Kate Hinds

South Orange commuters waiting in line for a bus (photo by Nancy Solomon)

(With reporting from Nancy Solomon) New Jersey commuters, many of whom still don't have power at home, struggled Monday morning to get to work. Gas is still in short supply, and New Jersey Transit's rail lines are only running limited service due to the "devastating damage" inflicted by Hurricane Sandy. The agency has set up emergency park-and-ride service and is using buses to get people into New York. But the wait time can be crushing: in South Orange, along the shuttered Midtown Direct line, train commuters waited two hours for buses.

The Department of Transportation says it's sending 350 buses to the state to fill in where commuter rail service has been disrupted. "The good news for commuters," writes Secretary Ray LaHood, "is that seventy of those buses will arrive ready for service this afternoon in New Jersey and many more will arrive throughout the week." Philadelphia's transit agency (SEPTA) has also sent 31 buses.

A spokeswoman for New Jersey Transit says the agency is trying to cope with multiple challenges and that it is difficult to add express bus service into New York.

For a slideshow of NJ Transit's storm damage, go here.

(image courtesy of UMTRI)

The average fuel economy of new vehicles sold in the U.S. last month was 24.1 mpg--the highest level since the UMTRI began tracking it in 2007.

The University of Michigan's Transportation Research Institute calculates that number based on vehicle sales and the "window sticker" number, which is verified by the EPA.

The UMTRI notes their numbers have been corrected to reflect changes in ratings for Hyundai and Kia models. Earlier this month, an EPA audit found that those car makers had overstated gas mileage.

For more, see the UMTRI's report here.

Top stories on TN:
Line By Line: Here’s What’s Running For Monday’s Commute: MTA Subways, Buses, LIRR, Metro North, NJ Transit (link)
Or check out our Transit Tracker (link)
Cuomo: Subway Service “Will Not Be Normal” Monday (link)
PHOTOS: The Last Ride for Shuttle Atlantis (link)
Subway Flooding Predicted, Eerily Matches Climate Change Model (link)
Why Sandy Emergency Aid Is for Roads, Not Subways, Buses: Congress (link)

Post-Sandy docks at the 79th Street Boat Basin, on the Manhattan side of the Hudson River (photo by Kate Hinds)

Sandy:
Philadelphia's transit system is loaning 31 buses to NJ Transit. (Star-Ledger)

And it can use them: NJ Transit had 257 rail cars and 65 engines -- 23 percent and 35 percent of its totals, respectively -- ruined or damaged by Sandy. (Bloomberg)

Oyster-studded barriers and mossy wetlands fringes: can "soft" infrastructure protect New York from the next storm? (New York Times)

On Sunday, 27% of gas stations in the New York metropolitan area did not have gasoline available for sale -- a decrease from 38% Saturday. (U.S. Energy Information Agency)

Other news:
Why isn't transportation a hot campaign topic? Because neither candidate has a good idea how to pay for what needs to be done. (Washington Post via AP)

Parkmobile, the pay-by-phone parking contractor in Washington, is apologizing after it blamed a recent fee hike on federal financial regulations. (WAMU)

The Twin Cities' bike share program had a record year. (MPR)

Some Los Angelenos opposed to a transit tax say the cost of running new rail lines ahead of schedule will leave Metro no choice but to sharply hike fares, reduce bus lines or both. (Los Angeles Times)

Hyundai and Kia overstated the gas mileage on most of their models from the past three years in an embarrassing blunder that could bring sanctions from the U.S. government and millions of dollars in payments to car owners. (WBEZ)

Meet Stroller Cat: a controversial feline who regularly makes the rounds on the Boston T. (Boston Herald)

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Waiting on line to pay cash for gas to fill gas cans at the Hess station on Union St. and 4th Ave. in Brooklyn (photo by Amy Pearl)

To ease widespread gas shortages in the Northeast, the federal government has temporarily lifted a restriction on foreign fuel tankers.

The Jones Act (pdf) -- formerly known as the Merchant Marine Act of 1920 -- was originally intended to ensure that the U.S. has a strong merchant marine during times of war. It also prohibits foreign ships from touching two U.S. ports consecutively -- meaning all goods that move between two domestic ports must do so on ships that are U.S. flagged and staffed.

