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That would destroy the subway’s electrical and hydraulic systems, and the water damage would be compounded by the corrosive nature of sea salt. Water would also flow downhill into the long, deep tunnels that pass under the East River between Manhattan and Brooklyn and Queens, further crippling the system. If water rises to a track’s third rail, where electric power is delivered to the train, trains cannot run.

Lower Manhattan contains a high concentration of subway stations that serve nearly all the city’s lines. Throughout the system, Bowman counts 25 subway stations whose entrance stairways are about 15 feet or so above sea level, while most are on higher ground.

In the end, Irene did not deliver as strong a blow as feared. Transportation officials declined to predict Sunday when the subway system would be back up and running. Inspectors are checking the tracks and pumper trains have been sent to places where flooding from rainwater occurred. After that is finished, trains without riders must be sent through the system to test it.

Still, Irene offered a troubling glimpse of what might be possible if a future storm brings more intense flooding. While a storm like Irene is a rare event in New York, it is not unheard of.

In 1992, a winter storm drove an 8-foot surge that flooded the entrance of the underground commuter train station in low-lying Hoboken, N.J., just across the Hudson River from Manhattan. Half a mile of track was inundated, and the train system was out of service for ten days.

An 1821 hurricane drove an even higher surge. The exact extent is not known, but the water rose 13 feet in one hour at Manhattan’s southern tip, according to the city government’s website.

Hurricane expert Jeff Masters cites a National Oceanic and Atmospheric Administration model predicting that a Category 2 hurricane could drive a 15- to 20-foot surge into New York. That would flood JFK Airport and Manhattan as far north as Canal Street.

Bowman says New York should build flood barriers to protect the city, much like London has had since building the Thames Barrier in 1982.

Bowman believes threes such barriers are necessary to protect New York: one across the upper East River, to shield against surges funneled through Long Island Sound; one across the narrow waters between Staten Island and New Jersey; and most dauntingly, one spanning from New York’s Rockaway beach community across five miles of water to New Jersey’s Sandy Hook.

“It’s not as big of an engineering problem as you might think,” Bowman said, because apart from shipping channels, the water of the Lower New York Bay is only 20 feet deep. He puts the cost of the entire project at $5 billion to $10 billion.

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Jonathan Fahey can be reached http://twitter.com/JonathanFahey. Peter Svensson can be reached at http://twitter.com/petersvensson.