As President Barack Obama selects his second-term Cabinet, all eyes are on the big departments - State, Treasury, Defense and Justice. Yet he can set the tone for his new term with changes in a less-likely place: the Department of Transportation.

The current secretary, Ray LaHood, is probably stepping down in 2013, and Obama's signature transportation policy, a national high-speed-rail network, is in disarray. The president's original goal was to give 80 percent of Americans access to high-speed rail within 25 years, but so far only California's increasingly embattled system is scheduled for completion by then.

High-speed-rail lines in Wisconsin and Florida were canceled by the states' Republican governors, and Amtrak's $151 billion plan to bring real bullet trains to the Northeast corridor is a nonstarter.

With a divided Congress unlikely to finance any significant portion of Obama's high-speed-rail projects, he has to nominate a secretary who cares as much about reform and good engineering as securing funding and undertaking flashy projects. A focus on efficiency over spending should please House Republicans, whose support the administration will need if it ever hopes to increase federal transit funding.

David Gunn, the president of Amtrak from 2002 to 2005, cited a lack of technical knowledge as the biggest problem at the Transportation Department, which he said has devolved into "an agency that just distributes money."

"If you look at the Federal Railroad Administration and the Department of Transportation, they've never really had professional leadership," argued Gunn, who managed most passenger trains on the Eastern seaboard at one point or another during his career. (Gunn was fired by President George W. Bush's Amtrak board in 2005 after objecting to what he viewed as the administration's politically motivated attempts to break up the railroad.)

Although most transit advocates view a lack of funding as American transit's biggest obstacle, some, such as David Schonbrunn, a longtime San Francisco Bay area transit activist who is suing to change California's high-speed-rail plan, agree with Gunn's assessment.

"We're spending our money in incredibly stupid and political ways," Schonbrunn said, "and the only answer from the leaders of these agencies is 'Give me more money.'"

Gunn was also critical of the way the Obama administration allocated the $8 billion in stimulus funds for high-speed rail.

"There are two groups that are absolutely critical to getting high-speed rail done: freight rail and Amtrak," he said. Yet the administration went to state transportation departments and local politicians, who, Gunn said, don't know what they are doing.

The administration has shut out the freight railroads and Amtrak California from its high-speed-rail plans, instead vesting power in the new California High-Speed Rail Authority, which has little operational experience and a barebones staff.

Silo approach

Another problem, Gunn says, is the silo approach that the Department of Transportation takes to financing air, highway and rail projects.

"They desperately need somebody who understands the interaction between modes," Gunn said. He cited a costly O'Hare International Airport expansion in Chicago, where he says passenger capacity goals may have been better addressed by a high-speed-rail network for the Midwest.

Right now, air, highway and rail interests frequently compete against one another to fill the same need.

The government often finances projects to widen and build new highways parallel to new rail routes, depressing ridership and limiting the cost-effectiveness of transit.

David Schonbrunn had praise for Peter Rogoff, the current head of the Federal Transit Administration.

"Peter Rogoff made some really excellent comments about how we can't continue to throw money into new projects without maintaining our current infrastructure," Schonbrunn said. He credited Rogoff with canceling the federal contribution to a widely panned elevated-rail connector from the airport in Oakland, Calif., to a Bay Area Rapid Transit station.

But Rogoff also signed off on and defended federal appropriations for San Francisco's controversial Central Subway under political pressure from House Minority Leader Nancy Pelosi.

Transit advocates have roundly criticized the project for its high cost and limited utility.

Beyond spending existing funds more responsibly, the Transportation Department must make regulatory changes if Obama's goals for high-speed-rail access are to be met.

The Federal Railroad Administration is already making progress on one long-overdue reform: rationalizing crash-safety rules for suburban and intercity passenger rail.

The agency's current safety standards require trains to be bulked up to survive crashes, whereas regulators outside of North America allow lightweight trains, which are faster, cheaper and more efficient, on existing freight and intercity tracks. Crumple zones built into modern European and Japanese designs protect passengers during accidents, and advanced signaling technology makes such accidents unlikely to occur in the first place.

In June, federal safety regulators issued a waiver to a small Dallas-area commuter rail line to use lightweight Swiss railcars, and the FRA also indicated a willingness to grant more such waivers in the future. This first move toward modern trains was driven from within the agency, and reform could be sped up with political support from higher-ups in the department.

Another aspect of rail policy under the administration's control is labor. The president nominates members to Amtrak's board and could use this power to push for desperately needed staffing reforms.

One candidate whom Gunn said he could recommend for transportation secretary is Eugene Skoropowski, who made a name for himself managing California's Capitol Corridor between San Jose and Sacramento via Oakland. During his tenure, ridership tripled and the number of trains scheduled per day quadrupled, turning it from a lowly intercity line into a bustling commuter system. And he did this without any additional state subsidies.

Because Capitol Corridor trains run on tracks owned by the Union Pacific Railroad, Skoropowski had to work with the freight carrier to achieve these ridership gains. Today he works for Florida East Coast Industries, a freight railroad that is starting private passenger rail service between Miami and Orlando, the first in more than a half-century.

Skoropowski's history of cooperation with the freight-rail industry stands in marked contrast to the California High-Speed Rail Authority's hostile relationship with the Union Pacific - hardly the cooperative partnership that David Gunn suggested is necessary for high-speed rail to succeed in the U.S.

Other transit analysts, such as Joshua Schank of the Eno Center for Transportation, a research group, agreed that it might be time for a transportation secretary from a technical rather than political background. (The office is sometimes used for bipartisan gestures: LaHood, Obama's first-term transportation secretary, was a Republican representative from Illinois, and Norman Mineta, who served under George W. Bush for five years, was a Democratic congressman.)

"With a technical nominee, you usually give them more leeway," Schank told me in an interview.

Whomever Obama nominates, the administration should learn from the failures of its grand and expensive first-term ambitions. If the White House is willing to listen to the engineers and technocrats within the department, it might find some of its goals within reach.

As Gunn put it, "They need somebody that understands how you accomplish physical things."