There is romance and mystery in fog, flowing down the shrouded city streets, shadowing Dashiell Hammett’s quick-talking detectives, churning into the “gray primordial vastness” that bedeviled the sailing ships of Jack London. To borrow a line from noir, it would be a shame if anything happened to the fog.

That’s because fog is not just a moody background; it’s a vital control on Northern California weather. Without it we’d have no redwood trees and no salmon, and we’d have uncomfortable people living in what we could call Nevada-by-the-sea. It would be hot and, with climate change, getting hotter. If you’ve been to Las Vegas in July, you know what that would do to your enjoyment of life, not
to mention your air conditioning bill.

But it’s only in the last few years that scientists have started to get a handle on the conditions that make fog happen here, and how fog might have changed—and be changing—as the climate does. Fog, even as a scientific entity, is elusive and wily and ethereal, defying our attempts at easy prediction.

Fog is a low cloud. Northern California summer fog—also known as a marine layer—is a type known as “marine advection fog,” different from the nine or ten other types that form in different ways and feature different types of clouds. Marine fog forms when wind pushes a warm, moist air mass over a cold surface, in this case, the ocean. As the air cools, it loses its ability to hold as much water, so
droplets condense, form a cloud and hang around in the sky. That’s a relatively simple equation, and works anywhere in the world, including your bathroom when you take a hot shower and pass warm moist air over a cold mirror.

Summertime fog is probably the most vital regulator of the climate in Northern California, and changes in the fog could spell big changes for the species—humans included—that depend on it. But before anyone can offer any kind of confident prediction about the environmental future of Northern California, they need to understand fog, which means understanding the factors that create that warm air and that cold surface, and move all the parts around in the right way.

And there are a lot of moving parts. To name just a few, the formation of summer fog is influenced by the difference in temperatures between the Central Valley and the coast, by large-scale pressure patterns over the entire Pacific Ocean and western United States, by the difference in pressure between, say, Nevada and Seattle, by sea surface temperatures, and by the difference in sea surface temperatures between different parts of the Pacific. Like a Facebook romance, it’s complicated.

Just understanding all that stuff in order to come up with a good description of how and why marine fog forms in Northern California is difficult enough. But now all the factors that conspire to create the fog are changing with global warming. Sea surface temperatures, for example, are heating up, although they also change every year on their own, thanks to regular events like this year’s El Niño or longer-term gyroscopic swings like the Pacific Decadal Oscillation.

Air temperatures are heating up, too, but more so in some places than in others, and it’s not a steady uphill climb everywhere. Coastal maximum summer temperatures, for example, have increased on average over the last hundred years, but decreased during the last thirty, while the inland daily temperature average increased only slightly—meaning that in some places the average temperature rose slightly, while in others it decreased. And since fog is affected by the difference in temperatures between places, but also affects the temperature… yikes.

With so many factors in play, it’s hard to know if the state is in for more fog or for less. One recently published scientific paper argues that we used to have fog more often: Fog was 33 percent more frequent in the first quarter of the 20th century than during the last half, for reasons that appear to
be unrelated to global warming. Another study suggests that warming may actually result in more fog for the coast.

So what will happen to fog? Now that is a good mystery.

Dave Reynolds, the climatologist in charge at the National Weather Service’s Northern California
forecasting office, lives on the boundary of the Mark Twain witticism “Climate is what you expect, weather is what you get.” Reynolds models and monitors the big-picture weather and climate patterns of the entire globe, then tries, along with his colleagues, to predict the Bay Area’s weather.

Our weather, fog included, is determined by the globalclimate—stuff like whether a jet of air blowing off the Himalayas (yes, those Himalayas) makes it all the way to California or gets stopped just short by a high-pressure ridge over the coast. In the summer, the forecasters are looking at worldwide phenomena in the service of one big task: “Forecasting the depth of the marine layer”—the fog—“is the number-one challenge from May 15 to October 15,” Reynolds says. “That drives how warm it’s going to be inland, how cool it’s going to be on the coast, how far the clouds will drive in.”

Reynolds needs to be accurate about the depth of the fog, because the rest of his forecast depends on that, and because a lot of people—not just San Franciscans complaining about a 75-degree heat wave—depend on his forecast. Firefighters need to know whether they can do controlled burns in the mountains. Boaters need to know the marine navigation conditions. Air traffic controllers need to know whether they can open all the runways at SFO. Water resource managers need to know what demand will be like and how hot it will be. Energy grid monitors need to know how many air conditioners will be running. Hospitals need to know if the heat or air quality will be a health issue.

Now, for the forecaster’s challenge: In Northern California in the summer, warm, moist air masses are usually blowing across the Pacific from the tropics, borne of, and propelled by, sea surface temperature variations in the western equatorial Pacific. Meanwhile, a general high-pressure area
over the Northern Pacific and a low-pressure area caused by high inland air temperatures causes wind to blow roughly south along the coast of the western United States, churning up the ocean and creating an upwelling of cold, nutrient-rich water called the California Current. On a typical summer
day, when the warm air meets the cold water—poof!—marine advection fog appears over the coast. When there’s such a temperature difference between inland and coast, the ocean cooled air will try to expand into areas where it’s warmer. In the summer, the inland areas get hot, and so the cold, foggy
air marches inland, conquering local heat areas as it goes.

It doesn’t take much of a change in the big picture to affect the fog. Say the high pressure area moves a bit, or the sea surface temperatures change—and remember, these are sea surface temperatures out near, like, Tahiti, and pressure areas covering thousands of square miles off the coast of Seattle—and the fog could go away for a week. You can, perhaps, understand why Reynolds has a tough job.

Reynolds’ workstation sits in the middle of a NORADesque command center, with banks of monitors displaying maps of various resolutions, each grid covered in splotches of color to represent different aspects of the weather. Reynolds sits surrounded by displays of the factors that cause fog: sea surface temperatures, inland temperatures, pressures, pressure gradients. Computers show the current state of all these factors and then forecast how they’ll change on an hourly scale over the next day, week, or month.

While the models are generally pretty accurate at predicting the next 24 hours, both computer weather and climate prediction models are not good at forecasting clouds more than a day or two in advance. There is a reason for this, and it is that long-term clouds, from a mathematical and
computational perspective, suck. Try modeling the physics of a bunch of water droplets condensing in air around an almost infinitely variable local topography with its own microclimates and slight temperature gradations and pressure gradations and elevation changes, all of it depending on subtle
differences in far-flung pressure and sea surface temperatures and…blast, you’ve just burned down your computer.

Even worse, Northern California’s coastal climate is particularly tricky to predict. We live right on the border between different types of climate areas, the wetter northwest and the drier southwest. The farther you get from here, the more confident climate predictions become.

Since computers struggle to predict weather, say, a full month ahead, Reynolds is left trying to predict a warm or cool summer based on a reading of all the other variables. He prefers looking at sea surface temperatures. “The colder the waters are over the ocean, the higher the probability
you’re going to get marine stratus,” Reynolds says. “It’s our view [that] the colder the ocean temperatures, the higher the probability of a cold summer.”

For climate change researchers, who are looking at much longer trends, there’s little hope of deterministically modeling individual cloud behavior. Generally, for a climate scientist to describe something as an actual change, rather than just a decadal shift, a thirty-year observation period
is required. But running a thirty-year simulation of how climate change may affect fog is just too uncertain, time-consuming, and hard on currently available computers.