The waiver means tankers that would otherwise be barred can immediately begin shipping petroleum products from the Gulf of Mexico to the Northeast.

According to a recent Wall Street Journal article, "it is either essential for national security or a vast barnacle on the hull of U.S. growth, depending on your point of view." Bob Parrish, the president of the Maritime Law Association of the United States, told TN the Jones Act is "really a deep subject that's been debated."

At a press conference Friday morning, New York Governor Andrew Cuomo said the waiver was necessary to speed delivery of fuel to area ports. Soon after, the Department of Homeland Security released a statement that read, in part: "As a result of impacts caused by Hurricane Sandy, today Secretary of Homeland Security Janet Napolitano issued a temporary, blanket waiver of the Jones Act to immediately allow additional oil tankers coming from the Gulf of Mexico to enter Northeastern ports, to provide additional fuel resources to the region...Secretary Napolitano's action immediately allows additional ships, that would otherwise be barred, to begin shipping petroleum products from the Gulf of Mexico to Northeastern ports, increasing the access to fuel in the storm damaged region."

Also on Friday, Cuomo signed an executive order allowing distributors and transporters to bring gasoline, diesel, and kerosene into New York without having to meet the usual registration requirements. "I don’t like to waive the tax, I don’t want to lose the money," he said, "but we do want to accelerate the flow of gasoline."

The waiver of the Jones Act lasts through November 13.

MTA head Joe Lhota stopped by the Atlantic Avenue-Barclays Center station in Brooklyn on Friday morning to greet passengers waiting in line for the buses over the Manhattan Bridge.

Lines are long but from this video it looks like they were moving quickly.

The buses will be in place until subway service between the two boroughs is restored.

The first Staten Island Ferry since Sandy (photo courtesy of Bob Moses)

(UPDATED 11/2/12) The first Staten Island Ferry since Hurricane Sandy will depart at noon Friday, followed by half-hourly service in both directions.

New York City Department of Transportation Commissioner Janette Sadik-Khan had Transportation Nation Thursday: "I'm hopeful that by tomorrow afternoon, I'll be talking to you live from the ferry terminal."

The city shut down ferry operations in advance of Hurricane Irene. Although the fleet wasn't harmed in the storm, the docks suffered damage.

Sadik-Khan also said high-occupancy vehicle restrictions would remain in place through midnight Friday. "Then we'll revisit it," she said, pending restoration of subway service.

The DOT has been working with the city's Metropolitan Transportation Authority to bridge the gap in subway service between Brooklyn and Manhattan, and has instituted special shuttle bus service and bus-only lanes to speed travel over the Manhattan and Williamsburg Bridges. Temporary bus lanes have also been set up on either side of the bridges on Third and Flatbush Avenues.

On a normal weekday, said Sadik-Khan, 728,000 people take the subway into Manhattan from the Jay Street, Atlantic Avenue/Barclays Center and Hewes Street subway stations. Over 200,000 people usually drive over the East River Bridges.

Sadik-Khan said the dedicated lanes were working. "Traffic was tough today," she said, "but it's pretty good flow considering the challenges that we face."

Residents of Newark, NJ, lining up for gas to power generators. (Photo by Anna Sale/WNYC)

Here's a list of what's transit is running in the NYC area this morning.

The current NYC subway map is fluid -- see the latest one here.

Because: the MTA says it can have subways running in the tunnels between Brooklyn and Manhattan in two hours once electricity returns. (Link)

Other transit/transpo questions? Our Transit Tracker has it covered.

Gas shortages continue to plague the area -- but the ports were opened yesterday. (Link)

Bus Bridge from Brooklyn: Jay Street was the best bet on Thursday. (link)

HOV restrictions are still in place for most area bridges. Exception: GWB.

And: the Staten Island Ferry could resume limited service later on today.

NJ Transit is slowly resuming some rail service, despite devastating damage. (Photos here)

Food for thought: NYC's subway flooding was predictable and eerily matches climate change models. (Link)

Speaking of climate change: NYC Mayor Michael Bloomberg says: "One [candidate] sees climate change as an urgent problem that threatens our planet; one does not." He's endorsing Barack Obama for president. (Link)

Been wondering what happened to subway rats during the flood? We were, too. (Link)

Questions about power? Shelters? How to help? Answers for other post-Sandy questions, here.

