Our tour begins with a beautifully landscaped front yard

Imagine this audacious plan: we return our grid of manicured yards into watershed and wildlife-friendly spaces. From a bird or butterfly’s perspective, it would be a transformation from sterile segmented turf fields to bounteous habitat full of nectar plants, insects, hiding places and nesting spaces.  This "Bay-Friendly"
gardens initiative is underway around the Bay Area under the sponsorship of Stopwaste.org. Last weekend some generous, certified “Bay-Friendly” garden owners opened their yards for tours.

A red fox squirrel scampers through the garden

We were able to purchase a tour booklet and tickets to gain entry to meander around and view the seven principles of "Bay-Friendly" gardening used in very different ways.  As their website states, "It’s an approach to landscaping with room for lots of personal preferences and interpretations." The gardens were beautiful, creative, and a great way to bring the natural world into people’s every day lives.

What struck me was the amount of insect and wildlife activity in the featured gardens.  These gardens were busy with insects visiting flowers on the sunny Sunday afternoon.  Squirrels scampered through the trees and a variety of birds were flitting about and calling from the shelter of trees and shrubs.  Like little wildlife havens, the yards were alive with an abundant diversity of plants and wildlife compared with other nearby yards of traditional turf grass and ornamental plants.

Garden creekside retreat featuring water permeable surface and artistic seating area

"Bay-Friendly" gardening also calls for the limited use of pesticides. Toxic chemicals, along with trash pollution, pose big problems to our bay and creeks.  Diazinon and chlorpyrifos are two commonly used insecticides.  According to a report by TDC Environmental, the two are “of great concern, because elevated levels of the two pesticides have been linked to findings of toxicity in wastewater treatment plant effluent, storm water runoff, urban creeks (including all San Francisco Bay area urban creeks), estuaries (including San Francisco Bay), and the Sacramento River.  Much of this toxicity occurs in urban areas, apparently reflecting urban releases—rather than agricultural releases—of diazinon and chlorpyrifos.”

Thimbleberry provides food for native birds and insects

"Bay-Friendly" gardens seem to need fewer pest control measures because the owners strive to create healthier soil conditions, choose plants that are best suited to our climate and location in the garden which, in turn, encourages beneficial insects.  Ultimately this combination keeps the pest populations in better balance.  When control measures are called for, there are resources available to help you choose those least toxic to the environment. Our Water, Our World website has some great resources including a downloadable pocket guide.

The "Bay-Friendly" garden website is a great resource, too, for both home gardeners and landscaping professionals.  There’s an interactive page showing some examples of good gardening practices. There is still one more tour you can attend in Marin County on May 19 to gather ideas for your own "Bay-Friendly" garden.  We’ve also been working on creating a "Bay-Friendly" landscape around the Crab Cove Visitor Center.  Maybe you’ll see us on the Alameda County garden tour, once we get certified, in the next couple of years!

Additional Links:

Pesticide pollution prevention ideas

Sunset Magazine landscaping ideas with less lawn

Harbor porpoises as seen from the Golden Gate Bridge. (Photo: William Keener/Golden Gate Cetacean Research)

Harbor porpoises haven't been seen in San Francisco Bay for more than 60 years. But now, they're coming back through the Golden Gate in growing numbers and researchers are trying to understand why they’re returning.

The best place to look for them is 220 feet above the water on the pedestrian walkway across the Golden Gate Bridge. That's where Bill Keener of Golden Gate Cetacean Research photographs them, holding a massive telephoto lens over the side of the railing.

"There's a porpoise right there, coming very, very close," he says pointing. A dark shape appears in the water. It's a harbor porpoise, coming up for air. "And here's a mother and calf coming straight at us."

The porpoises have dark gray backs and pale bellies. They're about five feet long, smaller than most of their dolphin relatives.

"Look at that! That one's on its side," Keener says. "The porpoise turned on its side. It's spinning and it's feeding."

