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(The following story by Andrea Estes and Mac Daniel was published in the the January 23 online edition of the Boston Globe.)

BOSTON — The family of a Wellesley scientist who suffered a fatal heart attack last summer on an MBTA commuter train that continued to pick up passengers for 20 minutes after he collapsed is seeking $25 million in damages from the MBTA and Amtrak.

Lawyers for the family of Dr. James Allen, a nationally known scientist for the US Geological Survey, last week served Amtrak and the MBTA with a 13-page demand letter that raises new allegations about his death on July 30.

According to the lawyers, the conductor of the Boston-bound commuter train ignored the pleas of several passengers, including a doctor, who begged him to stop the train so that Allen could get medical help, his family alleges.

Instead, according to the letter, the conductor kept collecting tickets and seemed more concerned about passengers waiting on the platform. Even after Allen’s heart stopped, the train continued to pick up passengers at three more stops before reaching Back Bay Station. Paramedics there could not save him.

The letter, a precursor to a lawsuit, cites the ”shocking and appalling facts of this case” in asking for $25 million. According to a lawyer for Allen’s family, they hope to settle the case without filing suit.

”This is a very private family,” said attorney Leo Boyle. ”We’re talking with the MBTA in an effort to resolve the matter and avoid the trauma of litigation. I would like to defer any detailed discussion if at all possible. We’d like to honor the family’s privacy.”

Amtrak officials declined to comment. MBTA spokesman Joe Pesaturo said, ”The T is in receipt of a letter of demand and lawyers for the MBTA and the estate of James Allen are discussing all aspects of the case in an attempt to achieve a resolution.”

Allen, 61, was pronounced dead at 10:14 a.m. on July 30, more than an hour after he collapsed in his seat on the commuter train.

Allen’s death made headlines nationwide and raised troubling questions about passenger safety on MBTA commuter trains, which are operated by Amtrak.

It led the MBTA to look for a new contractor to run its commuter rail lines, with T officials vowing never to work with Amtrak again.

The head conductor on the train Allen was riding in was suspended with pay after the incident and returned to work in September, according to officials.

The demand letter, prepared after a private investigation that included interviews with several passengers, alleges that the crew’s negligence was far worse than originally described.

The workers knew almost immediately that Allen was gravely ill but didn’t stop the train, alleges the family, contradicting previous accounts that workers thought he had merely fainted.

Within a minute after leaving the Wellesley Farms station where he had boarded the train, Allen began to wheeze and gasp for air and then slumped in his seat, according to the demand letter.

Passengers rushed to his aid and two assistant conductors called for passengers with medical training. Two passengers, including Jeanne Hathaway, a Massachusetts General Hospital/Harvard researcher with a medical degree, administered CPR. Assistant conductor Susan Bergeron, who had been largely credited with trying to resuscitate Allen, only assisted the others, according to the family’s lawyers.

”According to more than one passenger,” the letter alleges, ”even before arriving at Auburndale at 8:54:19 it was quite clear to the crew that they had a critically ill passenger on their hands. Tragically, as the train departed Auburndale, the crew had still made no attempt to contact emergency medical services or, for that matter, to even report the situation as an emergency either to dispatch or to anyone else.”

Assistant conductor Walter LaCombe challenged the head conductor’s decision not to stop the train in Auburndale, but was ignored, according to a passenger cited in the letter.

Passengers repeatedly demanded that the conductor stop the train, but were rebuffed, the letter says.

When one commuter asked why the train was continuing to pick up passengers, head conductor James Peros seemed confused by the question, the letter alleges.

”What about the people on the platform?” he allegedly asked the man, urging him to ”Take it up with the T” if he had a problem with his answer.

”Meanwhile, passengers looked on in disbelief” as the train continued to make two more routine stops to pick up and drop off passengers,” the letter alleges. ”Many on board began yelling at the crew to do something.”

Had the conductor stopped the train at Auburndale, West Newton, or Newtonville, the lawyers allege, Allen probably would have survived. Within blocks of the stations were emergency personnel – at Newton Wellesley Hospital and Newton fire and police stations – and defibrillators, devices that could have re-established his heart’s normal rhythm.