TN's regular Moving Stories will resume Monday. Subscribe to our daily email here. And follow us on Twitter for updates. Check out Tumblr, too.

The totality of the damage done to New Jersey Transit by Hurricane Sandy can't be fully ascertained at this point, but the list on the agency's website is daunting.

Rail lines have suffered catastrophically: washouts, downed trees, waterlogged equipment, and track damage. The iconic Hoboken Ferry Terminal is flooded. The agency reports that even the Rail Operations Center--"the central nervous system of the railroad"--is engulfed in water. Although most bus service returned Thursday, nine of its bus garages continue to operate on back-up generator power. And in a letter requesting federal aid, Senators Lautenberg and Menendez write: "the only passenger rail tunnel into New York City—which connects thousands of people to the city each day—is shut down."

Earlier this week, Governor Christie said it could take seven to 10 days to resume PATH train service.

There is no timeline for resumption of rail service. The agency says it is continuing to inspect the system and that "the blow delivered by Hurricane Sandy will continue to impact customers for days to come."

This guy might have pulled through. (Photo by laverrue via flickr)

It's not just New York's two-legged population that could take a while to get back to normal.

While most subway riders have other concerns -- like when will the currently truncated service return to normal -- another nagging question remains: how did the subway's rat population fare?

We reached out to the New York City's Health Department, which runs the city's Rodent Academy. Turns out: the answer is mixed.

According to a DOH spokesperson: floods push some rats to the surface, but they also kill lots of rats -- particularly young rats -- in their underground burrows. As a result, floods tend to reduce the overall rat population.

The DOH said it was unclear at this point what affect Hurricane Sandy might have on the rat population, but noted the agency hasn't heard any reports of significant impact.

But other musings about rat society point to a more nuanced view of exactly what kind of rat might have survived. New York Magazine reports that dominant rats may live deeper below ground -- increasing their likelihood of drowning -- while the more "submissive" rats cluster closer to the surface.

Under this theory, the meek rats shall inherit the subway.

Other facts from the NYC DOH:

• No research has demonstrated an increased health risk from flushed rats from underground.
• DOH is monitoring for signs of increased rat activity and will respond accordingly.
• Dead rats do not pose a health risk. "We have not received reports of large piles of dead rats, but we are monitoring this and can take steps to get rid of them as appropriate."
• There are no reliable estimates of the rat population in NYC.
• The main rat in NYC is the Norway rat.

Brooklyn "bus bridge" locations

(SEE UPDATE BELOW) Manhattan-bound Brooklynites: Go to Jay Street, not Barclays -- it will immeasurably improve your ride into Manhattan.

We're getting reports this morning that Thursdays' Brooklyn-Manhattan commute is proving...challenging. But once riders clear daunting lines at the three bus bridge locations in Brooklyn, traffic over the bridges into Manhattan is moving quickly.

But because the line at Barclays Center is longer than the line at Jay Street -- and Jay Street is closer to the Manhattan Bridge -- riders are being directed to the bus bridge stop at Jay.

Here's what we know: this morning, TN's Andrea Bernstein was at the Barclays Center in downtown Brooklyn. The arena was built at this site because of its 11 subway lines and Long Island Rail Road service. And now it's functioning as the site of one of three MTA-operated "bus bridges" that must shuttle passengers between the two boroughs until the subway tunnels can be restored.

(Subway and LIRR service to Atlantic Avenue-Barclays Center was relatively uneventful -- even uncrowded. To encourage transit use, the MTA isn't collecting fares.)

Subway fares have been waived (photo by Caitlyn Kim)

But as those transit riders pour out of the Atlantic Avenue terminal, they are confronted by bus lines that she says wrap entirely around the arena.

"Thousands of them are in line," Andrea said. She said MTA workers were getting people onto buses as quickly as they can -- but once the bus is loaded, it must confront traffic. "They are waiting for a police escort to help take them down Flatbush Avenue across the Manhattan Bridge," she said.