Porpoises spin as they go after schools of herring and anchovies, which means these porpoises are feeding in the middle of a heavily-trafficked shipping lane. "The porpoises have found a way to not only avoid the ships, but it's also the noise they make," says Keener.

Studying a Shy Marine Mammal

Seeing this behavior is huge for Keener. Harbor porpoises are notoriously shy in the open ocean, so they're tough for researchers to study. Here in the bay, Keener and his colleagues have identified 250 individual porpoises with their photos by looking for unique scars and color patterns on the animals.

Porpoise mating display as seen from the bridge. (Photo: William Keener/Golden Gate Cetacean Research)

When these researchers first started their work on the bridge, they caused a bit of a stir. "You noticed there was a Golden Gate Bridge patrol officer here just a few minutes ago," says Keener. "Well, we're staring down at the water for hours. They'd start getting worried about us. But they know us now. They know what we're doing."

Of course, the big question is why harbor porpoises disappeared in the first place. Keener says the bay has historically been porpoise habitat. Their bones have been found from hundreds of years ago.

"And then there were reports in the 1930s. And then we don't really have reports from around World War II. And there were a lot of things going on during World War II that could have caused that."

San Francisco Bay became a wartime port and a major ship-building center. The Navy strung a seven-mile-long net underwater across the opening of the bay to keep out Japanese submarines. Hundreds of mines were planted in the waters outside the Golden Gate.

Keener says all that activity certainly would have disturbed the porpoises. But there's a bigger change that may have driven them away.

The Changing Bay

To see it, we head toward the Golden Gate Bridge on a twenty-two foot boat with Jonathan Stern, a whale researcher at San Francisco State University. Stern was the first person to spot the porpoises in the bay three years ago.

"I just couldn't figure out what they were doing here. It's like when you see somebody you're used to seeing at work and you see them somewhere, in Hawaii or something. What are you doing here? You're out of place," says Stern.

The bay we're gliding over today is a far cry from the bay in the 1950s and 60s. As the Bay Area boomed, so did water pollution. Keener says raw sewage used to flow right into the bay. "I remember coming across the Bay Bridge when I was very young and it would just smell. It would stink."

After the Clean Water Act was passed in 1972, the bay's water quality began to improve. But Stern says it took time for the food web to come back. "It takes the biology a while to track the chemistry. So it's not surprising that it's taken years for this ecosystem to generate like this."

Stern says it's also possible that the porpoises had to rediscover the bay. "Because over 60 years, we're talking about a number of generations of porpoises. So it's quite likely that San Francisco Bay as a location, as a habitat was out of the institutional memory of the harbor porpoises off the coast here."

Bill Keener and Jonathan Stern search for porpoises in the bay.

As we slow down under the bridge's span, Keener keeps an eye out. "There are porpoises between us and the south tower at 200 yards," he says.

Keener and Stern have a special permit that allows them to approach the porpoises. We wait, listening for them to surface.

"I just heard one here. Here's a cow-calf pair close to the boat and we'll hear this puff," Keener says.

We hear two loud puffs as the porpoises surface just off the bow. "The old time sailors used to call them puffing pigs. That's the exhalation," says Keener.

The harbor porpoises seem calm around boats in the bay, which Stern says will let researchers study their life cycle and social structure, as well as how they might react to big events like the upcoming America's Cup race. Overall, he says it's a good sign that the porpoises are here.

"It's one of those very few good news environmental stories. And it's in our backyard. You know, there was the will to get the bay cleaner and we're now starting to see the effects of that. It gives one hope."

The Golden Gate transmits a vast volume of water back and forth from the Bay twice each day, regular as clockwork but in a much more complex rhythm. Photo by Andrew Alden.

These days, most people in the San Francisco Bay Area arrange their daily lives around the clock. But in former times it was the sun, moon and tides that governed the rhythm of our days. Nowadays the sun and moon attract notice only on the rare occasions when they have eclipses. But the tides still matter.

