A cold, salty wind blows from the west. The gray Pacific Ocean – incubator of slimy life, cycler of nutrients, composer of storms – doesn’t seem like itself lately.

The bully they call El Niño seems to be coming around more often, screwing with every fishery he touches. Niño plays games with the world’s weather, flooding dry Peruvian coastal towns while parching lush Indonesia.

Expanding offshore twilight zones of low oxygen turn fish into refugees and kill whatever can’t swim away. Oregon fishermen pull up buckets of dead crabs while jumbo squid pulse poleward, happier than clams in the suffocating layer. Other warm-water species are hanging out in places that used to be too cool for them. Tropical storms are getting meaner; jellyfish are swarming.

Meanwhile, the mad chemist known as pH is tinkering with the ocean’s ions, making California’s coast more acidic than the psychedelic ’60s. Dolphins file noise complaints, the shells of microscopic snails dissolve, and light-reflecting plankton retreat.

The sea’s weird behavior is a tough nut to crack, but some of the world’s sharpest minds are on the case. Their chief suspect is carbon dioxide, code-named CO2: atmospheric loiterer, weather tweaker, planet heater.

CO2 and his gaseous co-conspirators have already been indicted for stealing ice from polar bears, provoking the Creole villainess Katrina, and sparking record-breaking forest fires across the western U.S. Celebrity prosecutor Al Gore made headlines with his brief on the crime streak, which he called global warming. (Defense lawyers prefer the term “climate change.”)

But outside the media bubble, CO2 may quietly be torturing another victim – one that’s easy, but foolish, to ignore. Scientists have found carbon’s fingerprints on the acidifying, oxygen-depleted and alien-invaded sea. This may be the grisly underbelly of global warming.

But despite the evidence against carbon, the law hasn’t been able to lock him up yet. He’s still on the lam, growing more powerful by the day.

Moss Landing, California

Our sleuths at the guano-speckled Monterey Bay Aquarium Research Institute are on CO2’s trail, plying the mystery with underwater robots and deep-sea simulation chambers. Their bosses are fully committed to the investigation: The future of California’s coastal waters, and the life that inhabits them, is at stake.

Me, I’m just out for a scoop. The economy’s slumping worse than I do in my ergonomically correct desk chair at The Daily Weekly, and the editors are starting to get that praying mantis look. If I can break this CO2 story, I might be able to score a corner cubicle.

An offer of lunch at the Haute Enchilada lands me a meeting with one of the smartest MBARI detectives, Senior Scientist Francisco Chavez. Sensing that I’m a rookie, he uses his Professor Voice. A crow perches on a nearby chair, eyeballing his rice.

We pumped more than 31 billion tons of CO2 into the atmosphere in 2007 by burning fossil fuels and making cement, Chavez says. The sea absorbs about one-third of that, sparing us an even hotter fate. But as the ocean takes in CO2, it gets more acidic – the same chemistry that carbonates soda. Sprite dissolves teeth; ocean acidification dissolves shells.

On average, the top layer of the world’s oceans has become almost 30 percent more acidic over the last two centuries, dropping from about 8.16 to 8.05 units on pH’s logarithmic scale. California’s coast is already more acidic than that average – but Peru’s waters are even more corrosive, thanks to natural upwelling.

“We know that the ocean is going to get more acidic,” Chavez says, forking his beans. “Unless we stop burning fossil fuels or we do some engineering thing to make the ocean more alkaline, there’s no way around that. California will become more acidic over time and maybe reach the levels Peru is at today.”

A chill ripples down my spine. The crow, now at Chavez’s feet, snaps up a jalapeño kibble.

Lima, Peru

The air smells of fishy diesel. From the balcony of Peru’s Ocean Institute (IMARPE), the Port of Callao is a gray watercolor divided in half by a blurry horizon. Anchovy fleets, cargo ships and a solitary research vessel drift in the polluted water, looking as weightless as the fog above.

On the street below, my sidekick, photographer Robin Parrott, scampers over to the bad side of town, snapping portraits of plastic bags hemming the rocky shore like stiff ruffles. An IMARPE guard trots after her with true caballero concern, protecting her from any would-be hoodlums.

