SAN FRANCISCO – When he was running behind schedule back in the day, San Francisco Bay ferry boat Capt. Keith Stahnke used to unscrew the knobs from the tops of the throttle levers to squeeze a few more knots of speed from his engines.

Nowadays, he says, that trick wouldn't work aboard the bay's modern fleet of sleek, computer-controlled, twin-hulled catamaran vessels.

"In our newest vessels, the pilothouse looks more like an aircraft cockpit than anything else," said Stahnke. "It features joystick controls, digital gauges and readouts and has redundant fly-by-wire control technology."

A part of the Bay Area water transportation industry since 1979, Stahnke no longer commands ferry vessels: He helps manage an entire fleet of them.

He spends his days helping an obscure state-created, regional agency morph from what was purely a planning entity to a hands-on operator of vessels and a post-disaster emergency responder – one that could help San Francisco cope if a "big one" hits.

Stahnke is operations manager for the recently reconfigured San Francisco Bay Area Water Emergency Transportation Authority, or WETA .

In 2007, when the California Legislature voted to change the authority by adding an "E" (for emergency) to its name, life became very complicated for Stahnke and his colleagues at the tiny agency, which has its headquarters on Pier 9 off San Francisco's waterfront.

Their task was to form an agency that would be responsible for promoting alternative water-borne transportation and for providing the first steps toward recovery following a major earthquake or other disaster that leaves the area's network of bridges unusable.

But when you consider that an estimated 300,000 people use the San Francisco-Oakland Bay Bridge each weekday, you quickly get an idea of how many could be left isolated if the massive span were to become impassable, as it did following 1989's Loma Prieta earthquake.

And while most laud the idea to modify the ferry system – now run by separate municipal operators – into an integrated post-disaster, stopgap transportation system, WETA officials quickly understood what a tall order they had been handed. Adding to that challenge was that the state provided no additional funding.

With only eight full-time employees and an annual operating budget of just $4.5 million, WETA Executive Director Nina Rannells said she and agency staff realized it would take time to develop a ferry fleet big enough to make a significant impact in the aftermath of a large-scale disaster.

"It is a little frustrating at times. We were given the charge of becoming an operator and an emergency responder, but we weren't given the money that you would think would come with those new responsibilities," Rannells said.

The agency first needed to detail exactly how it would make the transition. Soon after Gov. Arnold Schwarzenegger signed SB 1093, WETA staffers began the arduous process of writing blueprints for the transition.

Out of that planning came a five-year financial road map that spells out the agency's short-term goals. By 2014, WETA leaders say, the agency should be moving as many as 500,000 more passengers a year (up from 1.2 million now) aboard an estimated 14 vessels. The fleet will be calling on at least two new multimillion-dollar terminal facilities to be built in South San Francisco's Oyster Point and in the Berkeley Marina within that five-year time period.

To pay for it all, Rannells said, the agency must depend on a patchwork of state and federal transportation grant funds, toll booth revenue, regional voter-approved transportation initiatives and other sources of money that can vacillate wildly as economic conditions and political winds change.

As is the case with many other transit systems, farebox revenue pays for well below 50 percent of the system's costs.

Among WETA's first moves was to begin the complicated process of acquiring the operations of the Vallejo Baylink and the Alameda-Oakland and Harbor Bay ferry systems.

Then it ordered four new ferry vessels. The first two, Gemini and Pisces, have been put into service. While not inexpensive – they cost about $16 million for the pair – the sleek, colorful, 118-foot-long vessels will help increase public awareness of WETA's new mission, agency officials say.

In both vessels, the captain is afforded a sweeping 360-degree view. The skipper sits in a custom-designed chair and has an array of closed-circuit cameras to assist with docking and undocking operations, and for security purposes.

Pisces and Gemini can accommodate as many as 149 passengers each in cabin seating areas that are both noise- and vibration-dampened and feature plush, wide seats.

The boats offer free Wi-Fi, 120-volt outlets to recharge laptops and carry-on storage space for 34 bicycles. Both can travel at a top speed of about 25 knots (approximately 29 mph) thanks to two 1,410-horsepower engines that run on biofuel and low-sulfur diesel fuel.

The new boats were also designed to be easy on the environment.

Authority spokeswoman Shirley Douglas said their "environment friendliness" starts with the way the two hulls are designed to slice through the water, creating a minimum amount of wake and wash in order to protect marine life. Their engines emit exhaust that is 85 percent cleaner than federal marine engine emissions standards and are 10 times cleaner than those of any other ferry boat operating on San Francisco Bay.

The other two vessels on order, with larger seating capacities, are expected to be delivered this fall.

"These new boats have been designed with the passenger experience in mind," Stahnke said. "Compared to some, it will be like going from coach to first class."