The twice-daily ebb and flow of the tides is not just a factor for ships navigating the San Francisco Bay shallows, although that is important. The tides are how the Bay breathes. The Bay's windpipe is the Golden Gate, a deep channel that enables seawater to spread nutrients and oxygenation to its lungs—wetlands as far away as the Central Valley. In turn, sediment from nearly half of California's surface area is exhaled to the Pacific where it piles up in a great furrowed berm just off the Golden Gate.

Tides arise from the interactions of the sun and moon with our planet; they are where the heavens most truly move the Earth. While mariners always had a good sense of the patterns of the tides, it took science to make them predictable. When Isaac Newton first grasped that the motions of heaven and Earth fit the same mathematical laws, in the mid-1600s, he saw that one very practical application would be in precisely describing—in modern terms, modeling—the tides.

Newton's tantalizing task is considered fairly well solved today, but it has taken centuries to arrive at this point. (Wikipedia has a good introduction.) Today Bay Area tides are monitored and forecasted by the National Oceanographic and Atmospheric Administration; NOAA's Tides and Currents website will serve you official tide data for many stations (like San Francisco's station at Crissy Field).

But even the most exacting mathematics gives us only a partial picture. Weather and climate both matter, too. As weather fronts and storms and winds impinge on the Bay's water, they can change the tides by as much as two feet. Semi-annual climatic cycles like El Niños add their slower influence. And sea-level rise adds its inexorable direction over the scale of a lifetime. For the best view of the day's exact coastal conditions, I look to surfers and the surf-forecast.com site. The tide is important for beach geologizers, too.

The other big influence on the tides in any given place is bathymetry—underwater topography. Mathematical modelers can treat the different parts of the Bay as giant bathtubs, each sloshing back and forth in its own rhythm and spilling into its neighbors, but that analytical approach has limits. For serious analysis of things like stormwater surges, major shoreline construction and channel dredging, the old-fashioned scale model—the Army Corps of Engineers' Bay Model in Sausalito—still matters.

Bay Model in Sausalito photo by hairygrumpy of Flickr under Creative Commons license

It's a painstakingly calibrated replica, one-thousandth true size or about one and a half acres, whose pumps and sumps produce realistic versions of the Bay's complicated breathing. (Unfortunately it's being renovated as I write this, but the Visitor Center is still open to help you learn about the Bay in other ways.)

"The bay was choked with sewage and toxic waste. There were no environmental laws, no regulations. The bay was really dying before our eyes."

The SF Bay was a convenient place fo dump garbage.

Lewis is executive director of Save the Bay. For decades, he says, the bay had functioned as official and unofficial trash dump for nearly every city on its perimeter.

San Francisco Bay's Grim Future

Dumping garbage into the bay wasn’t only convenient, it served the larger goal of getting rid of the bay entirely.

"There was a proposal by the Rockefeller brothers," says Lewis, "to actually chop down the top of San Bruno Mountain and move it by conveyor belt to the west side of the bay, creating more fill the size of Manhattan out in the bay."

According to Richard Walker, a professor of geography at UC Berkeley, this was the ethos of the day: The bay served no purpose. To fill it up was to make it useful.

"We’d had the depression, the war. There was lot of money to be made in expanding cities, expanding highways, building bridges," he says.

In 1959, the United States Army Corps of Engineers released a study showing that 70 percent of the San Francisco Bay could be filled and transformed into usable land. The City of Berkeley, meanwhile, had proposed to double its size by extending three miles into the bay.

Save the Bay's founders: Kay Kerr, Sylvia McLaughlin, and Esther Gulick

This caught the attention of three Berkeley women: Sylvia McLaughlin, Catherine "Kay" Kerr, and Esther Gulick. Married to prominent UC Berkeley faculty members, the women had strong political connections in the area, as well as to local groups such as the Sierra Club.

They decided to call a meeting of local conservationists (the word "environmentalist" didn't exist yet). Once those activists found out about the plans for the bay, surely they'd swing into action.