I’m hanging with a guy from my own neighborhood: Dave Field, an MBARI post-doc visiting IMARPE for an international seminar. The blond, 6-foot-7-inch researcher outsizes his Peruvian colleagues like a yellowfin tuna among sardines. But he fits right in, having researched in Lima for more than a year; his local Spanish dialect gives him honorary paisano status.

Field’s research team, about 20 scientists from Peru, Chile, France and the United States, is in the business of cutting sediment cores from low-oxygen waters called oxygen minimum zones. OMZs, like deserts, are great preservers of the past because they’re inhospitable to crawly critters that would otherwise mess up the sediment.

Good cores are like tree rings, mapping the sea’s history. By analyzing the geochemistry at different layers, Field’s team can reconstruct hundreds of years of marine history. CO2 and oxygen levels change naturally in the course of annual, decadal and centennial ocean cycles, he explains, so it will take some sleuthing to figure out whether recent changes are really a symptom of global warming.

“What’ve you found?’’ I press.

“It’s looking pretty abnormal,’’ Field says.

“Global warming?”

He hesitates. It’s not that straightforward.

I’m pushing Field to go harder on CO2, give me something to work with. But IMARPE researchers – despite the fact that Institute President Admiral Hector Soldi is a graduate of Monterey’s Naval Postgraduate School – are even more cautious than he is.

Kicking back in the absent director’s office, IMARPE Fisheries Biologist Carlos Benites gently derides Field for insisting that global warming is changing the sea. “Dave is a believer,” he says with a laugh.

Pinned between the two of us, Field takes a just-the-facts-ma’am approach, citing data that link fossil fuel burning with ocean temperature and pH changes.

IMARPE may be slow to recognize those connections, Field tells me later, because it’s a government agency, an inexorable part of the country’s economic engine. Its mission is to generate data for the national fisheries, not dive into the unprofitable waters of climate change.

Then there’s the issue of proof. It’s easy to blame melting polar ice on a warming planet, he says, but the closer you get to the equator, the harder it is to prove causality. At Peru’s low latitude, scientists would have a hard time linking expanding OMZs, opportunistic jumbo squid and fiercer El Niño events to atmospheric CO2. There are so many other suspects: upwelling, wind patterns, commercial fisheries, pollution.

This villain CO2 is proving to be a slippery bastard. I have to move on.

San Andrés, Peru

The air is sharp with salt and fresh death. Fishermen unload their catch, bosomy old women sort fish and customers haggle for bargains. A live she-crab escapes her net, tap-dancing sideways in a vain attempt to protect her spongy orange cluster of eggs. Women in spattered aprons smash piles of snails, tossing the curls of meat into buckets of water. A man squats on the concrete, bisecting rays into bloody triangles.

Marine invertebrate specialist Antonio Cabrera identifies the unfortunate fish by their Spanish common names: merlusa, pejegallo, cabinsa, bobo. One solitary spotted specimen with no scales or teeth stumps him.

He examines it under the sunlight, then wraps it up to take to the nearby IMARPE lab on the edge of Paracas National Reserve – a parched desert peninsula cracked by earthquakes, scraped smooth by tsunamis and rimmed by some of the most biodiverse waters in the Americas.

The money-making life in those waters is IMARPE’s research priority. The institute mainly focuses on Peru’s superlative anchovy catch, which accounts for 90 percent of the national sea harvest. Even so, there used to be more fish in these parts, Cabrera says. Environmental changes have big impacts on the catch.

My ears perk up. Changes? Is that code for global warming?

No such luck. In Peru, upwelling and El Niño events cause such profound seasonal and annual variations that it’s futile to try to isolate the slower influence of carbon accumulation, Cabrera says with a frown.

Peru’s not helping my CO2 exposé. The waters are too intense, too unpredictable.

I’ve got to head for common ground.

Concepción, Chile

Equinox, Sept. 22. The sun hovers over the equator, rising due east and setting due west. Every point around the globe sees roughly 12 hours of light and 12 hours of darkness.

