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

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

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

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

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

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

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"Anti-shark cage? You go inside the cage? Cage goes in the water, you go in the water? Shark's in the water. Our shark." (from the film JAWS)

Like any good fishing trip, the day started before the sun came up. Our boat, the New Superfish out of the Berkeley Marina, had been specially outfitted with a shark cage and hot-tub, what they called the "TRU" or "Thermal Recovery Unit." The under-caffeinated passengers stowed their gear, the crew cast off and we began our trek to the Farallon Islands in hopes of encountering great white sharks.

We would cross under the Golden Gate Bridge just as the sun was rising over the East Bay Hills– a beautiful sight on a clear crisp morning. From there it was fairly smooth sailing out to the Farallones. We had been trying to make this trip for years. Weather and rough seas always seemed to keep us cooling our heels on land. Even on a good day this is generally not a trip for the faint of heart or weak of stomach. But now we were finally on our way.

Like many people, I'm fascinated with sharks. I can’t remember a time when they did not interest me. Growing up we had a collection of National Geographic magazines that my brother and I would page through. The one that I'd return to again and again was a well worn copy from 1968. On the cover was a shark and inside there was an article titled "Sharks: Wolves of the Sea." I was equal parts frightened and captivated and it sparked my curiosity to check out every book I could find about sharks at the library. Then when I was in 4th grade, I did an incredibly in-depth presentation on Great White Sharks. I considered myself the class expert. This was a couple years before a famous movie came out that made the great white an infamous villain. I think Jaws was the first R-rated movie I ever saw. I don't know if it was the result of one of my friend’s parents being lax or if my buddies and I managed to sneak in, regardless, I saw that movie at a far too young and impressionable age. And it permanently colored my perceptions of being in the ocean. That was when my interest in sharks tipped from mainly curiosity to just being terrified.

I think most surfers in California always have the thought of white sharks somewhere in the back of their minds. But when I surfed it was always in the front and center of my thoughts, "I am bait." As great a day on the waves might have been, it was always partnered with my ever-present fear, irrational as I knew it was…makes for a fun time. I was looking forward to meeting the bully of my imagination head on and hopefully getting past this.

Prior to our trip I had the great honor of meeting one of my all-time heroes, Dr. John McCosker at the California Academy of Sciences, to talk sharks. Dr. McCosker is one of the world's foremost experts on the great white shark. It's not hyperbole to say his work has set the foundation of nearly all white shark research over the last 30 years. He has also been particularly instrumental in of our understanding of why white sharks occasionally attack humans. Since 1950 there have been around 100 shark attacks that have occurred along the entire California Coast. Most of these were not fatal. Needless to say, I know the numbers but always thought, "But with my luck…" When I expressed my goofed up fears, Dr. McCosker put it into perspective for me. "What's so remarkable that if the numerator is 99, (Amount of shark attacks) the denominator is in the billions. How many human beings or human being-hours have been spent in the water over the past 60 years? The sharks are clearly not hunting us. So why are we so afraid? I guess because we are terrestrial animals that are accustomed to things on land that we understand, and when we put our foot in the ocean, we are out of our element and no longer in charge. So we're afraid of white sharks because of the exaggeration and what we've created with our own imaginations. And there's no reason we should be. We should be more afraid of the disappearance of white sharks, because an ocean without white sharks is a very unsafe place for every human being."

I also asked Dr. McCosker what the chances were that we'd see white sharks at the Farallones. He said that no doubt the sharks would be there but he couldn't place odds on us seeing them. Shark dive operators in the Marine Sanctuary are not allowed to bait or chum around the Farallones. The sharks know that the boats don't have much to offer in the way of food or sport. But Dr. McCosker then said, "You might not see them but no doubt they'll know you're there."

We reached the Farallon Islands and the cage was dropped into the bitter cold water. Divers pulled on their wetsuits and fitted their masks. I would be in the first group getting into the cage. We tested our regulators, hooked up to a hookah unit pumping air down to us from the surface, and heavy weights were strapped to our ankles. I clambered out over the rolling cage and slipped into the frigid water. From the start I had a hard time controlling my breathing and thought I might hyperventilate. Was it the burst of cold water entering my wet suit or the adrenaline hit from me thinking I'd be breaking the surface and entering the opening jaws of a great white? As I calmed down I scanned the murky green depths. The rays of sunlight draped down from the surface. Jellyfish pumped by in a leisurely fashion. The cage pitched up and down with the rolling waves and my leg slipped between the bars behind me. I immediately spun around and reeled it back in with the thought that it was about to be snapped off by a waiting monster. I frantically scanned the green shadows below and around. In a short time my breathing normalized. I was in their world but I suddenly found a peaceful calmness take over.

We did not see sharks on our dive. It was disappointing but not unexpected. But in many ways I saw much more. I saw their realm for what it really is: a fragile and beautiful place where white sharks are the masters but not monsters. In order to complete our story I would rely on the footage taken by white shark researchers such as Scot Anderson out at the Farallones and other footage taken by the folks at Great White Adventures during past dives in the clear blue waters of Mexico. In any case I would not trade my experience. Knowing that I was sharing the water with these amazing animals, unseen but out there, has given me something back. No more irrational fear, all wonder.

