The whale-watching boat Superfish drifted up and down with the surging waves that crashed over the rocky shore of the Farallon Islands, an ancient archipelago 27 miles off San Francisco's coast.
Derek Lee, a 35-year-old biologist who has spent the past five winters on the islands, puttered up in a small motorized raft the other day, tied up to the side of the boat and grabbed baggage handed down from the vessel.
Lee's little raft is the only way for people to get onto Southeast Farallon Island in this 211-acre chain of craggy rocks that is part of the Farallon National Wildlife Refuge. Storms and rough waters have consistently destroyed all landing docks that were built, so Lee has to ferry passengers over to a diesel-fueled crane that lifts them on, or off, the island.
It can be rough going for the small band of biologists who live in a 120-year-old Victorian house on the cold, weather-beaten rocks. But this isolated outcropping jutting out of the often stormy sea is where some of the world's most important marine wildlife research is now taking place.
"It definitely is a laboratory of ecosystem science," said Lee, a specialist in species demography for the Point Reyes Bird Observatory, now called PRBO Conservation Science. "Absolutely we are reaping a huge harvest of information about the ecosystem and about the Pacific Ocean, which is the single largest factor in global climate after the sun."
The studies on marine mammals, birds and the ocean ecosystem at the Farallon Islands are as important as any research going on anywhere in the world, especially given the recent findings of the United Nations' Intergovernmental Panel on Climate Change, which predicts lasting ecological impacts from an ocean that is heating up and rising fast.
Data from Farallones researchers are already showing how changing ocean climate conditions are devastating the Cassin's auklet, a small North American seabird that feeds on krill. Lee said the species' population has declined about 80 percent over the past three decades, and disaster has struck in the past two years.
"The species has had an absolute and complete breeding failure," he said. "Not a single egg has hatched for the last two years. That's unprecedented in the last 35 years of our data."
Studies on the islands are showing that the reproductive and dietary habits of other seabirds are also changing with ocean temperatures.
Lee's team established a connection between El Niño weather conditions and the migration of California sea lions from their usual home on the Channel Islands to the Farallones. Climate also has a mysterious effect on marine mammal reproduction, he said.
"We just started analyzing the elephant seal population and how climate affects how many males and females are born," Lee said. "We've determined that El Niño causes more males to be born. We don't know why, but we are trying to figure it out."
Even during these changing times, the archipelago and the water surrounding it are teeming with life, including five species of seals and sea lions, 13 species of seabirds and one of the largest concentrations of great white sharks in the world. Dolphins, humpback whales and blue whales are regular visitors, and fur and elephant seals are beginning to thrive on the islands after being absent for nearly two centuries.
The common murre is also making a big comeback after egg collectors nearly wiped them out a century ago. A pod of killer whales from Washington state was recently spotted near the Farallones, and a prominent computer scientist and his sailboat vanished, adding a touch of mystery to the place.
All of which contributes to a bounty of information about the health of what researchers call the California Current, the band of coastal water from Baja California to British Columbia that flows past the islands. In fact, this forlorn-looking collection of rock is one of the richest marine environments on the globe, thanks to its proximity to the continental shelf, which provides deep upwellings of cold, nutrient-rich water.
"The ocean provides a huge portion of the protein humans eat, and the California current is a big part of that productivity," Lee said. "We're talking about the food on our plate and how global climate change may affect that. The ecosystem knowledge that we provide from this natural laboratory definitely has fisheries management implications."
The current status of the Farallones as a weathervane for global climate change represents a historic new era for a place that 19th century sailors dubbed "the devil's teeth." For hundreds of years, the archipelago was used to harvest food, not information.
American Indians called these rocks the "Islands of the Dead," an earthly hell where bad spirits lived, according to historians. The Portuguese explorer Juan Rodriguez Cabrillo was said to be the first European to see them in 1542, but he never went ashore. Sir Francis Drake was the first to do that, gathering seabird eggs and killing sea lions for meat in 1579, after his five-week stay on the Point Reyes peninsula. The islands were a source of food for passing seafarers and egg hunters for the next three centuries.
