For now, we can expect some six weeks of repairs in July and August, knocking out a quarter of Amtrak, New Jersey Transit, and Long Island Rail Road trains.
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In recent weeks and months, you've heard the voices of frustrated commuters as problems arise at Penn Station. Monday we heard from a different voice.
"No engineering problem is insurmountable," said Robert Paaswell, Professor of Civil Engineering, City College of New York
He's including Penn Station, and what promises to be an engineering rebuild and replacement project.
It will happen in the underground railroad labyrinth with a spaghetti junction of tracks and switches, much of it being replaced by Amtrak this summer.
"You have to have probably a two- or three-year program. This isn't all going to be done in one summer," Paaswell said.
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In the months of July and August, Amtrak officials say there will be 25-percent fewer trains during the height of the repair work, forcing riders to alter their commute.
"So you are going to have to find ways of moving those people whether it's by express buses by trains into, for New Jersey perhaps trains into other stations," Paaswell said.
So far, New Jersey Transit and the MTA have not announced their scheduling which they are working on with Amtrak.
In addition to repair work, Amtrak has announced an ambitious plan to improve passenger areas, create a joint railroad operations center and improve security.
"Penn Station is the link to that, to all the commuter rails, the subways come in here. It's really a transportation hub and if you take it out you have really messed up what is really New York," Paaswell said.
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The governors of New York and New Jersey have also suggested bringing in a third party to oversee Penn Station.
"Is there somebody out there who can do that?" Eyewitness News asked.
"Oh I'm sure there are many firms. European firms in Spain and France," Paaswell said.
For now, Amtrak will be looking for federal money to cover some of these improvement costs.
"People have to understand that these are public investments and you have to find the money because the returns on those investments are enormous," Paaswell said.