But they didn't.

"They were all busy doing their own things," recalls McLaughlin, who is now 94 and lives in the Berkeley hills. "They were saving the redwoods, this and that. They said they they understood the need but they were too busy to help."

A New Movement Takes Shape

And so, in 1961, Save the Bay was born as a campaign to stop cities from filling in the Bay. McLaughlin says it was not always a popular position to take. "I got called all kinds of names, not very complementary," she recalls.

But while developers complained, Save the Bay was growing as an organization, in ways that other groups hadn’t thought to do in the past.

"They very wisely turned themselves into a mass organization by charging $1 for membership," says UC Berkeley's Walker. "And they very quickly had thousands, even tens of thousands of members within two years."

In addition to its vast membership, Save the Bay rallied the media. Pete Seeger even wrote a song about the Bay, calling it a "sludge puddle, sad and gray."

Until this point, says Walker, environmentalism had been a small, elite movement. But Save the Bay changed that. It resembled other major movements of the day, civil rights, free speech, and, eventually, the anti-war movement: Popular movements of ordinary people, trying to change policy.

"Save the Bay is absolutely there at the birth of that kind of popular environmentalism," says Walker.

It Worked.

In 1965, California passed the McAteer Petris Act, which created a new agency, the Bay Conservation and Development Commission, which has the power to stop development on the Bay.

Thanks to that, to the 1972 Clean Water Act and other laws, the bay is much cleaner. And after decades of shrinking, it’s getting bigger, thanks to wetland restoration. That leaves a host of new challenges, including sea level rise and invasive species.

But we’re starting from a different place now than we were in the sixties. And that is thanks to the deceptively simple idea that occurred to Sylvia McLaughlin, while looking out of her window, half a century ago.

"This is something we don’t have a lot of other places," she says "and we have to take care of it."

You can watch excerpts of the wonderful, four-part documentary "Saving the Bay," on the show's website.

Gulls making fast work of AT&T Park leftovers. Credit: Flickr, Malingering.

In a QUEST radio story on Monday, I cover the Bay Area's California gull population becoming a major concern for the South Bay Salt Pond Restoration Project. Thousands of acres of industrial salt ponds are being restored for shorebirds and other wildlife. And that restoration work is creating a big opportunity for some very aggressive gulls.

While reporting the story, I stumbled upon a mystery that's well-known to San Francisco Giants fans: Some gulls have an uncanny way of showing up at AT&T Park during the eighth or ninth inning of a ballgame.

Day game or night game, the gulls bizarrely seem to know when the game is close to ending, pouncing on leftover hot dogs and garlic fries. As Giants broadcaster Mike Krukow said, "if you were a gull, where would you be?"

There are a lot of popular theories about how the gulls time their arrival so well. Do they recognize the illustrious beard of Giants closer Brian Wilson? Do they know “Take Me Out to the Ballgame,” a tune that's always sung during the seventh inning stretch?

I spoke to a few local experts to get their take…

Dan Murphy, Volunteer with Golden Gate Audubon:

It's a crime of opportunity. They're very well attuned to our behavior and our trash. When there are large numbers of people in the stands, gulls don't come into the ballpark. But they can sense when things are starting to wind down. A lot of people leave the game before it's over, so they might be clued in by people moving out of the upper deck toward the eighth inning. That makes sense since they seem to settle on the left field side first.

If a game goes into extra innings, the gulls still seem to know when the ninth inning is. You'll see them sitting on the roof or on the big glove in the outfield, waiting for the game to end. That may still be due to the fans that leave early, but they seem to have a sense of how long games normally go. It's likely that a few birds are always watching and as soon as a few birds go in, others will follow. They're really good at what they do. They find food sources and use them to the max.

David Shuford, Biologist with PRBO Conservation Science:

Gulls spend their day cruising around a lot. But once they figure something out, they tend to come back. So even though the ninth inning doesn't happen at the same time each day, once a few gulls pick up on it, you'll soon have a crowd. It's possible that they can recognize the sounds, too, like songs that are played during the game. Gulls are pretty good about sound.