People whose commute normally takes 45 minutes told Andrea that it's taken them an hour and a half just to get to the Barclays Center, and that's before taking the bus to Manhattan.

The line to board a bus on Hewes Street, Brooklyn (photo by Jim O'Grady)

Meanwhile, in Williamsburg, WNYC's Jim O'Grady said Hewes Street isn't quite that crowded--but not by much.

Speaking by cell phone, he said "I'm looking at a line that is a block long." Or it was a block long, before another J train disgorged dozens more people who promptly got in line for the bus over the Williamsburg Bridge.

Boarding the Hewes Street bus (photo by Jim O'Grady)

Jim said the crowds boarding buses was reminiscent of a Tokyo subway: "There are MTA workers in orange vests, and they are pushing people onto the buses and forcibly closing the doors on them."

It sounds dire, but Jim said the 10 MTA workers were efficient and doing a good job.

But, like Barclays Center, the buses are pulling out into traffic.

Jim said police are checking to make sure each vehicle has three passengers in it -- ensuring compliance with the new HOV rules. Once drivers clear that checkpoint, he said, traffic seems to be moving well over the bridge.

(UPDATE 10:20) Once buses make it to the Manhattan Bridge, the ride over is a stark contrast to the line gridlock.

Or, as Andrea says: "That was awesome! I got to Manhattan so quickly that I missed my stop!"

Later, Andrea reported that she was seeing a lot more police officers directing traffic. "They were really there, they were really doing it."

It sounds like the dedicated bus lanes are working as intended: they are speeding traffic over the bridge. Andrea also said that southbound riders told her they made great time from 57th Street to Spring Street -- it was a 15 minute trip.

Andrea reports that someone on the bus was so happy with the speed it was traveling he told her: "imagine if we had rapid bus transit, then the buses would be like this all the time."

Remember, transit riders: MTA head Joe Lhota warned riders Wednesday night that the commute would be tough. “Be flexible about your travel times," he added in an emailed statement. "We have come a long way in a short time to repair the damage from the most devastating event to strike our transportation system.”

For more travel info, visit our transit tracker.

Put away your MetroCard and commuter rail passes: transit fares have been waived in New York through Friday

Take a look at the Thursday subway map and find out where to catch a bus bridge here

No word yet on when Staten Island Ferry service will resume, but rivers are plying the East River again (link)

No rail yet for NJ Transit, but they have restored most bus service

Amtrak says limited service in the Northeast will resume Friday (link)

Let's hope that the bus/subway combo works better than Wednesday's bus only #commutefail

Looking for more details? Visit our Transit Tracker.

WNYC's Jim O'Grady says the phrase of the day: "Yo yo yo I need three!"  Drivers are looking for passengers to comply with the HOV requirements on bridges.

Wait times to board the "bus bridge" to Manhattan stretched to over an hour, tweeted one person waiting in line at the Barclays Center in Brooklyn. Others tweet it's more like four.

Remember MTA head Joe Lhota's words: "Bear with us."

Line for a "bus bridge" at Brooklyn's Barclays Center (photo by Alohaimchelle via instagram)

Meanwhile, on Metro-North's Harlem Line:

An uncrowded Metro-North train (photo by @DonChenNYC)

Flooding at the South Ferry subway station (photo courtesy of NY MTA)

New York Governor Andrew Cuomo announced Wednesday night that he was "declaring a transportation emergency" and authorized the MTA to waive fares on subways, buses, and rail lines through Friday.

Cuomo said that decision was prompted in part by the grueling traffic in Manhattan on Wednesday. He called the gridlock "dangerous" and said he wanted to encourage people to use transit.

But the subway system that will be up and running Thursday will not be the system New Yorkers are used to. Only 14 of the 23 lines will be operational, and even those will be running in segments. LIRR service is being slowly phased back in. Cuomo said one bright point was that roughly 50% of regular customers would have normal service on the Metro-North commuter rail line.

"Bear with us," said MTA head Joe Lhota, who was seated next to the governor at the last-minute press conference. He called the damage done by Hurricane Sandy the "most devastating event ever to happen to the MTA."