Concepción Bay is a mirror to home – 36.6 degrees south to Monterey Bay’s 36.6 degrees north. The two bays look startlingly similar on Google Earth, with backward C shapes and jutting southern peninsulas. Both experience upwelling, which makes for strong commercial fisheries. Military bases and marine research institutes cluster near the ports.

It’s not a perfect reflection. Concepción Bay is almost 50 longitudinal degrees east and three hours ahead of Monterey Bay. It’s the start of Chile’s spring, when chilly, nutrient-rich waters well up from the deep, and California’s fall, when upwelling subsides and surfers enjoy a window of warm.

Trusty Parrott is a bit green as she battles a South American intestinal bug, but she manages to capture a flurry of commerce at Concepción Bay’s Talcahuano port. Fishermen unload hake under the hungry gaze of pelicans, seagulls and sea lions. Market workers arrange fresh surf perch and cusk eel into appetizing displays. A mustachioed salesman poses with a pretty, red fish called splendid alfonsino, whose species is in danger of collapse from overfishing.

On the flip side of the equator, at Monterey’s Wharf 2, Weekly photographer Nic Coury recons a similar scene. Commercial fishing boats bob at the dock, still water reflecting blue sky. Sea lions crowd onto tire buoys and sniff the fishy air while fishermen offload catches of silvery sardine. A tattooed worker fillets rockfish, another fishery flirting with collapse.

Meanwhile, I nose around Concepción University, where students flow between classes like currents in a lazy stream. Outside the oceanography building, a giant whale skeleton swims in the air. Inside, my head swims during a bilingual briefing from Silvio Pantoja, deputy director of the university’s Center for Oceanographic Research in the Eastern Pacific (COPAS).

The surface water off the Central Chilean coast has warmed over the past 350 years, Pantoja explains, but it’s cooled over the same timeframe in northern Chile and Peru. “We think both are global warming,’’ he says.

Rising air temperature heats the ocean’s top layer, he explains, creating a pressure difference between land and sea – especially in arid regions. That drives stronger coastal winds, which cause more upwelling, which brings colder deep-sea waters up to the surface.

Got it: the surface is a moody place. But what about the deep ocean? Is it warming?

Pantoja swivels toward his computer and pulls up a graph produced by COPAS researcher Wolfgang Schneider. While the temperature in the ocean’s top 300 meters fluctuates in response to seasonal changes, the interior ocean – from 300 to 5,000 meters – has warmed by an average 0.02 degrees Celsuis between 1999 and 2003.

That may sound piddling, but it would take energy from all of the world’s nuclear power plants working nonstop for 20 years to warm the sea that much, Pantoja says. If the ocean temperature rises an average 0.8 degrees Celsius in 100 years, as Schneider projects, we can expect tropical storms and flooding to make Katrina look like a schoolgirl.

I start to space out, imagining the headlines. Just in time, a smiling young scientist appears in the doorway, thumbs in his jean pockets. With his effortless American English and intricate knowledge of Californian and Chilean shores, Fabián Tapia is an ambassador for eastern Pacific marine science.

Tapia studied coastal marine ecology during his two years at Scripps Institution of Oceanography. Now he’s working with colleagues from Oregon State University and UC Santa Barbara to monitor near-shore intertidal ecosystems. The scientists call their team Partnership for Interdisciplinary Studies of Coastal Oceans, or PISCO – a toast to the idea’s conception over a few rounds of Pisco sours, the tart drink that’s managed to throw my sheets to the wind in both Peru and Chile.

Tapia escorts me across campus, past invasive eucalyptus groves and pre-Pinochet student dorms, and into the office of Osvaldo Ulloa, a shiny-eyed oceanographer who seems perpetually rushed. He seems to consider brushing me off, then launches into a half-hour crash course on the future of life as we know it.

The Pacific is the biggest ocean in the world, Ulloa explains, spreading his hands along the length of his desk as if to scoop up that unfathomable mass of water. Its huge heat storage capacity means it has the biggest potential impact on worldwide weather.

