A Gold Rush-era ship is excavated from historical fill at a San Francisco construction site in 2005. Photo by Andrew Alden.

Humans have been making land for thousands of years. Lately we have gotten better at it, but nature has a head start of a few billion years, and we don't work with nature's infinite care.

On the largest scale, land grows because volcanoes and tectonic movements elevate rocks above sea level. The Bay Area has no volcanoes at present, and the basic framework of our terrain is tectonism organized around the San Andreas fault system. On the scale of human history, that's too slow to be relevant. For growing new land, erosion and deposition matter more to us.

New land grows naturally around the Bay as wetlands capture sediment washed in with the seawater. Unfortunately for builders, it's soft black mud and it's barely at sea level. And unfortunately for shippers, "bay mud" bars vessels from approaching the shore almost everywhere except around steep bodies of bedrock, like Yerba Buena and Alcatraz Islands. When Gold Rush settlers came here to stay, making bay mud into useful land—reclamation—was one of their chief concerns.

In San Francisco there were so many abandoned ships in the harbor that many were simply scuttled and buried in fill—dredged sand and mud from the Bay, mostly, along with waste rock and debris. We dig up the old ships occasionally while building around the Financial District.

More land was made elsewhere simply by diking off sections of the Bay, letting it dry out, and putting it to use growing crops or harvesting sea salt. (Today the salt ponds of the South Bay are carefully being restored to working wetland.) In San Mateo County, levees were built to create Brewer's Island around the turn of the last century. The dry bay mud served as hayfields and salt ponds until T. Jack Foster set out to turn Brewer's Island into a complete planned city. The creation of Foster City in the 1960s was overseen by geotechnical engineers, but the basic method was age-old: dredge, dump, drain.

The U.S. Geological Survey has mapped artificial land along with all the other geologic units around the Bay. The majority of this reclaimed land is in the central Bay, in San Francisco and Oakland.

Major land reclamation areas of the central Bay are shown in purple, marked afbm for artificial fill on bay mud. Map from USGS Open-File 00-444. Click to view it at full size.

Reclaimed land shows its weakness in earthquakes. In the 1906 quake it was widely noted that buildings placed on "made land" were prone to failure. Nonetheless the city's rubble was used for fill at the site of the 1915 Pan Pacific Exposition, which later became developed as the Marina district. In the 1989 Loma Prieta quake the Marina had the deadliest damage in the city. Likewise, the Cypress section of Interstate 880, in west Oakland, failed where it crossed old fill. In San Francisco the notorious Embarcadero Freeway, also built upon old fill, was torn down shortly after Loma Prieta, before it could fail. Our areas of fill, old and new, will continue to be tested by earthquakes while our reclamation practices continue to improve.

For geology enthusiasts, Oakland's reclaimed land has given us an unexpected treat, seen in the new Middle Harbor Park.

A replica seawall recycles rock from an early land reclamation project: the port of Oakland. Photo by Andrew Alden.

In the 1880s, early in the creation of Oakland's harbor, a pair of "training walls" was built to guide the tides into scouring the ship channel clean. The project required lots of large boulders, and every quarry along the Bay Area shoreline was recruited to supply the stones. When the old north training wall was demolished in 2001, some of the best rocks were set aside. These were made into a replica pier, nicely laid down in drystone masonry, that displays excellent specimens of Bay Area rock types.

San Francisco Bay is home to hundreds of invasive species. Many arrived in the ballast water of large ships.

Hundreds of invasive species have been found in San Francisco Bay, according to biologists. That makes the bay one of the most invaded estuaries in the world.

Hoping to restore native fish and wildlife, California has passed the strictest rules in the country to prevent ocean freighters from introducing more foreign species to the bay. But the standards are so tough, officials may not be able to enforce them.

"Let's see we've got one, two, three exotic organisms, four exotic organisms…"

On a muddy beach in Alameda, Biologist Andrew Cohen of the Center for Research on Aquatic Bioinvasions scoops up a clump of seaweed that’s home to clams, snails, and strange globs.

"Those yellow dots are the eggs, the egg mass of a Japanese sea slug which show up here a few years ago." Almost all of the animals in Cohen's hands are invasive species – originally from places like China, Australia, and the Atlantic.

Listen to the QUEST radio story Combating Bay Invaders

"Anytime I go out in the bay, there's a reasonable chance I'm gonna find something I've never seen in the bay before – something no one has seen on the Pacific coast before. That's just astonishing," says Cohen.