There are still subway tunnels flooded with water from "floor to ceiling," said Cuomo. Beginning Thursday, the Army Corps of Engineers will begin deploying 250 "high-speed pumping devices" to aid water removal. These will be operated around the clock until the tunnels are clear.

Meanwhile, to shuttle passengers between Brooklyn and Manhattan, the MTA will put 330 buses into service to act as a bus bridge. Late Wednesday night the New York City Department of Transportation released more details about how the bus lanes will be structured. DOT spokesman Seth Solomonow said the city was creating a "surface subway."

Starting at 6am tomorrow -- timed to coincide with the start of the subway -- buses will operate over Manhattan Bridge via a two-way bus lane on the lower level. These bus-only lanes will be operational 24/7 and will be enforced by the NYPD. Buses will also go over the Williamsburg Bridge. In both cases, buses will make major stops on their way uptown via the Bowery and Third Avenue along a dedicated curbside lane -- which he said will also be enforced by the NYPD.

The buses will run up to 55th Street, then turn around and head back to Brooklyn on Lexington Avenue.

For more information about transit service in New York, visit our Transit Tracker.

No fares = back door boarding -- IF you could get on (photo by Kate Hinds)

I left my Upper West Side apartment at 9:53 this morning, aiming for an M7 or M11 bus -- only to see a packed M11 pulling out of the bus stop on Columbus Avenue and 80th Street, leaving a trail of would-be passengers in its crowded wake.

The Columbus Avenue bus was my stand-in for the C train, which I normally take down to Spring Street. I had adjusted my expectations about my Wednesday commute, but even in the new reality of post-Sandy transportation it was grueling.

I had ridden my bike the 80+ blocks to work on Tuesday, which I often do -- but the return trip home, in the dark, with no streetlights, was harrowing. So I was glad to see the return of some transit.

But by 10:12 a group of us were still waiting for a downtown bus we could actually get on. I was busy both talking to people and eavesdropping (overheard at the bus stop: one man complained to his friend that he was sorry he sold his car; his friend said to him "man, you don't want to own a car in New York -- it's too expensive!")

A couple of crosstown M79s went by, comparatively empty. The crosstown bus line -- often used by people getting to subway lines on either side of Central Park -- was nowhere near as popular as the uptown/downtown ones.

New Yorkers who wanted to go downtown could only gawk in envy at the relatively empty M79s (photo by Kate Hinds)

"The crosstown was terrific," said woman I spoke to. Sue Breger was going from her home on East End Avenue to her office at Primary Stages, on 38th and 8th. She was one of the few sanguine commuters I spoke to. "I think we've been through worse, and I love this city," she said.

By 10:20, two M7s had come and gone, too full to pack on to. A few minutes later, two M11s followed, so crowded that people were riding in the door wells. By 10:38, I was debating the merits of bailing on Columbus with another woman, only to be told by a third person that the lines -- and gridlock -- on Broadway were no better. I considered the M10 on Central Park West and discarded it, for the simple reason that I rarely see it running on a good day.

Meanwhile, I waited. I felt like a desert island castaway, ceaselessly tracking the horizon for rescue. "I think I see an M7! I think it has room! Oh, never mind, it's too crowded."

At 11:05, I was able to push my way onto an M11.

Welcome to your Wednesday morning, post-Sandy commute (photo by Kate Hinds)

But did I mention what Columbus Avenue looked like?

Sure, you can get on a bus, but will it actually move in this traffic? (Photo of Columbus Avenue by Kate Hinds)

Twenty-three minutes later, I had only gone 15 blocks. Which was a walk in the park compared to a man whose personal space I was invading. Newman (as he identified himself) had been on the M11 for two hours, after boarding at 125th Street. "My shift started at 10," he said. "It's terrible." He was trying to get to his job at B&H photo on 34th Street. "I don't know why, but they're open," he said. "But that's business."

At that point, I overheard a woman talking to a friend on her cellphone. "I want to go to Dubai or Monaco," she said wistfully. "Places you go to by helicopter or Maserati."

