Scanning the slate-gray waters of San Francisco Bay on an overcast spring day I spot more eider ducks and gulls than barges or ships. We’re patrolling past Alcatraz in a 41-foot Coast Guard utility boat that’s almost as old as its blue-eyed 30-year-old coxswain, Chuck Ashmore. Ironically, this old workhorse, with its aging marine radio and soon-to-be-installed Vietnam-era .60-caliber machine gun, is on the cutting edge of a revolution in homeland-or, I should say, home water-security.

Long the threadbare cousin of the Navy and Marines, the Coast Guard has transformed its mission since the attacks on the World Trade Center and the Pentagon. Then, just 2 percent of Coast Guard resources were directed at security; the agency was primarily focused on enforcing fishing quotas, catching drug smugglers and marine polluters, and rescuing distressed boaters. But in the immediate wake of the attacks, 2,900 reservists were called up to augment the agency’s 35,000 active officers, and security work commandeered 58 percent of the agency’s resources.

September 11 put airport security high on the public agenda, but military strategists acknowledge that a much more disturbing vulnerability may be our 95,000-mile coastline, where 14 of the nation’s 20 largest cities and more than half the U.S. population are located. Whatever their tool of choice-chemical or biological weapons, high-grade explosives, or radiological “dirty bombs”-terrorists could smuggle it in through one of the nation’s more than 360 ports.

Another sort of contraband could be the terrorists themselves: In May, reports surfaced that as many as 25 Middle Eastern extremists had likely infiltrated U.S. borders by stowing away aboard container ships that had recently docked in California, Florida, and Georgia. Other disturbing possibilities: The ports themselves could become terrorist targets: A boat could be used to ram or bomb shoreside nuclear power plants, military ammo dumps, or petrochemical complexes in highly populated areas such as coastal Texas or the lower Mississippi. Then there’s the potential for eco-terrorism-say, disgorging the contents of an oil tanker into a harbor.

Until recently, such scenarios had been only dimly imagined. “If you think the aviation community is bad, the maritime community has never thought about security other than antipiracy,” says Ian Gilchrist, a 10-year veteran of the United Nations’ International Civil Aviation Organization, who is now a consultant with Hill and Associates, a security services firm in Stamford, Connecticut.

With some 17 million privately owned boats and 10,000 commercial and cruise ships plying U.S. waters each year-and 2 billion metric tons of trade goods passing through U.S. ports-building a taut security net is a daunting project. Recognizing the challenge, U.S. Sen. Charles Schumer of New York has introduced a bill that would provide $250 million to develop nuclear screening devices for ports and toll booths, and $150 million more to buy mobile X-ray scanners for the Customs Service. Meanwhile, the House has passed legislation, which at press time was pending in the Senate, to allocate an extra $75 million a year to the overextended Coast Guard for security. (The emergency funding the agency received after September 11 quickly ran out, and many reservists were sent home.) The Coast Guard, meanwhile, has requested a 36 percent budget increase, to $7.3 billion, for the 2003 fiscal year.

The Coast Guard’s protection strategy is twofold. The first step is to tighten security on U.S. coastal waters by creating an integrated network of low- and high-tech counterterror operations. Such a network would of necessity employ antiquated equipment like Ashmore’s utility boat but also innovations such as top-end sonar systems and specially trained armed teams to act as ship escorts and emergency responders. Step number two in the Coast Guard’s plan is even more ambitious: The goal is to detect and defuse threats before they ever reach our shores. Through better mapping, surveillance, and global maritime intelligence, officials hope to make the oceans more “transparent”-effectively pushing back our borders to many miles offshore. “If a container has some nasty stuff in it, once it gets to this port it’s already too late,” says Tay Yoshitani, executive director of the Port of Oakland. “You want to go back to the source.”

San Francisco Bay is home to one of the nation’s busiest shipping-container ports, and one of the major Coast Guard stations there is on Yerba Buena, a pine- and lupine-covered island that divides the cantilevered and suspension sections of the Bay Bridge. At the top of the island, within a prefab structure beneath a field of microwave and radar antennas, resides command central, and at its heart is the Vessel Traffic Service. The equivalent of an airport control tower, the system consists of more than two dozen computer and video terminals that are manned 24/7 and that daily track some 350 to 400 vessel transits, both on the bay and under the Golden Gate Bridge.