In general, they're really good at figuring things out. Like when local dumps are closed on the weekends, the gulls seem to know that and don't show up on those days. It's hard to know if they truly know what Saturday is. They may just be cruising by and not see any action, so they don't land. But they seem to recognize the pattern.

Gulls have an advantage – they're total generalists. They're smart and they're tough. They can eat just about anything too. They go after fish, garbage, and other birds. Some of our work on the Farallon Islands has shown that gulls can actually recognize certain individual people as well.

Josh Ackerman, Research Wildlife Biologist with USGS:

They do exactly that same thing at the landfills in the Bay Area. We've done studies on gulls where we've tagged them with transmitters and tracked them daily for two years. California gulls depend on a few of the landfills in the South Bay for food. They arrive exactly when the dumps open and leave right when they close, since the trash piles are covered up when the landfill isn't operating. From our studies, we know that the gulls cover a lot of territory during the day, so it's not a big deal for them to travel to find food.

George Costa, Senior Vice President of Ballpark Operations at AT&T Park:

We've seen an uptick. There seem to be more gulls lately. They always time their arrival to an inning or two innings before the game ends. They're creatures of habit. They know where the food is and that crowds mean food. They're never here except for game days, but if there's a game, they crash the party every night.

It's a series of triggers that tells them it's time. They see the lights and the crowds. There are food smells, like the garlic fries. It's a combination of all those things. You'll see the gulls line up on the left field roof before the game ends. We see the scouts come in and they cue the rest of the gulls.

It's a nuisance really and the fans don't enjoy it. So we're looking at a variety of possibilities to deal with it, including having a falcon on site. They've used them at other ballparks and they seem to work there. You won't get rid of the gulls completely, but we think it would get rid of about 80 percent. We have to retrain these gulls.

The San Francisco Bay Trail project was started in the 1980s to build a "ring around the Bay." The project has been compared to the 2,200-mile Appalachian Trail in that it connects the communities along the way.  But the Bay Trail is unique because it circles a body of water and does so in a major metropolitan area.

Some 310 miles of the San Francisco Bay Trail have been completed as of this summer, and it turns out that Richmond is the city with the most miles of trail so far: 30. It makes sense if you think that Richmond is the city with the longest shoreline in the Bay Area. The city has also been lucky enough to have a group of volunteers who in the late 1990s created the Trails for Richmond Action Committee with the goal to finish the Bay Trail in that city.  They have 11 miles left to go.

Our video takes you on a journey along several sections of the Bay Trail in Richmond. We start out bird-watching at Miller/Knox Regional Shoreline, then ride to the wetlands north of Pt. Isabel Regional Shoreline, and end up at the newest section of the Bay Trail, which circles a former landfill off the Richmond Parkway.

In our video, we wanted to somehow recreate the experience of watching the scenery change as you move along the Bay Trail.  So we asked Bay Trail project manager Laura Thompson to ride her bicycle as we interviewed her, and we came up with our own low-tech "dolly" so that we could film her as we rode alongside.  Check out the photos:

Want to recreate our journey? Find the locations on this map:

View Journey of the San Francisco Bay Trail in a larger map

San Francisco's Pier 39 is home to only a few sea lions this summer.

I spent Saturday sightseeing in San Francisco with a friend visiting from out of town, and I thought I’d check in on the sea lions at Pier 39. Just a few years ago, there were about 1600 of them, slithering on and off the wooden docks, basking in the sun, and barking at one another. Then in 2009, most of them swam away, as QUEST blogger Amy Gotliffe explained. The sea lions’ favorite food, herring, was in short supply, so they went to Oregon to feast on anchovies and salmon. Now the herring are making a comeback—will the sea lions return too?