Our unMaserati-like pace gave me plenty of time to meditate on what was slowing progress: hyper-crowded roads hampered by the dangling crane at 57th Street, which had caused street closures. Another complicating factor: Columbus Avenue turns into Ninth Avenue, which runs into...the Lincoln Tunnel, the only avenue of egress to New Jersey on Wednesday morning. And there was undoubtedly a ripple effect caused by the power outages south of 26th Street on the West Side.

By 11:40 a.m., I was only on 57th Street, and had gotten the word from my editor to return home. I made it back to my apartment, on foot, in under 30 minutes.

New York Governor Andrew Cuomo announced during a press conference Wednesday that some rail service is returning -- but there will be no subway service below 42nd Street. He also said that the LIRR and Metro-North will begin limited service this afternoon at 2pm. More when we have it.

From the MTA's website:

Governor Andrew M. Cuomo announced that beginning this afternoon, both Long Island Rail Road and Metro-North Railroad will begin to provide limited service on part of their respective networks. The Governor also announced that beginning Thursday morning, there will be limited subway service on several routes, supplemented by a bus shuttle between Downtown Brooklyn and Midtown. There will be no subway service between 34th St in Midtown and Downtown Brooklyn.  Earlier today, Local, Limited-Stop and Express Bus service began operating as close to a normal weekday schedule as possible. As was the case yesterday, bus service will operate on a fare-free basis today.  Access-A-Ride also began limited service today, as well as accepting reservations for travel after Noon tomorrow.

NYC began restoring bus service at 5pm Tuesday. (Photo by Metropolitan Transportation Authority / Patrick Cashin)

TN/WNYC has put together a Transit Tracker for the New York/New Jersey/Connecticut region. Check it often for the latest transit updates.

Bus maps of operational NYC routes can be found here.

The MTA says it will provide a schedule for subway service restorations by midday Wednesday.

The Tri-State Flood Tracker gauges water levels in real time.

The head of the MTA says the city's transit system is experiencing the “worst devastation" it has seen in its 108-year history. All seven subway tunnels were flooded with salt water.

Buses are running on city streets again, but New Yorkers will have to be creative with their commutes.

This MTA video of flooding in the South Ferry subway station demonstrates how hard the subway system has been hit.

NJ Transit says it's suffering “unprecedented damage” and "there is no estimate for service restoration" at this time.

Amtrak service to New York is hampered by flooding in the Hudson River tunnels.

Check out some photos from the storm and its aftermath.

Storify: WNYC wants your dispatches from the field.

Read how climate change is imperiling transit.

Follow us on Twitter to stay current on the aftermath of the storm. We're also posting photos to Tumblr.

New York's MTA just released a startling video of the extent of the flooding at the South Ferry - Whitehall station, located at the southern tip of Manhattan.

The station recently underwent a $530 million overhaul. When it reopened in 2009, it created a new connection between the 1 train to and N/R line and was the first new subway station in the city to open in 20 years.

Below, for comparison, a photo of the station pre-Hurricane Sandy.

10:11am: A beheaded subway entrance. (photo by Jim O'Grady)

UPDATE: Tuesday 4:50 PM: The MTA's Charles Seaton says not all bus routes will be running Wednesday morning, that limited routes will be running. Those will be announced later Tuesday evening.

UPDATE Tuesday 11:50 AM: The latest on MTA and NYC transpo is always at our Transit Tracker.

Some bus service will begin at 5 p.m. on a Sunday schedule.

There is no timetable yet for subway service resumption. Governor Andrew Cuomo and MTA Chairman Joe Lhota said in a joint press conference Tuesday morning they hope to have full bus service restored Wednesday morning. No fares will be charged through Wednesday.

Portions of subway service will return in pieces as it is able. Buses will be used to connect fractured sections.

Flooding could keep east river crossings shut for some time. The Clark, Steinway, Rutgers and Strawberry Street tubes under the East River are all flooded. Lhota said pumps are clearing the Joralemon Street tube and will have it dry in a few hours.

No buses or trains were damaged because of effective shut down preparations. Assessment of the extent of the damage on the tracks "will take a little bit more time than we thought," Lhota said.

Lhotoa said flooding at the South Street subway station was "literally up to the ceiling."

Pumping is underway in the Battery Tunnel.

Metro-North has no power from 59th Street to Croton.

