BART passengers could someday see a second route across the San Francisco Bay, with a parallel but totally new alignment and crossing points on the either side of the bay.

"BART officials are starting to study a second Transbay Tube," reports Michael Cabanatuan. That news follows "years of supposition and pie-in-the-sky conjecture from planners and passengers alike," according to Cabanatuan, but now the real planning can finally begin.
"Much of the talk about a new rail tunnel has centered on its location, or alignment, including where the BART lines would head once they emerge from the tube, and how they could connect with jobs and housing," according to Cabanatuan. The project could eventually cost $12 billion to $15 billion, and the possibilities for crossings and alignment are still wildly speculative, but lots of fun for fans of BART and The Bay Area, or public transit and metropolitan areas more generally.
As for the expected cost just to study the idea, "BART plans to pay for a variety of studies and some early engineering with some of the $200 million set aside in Measure RR, its $3.5 billion system modernization bond. Regional Measure 3, the Bay Area toll increase proposal on the June ballot, would set aside $50 million to further study the new tube, and Caltrans and the state Transportation Agency have said study money should be available as well, reports Cabanatuan.
Oddly enough, there's been renewed talk of a second Bay Bridge span in recent weeks—mostly speculative talk originating from the office of U.S. Senator Diane Feinstein that stands in obvious juxtaposition of the BART plan.
The source article includes a lot more detail about the various regional organizations and powers that will partner on the planning process and could eventually sway the final alignment of the second Transbay Tube.
FULL STORY: BART gets serious about a 2nd East Bay-S.F. Transbay Tube

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