles trains spaced much closer than that. It cites several examples of Amtrak trains that run as close as 5-8 minutes apart.

An example of the cascading delay cited in the MBTA analysis is actually caused by a train that does not exist, Nelson said in his April 19 report. The MBTA simulation showed a New Bedford train causing major delays when introduced into the morning schedule but Nelson said the actual Attleboro alternative plan does not include that train at that time.

Nelson’s reports also criticize the MBTA for not considering the benefits of mixing transportation modes. While the MBTA considered and rejected enhanced bus service from Fall River and New Bedford because of traffic congestion in Boston, Nelson said it did not consider express bus service to existing commuter rail stations. Express bus service to commuter rail stations could result in shorter commutes than either bus or rail service alone, Nelson said.

PEER’s Bennett said that her organization is involved because it had been contacted by public employees upset that scientific and legal issues were taking a back seat to political considerations. In the 2000 Transportation Bond bill the legislature dictated that the route should go through Easton, she said.

“The legislature has involved itself,” Bennett said. “They have mandated which route it should take. What’s the point of the process if they are going to do that?” The EPA and Natural Heritage letters give her hope that the route choices will be looked at again, Bennett said.

Easton’s White said that, in her opinion, it is still one of the pivotal issues and a point of vulnerability in the MBTA’s plan. If the MBTA can’t convince the EPA that the Stoughton route is really the only one then the entire plan is in jeopardy.

Of the politicians that attempted to force the issue, White said “they may have just shot themselves in the foot.” DOT’s Carlisle said that the MBTA will be filing for the permits it needs soon. The target date for the trains to be running is 2008, he said.