Most of these marine invaders arrived as international hitchhikers. Ships that carry cargo on the open ocean have to be balanced, so they don't tip over. To do that, they fill massive onboard ballast tanks by pumping water in at one port and pumping it out at the next.

"For a long time, people didn't think too much about this, cause it was just water. But eventually, we found that we were moving virtually everything that lived in the sea," Cohen says.

Marine organisms like crabs and snails have tiny free-floating larvae. So, a tank full of ballast water is like a soup of marine life. "They're so effective at dispersing because a single individual might produce a million young."

Some invaders have brought parasites that cause swimmer's itch at local beaches. Other foreign species, like the Asian clam, have altered the entire food web in San Francisco Bay. Millions of dollars have been spent trying to eradicate the worst invasive species. But Cohen says those efforts rarely work. So, the strategy has turned to prevention.

Testing New Treatment Technology

Inside the Golden Bear, a 500-foot ship at the California Maritime Academy in Vallejo, Engineer Bill Davidson switches on the ballast pumps. "The ballast tanks we use are right above us, which are our treatment and control tanks," says Davidson.

Davidson is testing new ballast water treatment technology. The idea is pretty simple – kill the organisms in the water, so they don't spread when the ballast is released. The system has two steps. First the ballast water is filtered. Then, chlorine is added. "And you take this chlorine and you feed it back into the ballast stream and so that will ideally oxidize or kill any live organisms," says Davidson.

The chlorine is neutralized before it’s released by the ship. But getting this system to work is trickier than it seems, because the organisms are very, very small.

In a lab on the ship, Julie Kuo of Moss Landing Marine Labs looks through a microscope at a tiny, cone-shaped plankton. "So right in your center field of view… That's a tintinnid and those guys pretty much get to as large as that."

"As large as that" is about half the width of a human hair. As part of the tests, Kuo counts the organisms in water samples from the treatment process – and, most importantly, sees if they're dead. "If they’re kind of sitting there and you don’t know if they’re alive or dead, you poke them with a probe," says Kuo.

The Frontlines of Regulation

This treatment system is designed to meet international standards that limit the number of living organisms in ballast water. Right now those standards are voluntary.

But California has adopted a goal that’s a thousand times tougher. It applies to all newly-constructed ships starting next January. The only problem is – the technology to meet California’s higher standard isn’t quite ready for prime time.

"We aren’t going to be able to go out there right now and say well, 100% you met the standard no matter what," says Nicole Dobroski with the California State Lands Commission, the agency overseeing the regulation.

She says none of the treatment systems being developed consistently meet California’s standards yet. Still, the state is moving ahead with the regulation.

"We recognize that that’s a challenge, but there's a good reason we wanted it to be a challenge. We wanted them to be innovative. We wanted them to think out of the box."

But ship operators may not have much to worry about if past enforcement policies are any indication. Ships are currently required to exchange their ballast water at least 230 miles from shore if they plan on discharging it in port. But even though hundreds of ships a year are not complying with these requirements, the State Lands Commission has only fined two ships in the past ten years.

"Our goal isn't just to come in and slap a fine on these vessels because we find that isn't necessarily the best approach. We try to work with them as much as possible, make sure they’re educated about all the necessary regulations," says Dobroski.

California's progress is likely to have a big impact on federal efforts as both the US Coast Guard and the EPA develop new national ballast water standards.

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A lot of folks in the Bay Area know the "mothball fleet." You can spot the aging Navy and merchant vessels as you drive over the Benicia bridge (check out our Google Map here to see the fleet). Most of them are waiting to be recycled – and they've been waiting for quite some time.

As I talk about in Monday's radio story, a lawsuit over these ships was finally settled this week. At issue was the paint flaking off the hulls of the ships.  After so many  years, it's weathered and fallen into Suisun Bay. That's a problem because the paint contains toxic metals like lead, cadmium, and copper. A study in 2007 found that more than 20 tons of these metals had fallen into the bay, which is a critical habitat for some endangered species.