(Undaunted, scientists at the Lawrence Berkeley Laboratory are working on the requirements for a one-of-a-kind computer that will try to model long-term global cloud behavior. It will be called the “Green Flash” and use special software being built at an atmospheric science research lab in Colorado, with contributions from Lawrence Berkeley engineers. They hope to have it up and running in a few more years.)

In the meantime, land managers often need scientists to take a stab at predicting the future of fog, anyway. For example, the Farallon Islands National Marine Sanctuary has been working on a climate change scenario for the islands, and last year the organization asked Reynolds to provide a
spring-and-summer cloud forecast. He wasn’t comfortable doing it but, when asked to say something, went with the occasionally advanced theory that, if inland areas heat up faster than the coastal areas over the next few decades—and recently, they have—fog should increase. (The pressure gradient caused by higher inland temperatures would increase both the winds that stir up the California Current to create fog, and the breeze that then blows fog in from the ocean.)

“The physics of it says that stratus should increase,” Reynolds says. “All things staying the same.” And then, at the idea of all things staying the same, he pauses for a minute to laugh.

Figuring out what will happen to the fog in the next century is not merely speculative research for the benefit of postcard photographers. Fog—both the clouds and their cooling effect—enables life of all kinds in California. It makes it a pleasant place to live, serving as natural air conditioning, which is important in an age of energy dependence and global warming. Fog sustains redwood trees, and everything that lives in them, because redwoods are somewhat inefficient plants that lose more water than other plants on sunny days; redwoods need cloud cover so as not to become desiccated.

While redwoods exemplify fog dependence—coast redwoods live only in the narrow coastal fog belt of Western North America—a great many other species need the fog. Salamanders, frogs and other amphibians, for example, are particularly sensitive to both temperature and humidity. Some salamanders suffer heat stress and die at temperatures in the mid-70s. The fog provides vital temperature control, allowing coastal amphibian species to survive (although some species hack it in the hotter Central Valley by hiding out during the day). Other plant species, like huckleberries, prefer shade and cool temperatures to avoid losing too much water.

The Central Coast’s endangered Coho salmon also desperately need the redwoods and the fog. The fish can’t reproduce in streams warmer than about 60 degrees Fahrenheit, a boundary to which many streams come perilously close in the warm summer spawning months. Without the cooling effects of fog and redwood shade, the salmon would face one more problem on a list that’s already near unmanageable: reduced spawning habitat, lowered summertime water flow, reduced food availability, and decreased genetic variability. A recent estimate put the total number of Central Coast Coho at 500 fish, and scientists warn that the subspecies is near extinction. “Redwoods and Coho are inextricable with each other,” says Charlotte Ambrose, a salmon recovery coordinator with the National Marine Fisheries Service. “If we can manage our redwood region for a diversity of ages in the redwood stand, we are likely to be managing for Coho salmon.”

As one way to help, Norman Miller, a climate scientist at Lawrence Berkeley National Lab, has proposed an investigation with the fisheries service to use a climate model to simulate where future stream temperatures might stay low enough to harbor spawning salmon. The project would look at fine-scale water temperature as a function of the presence of fog, while also taking into account tree shading and dew. “The question becomes, how do we quantify regions that don’t get above a temperature like that?” Miller says. “Because stream temperature is a key to salmon recovery.”

The end goal would be to identify good spawning streams in advance, and preemptively work to protect them. “We really don’t have good models in place right now to help us identify where those areas are where we can protect them now, or work with whoever the landowner is now to preserve those areas,” Ambrose says.

There’s also a human factor to fog. We rely on its cooling effects for agriculture—the wine grape-growing conditions of Napa, Sonoma, and Mendocino counties, for example, are shaped by the fog to such an extent that even minor changes could be career-ending for some vintners. Summertime
clouds are also a major transportation issue for boats and airplanes, and have been throughout history. In the era before the Bay Bridge, when you still had to go from Oakland to San Francisco by boat, fog was a menace to navigation, a dark, ominous, terrifying shipwreck-waiting-to-happen. The
San Francisco Bay was once the most shipwreck-prone place on Earth. Fog, in other words, is a weather condition that matters. Just ask the pilot of the Cosco Busan.

Several recent research papers take some steps toward a better understanding of Northern California fog. One is the dissertation of UC Berkeley geography graduate student James Johnstone, now a postdoc at the University of Washington. In a 250-page paper that is considerably more thrilling
than its title, “Climate Variability in Northern California and Its Global Connections,” as well as in a paper published this February in the Proceedings of the National Academy of Sciences, Johnstone set out to define the global patterns that control fog in the summer and rain in the winter in an attempt to see what might happen to redwood trees.

One of the curious things about Northern California fog is that the observational record for it is extremely poor. The National Weather Service started tracking fog measurements at the San Francisco airport in the mid-1990s, but that’s not yet the kind of time scale a climate researcher needs. Miller and others use summertime relative humidity data measured by several offshore buoys along the coast—if the humidity is 100 percent, they assume there’s fog.

Johnstone used regional airport data. Airports take hourly measurements of the height of the cloud ceiling, which is a nice way of identifying foggy days. Johnstone used observations from the Arcata and Monterey airports, which had records going back to 1951. The observational record shows a weak, insignificant decrease in fog between 1951 and 2008, with considerable year-to-year shifts. (In the peak year, 1951, there was more than twice as much fog as in 1997, the minimum year for fog.) But Johnstone wanted to extend his records to cover the entire century, and so he went looking for a way to identify fog by proxy.

He matched up the observed fog records with the big-picture stuff over the same time period, to see how well temperature, pressure, and sea surface temperature worked as predictors of fog. They all did, to some degree. Movement in the North Pacific Pressure High and changes in global sea surface temperatures both appeared related to the presence of fog in Northern California. But temperature variability—the difference between inland and coastal daily maximum temperatures across the western United States—stood out. “It correlates amazingly well with fog,” Johnstone says. “This just blew my mind that they correlate so strongly.”

Temperature records go back much further than the cloud ceiling observations, to the beginning of the 20th century. If the inland-coast temperature differential is reliable enough an indicator of fog, which Johnstone thinks it is, it allows an estimation of what fog has done over the entire century.

This time, there was a stronger trend: Johnstone’s analysis showed that fog in the early 1900s was about 33 percent more frequent than in recent decades since 1951. While 1951 was extraordinarily foggy, by extending the study backward, Johnstone inferred that years like that were much more typical between 1901 and 1925. He credits the long-term reduction in fog to coastal circulation and temperature changes, including the roughly thirty-year cycling of the Pacific Decadal Oscillation.

Johnstone cautions that making any predictions now would be premature. His study shows such considerable year-to-year variability in fog—even decade-to-decade variability—that he concludes crediting anything to global warming is probably still unsupportable. “The future is anybody’s guess,” he says.

One of the few well-known predictions about fog comes from Bereket Lebassi, a graduate student at Santa Clara University, along with a number of local researchers including Norman Miller and San Jose State professor Robert Bornstein, in a paper published last year in the Journal of Climate.

Although Johnstone’s work shows an overall decrease in the difference between inland and coastal temperatures, due in part to uncertain trends in the inland summer temperature maximums since 1901, those inland temperatures have rebounded since about 1970, warming relatively faster than the coast, which has actually seen its daily temperature maximums decrease, according to the Lebassi paper. The authors argue that this is fog cause-and-effect: The increased temperature differential causes more fog, which in turn further cools the coast, which further increases the temperature differential.

