Palo Alto's ambitious effort to redesign its rail corridor is starting to pick up speed in the southern half of the city, where officials are narrowing down options for separating Charleston Road and Meadow Drive from the train tracks.

If the city succeeds in its "grade separation" effort, these two rail crossings are likely to see the most dramatic changes, potentially involving a trench for trains. By contrast, the city has scaled down and delayed its plans for the two crossings in the northern half of the city: Palo Alto Avenue and Churchill Avenue.

The council's Rail Committee has recently abandoned the exploration of any significant engineering solutions for Churchill, where a trench or a viaduct would require property seizures (the city is still exploring a scenario in which Churchill would be closed to traffic near the grade crossing). At Palo Alto Avenue, the city is still evaluating a "hybrid" option that would combine raising the tracks and lowering Palo Alto Avenue. But the solution, several council members have argued in recent weeks, may be best explored as part of separate plan that focuses specifically on downtown.

At Charleston and East Meadow, which are being explored jointly, the city is hoping to come to a big decision in early 2019. On Wednesday morning, the Rail Committee signaled its intent to further narrow down options for these two crossings when three members voiced support for eliminating the "viaduct" alternative in which trains would be elevated over the roadway. If the council does that, the only options on the table for these two intersections would be a train trench or a "hybrid" option, which combines lowering the tracks with raising the roads (or vice versa).

While they stopped short on Wednesday of actually recommending the elimination of the viaduct option because of concerns about issuing public notices, committee Chair Cory Wolbach and council members Greg Scharff and Lydia Kou all indicated support for doing so in November, when the item returns to the committee for further discussion.

For the city, the issue of what to do about the south Palo Alto grade crossings is a quandary that is both deeply urgent and extremely complex. The city is competing with Mountain View and Sunnyvale for funds from Measure B, a 2016 county measure that allocated $700 million to the three cities for grade separation, and Palo Alto council members recognized in February the urgency of developing a preferred alternative by the end of this year.

And with Caltrain recently launching work on the Palo Alto segment of its electrification project (which is set to be completed in 2020), city officials are keenly aware that it won't be too long before train traffic is significantly increased, bringing more gate closures and gridlock to local streets near the rail crossings.

But while council officials agree on the problem, they remain torn on solutions. The idea of building a viaduct for trains over the two south Palo Alto crossings remains deeply unpopular, with nearly every public speaker at Wednesday's meeting of the Rail Committee speaking out against it.

A much more popular solution is building a trench for trains. Davina Brown was one of about a dozen residents who said Wednesday that they would far prefer underground trains over overhead ones. Elevated trains are noisy and difficult to maintain, she said.

"Let's do the right thing now and put a train in the trench," Brown said. "It's safer, it's aesthetically more pleasing."

The popular option, however, is both the most expensive one (with costs exceeding $1 billion, according to one recent city estimate) and the one that would face the steepest permitting hurdles. It would need to win approvals from various state and regional agencies, including Caltrain, and officials are far from certain that they can get these agencies to buy in.

One thing that Palo Alto officials are hoping for is an "exception" from Caltrain that would allow the construction of a trench with a 2 percent grade, which exceeds Caltrain's design standard of 1 percent (a trench with a 1 percent grade would have to be longer and more expensive). Etty Mercurio, Palo Alto's project manager for grade separations, said that the only place in the Caltrain corridor that has a grade of greater than 1 percent is San Bruno, where there is a short stretch with a 1.3 percent grade.

"Getting a design exception is a long process and you usually have to have a very, very good justification for that process," said Mercurio, a consultant with the firm Aecom.

Another potential obstacle is creeks. Mercurio said she had recently spoken to officials from the Santa Clara Valley Water District who expressed concerns about the proposed trench blocking Adobe and Barron creeks. She said she was advised by water district officials to consult with the U.S. Army Corps of Engineers, which may have additional concerns, she said.

Gary Kremen of the Santa Clara Valley Water District told the Weekly in an email: "We stated that any changes to the fish-bearing creek requires environmental permits from State and Federal agencies. We immediately provided information to Palo Alto staff of our contacts with the key environmental regulatory agencies so they could get started investigating permits."

These obstacles are unlikely to be resolved by the end of this year, when the council had initially planned to select a preferred alternative for grade separation, or by next February, which is the current goal.

But if other agencies may ultimately determine whether Palo Alto can move ahead with a trench, council members indicated Wednesday that they would be perfectly willing to kill the viaduct option without external input. While Councilman Adrian Fine chafed at the idea of eliminating the viaduct without gathering more data, Councilman Greg Scharff argued that scrapping the option makes sense.

He noted that it is costing the city about $250,000 to fully explore each grade-separation alternative.

"I think people have a fairly good sense of what a viaduct will look like," Scharff said. "It's a quarter of a million dollars to explore, it causes a lot of anxiety in south Palo Alto and it causes me a lot of anxiety. It would be really unattractive and it would impact people's quality of life."

The committee initially considered recommending the removal of the viaduct option, but held back after Fine expressed his concerns and agreed to place the item on its November agenda. Fine noted that given the challenges with tunnels and trenches, that may end up being the only feasible option. The decision should not be based solely on the fact that many people oppose it; it should be consistent with the city's big-picture goals and objectives.

"We could be boxing ourselves into a solution that isn't possible,” said Fine, the sole dissenter in the 3-1 vote to place the item on the November agenda.

His colleagues all recognized that given the uncertainties about a possible trench or tunnel in south Palo Alto, eliminating the viaduct would leave the "hybrid" option as the only grade-separation option on the table for Charleston and Meadow. Given the uncertainty over the underground options, Wolbach suggested Wednesday that the city prepare different scenarios: One that assumes the city will get the needed approvals for a trench and another one that assumes it does not.

"I think we should be looking at two alternatives at the end of the process, not one, because we don't have answers from Caltrain and we probably won't have answers in a couple of months," Wolbach said.