POSTED Tuesday 9:05 AM: MTA chair Joe Lhota spoke to WNYC's Soterios Johnson Monday morning about the extent of the damage to the subway system. Listen to the interview below, and read the partial transcript of his remarks.

Lhota said he knew last night there was a problem. "Last night I was downtown and it was pretty obvious...I saw the water surge coming up, realizing that the systems were going to be affected. Our electrical systems, our alarm systems, tell us when there's water down there. They basically shut off. It's an automatic system...they would only shut off if there was water down there."

Johnson asked Lhota just how bad the flooding was. "The assessment is ongoing. Dawn is just cracking right now," Lhota said, adding that the sunlight would help with the assessment process, "which is going to be ongoing. We'll report back to New Yorkers later in the day as to what we have assessed, and determine how long it's going to take to get the system back up and running. One thing I do want everyone to focus on is the fact of how dynamic and how robust the New York City subway system is." And New Yorkers need to understand: "We're going to be flexible, we're going to try to be creative. Those systems that can be up and running, those portions of the system that can be up and running -- I want them up and running as quickly as possible. Then use our bus service and our buses -- re-route them in such a way that they supplement and complement each other. And that's what I mean by creativity: if there's a portion of  the system that's going to take longer to repair, that doesn't mean the whole system is down...we're New Yorkers, we adapt very very well."

Johnson asked if salt water had flooded the subways. "I can't imagine that it's fresh water, it's going to be at best brackish, but for the most part it's salt," Lhota said. "Water and electricity never mix properly, but when you add salt to it, once the water is gone, the salt leaves a film...the way electronics work on the subway system is two pieces of metal running together conducting electricity. And it there's anything in between those two pieces of metal -- like film left over from salt -- that needs to be cleaned off because the connections need to be clear and straightforward for us to manage the process of making the subway system safe."

Johnson asked Lhota what his worst-case scenario for restoration of subway service. "I literally can't answer that until later today," Lhota said. "his happened overnight, it's been ongoing, the assessment's been ongoing, and we've called...all of our workers backs." "Are we talking days or weeks?" asked Johnson. "It's unfair to me -- I'm going to  try to get this up and running as quickly as I possibly can," said Lhota. "I really don't want to be tied down to answering that question the way you've asked it because it'll be something that will linger out there...it would be a scientific wild guess on my part to answer it that way and I just need to get better information and then determine it."

As to when the bridges and tunnels will be open: "I literally just sent a text message to Pat Foye, the head of the Port Authority," said Lhota. "He and I need to figure out how to open up the bridges, how to open up the tunnels. The wind has calmed down significantly...the tunnels, if they're dry, the assessment can be relatively straightforward. [But] the bridges, given the extent of the wind, we're going to need a couple hours having the engineers assess that there's no damage to any of the bridges. We experienced at the Triborough - RFK bridge wind gusts over 100 miles an hour last night. That's extraordinary. We've got to make sure that the integrity of the bridge is there. I'm confident that it is, but out of an abundance of caution we're going to need at least two hours for our engineers to go through and assess to make sure that the bridges are safe. I think they're safe -- in fact I'm almost positive they're safe -- but out of an abundance of caution, we will do the work we need to do."

Johnson asked about the Metro-North and Long Island Rail Road commuter rail lines. "First off," said Lhota, "we're trying to count the number of trees that are downed on Metro North and it's going to be in the hundreds...we're going up in a helicopter today to assess the entire system from the air to determine where we have our problems. The Long Island Rail Road experienced an enormous amount of flooding all through the South Shore, the Babylon branch all the way out to ...Montauk. We're assessing that right now and will determine how far we can go." He continued: "I am very worried about power....the power is a problem. It's an electric subway system for the most part. Some of our commuter rail system is electric as well, some it's diesel, or a combination...we need electricity to run. So this power problem in the tri-state area is significant for getting us up and running on the commuter rail front...the power on Metro North is down from 59th Street in Manhattan all the way up to Croton-Harmon on the Hudson line, all the way up to New Haven, Connecticut on the New Haven line. We have no power on the system at this time."