“As global warming is warming the interior, that would mean—in theory, and our observations back this up—there would be increased onshore sea breeze activity, bringing in cooling air, and bringing in fog, which would block the sunshine, and therefore the temperatures along the coast would be cooling,” Bornstein says. “And that’s what we found.”

This is a fairly remarkable-sounding idea: The effect of global warming could be to cool coastal California. Bornstein, like Reynolds, says that in theory, in the future the cooling trend could continue, since current global warming predictions call for temperatures to increase more quickly inland than on the coast. If coastal maximum temperatures continue to cool, as they did during the study period, that would be good news for hospitals worried about human heat stress and vintners worried about the extinction of wine grapes in the Napa Valley. Bornstein has started to look at energy consumption, and how more fog in the future might help coastal California keep its energy use down.

Still, the data wasn’t complete enough to nail down any conclusions. (And, Johnstone points out, the increase in fog over the last thirty years amounts to a small uptick in a century-long decline.) “I’m not willing to say anything,” says Berkeley Lab’s Miller. “The real questions behind that are, what changes will we see in the mechanisms that are conducive to fog formation, the controls? You can ask the same question about hurricanes—what are the big controls?”

These controls are moving targets—sea surface temperature gradients, inland temperature gradients, pressure gradients, changes in the upwelling. Sea surface temperatures, for example, are warming everywhere, but asymmetrically. Even the tropical jet stream appears to be changing, shifting slightly to the north, which could alter weather over the entire mid-latitudes. None of it is changing uniformly with respect to fog, meaning that in some sense, researchers have to pick their poison. Will stronger winds lead to a stronger upwelling and therefore colder water—and so more fog? Or will globally warming ocean temperatures cancel that effect out and weaken the upwelling, leading to less fog?

Park Williams, a postdoc in UC Santa Barbara’s geography department who worked on his own fog study for his dissertation, is the first to admit that, after years of studying fog data, the future is still unclear. It’s more important than ever, though, he says, particularly when you look at predictions for temperature changes in California and realize that those are completely dependent on fog. (In the Intergovernmental Panel on Climate Change report, for example, coastal California is a tiny, cooling dot in a sea of red warming areas.)

“Cloud cover along the coast reasonably dictates summer temperatures,” Williams says. “Until we have a more accurate picture of how summer cloud cover may respond, we have no idea what our temperature outlook is for a global warming picture.”

But for now, the fate of fog defies easy—or complete —explanation. It’s the kind of thing that keeps scientists going: a real, complex puzzle that could take years or decades to fully untangle, with tremendous implications for human health, navigation, agriculture, native species, and energy use.

In The Sea Wolf, Jack London compared fog to “the gray shadow of infinite mystery, brooding over the whirling speck of earth.” London wrote that line in 1904, a few decades before the first researcher proposed—and was ridiculed for suggesting—that greenhouse gases might change the climate. We know more now about almost everything, including about fog and what causes it. But we do not understand everything, and so fog remains a gray shadow of infinite mystery.

No one’s quite sure why, but for the last six years, California has had a squid problem. “Invasions have been documented throughout the past century,” John Field, a researcher for the National Oceanic and Atmospheric Administration, wrote in a recent paper, but “the spatial and temporal extent of the ongoing invasions appear to be unprecedented in the historical record.”

John McCosker, an eminent research scientist and director of the California Academy of Sciences aquatic biology program, is more blunt: “The squid are moving north, eating most everything in their path,” he says. “It’s like a horror movie.”

The squid’s encampment raises a host of unanswered questions: Does the shrinking of tuna and shark populations mean that there aren’t as many large predators to keep squid in check? Are squid reproducing here or just swimming up from more southerly breeding grounds? Will their eating habits depress local populations of commercially important fish like hake, rockfish, and smaller squid? Most glaringly: Will they ever go away?

One factor that may have prompted their invasion is the ongoing “shoaling” of low-oxygen zones in the Pacific Ocean. Parts of the ocean, particularly in warmer tropical waters, have always had a low oxygen level, but during the last decade, that zone has spread into shallower water along the West Coast. The squid appear to thrive in it—although no one’s certain why.

That’s maybe the most worrying thing about the squid invasion—the possibility that it’s a symptom of broader ocean changes that are altering the habitat for thousands of species. Scientists still lack definite proof, but recent news suggests that it’s a depressing time for ocean health: Warming. Acidification. Dying coral. Chemical and hormonal pollution. Doomed salmon fisheries. Beach-closing blooms of jellyfish.

Some scientists have even suggested that worldwide, we’re watching our oceans go backward 550 million years to the conditions of the Cambrian era, when invertebrates ruled the warm seas and bony fishes hadn’t been invented yet. Could the California squid invasion signal the dawning of the age of a warm ocean full of ill-tempered invertebrates? Or can our local back-boned species hang on, forestalling what some researchers worry may be the end of fish?

The Changing Ocean
About a year ago, Chris Harrold, the Monterey Bay Aquarium’s conservation research director, and I stopped at the aquarium’s signature exhibit, the kelp forest tank: 340,000 gallons of what you would have seen scuba diving in pretty much any kelp forest in the state—thirty years ago. “Can you see this along the coast right now?” I asked.

Harrold paused for a moment. “If you dive the offshore Channel Islands or go down along the coast of Big Sur, to areas that are remote, those are sort of de facto marine reserves because people can’t get there,” he said. “Those kelps forests would look an awful lot like this one.”

“But,” he continued, echoing a common lament among California’s fishermen and divers, “if you dive in areas that are heavily dived, like along the coast of Monterey, it would be quite a bit more sparse. The fishes would be smaller, because scuba divers and recreational fishermen can fish there. And that leads to fewer fish and generally leads to smaller fish as well.”

Others will tell you that marine life isn’t as abundant as it used to be: Fishermen who now have to boat thirty miles to find fish tell stories of friends limiting out in an evening at the dock twenty years ago. Scuba divers talk of picked-over reefs and quiet kelp forests. Free divers and spear fishermen remember rocks plated with abalone and chasing after gigantic fish like white sea bass.

To scientists like Harrold, with decades of experience studying California’s marine environment, it’s clear that the Pacific Ocean is changing. But measuring how much, and which of these changes are normal, cyclical events and which are our fault, he says, “is just a very difficult nut to crack.”

The ocean, and the Pacific in particular, is always under stress. There are dramatic events like El Niño, as well as cyclical fluctuations in currents, temperature, oxygen levels and nutrient upwelling and that’s not even the half of it. “There are so many [factors] that we know,” Harrold says, “and we don’t even know how many we don’t know.”

Here’s what we do know: The ocean is warming, but what portion of that is random fluctuation and what’s long-term change is hard to say, particularly locally. Worldwide, the ocean is becoming more acidic, as the water takes carbon dioxide out of the air and turns it into carbonic acid. Its pH has dropped about a point, which scientists suspect is bad for coral reefs and shelled animals like mussels and oysters, because even a slight change is damaging to their shells.

Meanwhile, polluted water runoff from cities and farms has carried nitrogen and phosphorous out into the ocean, where, along with carbon dioxide from the air, it’s gobbled up by algae and bacteria that quickly suck up all the oxygen in an area, leading to red tides—giant algae blooms—and low or no-oxygen seas. The most famous example is the 20,000-square-kilometer “dead zone” at the mouth of the Mississippi River that appeared in the 1950s and has yawned out ever since.

