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(The following story by Carl Nolte appeared on the San Francisco Chronicle website on October 18. Rocky Conner is a member of BLET Division 283 in Oakland, Calif.)

SAN FRANCISCO — Engineer Rocky Conner leans out of the cab of his big yellow diesel locomotive and blows the traditional signal for the crossing – two short blasts, a long and a short – and the last freight train in San Francisco rumbles across Third Street, clanking across the tracks of the Muni’s newest streetcar line.

Seeing the Union Pacific freight train is a surprise to the neighborhood, says Jose Abantao, the train conductor.

“Guys walking on the street always say, ‘I didn’t know you had trains here!’ ‘Every day,’ I tell them,” Abantao said.

Despite San Francisco’s reputation as a home to corporate headquarters and a high-tech capital, freight railroading is still alive in the city, with one Union Pacific freight train a day connecting with a short-line railroad that is planning a major expansion.

Once upon a time, when San Francisco was a port city, freight railroad tracks ran all over the waterfront and South of Market like a spiderweb. Rails snaked into every pier on the waterfront, and freight trains chuffed down dozens of streets.

Mission Bay – now the site of a UCSF campus and the city’s newest neighborhood – was a rail yard, one of six marshaling yards that handled as many as 2,000 freight cars a day.

Passenger commute trains still run and are prospering under Caltrain management, but the freight business has faded away like the soot-stained memories of yesteryear.

Since 1992, LB Railco has run the short-line railroad, a switching operation that folds 10,000 feet of track into a railroad about half a mile long on the southern waterfront, an out-of-the-way district between Potrero Hill and the Bayview neighborhood.

LB Railco’s main business is loading contaminated soil from construction projects into railcars and shipping it to a landfill in Utah. The company’s connection with the nation’s rail network is a Union Pacific spur track that leaves the Caltrain main line near Oakdale Avenue and runs down Quint Street, across Third and to the Railco switching yard on Cargo Way.

As soon as a rail drawbridge is completed across Islais Creek, one of the city’s lesser-known backwaters, LB Railco will be able to offer rail service to ships calling at Pier 80, one of San Francisco’s last cargo piers.

This all sounds faintly nostalgic, but according to David Gavrich, president of LB Railco, economics trump nostalgia. “Look,” he says, “our typical trains are 60 cars long, and each car can carry 100 to 110 tons. That is approximately 6,000 tons. It would take 300 trucks to carry that much.”

The contaminated soil, which is the principal cargo, comes from construction sites around San Francisco, from Mission Bay, South of Market sites and other places. Much of it, Gavrich says, is remnants of an older San Francisco, rubble from the 1906 earthquake, used as landfill.

Nearly all of it is contaminated by modern standards: full of lead, arsenic and hazardous chemicals. “Every time you have a big construction project, for a high-rise, for an underground garage, you find this stuff,” Gavrich says.

Railco and its linked organization, Waste Solutions Group, figured they could use gondola cars that hauled coal from Wyoming to West Coast ports for export to China. The gondola cars come west full and go back empty. So the company uses some of the empties for the waste business.

The trackage came from a project called an Intermodal Container Transfer Facility, built 20 years ago to try to keep container shipping in San Francisco. The ship line that used the facility moved its vessels to Oakland, and the terminal sat empty.

The port also had two locomotives, 100-ton switch engines left over from the days when the city-owned San Francisco Belt Line Railroad had 68 miles of track stretching along the waterfront from the Presidio to what is now the baseball park.

The switchers, which generate 1,000 horsepower apiece on a good day, are 60 years old. “You are looking at a piece of San Francisco history,” said Bob Grady, Railco’s engineer.

LB Railco uses high tech and low. Gavrich says the company plans to convert the two vintage switch engines to clean-burning biodiesel fuel, made from such material as used cooking oil and kitchen grease.

To remove the weeds on the rail tracks, the company leases a herd of goats twice a year.

Railroading and loading contaminated soil is scruffy work. To load the soil in the railcars, LB Railco employees use a crane to pick up an open container of soil from a truck and carefully dump it in the open railcar.

Gavrich is proud that one of his employees, a crane operator named Bobby Barnes, invented a device called Tipper Technology to make it possible to load the cars without stirring up toxic dust.

Gavrich says he hires employees from the Bayview-Hunters Point neighborhood. “Most of them only have to walk five minutes to get to work,” he says.

The loading goes on all day, but the main activity is between 10 a.m. and noon, five days a week, when the Union Pacific train shows up to make the rail connection with the outside world.

The UP train, which is called “the South City Switcher,” comes up from South San Francisco along the Caltrain tracks, running between regular passenger trains.

It’s like a ballet with trains weighing hundreds of tons. The passenger trains have the right of way, so the freight has to duck into a siding to get out of the way.

The UP freight also handles a handful of other San Francisco freight customers – a lumberyard and a frozen food plant on Carroll Street in the Bayview and a rendering plant near the LB Railco facility.

The whole operation looks a bit like a model railroad in the window of some hobby shop. “It’s fun,” Gavrich said. “I have goats trimming the weeds, and I get to play with real trains.”