Watch The Great White Shark: Meet the Man in the Gray Suit TV story online.

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The Galapagos of California: The Farallon Islands.

Every so often the fog retreats from my neighborhood in San Francisco, moves out to sea and we are blessed with a world-class sunset. Adding to the oranges and reds, yellows and spiraling indigos of the evening sky, it also gives us a special chance to see the silhouette of the strange jagged fist of rock breaking up the crisp line of the horizon. I have gazed out upon the Farallon Islands for years. The archipelago is clearly the wildest part of The City-seemingly always just out of reach. (Many people don’t realize that these little islands are actually part of the City of San Francisco.) Since they are a federally protected wildlife refuge, they’re completely closed to the public. So to get a chance to actually set foot on South Farallon Island was an absolute honor.

We’ve tried to share the experience in as many ways as we can. I encourage everyone to really explore the islands through Quest. In addition to the television story, we have a radio presentation with reporter’s notes, a web exploration with video and stills, a unique audio slideshow, an interactive history timeline (also embedded below) and a Flickr set. We’ll also be adding another web-only video story and education guide. The only things we couldn’t bring you are the smell and chill of the wind. But we’ll get on that.

Farallon Islands History: Interactive Timeline

Watch the The Farallon Islands – "California's Galapagos" television story online.

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Each year the Marine Mammal Center treats somewhere between 600-1000 animals, including California sea lions, Pacific harbor seals, Northern elephant seals, and steller sea lions. About half of them are treated successfully at the center and released into the Pacific. The other half either die naturally or have to be euthanized.

Most of them end up at the center's hospital after passersby spot the animals on the beach and sense something’s wrong. (The Marine Mammal center responds to calls anywhere between Mendocino and San Louis Obispo Counties — some 600 miles of coastline.) Some problems are human-caused, like boat-propeller injuries or ingested fishing nets and hooks. Other times, it's cancer, domoic acid poisoning, or leptospirosis. Sometimes, it's hard to tell exactly what happened — hence the need for necropsies.

On the day that Quest intern Jennifer Skene and I visited the center, veterinarian Nicola Pussini performed two necropsies, both on sea lions. One animal seemed to have died from a tumor underneath his fin; the other was a suspected domoic acid intoxication.

Each necropsy takes about an hour and a half. First Pussini measures the animal, then he slices it open and inspects every part, from tongue to tail. He inspects the teeth, pulls out all the organs, checks to see how much fat the animal has. The data, along with tissue samples, are archived and shared with other research institutions. This is the kind of basic research that Marine Mammal Center staff cite when people ask why they devote so many resources (most of it from private donations) to animals whose populations are neither threatened nor endangered.

I should mention that I didn't exactly see this entire process firsthand. Let's just say that after my first strong whiff of sea lion intestine, I felt a compelling need to go check on things outside the necropsy room. Luckily for me, Jennifer has the stomach of a true scientist and managed to both hold the microphone and take photos. Luckily for you, we’re sparing you her gorier shots.

Listen to the Sea Lion Rescue radio report online, and watch our photo slideshow.

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For these notes, I thought I'd focus on something that didn't make it into the sea lions radio broadcast: the necropsy.

Each year the Marine Mammal Center treats somewhere between 600-1000 animals, including California sea lions, Pacific harbor seals, Northern elephant seals, and steller sea lions. About half of them are treated successfully at the center and released into the Pacific. The other half either die naturally or have to be euthanized.

Most of them end up at the center's hospital after passersby spot the animals on the beach and sense something's wrong. (The Marine Mammal center responds to calls anywhere between Mendocino and San Louis Obispo Counties — some 600 miles of coastline.) Some problems are human-caused, like boat-propeller injuries or ingested fishing nets and hooks. Other times, it's cancer, domoic acid poisoning, or increasingly these days, leptospirosis. Sometimes, it's hard to tell exactly what happened — hence the need for necropsies.

On the day that Quest intern Jennifer Skene and I visited the center, veterinarian Nicola Pussini performed two necropsies, both on sea lions. One animal seemed to have died from a tumor underneath his fin; the other was a suspected domoic acid intoxication.

Each necropsy takes about an hour and a half. First Pussini measures the animal, then he slices it open and inspects every part, from tongue to tail. He inspects the teeth, pulls out all the organs, checks to see how much fat the animal has. The data, along with tissue samples, are archived and shared with other research institutions. This is the kind of basic research that Marine Mammal Center staff cite when people ask why they devote so many resources (most of it from private donations) to animals whose populations are neither threatened nor endangered.

I should mention that I didn't exactly see this entire process firsthand. Let's just say that after my first strong whiff of sea lion intestine, I felt a compelling need to go check on things outside the necropsy room. Luckily for me, Jennifer has the stomach of a true scientist and managed to both hold the microphone and take photos. Luckily for you, we’re sparing you her gorier shots.

Watch the Sea Lion Rescue audio slide show online.

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