These factors are leading towards huge changes in the function and constitution of the ocean. Still, it’s a big, resilient place, and since most of the human-caused ocean changes result from accommodating 21st century human needs—feeding and clothing ourselves, getting around—it’s likely we won’t stop without proof that we’re doing great harm. Unfortunately, it’s just as likely the damage won’t be completely evident until it’s done. Given how we rely on a healthy ocean, it isn’t a great place for conducting uncontrolled experiments.

“I don’t know if anyone can tell you if we’ve gone past the point of no return on any particular parameter, but I’m sure almost every scientist could tell you there are points of no return,” Harrold says. “We just don’t know where they are. And we may not find them until we’re there. That’s what’s scary.”

The Missing Salmon
Not long after I met with Harrold, I visited a longtime recreational fisherman who was selling his boat. He couldn’t fish for salmon—once the main reason to fish in California—because the population has entirely collapsed, leading authorities to ban salmon fishing for the last two years. For many Californians, this record low has been one of the most compelling pieces of evidence that fish are in trouble. But how much is the changing ocean behind the salmon’s disappearance?

A clue surfaced in the mid-1990s, when the National Marine Fisheries Service received a petition asking it to list Puget Sound salmon as an endangered species. The NMFS responded with a 1998 report reviewing the status of all salmon species throughout the western United States. Among them were the Central California salmon known as fall-run Chinook.

At the time, the fall-run Sacramento River Chinook appeared to be in good shape, with numbers possibly approaching historic highs. But many of the report’s authors felt those numbers were misleading. While the salmon weren’t immediately in danger of extinction, the report concluded, they were “likely to become so in the foreseeable future.”

Those danger signs weren’t enough to convince politicians to protect the salmon. “Back then there were a million fish, and squaring that with the idea they might go extinct, it just wasn’t possible,” says fisheries service biologist Steve Lindley, one of the report’s co-authors.

Almost exactly ten years later, the population collapsed. More than a million salmon once swam up the Sacramento River every year to spawn. As recently as 2006, there were hundreds of thousands. By the fall run of 2008, there were only 66,000.

That year, for the first time ever, the fisheries service closed the salmon fishing season throughout California. Conditions didn’t improve this year; the economic damage for 2008 has been estimated at more than $250 million and thousands of jobs. “We are feeling a bit vindicated,”  Lindley says.

Lindley, still at the NMFS, was the lead author of a recent report analyzing the salmon collapse and its causes. His report, much like his review a decade ago, portrays a species ill-equipped to deal with environmental change. Salmon have low genetic variability because almost all of them come from hatcheries. Those that don’t must make do with spawning habitat degraded by water pumping, development, pollution, and the arrival of invasive species like overbite clams. While none of these problems individually precipitated the collapse, they made the salmon’s existence precarious enough that a random change in ocean conditions could. It was left to Lindley and his NMFS colleagues to figure out where that change had occurred.

Their conclusion: In 2004 and 2005, the current off California, which usually drives a strong upwelling of cold, nutrient-rich water, shifted, resulting in warmer water and changes in the food chain. Scientists watching the ocean that year noticed seabirds abandoning their Farallon Islands nests, emaciated gray whales, and sea lions swimming far offshore to find food. For that year’s doomed young salmon, the water warmed, and their favorite prey disappeared, just as they entered the ocean. Many starved to death, never returning to the river to spawn.

Ocean conditions returned to “normal” in 2006, so Lindley’s report predicts that the salmon population will probably rebound next year, and even more the year after. But while Lindley doesn’t believe the salmon face immediate extinction, he does think they face a problem with diminishing returns. Without environmental changes, such as improved spawning habitat and water flow, and reduced hatchery production to allow for greater genetic diversity, there are likely to be more of these boom-and-bust cycles as ocean conditions fluctuate.

After each bust, the recovering population will likely get a little smaller and a little more vulnerable. It’ll be like looking at a peak-and-valley line, with each peak a little lower and each valley a little deeper. “It’s just getting lower and lower, and eventually it’s going to crash,” Lindley says.

The Blooming of Jellyfish
Jeremy Jackson, an eminent marine scientist at the Scripps Institution of Oceanography, has looked into the future and predicted the “rise of slime”—the end of vertebrate fish and a dawning era of microbes, algae, and jellyfish. In some parts of the world there do appear to be more jellyfish than there once were. The Mediterranean, where jellyfish seem to have all but displaced fish, is a favorite apocalyptic case study, but around the world, from Puerto Vallarta to Phuket, jellies’ stinging tentacles regularly close beaches.

Jellies’ success has been attributed, in part, to humans: Overfishing has reduced their predators and competitors, farm runoff has created low-oxygen dead zones favorable to jellies because, unlike fish, they don’t need much oxygen to move around, and ocean warming appears to foster their favored planktonic prey while harming the plankton that fish prefer. The Mediterranean in particular has lent itself to slime’s rise: As an enclosed sea, it’s more susceptible to the unholy trinity of water pollution, invasive species, and overfishing.

Algae and microbes thrive in similar conditions, especially in polluted runoff areas. They so rapidly consume the water’s oxygen that their massive blooms leave giant dead zones. Fish swim in…but don’t swim out.

Nothing seems to inspire hyperbole quite like microbes and jellyfish. Daniel Pauly, a fisheries scientist at the University of British Columbia, has said that with oceans turning into a microbial soup, his kids will tell their kids, “Eat your jellyfish!” A similarly bleak report in the journal Trends in Ecology and Evolution earlier this year, written by an international team of scientists from Australia, Africa, and America, was titled “The Jellyfish Joyride.”

But while the idea of a future ocean so thickly filled with creeping jellies that you could walk across them may get scientists giddy, locally, we’re doing okay. “I’m not prepared to say we’ve seen a jellyfish increase,” says Steve Haddock, a jellyfish expert at the Monterey Bay Aquarium Research Institute. “I don’t think there’s any quantitative evidence that shows that.”

After all, he points out, jellyfish come in a huge variety of types, sizes, habits and politeness levels—there are hundreds of species—and they’re probably just as fragile as other parts of the ecosystem. Haddock has read news stories from India, where researchers are worried about jellies disappearing because they are the main food source for endangered turtles, and from China, where researchers are seeding the ocean with jellyfish to ensure a continued viable jelly fishery.

In fact, counting how many jellyfish are actually out there is tricky. That’s the thing about studying jellyfish:
It’s hard. Or rather, too soft. Those much-maligned slime are tough to capture, tag and track, or even find. Jellies live out of the view of remote sensing equipment and don’t show up much in the fossil record.

Researchers resort to approaches like counting them from airplanes, but you can guess at the uncertainties involved in doing that. And even though jellyfish blooms seem startling, they, too, are cyclical. Haddock says he’s seen reports of a massive jelly bloom that closed fisheries in the North Sea, off the coast of Holland—except that this one occurred in the 1700s. Huge blooms have similarly been recorded in the Mediterranean going back a hundred years.

But what is not part of the cyclical pattern, Haddock says, is the arrival of invasive species. Humans are quite talented at doing the Johnny Appleseed thing—ocean-going ships that carry ballast water transplant critters all over the world, including introducing jellyfish to areas where they’ve bloomed like crazy, along with other species that have paved the way for native jellyfish to go nuts. “Anything you do that throws off the balance of the ecosystem is going to have these kind of cascading and probably unanticipated effects,” Haddock says.

