The fear over turning downtown San Jose into a business-killing construction zone has transit agencies fighting over how to dig a 5-mile tunnel that will bring BART to the heart of Silicon Valley.

When the project is done by 2026 or so, BART trains will run all the way to Santa Clara, with three underground stations in San Jose. All but 1 mile of the 6 miles of track that must be laid from the nearly completed Berryessa Station in northeast San Jose will be underground, much of it beneath Santa Clara Street, a main artery through downtown San Jose.

Getting there, however, has San Jose officials worried. They look at other big BART construction projects through cities and foresee nothing but trouble.

“When BART was constructed on downtown Market Street in San Francisco, it took two generations for the core of that city to recover,” San Jose Mayor Sam Liccardo said Tuesday.

He and other Silicon Valley leaders are fighting BART’s preference to rip up Santa Clara Street in basically the same fashion that Market Street was torn up in the 1960s. It’s known as “cut and cover” — excavate the street for side-by-side tunnels, then cover it back over when done.

Cut and cover would mean taking much of Santa Clara Street out of service for up to five years, something South Bay officials say would hurt businesses, not the least of which is the planned 8 million-square-foot Google campus near the SAP Center arena.

They’re backing an alternative strategy hatched by the Santa Clara Valley Transportation Authority, which is in charge of building the extension that BART will then operate. The VTA wants to bore a single, 45-foot-diameter tunnel that would allow the BART tracks to be stacked on top of each other.

VTA officials say the single tunnel — drilled with a giant boring machine similar to what’s been used for San Francisco’s Central Subway — would be both faster and less disruptive than digging up streets.

BART says stacked tracks would make it harder to evacuate people in an emergency in the three downtown stations — in Alum Rock, near City Hall and by the SAP Center.

Another concern is cost: The VTA has been told its method could add $521 million to a project that’s already going to cost $4.7 billion.

Liccardo disputes the higher cost, but figures a little extra money would be worth it in the long run.

“In the heart of Silicon Valley, we should embrace innovative methods ... rather than clinging to construction approaches of the 1960s that will gut several blocks of our city’s core,” the mayor said

The fight has pitted BART General Manager Grace Crunican against Nuria Fernandez, who runs the VTA. Neither one wants to give, but they did agree to bring in a panel of outside experts last week to judge the two approaches.

The panel concluded that BART’s method was preferred, “especially in fire/life safety and emergency situations,” Crunican wrote to her board in a Nov. 15 memo released this week.

Fernandez shot off a separate confidential memo to her board a day later, saying that although there were “considerations related to fire/life/safety that would need to be addressed in the design,” the single tunnel “as presented could be operated.”

In other words, VTA spokeswoman Brandi Childress told us, “we are not hearing that the single bore is not doable.”

Meanwhile, time is running short. The VTA board must act by early next year if it hopes to get in line for federal funds. So where does that leave things?

“Basically there’s a standoff,” says one high-level transit source, speaking on condition of anonymity because the person needs to work with both sides. “The VTA is not going to build something it doesn’t want to build, and BART is not going to operate something it doesn’t want to operate.”

Gold rush: State Sen. Scott Wiener, who has adopted the cannabis industry as one of his major concerns, is taking aim at new state regulations for recreational marijuana that will allow for big growing operations in California.

“By not limiting the amount of land that can be cultivated by any one operation, we are basically inviting mega industrial-scale operations into the state,” the San Francisco Democrat said. “It will squeeze out the small farmers that have been at the forefront of the industry for many, many years.”

Wiener’s anger is directed at rules issued last week by three agencies — the Department of Health, Department of Food and Agriculture and the Bureau of Cannabis Control — that do not limit the number of licenses a grower can hold or the total acreage one can farm. He said he hopes to make some changes when the Legislature is back in session next year.

Although there were no limits written into the voter-approved Proposition 64 that legalized recreational marijuana sales, small growers had hoped the state would set a cap of 5 acres per farmer for the first five years. One of the 2016 initiative’s biggest backers, Lt. Gov. Gavin Newsom, said there would be no “new gold rush” of corporate cannabis as a result of legalization.

Newsom, who is running for governor, appears to be fine now with allowing for big growers.

“Legalization is a process unfolding over many years,” and regulations will need “constant re-evaluation,” Newsom said in a statement from Mexico City, where he is talking marijuana issues with trade officials.

But he added, “I’m not ideological about this; I’m watching closely to ensure that the rules are being applied with tough anti-monopoly standards that create favorable market conditions for small legal businesses.”

San Francisco Chronicle columnists Phillip Matier and Andrew Ross appear Sundays, Mondays and Wednesdays. Matier can be seen on the KPIX TV morning and evening news. He can also be heard on KCBS radio Monday through Friday at 7:50 a.m. and 5:50 p.m. Got a tip? Call (415) 777-8815, or email matierandross@sfchronicle.com. Twitter: @matierandross