In terms of the actual conditions of the rails: "We're going to have to evaluate it," Lhota said. "We're going to have to walk ths system to determine the extent of it and we're also going to have to cut up all the trees that are in the way and get them out of the way."

With reporting by Alex Goldmark

We’ll be updating this throughout the day. Send your photos to transponation@gmail.com or @transportnation.  ‘Cause we’d like to share them.

1:3opm: broken traffic light at King Street and Varick Street in lower Manhattan (photo by Kate Hinds)

10:27: from Jim O'Grady: "World Trade Center. Cop said PATH station flooded, didn't know how badly. My guess: badly."

10:11am: A beheaded subway entrance. (photo by Jim O'Grady)

10:11am: Staten Island Railway's Clifton Shop in the aftermath of Hurricane Sandy. (Photo by MTA via flickr)

9:55am: flooding at the entrance to the Hugh L. Carey (formerly Brooklyn Battery) Tunnel, via @NYGovCuomo

9:49am: Downed tree in Tribeca park (photo by Jim O'Grady)

8:14am: Rainbows over Brooklyn (photo by Andrea Bernstein)

MTA head Joe Lhota at New York City Transit president Tom Prendergast inspecting flooding at the Battery. (Photo courtesy of MTA/Adam Lisberg)

(UPDATED with Lhota's comments on WNYC radio at 7:40 a.m.) The head of the New York MTA, Joe Lhota, has released the following statement -- which, as of this writing, is on the front page of the MTA's website.

"The New York City subway system is 108 years old, but it has never faced a disaster as devastating as what we experienced last night. Hurricane Sandy wreaked havoc on our entire transportation system, in every borough and county of the region. It has brought down trees, ripped out power and inundated tunnels, rail yards and bus depots. As of last night, seven subway tunnels under the East River flooded. Metro-North Railroad lost power from 59th Street to Croton-Harmon on the Hudson Line and to New Haven on the New Haven Line. The Long Island Rail Road evacuated its West Side Yards and suffered flooding in one East River tunnel. The Hugh L. Carey Tunnel is flooded from end to end and the Queens Midtown Tunnel also took on water and was closed. Six bus garages were disabled by high water. We are assessing the extent of the damage and beginning the process of recovery. Our employees have shown remarkable dedication over the past few days, and I thank them on behalf of every New Yorker. In 108 years, our employees have never faced a challenge like the one that confronts us now. All of us at the MTA are committed to restoring the system as quickly as we can to help bring New York back to normal."

Speaking Tuesday morning on WNYC radio, Lhota said that he wouldn't wait for the entire system to be operational before putting subway lines back into service -- hinting that the city could be looking phased-in service. But when asked when he thought the subways might be running, he wouldn't be pinned down. "It would be a scientific wild guess" to put a time on it before the true extent of the damage is ascertained, he said.

We'll be following this situation closely. More when we have it.

Brooklyn Heights Monday night (photo by Sherief Elkatsha)

The entrance to the downtown 1 train at Broadway and 79th Street (photo by Kate Hinds)

(With reporting from Alex Goldmark and Andrea Bernstein) Earlier Monday, the head of New York's Metropolitan Transportation Authority said that salt water from the East River would put the city's subway system “in jeopardy.”

So when word went out earlier Monday night -- from the agency's official Twitter feed -- that the doomsday scenario of salt water flooding the system could be coming to pass, New Yorkers feared the worst.

The tweet: "Up to four feet of seawater is entering subway tunnels under the East River."

But now the authority says that was an error -- and it can't ascertain the condition of the tunnels right now. From a tweet just before 9:30pm: "Correction: Condition of under river tunnels unknown. Up to four feet of water was observed at a Lower Manhattan station."

Salt water could corrode the subway's signal system. And even after water is pumped out of a flooded station, salt deposits remain behind. The MTA says these damaged signal systems can't always be cleaned in the field and sometimes they must be replaced outright.

The subway system was shut down Sunday at 7pm. The mayor said earlier Monday that it would not be up and running by Tuesday morning, which gives the authority more time to determine the condition of the system.

The MTA says the pumps for clearing water from the stations are running on generators, not dependent on Con Ed -- one piece of luck for the agency, given the power outages in the area.