Nevertheless, he’s not worried about the rise of slime: “I don’t go into the ‘destroy all evil jellyfish’ camp—they’re kind of part of the ecosystem.” But, Haddock says, “I am worried that when I go scuba diving there’s no big fish, and everything’s totally picked over, and the environment is obviously being degraded by human activity.”

Which raises another question: How overfished is California?

The Plight of the Bony Fish
Overfishing has been rightfully blamed for many of the ocean’s ills. Books like The End of the Line or The Empty Ocean report that the North Atlantic has been picked clean, and that governments in Europe, Africa, and Asia have denied or delayed action while maximizing their harvest to the point of collapse. In California, the question of overfishing is more nuanced—it depends on the species.
First, though, what counts as a California fish?

It’s a surprisingly complex question. There are around one thousand different kinds of fish off the
Pacific Coast, most sharing the common characteristics of the animals that have lived here for the last 500 million years: backbones, gills, scales—although there are some exceptions.

Yet California-specific fish—the kinds you see in aquarium kelp forest tanks—vary wildly. There are native
fish everyone recognizes: salmon, rockfish, halibut, white sea bass, and bright orange garibaldi (the state marine fish, which, despite its diminutive size, is one of the most aggressive creatures in the sea). There’s the stuff the food chain is made of—mackerel, sardines, anchovies, pollock, hake. Then there’s the kind no one except marine biologists doing dissertations have ever heard of—infinite varieties of perch, smelt, gobies and things with funny names like the shortspine thornyfish (also known as the “idiotfish”).

To survey the health of every kind of fish in the ocean would be impossible, but the numbers for one kind of native fish tell a compelling story. Commercial fishing drove the state’s smaller, near-shore fish species, like rockfish, to record lows in the early 1990s. Fishermen took more than 16,700 tons of rockfish in 1991, the peak fishing year since the National Marine Fisheries Service started keeping data in 1950, when the commercial haul was only 3,700 tons.

But things have turned around since the ‘90s, thanks to stricter regulations. Bottom trawling—dragging a net across the seafloor and pulling up everything in it—is banned here. (The US government bans trawl-fishing in West Coast federal waters, as well.) The state has a number of no-fishing marine reserves; regulators are now working on a funding-and-controversy-plagued, but visionary, network of reserves that would be as effective a plan as any at conserving local species. As for the rockfish, the commercial haul in 2007 was only 640 tons. Today, scientists say, groundfish populations—fish, like the rockfish, that live near the bottom in the coastal zone, in roughly ten to one hundred feet of water—appear to be doubling or even tripling.

This is good news—but it only applies to species whose habitat is covered by California or US regulations.
The news for the globetrotting species that visit our waters like tuna, swordfish, and sharks is extremely bad. Bluefin tuna, for example, which can swim back and forth between California and Japan in months, are on the sushi boat to extinction. It’s simply impossible to convince a tuna or shark to stick around in California where the weather’s nice and the fishing regulations severe.

So while the outlook for open-ocean fish is dire, for California’s kelp forest natives, it isn’t too bad. “As long as we’re fishing, and continuing to impact the ocean through warming and other things, it’s not going to be pristine,” says John Field, a researcher at NOAA’s Southwest Fisheries Center, of the possibility that the coastline will return to the aquarium-like conditions that people remember. “But certainly in reserve areas things should look as close to pristine as possible.”

The Squid Invasion
In 2005, Field was out in Monterey Bay doing population surveys of shortbelly rockfish—or at least he was trying to, but his nets kept coming up filled with squid. Field wondered what the squid were eating, so he cut a few open and, sure enough, they’d been dining on shortbelly rockfish. “I thought, ‘Well, new source of mortality,’” Field says. “I’d better study this.”

The squid invasion is an international concern: They moved north from their traditional home off Central America, and south, too, into Peru and Chile. Many Chilean fishermen blame the squid for a hugely reduced catch of hake, and Field would like to know whether that’s true, and to what extent that applies up here as well. (Hake are an important and declining fishery in California.) There’s also recent, intriguing work done with remote hydroacoustic sensors showing that squid are chasing hake and changing their schooling behavior.

Squid may be bothering other species, as well. Although Field doesn’t think it likely that a squid could catch an adult salmon, researchers have discussed—and found plausible—the idea that marauding squid could disrupt salmon schools.

But the squid have predators—sharks, billfish, and tuna may benefit from the invasion. “There’d be winners and losers,” says Field. “Shortbelly rockfish and hake might be on the losing end, and sharks and marine mammals might be on the winning end.”

There’s a qualifier on that, though: It takes a big tuna to catch a big squid, and big tuna are increasingly
scarce. Sharks, tuna, and billfish have been fished to the point where there aren’t many big ol’ honkers around—and that may be one reason the squid are here in the first place.

Are squid here to stay? Settling in to raise a family constitutes a bad sign, but no one’s sure if that’s happening yet. Louis Zeidberg, a postdoctoral researcher at the Hopkins Marine Lab, spent the last year searching for squid babies and actually tried breeding them using in vitro fertilization. He hasn’t had any luck at the water temperatures commonly found in Northern California. “We have been able to do in vitro fertilization at 17 degrees [Celsius], maybe even 15, but I don’t think we’ve been able to do it at 12, which is a typical temperature up here,” Zeidberg says. “However, we are still refining our techniques for fertilization. It’s not a rule-out yet.”
T

he other conundrum is why the squid invasion appears to correspond with the expansion of the low-oxygen zone off of California’s coast. Technically, squid should do worse in those areas—scientists have always thought that squid need more oxygen than fish. But Zeidberg said recent tagging data indicates that instead of swimming willy-nilly after prey, the squid are swimming straight up out of the low-oxygen zone, and then gliding down through the water column—a energy-saving movement, like a human swimmer coming up to breathe and then drifting downward to conserve air—allowing them to thrive in low-oxygen water. Most fish, on the other hand, can’t swim in those zones very well, so the prey there is off-limits; fish that do swim through are often sluggish from lack of oxygen and can become prey themselves.

The squid have long followed the movement of the low-oxygen zone, but it’s changed shape in the last decade, covering more shallow water throughout the eastern Pacific Ocean. It’s happened before, most recently in the 1950s and 1960s. This time, though, the zone appears to be slightly larger. And that’s a reason to worry: Even though many of the events that are fostering the squid’s rise are normal and cyclical, they’re happening with increased intensity, or lasting longer.

“We are noticing very subtle signs everywhere that indicate that things aren’t in balance the way they used [to be],” Zeidberg says. “Maybe the squid’s only going to be here for ten years. But if the typical predator load and typical oxygen levels were in existence the way they were in the 1930s, they should’ve only been here for two years instead of ten. We see these little subtle examples that are pretty indicative of a low level of health for the Earth’s ecosystem. And [the evidence] is not going to be very straightforward until things are really bad.”

The End of Fish?

So here’s the big question. Fish: screwed, or not?

There’s good news: Salmon are expected to—at least temporarily—recover from their collapse. Habitat restoration in the Sacramento River and Delta could help ensure their survival. Groundfish are recovering. California can protect the marine environment and address the acidification and warming issues that go hand-in-hand with climate change. Even the squid invasion may not be the end of the world for fish—or at least for the kinds big enough to bite back.

But big-picture marine scientists are more pessimistic about ocean health and the future of fish than you might imagine. “The ocean you and I inherited was probably better than what we will leave for our children, or grandchildren,” says John McCosker of the California Academy of Sciences, “However, it’s not too late.”