Exhibit A: El Niño. It originates in the equatorial eastern Pacific but perverts coastal weather patterns from California to Chile, re-arranging the distribution of rain as far away as Africa and Indonesia.

Exhibit B: The Pacific’s pair of oxygen minimum zones, one each in the northern and southern hemispheres. If low-oxygen waters are indeed expanding, as a recent German study reports, they may accelerate global warming by releasing more nitrous oxide – the world’s third most notorious greenhouse gas, after CO2 and methane.

With help from Oregon State scientists, Ulloa and his colleagues plan to probe the mystery of unexplained low-oxygen episodes – dubbed “dead zones” – that are common off central Chile but have only recently become annual events off the coast of Oregon, killing masses of crabs and other invertebrates. OSU scientists suspect global warming, but Ulloa wants more proof.

He does, however, see the logic in Francisco Chavez’s hypothesis. As global warming acidifies the sea and drives OMZs toward the surface, California’s ocean could eventually mimic Peru’s current conditions.

“We already have a system that could look like the future,” Ulloa says. “If we keep changing the planet the way we do, it’s a possibility.”

These scientist types are slippery fish. I’m not sure I’ve got enough evidence to nab CO2, but at least I finally have his scent.

Coquimbo, Chile

Five hundred miles north of Concepción, the arid coastal town of Coquimbo is blooming. A rare early spring shower coaxed purple and orange wildflowers out of the normally brown hillsides spooning Herradura Bay. The students at Chile’s North Catholic University are making out on the grass.

My host is Javier Sellanes, a scruffy young researcher who studies bottom-dwelling marine life in the OMZs. He’s skeptical of the idea floated by MBARI and COPAS scientists, that the oxygen minimum zone has gotten thicker over time. “The truth is that I don’t know,” he says. “I don’t think anyone in Chile knows.”

Sellanes introduces me to his wife, oceanographic chemist Práxedes Muñoz, and sea-floor specialist Beatriz Yannicelli, a bohemian redhead who works in one of those poorly lit offices typical of post-docs.

After two weeks on the trail, my hair has taken on the shape of an anemone and my clothes exude the odor of fish. My scoop, like an angler’s 200-pound marlin, is slipping away. I can only assume they take pity on me when they agree to a mid-afternoon brainstorming session.

El Niño causes so much flux in Chilean waters that it’s next to impossible to tease out the impacts of global warming, Muñoz says a little apologetically.

Then she reconsiders. Rising CO2 levels drive acidification, which makes it harder for calciferous animals to make shells, she muses. In theory, the decline of armored micro-organisms could ripple up the food chain, possibly re-arranging entire marine ecosystems. Trace metals are also more soluble in more acidic waters, which could end up tweaking ocean chemistry in unexpected ways.

“This is pure speculation,” she hedges.

But her husband backs her up. As the ocean’s pH declines, Sellanes says, the acidity threatens corals and the species that depend on them.

Global warming affects ocean circulation and wind patterns, Yannicelli adds, which can shift production zones and alter habitats. Nature tends to change slowly enough for ecosystems to evolve, but the relatively rapid rise of CO2 could transform marine communities in the blink of a geologic eye.

“Oxygen levels are going down,’’ Muñoz says.

“But we can’t be certain OMZs are expanding,” Sellanes interjects. “Not without historical data.”

“If we need decades or even centuries of data in order to be certain about what’s happening now,” I ask, “how can science inform policy changes?”

“We don’t need 100 years,” Yannicelli replies. “We need money and an interdisciplinary effort to analyze the data we already have.”

“The Americans,” Sellanes adds glumly, “are better at that.”

Moss Landing, California

The day after I get home, MBARI announces that acidification is causing sound to travel farther underwater. The implications are serious for marine mammals that rely on sound to get around, communicate, find food and hump. Three weeks later, NOAA and the National Science Foundation launch the first national study on acidification’s impacts.

Meanwhile, MBARI researchers are experimenting their way to the bottom of the CO2 mystery.

Senior Scientist Jim Barry predicts deep-sea animals will be less adaptable to pH changes than those at the surface. To test the hypothesis, he immersed them in cages 3,600 meters deep, bathing them in an acidic plume of carbon dioxide for up to a month at a time.