This weekend the floating wooden palates at Pier 39 were mostly bare; there were perhaps a dozen sea lions. We would expect the sea lion numbers to be low this time of year, herring or no herring. In the summer, sea lions travel down south (the Channel Islands, San Diego, Baja) to breed. But there were still fewer sea lions at Pier 39 than in summers past.

Sea lions will eat a lot of different prey items: octopus, squid, small sharks. But their bread and butter is herring, which have been hard to find in recent years. The herring fishery is the only fishery still in operation in San Francisco Bay, and it closed during the 2009/2010 season (December through April), because there were so few fish. This year, the herring fishery opened again, but with a lower quota than in the past, to allow the fish to recover.

There are a few hypotheses about why the herring numbers dipped so low in 2009. First, herring lay their eggs in the brackish waters of the estuaries around San Francisco Bay. Each female fish can lay up to 50,000 eggs, which are a prized commodity in Japan. However, the years leading up to 2009 were drought years, so the estuaries were saltier than usual. That may have affected the herrings’ spawning success. Second, the 2007 Cosco Busan oil spill may have affected herring health. Researchers found oil-soaked embryos, which were deformed. Third, herring declines may be the result of climate change. As surface waters get warmer, there is less mixing with cold, nutrient-rich water from the bottom of the ocean. There are also big patches of the ocean that have very little oxygen. These hypoxic zones are deadly to their inhabitants, and are affecting many marine species.

However, the herring appear to be making a comeback, possibly because the past few years have been wet and the estuaries are sufficiently fresh, or because the spilled oil has been flushed from the Bay. Time will tell whether the sea lions follow their food and return to Pier 39. I hope they come back—along with the twists and turns of Lombard Street and the Golden Gate Bridge, the Embarcadero’s sea lions are one of my favorite San Francisco treasures to show off to visiting friends.

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^{Mount Diablo is seen with its foothills from Wildcat Canyon Road near Inspiration Point in the Berkeley Hills. Photo courtesy Seán O'Hara of Flickr under Creative commons license. Photos by Andrew Alden unless otherwise indicated.}

Mount Diablo, in the heart of the East Bay, is an interesting mountain in many ways. It has fossils. It has a lot of serpentinite in it, with the accompanying serpentine plant community. It's been mined for mercury and other metals. It's an exceptional structure even in a region of crazy-complicated tectonic structures. But I expect to get into the geological details some other time. Because first of all, Mount Diablo is just there.

Mount Diablo was always a landmark, so widely visible around the Bay and central California that in 1851 its peak was named the base line for land divisions. Around here and across the majority of California and all of Nevada, every township and section is numbered in relation to the north-south Mt. Diablo Meridian and the east-west Mt. Diablo Base Line. (Full details are given by the Mount Diablo Surveyors Historical Society.)

Today few of us have any awareness of land division, and we can simply enjoy the peak's prominence as we drive Bay Area roads or hike the hills. Around the Bay proper, Mount Diablo peeks over the Berkeley Hills as seen from Corona Heights in San Francisco . . .

. . . or from the hills above Marin City, where the "devil's mountain" overlooks Angel Island.

To see the peak's full extent we need to cross the hills of the East Bay, or at least climb them. Here the mountain is seen from the Los Buellis Hills, east of San Jose, looking up the valley formed by the Calaveras fault.

Once over the hills, your every vista centers around Diablo whether it's the view from Oakland . . .

. . . or from the Tassajara Valley . . .

. . . or from the Delta:

_{Photo courtesy Mark Johnson of Flickr under Creative Commons license}

On Interstate 5, Mount Diablo can be spotted from the Dunnigan Hills in the north to near Patterson in the south. From state route 99 it's visible from a much longer stretch, but only if the conditions are right. In fact, instead of driving everywhere to determine Mount Diablo's viewshed, it's more efficient to visit the peak itself on a perfect day and look outward. There's a handy sign pointing out what's possible on a perfect day.

