The noise of all these nesting and breeding birds is almost overwhelming (check out the slideshow below for a firsthand look), but these birds speak for a lot more than themselves. Our guides, PRBO Conservation Science, have been studying these birds for 40 years. As Biologist Russell Bradley explained, these seabirds are environmental samplers. In order to raise their chicks, they depend on the food web that blooms in the spring when coastal upwelling brings nutrient-rich water to the surface. If that is disrupted or delayed, the first place scientists will see it is in these bird populations, who will either have poor or non-existent breeding seasons.

Those changes in the upwelling patterns can be due to natural variability in the system. But increasing, scientists are asking whether the changes are due to climate change. That's not an easy question to answer. There are a lot of different factors in the mix.

I spoke with Zack Powell, a professor at UC Berkeley who studies climate and upwelling, and he said it all comes down to the timing of natural cycles. First, there's El Nino – where warm water spreads across the equator and heads up the California coast. That can happen every two to seven years and when it does, it acts a barrier to upwelling, interfering with the marine food web. Scientists recently confirmed that El Nino will return this year.

Looking at changes on a longer time frame, there's the Pacific Decadal Oscillation. It's a pattern of ocean warming and cooling that can last 30 years. Powell says it can also have an effect on marine life and fisheries.

And finally, there's climate change, which comparably may cause changes on the longest time frame. Powell says there's about 100 years of historical data about the ocean conditions off the California coast and it's not much when looking at such long-lived patterns. Powell and others work on climate modeling to help answer these questions. Some of the models show that the seasonal winds may become stronger, meaning upwelling patterns could be altered. And ocean temperatures could rise significantly, changing the way warmer surface water and nutrient-rich deep water mix.

Powell says right now his focus is the granularity of the climate models. They simply can't predict changes on a small geographic scale. "For most models, the smallest footprint is about 100km and all the upwelling takes place closer to shore than that." But he's hoping there will be drastic improvements over the next few years. And if extreme changes do take place, for whatever reason, the birds will certainly tell us.

Listen to the Journey to the Farallones radio report online, and check out our Farallon Islands Interactive Map for the sights and sounds of the island. Or watch the audio slideshow below for a first-hand look.

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.

The Eye in the Sea. Credit: MBARI.

The Eye in the Sea is one of the coolest, gee-whiz scientific projects you'll see. It's part of the Monterey Bay Aquarium Research Institute's so-called MARS project (that stands for Monterey Accelerated Research System). MARS is an undersea laboratory, set up deep on the sea floor about 30 miles offshore from Monterey.

The Eye in the Sea is one of the first research projects to be hooked up to MARS. It uses a small amount of red light to view what’s happening on the ocean floor, about 3,000 feet below the surface. The images travel through 32 miles of cable and go back to the control center on land, where researchers view real-time video of life at the "benthic" level – that is, a voyage to the bottom of the sea.

And you're going to be able to take that voyage, too.

Schoolchildren, teachers and eventually the general public will be able to see the spindly-legged crabs calle spiny kings, or the eel-like hagfish, or the giant, dark, blob-like Pacific sleeper shark.

The Eye in the Sea becomes operational in January, and researchers expect to have their school program up and running by late January or early February, depending on the success they have hooking up Eye in the Sea to the metal hub out in the middle of Monterey Bay.

All of that means that the public will be able to go to www.mbari.org beginning sometime in February and view video-cam images from half a mile deep on the sea floor.

How cool is that?

Watch video from the Eye of the Sea in the Underwater Laboratory audio slide show online.

Areas where the oil spread after the spill. See this map and others.

And November's the month last year when the Cosco Busan crashed, leaking 53,000 gallons of black goo into San Francisco Bay.

So biologists will be particularly attentive this November, one year after the oil spill, to see if there's a noticeable dip in the numbers of herring in the Bay, or the number of migratory birds that alight here.

The number of birds harmed by the oil spill is not really known. More than 2,000 birds were killed – but those are simply the birds that were identified, not the total number. Since many dead birds in remote areas were never found, and since predators took away many of the hurt birds, the estimate for the total number of birds harmed by the spill is many times higher than that. So researchers are conducting experiments to determine a provable, scientific estimate of the number of birds killed or harmed by the oil spill.

According to California Fish and Game scientist Julie Yamomoto, it only takes a spot of oil the size of a nickel to harm a bird. It's not just uncomfortable, she says, it's actually lethal – because the oil is like a hole in a wetsuit, and birds that have been oiled become hypothermic. And they also lose buoyancy, so birds can actually sink and drown in the ocean.

All the experiments and data on habitats, fish, birds and other wildlife will be compiled into something called the Natural Resource Damage Assessment.

It's nicknamed NRDA (pronounced "nerd-a") and that's pretty apt. It's a little wonky, to say the least. The data is supposed to be completed by the end of next year, and then the NRDA report is expected to be compiled and submitted sometime in 2010.

Listen to the Oil Spill Anniversary radio report online.

But even though it's in our own backyard, this place remains mostly unknown… probably due to its chilly temperatures. Let's face it, most of us are not donning our masks and snorkels and swimming in the hypothermic Pacific Ocean off our coast.

Lucky for us, some intrepid scientists and students are diving into this amazing place. Their job is to monitor how the ecosystems are responding to the new restrictions and protections taking place in the Marine Protected Areas. They gave us an amazing opportunity to see the natural world beneath the surface. And the world they shared with QUEST is truly inspiring. Playful harbor seals tease the divers while they weave through the gently swaying kelp forests. Fish dart through the rays of sunshine that cascades down to where starfish slowly go about their day. Through the eyes of these scientists, we witness the undersea life in bloom. They clearly have one of the best offices to go to work to each day.

Watch the Underwater Wilderness: Creating Marine Protected Areas television story report online.