The objections raise the prospect that the bullet train line may not reach San Francisco, one of its key destinations.
It's a hurdle that high-speed rail planners could face in other heavily populated areas of California as they embark on the nation's most ambitious intrastate rail project, threatening delays that could stall the project for years if extensive opposition surfaces.
If completed as planned, the rail system would stretch 800 miles and link the San Francisco Bay area, Sacramento, Fresno, Los Angeles, Anaheim and San Diego with trains running at speeds of up to 220 mph.
California's line and a Midwestern project are the likely front runners for $8 billion in federal stimulus money dedicated to development of high-speed and conventional rail. It's not clear whether delays, either through neighborhood opposition or lawsuits, would jeopardize California's share.
By the time the entire California high-speed rail system is completed, the total cost is expected to top $45 billion.
In some of the neighborhoods south of San Francisco, residents are urging the state high-speed rail board to consider tunneling, trenching or making San Jose the system's terminus in the Bay Area. That step would require riders to take commuter trains from the heart of Silicon Valley to San Francisco.
Others suggest a different route, perhaps taking the trains off the peninsula and reaching San Francisco through an underwater tube from Oakland.
Their allies in the California Legislature have inserted language into a pending bill that would require the rail board to consider a different San Jose-to-San Francisco route than the one currently selected.
"We're supportive of (high-speed rail), but we have some deep concerns over potential implementation," said Patrick Burt, a city councilman from Palo Alto, a peninsula community about 30 miles southeast of San Francisco.
Palo Alto and four other peninsula cities -- Atherton, Belmont, Burlingame and Menlo Park -- have joined to create a unified voice on the project.
Atherton, Menlo Park and Palo Alto also are involved in a lawsuit challenging the rail board's selection of the Pacheco Pass as the primary route for trains between the Bay Area and the Central Valley. They say a more northerly route, through the Altamont Pass, would be the better choice.
Making Altamont the primary route could leave all or some peninsula cities untouched by high-speed rail, depending on where tracks are placed.
Last year's bond measure designated the San Francisco to Los Angeles and Anaheim segment as the first built. State officials hope to have it finished by 2020. Links to San Diego and Sacramento could follow shortly after, depending on funding, said Mehdi Morshed, the rail board's executive director.
Planners have settled on the corridor used by the Caltrain commuter line as the best high-speed rail route on the peninsula, but they haven't decided if trains will run above or below ground. They also haven't determined if tunneling would be more expensive than other alternatives.
Part of the 52-mile-long corridor is wide enough for Caltrain and high-speed rail tracks to run side by side. In narrower sections, tracks might have to be stacked or the state might have to obtain adjoining property through eminent domain, Morshed said.
That has some residents worried that elevated trains will split their communities, that the rail board will need to expand the right of way or both.
A Web site established by a group of peninsula residents features pictures depicting the transformation of Menlo Park's picturesque, tree-lined Caltrain station into a barren place with trains on a cement berm.
"There's going to be a huge amount of unhappiness if they don't do it right," said Malcolm Dudley, a former Atherton city councilman. "Right means tunneling it. It's done all over the world in urban centers."
Menlo Park Vice Mayor Richard Cline estimates seven to 15 miles of tunneling could be necessary to avoid major impacts on peninsula cities.
Morshed said the board will have to consider terminating high-speed trains in San Jose if environmental obstacles and public opposition are too daunting. But rail board member Quentin Kopp, a semiretired judge and former state senator, said a San Jose terminus would violate voters' intent when they approved Proposition 1A.
San Francisco Mayor Gavin Newsom also would fight any attempt to stop the trains short of his city, a mayoral spokesman said. "The economics of high-speed rail depend entirely on connecting LA and San Francisco," said Michael Cohen, San Francisco's director of economic and workforce development.
Whatever option is chosen, peninsula residents simply want a transparent process that considers their opinions, said Nadia Naik of Palo Alto, who helped form a citizens' group, Californians Advocating for Responsible Rail Design.
"That would give us tremendous peace of mind," Naik said. "Nobody's done that. We get a lot of, 'Oh, you're just 50 people who complain."'
High-speed rail planners say they've held dozens of community meetings and will continue to reach out to peninsula residents to hear their concerns.
"Our prime responsibility is to do as little disruption and as little damage and inconvenience as possible...," Morshed said.
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