In the past, officers read information about boats entering the harbor off the system’s radar screens and then simply wrote the ships’ vital statistics on index cards. Today, operators use digital chart overlays of processed radar video imagery to track vessels, then color-code them by type and size. On a recent visit, I read some of the ships’ names off the screens: American River, General Villa, Eagle, Raccoon, Trig Lund. If any one of them attracts an operator’s interest he or she can call it up in the database, which describes the size, tonnage, ownership, and other vital aspects of every vessel that’s come into the bay since the mid-1990s.

The operations officer on duty, Lieut. Dawn Black, shows me another of the system’s capabilities: panning and zooming one of a set of five powerful 40-to-1 magnification video cams located around the bay. Soon we are peering into the inner harbor of the Port of Oakland, where several ships are waiting to have their cargo offloaded by a giant gantry crane. “Container ships are not always punctual, so this way we can keep an eye on what they’re doing,” Black says.

Before September 11, incoming ships had to give the Coast Guard 24 hours notice. Now ships are required to notify the Coast Guard a full 96 hours in advance and must provide more detailed information-such as where the ship originated, its most recent port of call, crew lists, and cargo manifests. That data is sent to a new office within the Coast Guard, the National Vessel Movement Center in Martinsburg, West Virginia, where it is checked against criminal and intelligence databases.

In the future, tracking global maritime trade and gleaning real-time intelligence may get even more efficient. Under new rules adopted by the International Maritime Organization, a U.N. agency responsible for maritime law, by 2010 the vast majority of oceangoing commercial vessels must be equipped with a transponder that broadcasts information on the ship’s ownership, cargo, and schedule, as well as its GPS-derived position, course, and speed. Any ship lacking this technology will immediately become a high-interest target for the Coast Guard and FBI.

For now, the data center in West Virginia transmits information about potentially high-risk ships traveling through San Francisco Bay to Cmdr. Jeff Saine. A year ago, Saine was a reservist working as a Safeway manager in Chico, California. Now he oversees the San Francisco arm of the Coast Guard’s new sea marshal program. In a watch-and-wait role that’s similar to that of the air marshals now assigned to commercial jets, armed teams of sea marshals board ships several miles from the harbor entrance and escort them to dock. Vessels of special interest include cruise ships, which, with as many as 5,000 passengers and crew, could provide a devastating target for terrorists. Decked out in blue jumpsuits and web gear, marshals station themselves in key spots on the vessel-the bridge, the engine room, and the rear steering compartment-places from which it would be possible to take control if, say, crew members tried to smash a ship loaded with crude oil against a bridge. “We’ll put people on the bridge from 12 miles out at sea to the (inland) ports of Stockton and Sacramento,” Saine tells me.

While the marshals board ships to ensure they arrive at the dock without incident, the Coast Guard’s Port Security Units patrol key harbors-Houston, Los Angeles, Seattle, and others-in heavily armed, 25-foot Boston Whalers. These reserve units will soon be augmented by full-time Maritime Safety and Security Teams. The first of these teams was formed on July 3; a dozen more are supposed to be created within the next three years. These dedicated groups of armed officers will include go-fast boat operators and gunners in marine blue camouflage who will not only protect their own harbors but-like waterborne SWAT teams-be deployed to other ports around the United States in case of an attack.

In addition, there will be help from the Navy. In April 2002 the Department of Defense created the Northern Command to coordinate the Pentagon’s responses to terrorism on U.S. territory, including navigable waterways: the shores along the East and West coasts, and the Gulf of Mexico. The Navy has also shifted 13 highly maneuverable, 170-foot Cyclone-class coastal patrol ships to the tactical control of the Coast Guard. “We’re going to bring our littoral warfare resources into domestic waters,” says Rear Adm. Richard West, oceanographer of the Navy.

Nearly 6 Million cargo containers are shipped to U.S. shores each year. Just 2 percent of those huge metal boxes are physically examined. But since 9/11, under the Customs Service’s Container Security Initiative, U.S. Customs officials have been stationed in foreign ports to prescreen U.S.-bound cargo ships. High-risk containers are identified and inspected, and in the near future special “smart seals” will be applied that will electronically indicate whether a container has been tampered with in transit.

Meanwhile, cargo inspectors here at home are getting a boost from a truck-mounted machine that costs about $1.2 million and resembles a heavy-duty cherry picker. Called the Vehicle and Cargo Inspection System, it shoots low-intensity gamma rays that are generated by the radioactive isotope Cesium-137 at shipping containers, offering inspectors a partial view of what’s inside. Gamma rays are more effective than X rays for this job because their shorter wavelengths are more energetic. As a result, they are less easily absorbed by solid material and can penetrate through more than 4 inches of steel.