The fleet, managed by the US Maritime Administration (MARAD), is meant to be a temporary holding ground for these ships, but a stalemate in recent years made it a bit more permanent. Since the closest ship recycling facility is in Brownsville, Texas, the ships must be towed there through the Panama Canal. But before they leave the bay, the marine growth on the hulls has to be removed to prevent the spread of invasive species. As we reported in a QUEST TV story a few years ago, MARAD wanted to do that cleaning in Suisun Bay.  The San Francisco Bay Water Quality Control Board ruled that method would release even more pollution.

Two things have happened in the meantime. First, in January, a judge ruled that the fleet was in violation of the Clean Water Act. Second, a new administration entered the White House.  As several people I spoke to mentioned, it lead to a noticeable thawing in relations.  As a sign of that, MARAD began moving a few ships out for recycling last fall.

The worst polluting ships will be removed by the fall of 2012, with all 52 ships under the settlement removed by 2017. (For more on the settlement, check out this blog post by NRDC's attorney Michael Wall). Where they'll be recycled is another issue. Instead of having the ships go to Texas, many would like to see them recycled here in the Bay Area. One company is currently working to open two dry docks on Mare Island in Vallejo. But since it's a former Naval facility, they're having some trouble getting permitted. In the meantime, the only work going on in the Bay Area will be the hull cleaning. Check out the slideshow below for more on that.

Listen to the Ghost Fleet On the Move radio report online.

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UPDATE on 10/23/09: From the San Francisco Chronicle – "Two World War II cargo ships moored among Benicia's fabled "ghost fleet" since the late 1940s will be towed out of Suisun Bay next month, scrubbed clean in dry dock and ultimately sent to Texas to be broken up and sold for scrap".

Read more about the clean-up effort in the Chronicle here.

On the surface of the story, the Ghost Fleet of Suisun Bay (commonly called the "Mothball Fleet" but most accurately referred to as the Suisun Bay National Defense Reserve Fleet) is leaking toxic waste in the form of peeling ship paint containing nasty heavy metals into an already stressed bay ecosystem. Bad guys: Mothball Fleet. Good guys: Enviros who are suing. Simple, right?

But when we began digging into the story, we found the origins of the problem and current impasse to be a bit more convoluted. I'll attempt to quickly summarize: The fleet has been there since the 1940's. It wasn't until 2006 that it came to light that the exterior paint is peeling from the ships and falling into the bay. Many tons of toxic heavy metals have already fallen into Suisun Bay and there's a lot more to be had. Oddly enough, the story was initially triggered by a study that was commissioned by the federal body who oversees the fleet, the Department of Transportation's Maritime Administration, or MARAD for short. So the Contra Costa Times got a hold of a draft of that report and now, the ships are at the center of a different kind of battle long after they've been decommissioned.

Environmental groups (NRDC, Arc Ecology and San Francisco Bay Keeper), community leaders and water regulators justifiably want MARAD to either remove or better maintain the ships so that they are not polluting these waters that serve as both fishing and nursery grounds for several fragile or threatened species. That includes humans who are often out there catching fish for dinner. Historically, MARAD has been regularly removing and dismantling the ships but like most federal bodies whose charter was drafted during WWII, alacrity is not at the top of their mission statement.

View Suisun Bay's Mothball Fleet in a larger map

The real issue now seems to be that MARAD has had to completely stop removing ships because they can't clean their hulls of potentially hazardous invasive biological species (to comply with the U.S. Coast Guard's National Aquatic Invasive Species Act of 2003) without scraping more paint into the bay. So, until someone develops a system to clean the hulls that doesn't scrape more paint into the water, the San Francisco Regional Water Quality Control Board says that MARAD can't remove the ships.

The one possible solution that everyone pretty much agrees upon is to dismantle the ships locally so that they don’t have to be cleaned of invasive species. There are currently no ship dismantlers operating on the West Coast but there's a company called Allied Defense Recycling located on Vallejo's Mare Island Naval Shipyard that's chomping at the bit to tear those ships apart. But they've also run into red tape. And while they await permits and approvals from multiple parties, the ships continue to rot and pollute.

It's always easier to write a story with clear heroes and villains. But to me, it does seem that MARAD, environmental groups and water regulators all agree that we have a problem that must be addressed. So, what now? I guess we wait. Perhaps this lawsuit will kick start some aspect of the clean-up process but in the meantime, frustration mounts for all parties involved and many pointing index fingers are suffering from overuse.

Watch the "Ghost Fleet" TV Story online, as well as find additional links and resources. Also, check out the online photo set of the ships and behind the scenes images.

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