McCosker says the best reason for optimism is that President Obama appears to have placed greater value on the work of scientists, which means that government will more carefully weigh the probable outcomes of our actions— like the “rise of slime” Jeremy Jackson warns about. (For his own part, McCosker has predicted that in Europe and Asia, hit worse by overfishing and jellyfish/microbe takeovers, “the future is muck.”) The Obama administration’s NOAA administrator, Jane Lubchenco, is a marine scientist who’s well-respected by her peers, and McCosker, Chris Harrold and others said they hope the change will mark the end of political interference with ocean science.

But even if Obama’s administration makes changes, the ocean moves slowly, and it may take years before its health improves. For endangered species, “years” is a long time to wait. “I’m hoping that nothing will go extinct in the meantime,” McCosker says. Chris Harrold doesn’t believe that this is the end of fish, but he’s not entirely optimistic either. “Fishes have been around for 500 million years,” he says. “I’ve got to think that humans would go extinct long before fishes or other marine life would. But there are some very disturbing trends, and I don’t think anybody can extrapolate where these trends will take us, because
the ocean is just too complicated.”

Meanwhile, as the conservation research director at one of the world’s largest aquariums—a place that has introduced millions of visitors to the idea of healing the ocean—Harrold has to find a way to keep the customers upbeat. “What hope can we give people?” he asks. “I guess I do believe that the damage that we’re doing is reversible. But the trend and our behavior is not yet there.”

Which is why marine scientists Katie Harrold and Aroon Melwani are standing waist-deep in the bay near Arrowhead Marsh, dragging a ridiculously awkward twenty-foot-wide seine net through the wetland in pursuit of tiny, bottom-of-the-food-chain fish. Frigid bay water laps at their rubber waders as they shuffle forward by inches to draw in the net. The bay-bottom mud is several inches deep, gooey like custard, clingy like glue, and stinky like the rotten cesspool of decay that it is. There is grumbling about the cold, and envious muttering about another scientist on the project who hurt his back and can’t participate in net-dragging excursions.

Once they’ve walked the net closed, Melwani and Harrold haul it out of the water and over to the bank, where both plop down in inch-deep muck and start unfolding the twine. At the bottom is their quarry, a giant blob of mud and inch-long flopping things, some of which are the crucial “biosentinel” fish they need to tell them how much mercury has entered the food chain in this corner of the bay. Using their bare fingers, Melwani and Harrold start grabbing fish, storing the useful ones in Ziploc bags and chucking the rest back into the water. Of course, there are not enough fish in the first round for all the testing they want to do, so they’ll have to drag the net another two or three times, at which point Harrold looks up at me, her face and glasses splattered, her hands dripping brown, and says, “So, you want to take a turn with the net?”

About a year ago, the US Environmental Protection Agency approved an updated plan for water quality objectives
in San Francisco Bay. One of the plan’s conclusions: It’s going to take time to get mercury levels in sediment where we want them, something on the order of 125 years. San Francisco Bay Water Board engineer Richard Looker presented this model to a group of scientists at a meeting in October, titling his PowerPoint slide “@@@!!! This is going to take a long time!”

The slide got an appreciative laugh from the scientists, although there are plenty of reasons to think that maybe it won’t be quite that hard. (“That 125 years is a really, really rough estimate,” Looker told me later. “People had wanted to know, and that was the best I could do.”) Ridding the bay of mercury won’t be easy, though. “There’s just a lot of mercury in the system,” Looker says. “The only way you lose mercury is it gets buried, it goes out the Golden Gate, or it evaporates. It doesn’t just degrade like a chemical, it has to be physically removed.” Even worse, the question of how mercury ends up in fish—and where it comes from in the first place—is still murky as bay mud.

These are the basics: Mercury gets into the environment in a number of different ways, from natural sources like volcanoes to urban sources like coal-fired power plants or stormwater runoff. In Northern California, mercury was historically used in gold mining, and many of the watersheds in the Sierra and Delta show high levels of mercury from California’s Gold Rush days. Most of the mercury used in gold mining came from mines in the New Almaden area of San Jose, where for decades it has washed down the Guadalupe River and into the southern part of the San Francisco Bay, which still has the highest mercury levels of any part of the bay.

But all this stuff in the air and water is regular ol’ mercury, and one of the odd parts of the puzzle is that regular ol’ mercury isn’t harmful to people or wildlife when it’s in the water. The damaging stuff, the kind that gets into the food chain, is a specific form of mercury called methylmercury. A confounding thing is that there isn’t necessarily a consistent relationship between the amount of mercury in the water, air, and sediment, and the amount of methylmercury in the food chain in that area. It takes a certain kind of bacteria to convert mercury into methylmercury (a process called methylation), and those bacteria are found in areas with lots of vegetation and living organisms. Which is confounding thing number two: In Northern California’s aquatic environments, those areas tend to be wetlands.

Ironically, these areas, which environmentalists have long struggled to save, can create and amplify methylmercury;
in some cases restoring wetlands may resolve one eco-hazard while accidentally worsening another. Even stranger, some areas methylate more than others, which has led to delays and confusion about whether to attempt restorations.

This nasty surprise became known in the mid-1990s, just as scientists and managers in the Bay Area were starting
to map out the West Coast’s largest wetland restoration project. The bay has lost eighty percent of its historic tidal wetlands, and getting them back is a huge priority for scientists and environmentalists. Wetlands are environmentally imperative for a huge variety of reasons: They sequester carbon, filter pollutants from the water, provide crucial habitat for birds and fish, control sediment, and are an important buffer against sea level rise.

The ambitious plan to have 100,000 acres of tidal wetlands ringing the San Francisco Bay by 2030—an almost unequivocally beneficial project—has had to confront the reality that no amount of restoration can return the bay to what it was. The omnipresent mercury that lurks in the environment, waiting to be methylated by restored wetlands, is one reminder that our attempts at restoration could just be making other problems worse.

“Wetlands are in virtually every respect a good thing, in terms of the benefits they provide to the environment and society,” Looker says. “It kills me that there’s a blemish on the reputation of wetlands. But they’re just doing what they do, and mercury methylation is a consequence.” If there was a king among Northern California’s mercury-
in-the-food-chain scientists, it might be Darell Slotton. A research ecologist at UC Davis, Slotton has defined the scope of the mercury problem in the bay and Delta and pioneered a key methodology for studying it. Starting with research in gold-mining-legacy Sierra watersheds, Slotton has spent years identifying the right kinds of small critters, called biosentinels, to study methylmercury patterns in the food chain.

For the most part, it’s useful to focus on animals that have very well-defined, local home areas (so you can identify where the mercury enters the system), wide distribution (so you can compare areas), short life spans (so you can better identify when the mercury enters the system), and regular habits (so you can test seasonally to see if methylmercury is more of a problem at certain times of year). Slotton works mostly with small fish, particularly certain smelts and Mississippi silversides.

After identifying rough patterns of methylmercury in the Sierra and Coast Range in the 1990s, Slotton and other
researchers funded by the CALFED Bay-Delta Program program turned their attention to untangling the wetland methylation scene. The Delta has had major restoration projects along its main channels, and as he set out Slotton expected to find higher levels of methylmercury in animals around those projects.