Customs Service Chief Inspector Steve Baxter and I are sitting in the cab of one of these machines. It backs down a line of parked trucks on San Francisco’s Pier 80, its double-jointed arm systematically moving over shipping containers that have just been offloaded from a Latin American cargo vessel. “Without this machine, that’s our main technology,” Baxter says, pointing to a pair of heavy-duty red bolt cutters and a pry bar lying on the cement quay.

The gamma-ray machine operator peers at a screen displaying a medical-film-like image of the first 20-foot container. It shows a dark mass resting atop a more open matrix. He colorizes the image to enhance the contrast. “The dark is dense,” he says. “They’re saying it’s empty wooden boxes, but that density on top is a problem. Density equals mass.”

A giant-wheeled front loader called a Port Packer lifts the container off its truck carriage and four burly customs inspectors force it open. Inside, they find that the “empty” wooden pallets have been covered with sheets of plywood. The unreported plywood, most likely filler that was added as an afterthought, was what showed up as density on the operator’s monitor.

So far so good, but the inspectors now go to work drilling holes in the wood. They’re checking for empty spaces where other sorts of dense materials-drugs or explosives, for instance-could have been hidden. “With inspections like this you don’t get much complaint,” Baxter says as the battery drills whine. “Now, with furniture shipments . . . ” He gives me a smile and shrugs.

Some of the most unusual security efforts in San Francisco Bay are taking place underwater, where a series of shore and dockside instruments and bottom-anchored sensors record the estuary’s shifting winds, tides, salinity, and currents, and report the information to shipmasters every 6 minutes over the Web and by dial-up voice mail. Called the Physical Oceanographic Real Time System (PORTS), it was originally a response to one of the worst bridge disasters in U.S. history. In 1980, the freighter Summit Venture, oblivious without real-time information about tides, currents, and winds, rammed into the Skyway bridge in Tampa during a blinding squall, killing 35 people.

The PORTS system has since showed it can mitigate other types of disasters. After a 1996 oil spill in San Francisco, PORTS, which now exists in nine major U.S. waterways, tracked the slick and, through computer models, predicted its trajectory. If terrorists released biochemical agents, radiological weapons, or other toxins into the water, PORTS could potentially track those substances as well. In addition, PORTS data tells Coast Guard officials which parts of the harbor are navigable at any given time. “It doesn’t predict where a bad guy may pop up, but it could predict-if someone’s coming in a small boat-where they could or couldn’t enter the bay and how,” says Alan Steinbrugge, director of external operations for the San Francisco Marine Exchange.

But the favorite new toys of both Naval and academic researchers are autonomous underwater vehicles (AUVs), which come in various shapes and sizes and are generally used for collecting data and other reconnaissance missions. The next generation of these electric vehicles will be able to automatically recharge, download data, and receive new instructions by docking at underwater stations linked to shore by fiber-optic cables. In addition, researchers at the University of South Florida have developed the torpedo-shaped Real-time Ocean Bottom Optical Topographer (ROBOT), which will be attached to AUVs and generate 3-D images of the ocean bottom. The images recorded by the ROBOT could be used to find mines on the seafloor or help locate a sunken vessel. Scientists at USF are also working on an underwater mass spectrometer that could be mounted on an unmanned sub to sample coastal waters for biological and chemical weapons. “Within 10 years I see swarms of them,” says Rick Spinrad, technical director for the oceanographer of the Navy, “a fleet of (AUVs) with smart sensing capabilities.”

Maritime trade is expected to more than double in the next two decades. As long as the United States participates in a global consumer culture in which exotic amenities-such as bottled water shipped not only from France and Italy but Fiji-are commonplace, our maritime transportation system will, by dint of scale, remain vulnerable to disruption, sabotage, or terror.

The good news is that last year’s terror attacks jump-started necessary changes in the agencies responsible for protecting our shores. “I never saw this sharing of information and intel (intelligence) before at my level,” says Ashmore, the coxswain patrolling the bay-a statement many wish could be made about the major intelligence agencies. And the Coast Guard’s security efforts will get a big infusion in coming years, thanks to a $17 billion contract awarded in June to Lockheed Martin and Northrop Grumman for dozens of new ships, helicopters, and fixed-wing aircraft. The key, experts say, is to remain vigilant. “After the Exxon Valdez we became more responsive to oil spills,” says the Coast Guard’s captain of the Port of San Francisco, Larry Hereth. “It’s similar with the terror threat. There are lots of challenges out there-prevention, coordination of effort. We’re just beginning to understand the threat, and to respond.”

Photograph by John B. Carnett

Coxswain Chuck Ashmore keeps an eye out for trouble on San Francisco Bay.