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(The following story by Mac Daniel appeared on the Boston Globe website on March 13.)

BOSTON — MBTA police were on a heightened state of alert yesterday and Amtrak stepped up police and canine patrols, prompted by the Madrid train bombings as transportation specialists acknowledged that US trains and rail stations remain vulnerable to terrorist attacks.

Passengers boarded a southbound Amtrak train at South Station yesterday under the watchful presence of a bomb-sniffing dog and two Amtrak police officers. At the same time, T officials began removing all bins in MBTA stations that were not bombproof while officers were reminded to remain vigilant about unattended packages, backpacks, or garbage bags similar to those used in the Madrid attacks.

“We can have a far greater impact by that approach than by deploying more officers,” said Michael H. Mulhern, MBTA general manager. The MBTA chose to refrain from deploying more police on the system because federal authorities had not raised the threat level, he said.

Meanwhile, passengers remained stoic. Noel Walls, who lives in South Boston and takes the MBTA commuter rail every Friday to work weekends at a care facility in Canton, was concerned by the Madrid bombings but refused to dwell on them. “I just pray that everything goes well,” Walls said.

The attacks in Spain, which killed 199 and injured more than 1,400, were a tragic reminder that 2 1/2 years after the attacks on Sept. 11, 2001, rail travel remains vulnerable. At South Station yesterday, MBTA police and Amtrak officials acknowledged that rail stations like the Boston terminal were porous, with no baggage screening of checked or carry-on bags similar to the lethal backpack bombs loaded with shrapnel used in the Madrid attacks.

“You cannot run a train station or a commuter rail station or a bus station like you run an airport. . . . We’re not surrounded by boundaries like an airport,” said MBTA Lieutenant Detective Mark Gillespie, commander of the transit police department’s investigative services. “Our main source [of security information] are the eyes and ears of the general public.”

New security measures at the nation’s airport that link every checked bag to a ticketed passenger are almost nonexistent on rail, although checked bags on Amtrak are required to be tagged with the owner’s names. Amtrak passengers are only required to show valid identification when purchasing tickets. Multiple unchecked entrances and exits abound at stations, while thousands of miles of rail on some of the nation’s busiest corridors are unmonitored.

Amtrak officials said random security checks of luggage are conducted, using bomb-sniffing dogs, in stations, baggage rooms, and occasionally on trains. “But we have nothing anywhere near what you see at airports,” said Amtrak spokesman Cliff Black. “It’s almost nonexistent by contrast.”

To help bridge the security gap, US Senators Tom Carper and Joseph Biden, both Delaware Democrats, introduced legislation yesterday allocating $515 million to the Homeland Security Department to conduct a risk assessment study of rail security threats and to offer security solutions. Yesterday federal officials said there were no immediate plans to increase security along tracks, bridges, tunnels, and rail stations because there was no intelligence indicating a direct threat. Still, several major cities stepped up security. In Manhattan, police carrying machine guns stood outside Grand Central Station while transit police, undercover officers, and the National Guards were inside the sprawling terminal. New York Mayor Michael Bloomberg said police would be stationed at subway centers across the city as well as along the commuter lines.

Bruce Hoffman, a terrorism specialist at the RAND Corporation, told the Associated Press yesterday that it is much harder to secure transit systems because of the large crowds. He also said the US government’s emphasis on airline and airport safety after Sept. 11, 2001, may have made public transit more vulnerable.

Still, passengers tried to go about their business yesterday.

James Powers of Carbondale, Colo., left Boston for New York on Amtrak’s Acela Express yesterday as he followed his wife to a series of East Coast meetings. He said he had not been on a train in 35 years and that the attack in Madrid “certainly crossed my mind.” But “it’s like being struck by lightning,” Powers said. “It seems very remote to me, and I don’t know if that’s fatalism or ignorance or some combination of the two.”

(Anthony Flint and Tatsha Robertson of the Globe staff contributed to this report.)