Yet when the results came back, the highest levels of methylmercury were actually in the periphery of the Delta. The restoration projects in the central and south Delta and Napa-Sonoma Marsh had relatively low levels. “It’s kind of the opposite of what we expected to find,” Slotton says. “There are certain kinds of wetlands that disproportionately
pump out methylmercury in certain conditions. But it looks like a lot of what’s out there being restored is fortuitously not a problem area.”

In some ways, that was great news. But because nobody quite understood why areas could behave so differently,
this mixed result made life very complicated for people who were trying to bring back the wetlands. A typical conversation between a scientist and a restoration manager around the turn of the century might have gone something like this:
Scientist: Not all restored wetlands amplify methylmercury.
Restoration Manager: Great!
Scientist: But some do.
Manager: Ah. Which ones?
Scientist: Uh, no one is quite sure.

So how did the people overseeing this gigantic wetlands restoration project know which areas to rescue?
That was Steve Ritchie’s mercury headache. Ritchie was the guy who, informed of the mercury-wetland connection
in the early 2000s, had to help the US Fish and Wildlife Service decide whether to proceed with wetland restoration projects in the South Bay’s salt ponds. Ritchie already knew that the salt ponds and restored wetlands ringing the area south of the Dumbarton Bridge have some of the highest total mercury concentrations in water and sediment of anywhere in the bay. He didn’t know what effect those new wetlands would have on methylation.
Ritchie convened a scientific working group and asked for a yes/no answer: “‘Should we do this at all?’ People said, ‘Yes, but look for ways to be cautious,’” Ritchie recalls.

“The consensus was that habitat is so much of a limiting factor for species that the risk is worth it.” In other words, they’d chance it for the sake of restoring badly-needed wildlife habitat. Especially risky was the area around the Alviso Slough, at the mouth of the Guadalupe River, where mercury had washed down the river and been trapped in the subsided salt ponds for decades. Ritchie asked a group led by Letitia Grenier at the San Francisco Estuary Institute to take a close look at salt ponds and nearby restored wetlands in the Alviso area, and to predict what might happen if the rest of the salt ponds were restored.

Grenier picked three biosentinels: birds, fish, and flies. Between 2006 and 2008, she and her colleagues collected hundreds of each, stalking through the marsh to collect tiny long-jawed mudsucker fish and brine flies (which are, as Grenier puts it, “sacrificed” for the cause), or jab needles into sparrows (which give blood and then are released). The South Bay hadn’t been studied in this way before, so it took a while to identify the best sentinel species and how to catch them. “The fun thing about all of this is you have to learn how to do it,” Grenier said. “You’re like a hunter-gatherer.”

The results were again encouraging: It appeared that animals in the salt ponds had higher levels of methylmercury
in their blood or tissue than animals in the restored wetlands nearby. Although the results from 2008 aren’t available yet, Grenier’s conclusion at the end of 2007 was that turning those particular salt ponds into wetlands would reduce the amount of mercury in the food chain. Ritchie decided to go ahead with a cautious, and reversible,
restoration plan.

“There’s nothing here that says you shouldn’t move forward, but whatever happens you’ve got to monitor it,” Grenier says. However, she says, it’s imperative to start now. “Given that the loss of our wetlands is happening, and sea level rise is happening, if we’re going to make marshes, we’ve got to start letting them accrete tomorrow, not in five or ten years as we dither about mercury.”

The apparent randomness of which areas are prone to methylation could have led to a great deal of dithering among experts about which areas to restore. Fortunately, over the last several years Slotton and others have isolated a pattern that appears to explain why some wetlands amplify mercury concentrations and others don’t. They started their research by getting better seasonal data, increasing the number of sites where they were collecting fish several times a year from three to 26. They noticed that their data showed huge seasonal spikes in mercury at some sites.
They started working backward, asking, “Well, what happened before this spike?” Slotton says. His answer: “Oh, the San Joaquin river jumped its banks and flooded a bunch of farmland. Six weeks later, we see mercury spiking in the little fish fifty miles downstream. You can link just about every one of the mercury spike events we’ve identified
to this issue of occasional flooding.”

Slotton says that there’s basic chemistry at work in the wet-and-dry cycles: When sediments containing mercury dry out, it changes the way the mercury is bound to the sediment, so that in the next flood it’s much more readily
converted into toxic methylmercury. In other words, seasonally flooded wetlands and floodplains seemed to be generating the most methylmercury.

In 2006 and 2007, Slotton added sites where he could test that hypothesis, and the two-year span of the project turned out to be perfect: In 2006 the region recorded historically high rainfall and severe flooding, and the following year there was a drought. The difference between the fish downstream of those areas during those two years was dramatic.

In July of 2006, at some sites downstream of major seasonal flooding, Slotton was capturing two-to-three-inch fish with mercury concentrations “that would be of concern in a thousand-pound swordfish,” he says. A year later, in the drought period, he captured the same kind of fish in the same place and found a tenfold decrease. “That was it,” Slotton says. “This is the most compelling evidence we’ve had to date.” Regardless of where the marsh is located—scientists have looked at similar data from Napa Marsh and sites in the South Bay—it now seems clear that episodic flooding plays a major role in creating new pulses of methylmercury, and moving them into the food chain.
Slotton’s finding was exciting for managers in the Delta region, where much of the wetland is in so-called “managed marshes”—diked-off areas where the flow of water in and out is controlled by private hunting clubs to make the habitat more friendly for migratory birds, particularly ducks. The results of the research suggest that the clubs could change the way they move water around, even slightly, and have a big effect on methylmercury concentrations. (Not that this would be easy—historically, the hunting clubs, scientists, and environmentalists have not necessarily communicated well with each other.)

But that’s the Delta. In the San Francisco Bay, where most of the marshes slated for restoration are tidal—not diked off, and not human-controlled—the question of where the mercury actually gets into the fish and birds of the bay is still a mystery. Isolating those sources would be the first key to controlling the problem. The second key would be figuring out which sources are more likely to affect wildlife. “If we can answer that second question, that gives us a tool to prioritize our actions,” Looker says. “If we find that industrial mercury is most likely to enter the food web based on its chemical form and where it is discharged, that may give us reason to have additional controls on industrial projects.”

If scientists can figure out what’s causing the mercury to get into the food web, and identify the methylation
hotspots, they might be able to reduce the bay’s level of harmful methylmercury even if its total mercury concentration remains high. That’s why Slotton and Ben Greenfield, a scientist at the San Francisco Estuary Institute, are currently conducting a huge survey of small fish from more than 100 sites around the San Francisco Bay, designed to give even more exact answers about how and where mercury gets into fish. And that’s why Katie Harrold and Aroon Melwani—and I, apparently—are standing in the bay collecting fish.

These topsmelt and gobies may hold clues that will help Greenfield and Slotton find a clear pattern for how methylmercury enters the bay. “What would be really useful is if we suddenly found that all the mercury in the bay was coming from one pipe, and we could just close that one pipe and all our problems would be solved,” Greenfield says, although it probably won’t be that easy. “The more likely outcome is it’s going to be a little bit of this and a little bit of that. We’re trying to figure out what is the this and that.” When they do, it may mean much greater control over the mercury side effects of wetland restoration projects, which is why collecting those small fish seems so imperative.

I accept Harrold’s offer of a turn at the net, don chest waders and rubber boots, and wade out into the water. Negotiating a heavy net full of mud and fish (and one Tecate can) while standing in bay mud that’s up to your shins is no easy task. As Melwani walks toward me to close up the net, one of my boots goes calf-deep into the mud. I yank, and my balance goes backward, but my foot doesn’t move. Then I’m teetering, taking my hand off the pole that holds up the net, wobbling. Finally, there’s nothing else to do but subside quietly backward, in my most dignified manner, into the muddy shallows.