_{Photo courtesy George Kelly of Flickr under Creative Commons license}

I've been up there on a perfect day, and while it's not geometrically possible, atmospheric refraction has allowed me to spot Mount Shasta. An example of a typical excellent (not perfect) day shows Pyramid Peak in the central Sierra Nevada.

_{Photo courtesy advencap of Flickr under Creative Commons license}

Such days were once more common. A. J. McCall, standing at the Sierra's crest on September 7, 1849, recorded "a picture of wonderful grandeur and magnificence":

"Below were a succession of innumerable pine-covered mountain peaks, growing less and less until they disappeared in a broad, yellow valley sweeping north and south until lost to view, and beyond another range of mountains. This was the far-famed Sacramento Valley, nearly a hundred miles distant. The purity of the atmosphere rendered vision almost illimitable, showing every line and shadow distinctly." (source)

Today the activities of ten million modern Californians make such purity almost unattainable—especially around Labor Day.

There's a common belief that when pioneer scout Kit Carson guided the Fremont Expedition over the Sierra in the winter of 1844 (at today's Carson Pass), he recognized his position by spotting Mount Diablo: "There is the little mountain—it is 15 years since I saw it; but I am just as sure as if I had seen it yesterday." But Bob Graham and Peter Lathrop argue convincingly that it was not Diablo, but the whole Coast Range that Carson meant. That's too bad; it was a good story.

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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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Suspended Sediment Concentration in the San Francisco Bay, USGS. Click here for a larger version of the image.

Much of the gold extracted from the Sierra foothills during the Gold Rush was in placer deposits. That is, it was mixed with the rest of the sediment naturally eroding from the mountainside. Flecks of gold have a greater density than almost all the other particles and, thus, can be concentrated through natural water movement. A similar process is seen when you go to the beach. When the mixture of minerals and waves are just right you might notice darker grains of sand creating streaks or patches in the wet sand.

Miners had to devise ways to extract the gold because it was still a minor component even in rich placer deposits. Methods like panning and simple equipment like sluice boxes were used with moving water to enhance the natural mineral separation process.

When all this relatively easy-to-get gold was extracted from the streams and rivers prospectors turned to hydraulic mining to obtain the riches. Hydraulic mining was the process of using high-powered water canons to artificially erode gold-bearing hills made of sedimentary deposits. These sedimentary deposits were ancient stream beds that contained gold in placer deposits much like the modern streams did. Essentially, hydraulic mining eroded ancient river sediment from the hillside and diverted the material into the modern river where miners then extracted the gold.

Unsurprisingly, the activity of hydraulic mining devastated the local environment. The landscape was scarred and the mountain streams choked with gravel and sediment. And the effects weren't just local. These rivers and streams flowed into the San Joaquin River and Sacramento River and deposited some of this sediment in the Central Valley causing flooding and navigation problems. Some of the finer sediment was transported even further, to the San Francisco Bay.

The effects of hydraulic mining practices are still measurable in the Bay today. Geologists from the USGS are studying the amount of sediment the Sacramento-San Joaquin Delta delivers to the Bay and are finding that the Gold Rush-induced sediment levels might be diminishing:

"[USGS geologist David Schoellhamer] says all the extra sediment has finally worked its way past the Golden Gate. The bay's water is about 30 percent clearer than it was 10 years ago."

It is taken many decades for this complex sediment delivery system to reach a new equilibrium. However, the readjustment of the estuary to these 'new' conditions might create new problems:

"Less sediment in the bay could spell trouble if scientists' predictions about rising sea levels come to pass. These delicate tidal marshes could be inundated over the next century."

What I find fascinating, yet also extremely challenging, is how the choices we've made as a civilization over the decades and centuries combine and sum to create the issues we face right now. There are no simple answers. Regardless of how well-intentioned some environmental programs may be there will always be some uncertainty about how natural systems respond. Continuing scientific research of these systems will reduce that uncertainty and inform policy decisions of the future.

Images: (1) California Water Science Center; (2) Wikipedia

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