Most of his subjects – including urchins, roundworms and microscopic foraminifera – didn’t like it. “A 0.2 unit pH change is pretty harmful for most of the animals we see down there,” Barry explains from his ocean-view MBARI office. “We’re asking animals in the deep ocean to live in a completely different environment than they evolved in.”

In a higher-CO2 ocean, most animals would have to expend more energy on staying alive, which saps their vim for reproduction and growth. That could be particularly true in the Pacific, Barry says, where the water is already more acidic than average.

His calm makes me antsy. I’ve gone to South America and back for this story; I want that corner cubicle. I’m looking for tears, desk-banging, mayhem. But seeing as scientists are not going to deliver, I settle for some futuristic gadgets.

Barry leads me to the bowels of MBARI, where he keeps tanks of clammy-looking brachiopods in a refrigerated darkroom, exposing them to different levels of oxygen, pH and CO2. When they’re acidified to a certain degree, they crash.

“This is one piece of the puzzle,” he says. “What’s the future for our ocean resources?”

His colleague, MBARI Senior Scientist Bruce Robison, is an expert on the dreaded beaky creatures that have been sniping fish from OMZs in the eastern Pacific. Jumbo squid have been invading toward the poles on both sides of the equator, but Robison smirks when I ask if it’s because of global warming.

“We’re all gonna weasel-word this, because ya can’t prove it,” he says gruffly. “We have compelling evidence that these things are related, but we don’t have a direct causal relationship yet. If we went around waving our arms and saying there was a definite relationship, no one would trust us.”

I slip out of Robison’s tentacles and locate Dave Field in his remote cubicle, contemplating digital photos of the latest Santa Barbara Basin sediment core. Like a tree stump, each pair of light and dark stripes represents one year. The core’s top layer, preserving deposits from 2002 to 2006, appears darker and redder than the rest. “That kind of matches up with the timing of the [dead zones] off Oregon,” he muses.

Is global warming the cause?

Field grins like he’s remembering an inside joke. He says he doesn’t know.

Scientists are finally in consensus about the reality of global warming, but the common ground ends at the ocean’s edge. I’ve spoken with some of the best marine scientists on this coast of the Pacific, chased CO2 through three countries, but the disagreement among researchers has only left my mental waters murkier.

Among all the research institutes I visited, MBARI is the deepest invested in the global warming mystery. And among MBARI’s faculty, even-keeled Barry may be the strongest expert witness for the ocean’s case against CO2.

Throughout the earth’s history, he says, spikes in atmospheric CO2 have accompanied mass extinctions. Some creatures – jumbo squid, jellyfish, blue-green algae – may benefit from the changes, but if the geologic record is any clue, most won’t.

Ocean pH has already fallen by 0.1 units since industrialization. If it drops a projected 0.3 more units by 2100, the sea will be 151 percent more acidic than it was in 1800.

If catastrophe is looming, I ask, why the caution? Shouldn’t scientists be rushing at the problem with beakers blazing?

“We’re in a shotgun period of acidification research,” Barry replies evenly. “It’s going to take a while to scale up to how this is going to impact populations, communities and ecosystems.”

We can be sure of one thing: The perpetrator is still at large. As we pump carbon from the Earth’s crust into the air, we tweak the fundamentals of life as we know it. The changes will be slower to manifest in the sea than on land, but the latter are likely to be more profound.

We can blame CO2 for its crimes against the sea. But we are the culprits.

This article was made possible by the World Affairs Journalism Fellowship, sponsored by the Ethics and Excellence in Journalism Foundation and administered by the International Center for Journalists.

BLOG -- The Acid Trip

DEEP CAMEO -- A fish considers the camera in MBARI Scientist Jim Barry’s deep-sea CO2 experiment, where caged animals are exposed to a plume of acidity.

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THREE HEARTS BUT NO SYMPATHY -- Jumbo squid, known for eating whatever they can stuff in their beaks, seem unruffled by the low-oxygen waters that make most fish sluggish.

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