There is a lovely squelching sound as I land on my back, and my hand, propped out for balance, sinks in up to the wrist. Melwani looks at me sympathetically, continuing to hang onto his end of the net; he is much more practiced at this than I am. “Sometimes,” he says, with his very best kindergarten-teacher voice, “we all have to sit down.” As I sit there in the mud, thinking about spending the next three days in a hot shower, I’m reminded again that with mercury science, nothing comes easy.

There’s ample scientific evidence that marine reserves help fish populations recover, and some evidence that these burgeoning populations then spill over into areas outside the reserve. There’s also ample evidence that California’s fish populations are, historically speaking, over-fished. Talk to someone who’s been diving in the state for a few decades, and they’ll tell you how the kelp forests once looked like aquariums, and about how you could just pick abalone off the rocks. Even fishermen lament the old days when you could fish for salmon just out of the harbor, or limit out on rockfish in a few hours after work.

With one recent study estimating that only four percent of the world’s oceans are completely unaffected by humans, and another (controversial) one estimating that, at current rates of fishing, the world’s fish stocks will vanish in forty years, marine reserves, even in popular fishing spots, seem like an imperative to many marine scientists and environmentalists. “Just from that big high-altitude perspective, I believe there ought to be chunks of the ocean that are set aside that aren’t supposed to be screwed up,” says Chris Harrold, a marine scientist and longtime director of conservation research at the Monterey Bay Aquarium. “It’s really as simple as that.”

After the final North Central California Marine Life Protection Act Initiative Blue Ribbon Task Force meeting in late April, the state is close to setting aside those chunks. It’s a measure of the project’s degree of difficulty that, when the decision-makers polled all the involved organizations about their proposal, they ultimately boiled their questioning down to: “Can you live with this plan?”

Here’s another measure: at the final north central coast Marine Life Protection Act (MLPA) meeting, a disgruntled environmentalist showed up intending to make a point with an authentic severed—and badly decomposing—seal head in a bag. (He was asked to leave, but there was no legal action taken against him, Department of Fish & Game spokesman Steve Martarano said, because the man had a permit. For the seal head.)

Saving the ocean, pleasing the constituents: Not easy. But when you can manage some sort of compromise that leaves everyone just mildly irritated, well, that’s when you get, as the Department of Fish & Game did, to trumpet your plan as the “milestone” that it is.

The MLPA orders state agencies to take a long look at California’s existing protected marine areas, then figure out some way to build a statewide, comprehensive, networked group to protect wildlife, improve research conditions, and enhance or at least maintain recreational opportunities.

To make it a little easier, the MLPA staffers split the map of California into study regions. They started last spring on the north central coast, which covers the area from Alder Creek in Mendocino to Pigeon Point in San Mateo. The region’s 45 appointed “stakeholders” then started the nearly year—long process of coming up with plans, commenting on the plans, running the plans by an appointed science advisory team, revising the plans, and coming up with new plans.

If you had stopped by one of these workshops, like the one held in Pacifica in January, you would have seen a motley assortment of ocean-lovers gunning for their own interests: an environmentalist in flowing silk, two fit young surfers from the Surfrider Foundation, an older man concerned about access for kayakers, a gentleman named Rolf who worried that he wouldn’t be able to drive his boat around, a thin, Lincoln-ish representative from California Trout in a maroon sweater vest and six-inch-too-short khakis, and at the head of the table, bellowing like something out of Robert Louis Stevenson, a party boat fishing captain with a name tag that read, “Hello my name is SMITTY,” all of them arguing passionately the finer points of ocean policy.

The most contentious battles were over “no-take” marine reserves; fishermen argued that environmentalists are trying to kick them off the water entirely by taking away all the good spots to fish. With Northern California salmon gone for at least the next several years, the catch in question, for fishermen, is mostly rockfish. And since rockfish are found in areas where there are rocks, and since areas with rocks and fish also tend to be obvious areas to put in marine reserves, recreational fishermen argued that the wrong plan could mean the end of their sport. (To be clear: fishermen aren’t against all marine protected areas, they were just against the particular protected areas proposed in this process by environmental groups. Some of the early plans would have put marine reserves in about ninety percent of the rocky areas, meaning that the only areas left open to fishing wouldn’t have any rockfish in them.) Suggested marine reserves at popular fishing spots like Duxbury Reef off Point Reyes, the area around Montara, and the Farallon Islands had many fishermen saying they’d sell their boats and do their fishing in Alaska or Mexico.

Calling it the “biggest political battle” his group had ever faced, Chris Hall, the president of the 13,000-member Coastside Fishing Club, said that the MLPA had “provided a vehicle for environmental organizations that wish for us not to be on the ocean a way to do it.” Environmental organizations and MLPA organizers disagreed. “This is not about trying to prevent people from fishing,” said Melissa Miller-Henson, the program manager for the MLPA Initiative. “It’s really about trying to maintain a healthy ocean ecosystem so that folks can take their children, their grandchildren, eventually their great-grandchildren out to go fishing because there are still fish out there in the ocean.”

Fishermen argue that California already has extensive marine regulations, and that after over-fishing in the 1980s and ’90s, California fish populations (especially rockfish and other so-called “groundfish”) have recovered to sustainable levels. Groundfish populations in California, after reaching a nadir in the 1990s, are increasing or holding steady. But Harrold argues that even a well-managed fishery still allows a lot of fish to be caught, and that we have really no idea what that means for the ocean ecosystem. “In large part, we’re conducting this big experiment in the ocean,” Harrold said. “Let’s extract hundreds of thousands of tons of fish—and see what happens.”

In late April, after a year of arguments, the north central coast stakeholder group presented three proposals to the Blue Ribbon Task Force, the group charged with taking a year’s worth of advice and picking one “preferred alternative” plan to send to Fish & Game for final approval. The three stakeholder proposals split along party lines: a “fishermen’s” proposal, an “environmentalist’s” proposal, and a slightly environmentalist-leaning compromise proposal that, in its backers’ defense, was “everyone’s second choice.”

The task force forwarded all three plans intact to the Fish & Game Commission and then set to mashing them all up into one giant compromise for its “preferred alternative.” For areas in the northern parts of the study region, they borrowed almost exclusively from the environmentalists’ plan, recommending the proposal’s suggested marine protected areas at Point Arena, Sea Lion Cove, Saunders Reef, Del Mar, Stewarts Point, and Salt Point, including a state marine park at the popular abalone-diving area near Salt Point. Then, as the task force moved south, they swung back toward the fishermen’s plan. They elected not to recommend any protected areas at Duxbury Reef, perhaps the most important area to fishermen, and also used the fishermen’s suggestions for Bodega Head and the Fitzgerald/Montara area. The task force’s “preferred alternative” covered twenty percent of the region’s waters and called for 160 square miles of marine protected areas.

Everyone now gets one more opportunity to make an argument. Again. The Fish & Game Commission started taking public comment on the preferred alternative and other proposals in June and has the power to change any of the plans as it sees fit. A final decision isn’t expected until at least December, and it’s likely the new MLPAs won’t be implemented until well into 2009. Meanwhile, the task force moves on. After a year of tension and argument and debate and passion, and a difficult compromise recommendation, their reward: They get to start all over again in Southern California.