Drake named the archipelago the Islands of St. James. Although the name didn't stick, one tiny island six miles north is still called the Isle of St. James.
In 1769, the explorer Juan Francisco de la Bodega renamed the islands Los Farallones de los Frailes, in honor of the Franciscan friars who were busy at the time enslaving California's natives. The islands fared better than the Indians until 1810, when a New England vessel called the O'Kain arrived with four sealing boats.
During the next 22 months, between 75,000 and 150,000 Northern fur seals and Northern elephant seals were slaughtered, their pelts sold as far away as China. When the New Englanders left, Russians from Fort Ross moved in, using Aleuts and Pomo Indians to help collect bird down, eggs, sea lions, fur seals and otters, according to various accounts.
By the time the Russians left in 1841, fur seals and elephant seals had been wiped out on the California coast, including the Farallones.
The common murre was the next victim of human gluttony. A shortage of eggs in San Francisco during the Gold Rush prompted entrepreneurs to begin collecting murre eggs on the islands. The eggs reportedly sold for $1.75 a dozen, prompting the formation of the Farallon Egg Co. and later the Pacific Egg Co.
The business was so profitable that rival gangs of eggers were formed and pirates began to ply the waters, hijacking egging vessels. A gunbattle reportedly broke out on the islands between rival eggers in 1863, leaving one man dead.
One tactic of the egg collectors, according to historians, was to break all the existing eggs, forcing the birds to lay new ones, ensuring fresh eggs for the trip back to the mainland.
As many as 600,000 eggs were taken annually from the islands. In all, an estimated 14 million eggs were removed from nests before the California Academy of Sciences and the American Ornithological Union halted commercial egg collecting some 40 years after it began. By 1900, the Farallon murre population, which was once well over a half million, had been reduced to only a few thousand.
By 1909, the North and Middle Farallon Islands had been declared a national wildlife refuge, but that wasn't the end of the trouble. Human habitation on the southeast island, which began with a lighthouse in 1855, meant the introduction of non-native animals like rabbits, mules, cats, turkeys, goats, chickens, house mice and children.
The invaders trampled nests and preyed on wildlife; ships regularly pumped out their bilges near the Farallones before entering San Francisco Bay.
The government, at various times, considered building military air strips, a harbor, a prison and a gas station for passing oil tankers on the islands. During World War II, more than 70 people lived in some 20 homes on the southeast island, which the residents referred to as Farallon City. There were movie nights, dances and even an island newspaper.
In 1969, South Farallon was declared a national wildlife refuge. The lighthouse was automated in 1972, ending 117 years of continuous occupation. The last rabbit and cat were removed from the islands in 1974. Mice, however, still scurry around the two houses.
The government established the Gulf of the Farallones National Marine Sanctuary in 1981, protecting the surrounding waters. Elephant seals returned to the islands to breed for the first time in 1972. In 1996, the first Northern fur seal pup was born on the islands, ending an absence of more than 150 years.
Monica Bond, a volunteer biologist, climbed from the Superfish into Lee's skiff. She would spend the next five weeks on the island monitoring elephant and fur seals.
The 36-year-old biologist, who has had two previous stints on the archipelago, said elephant seals have the longest migration and can dive deeper than any other mammal. The females have the richest milk, she said.
"Now's the time to study them," she said. "The females are giving birth and will be sexually receptive after a few weeks of nursing. The males are fighting."
In early January, the last time she was on the island, Nero, the alpha elephant seal, was killed in a fearsome battle with another bull named Don Francisco, throwing the seal hierarchy into chaos. She said fur seals are even more aggressive toward people than their bigger cousins.
"The reappearance of fur seals will definitely change how we do business out here, because they are so aggressive," said Bond, the only Farallon worker since seal hunters left the islands to contract "seal finger," a rare bacteria that infects the digits of people who handle the pinnipeds. "We stay really far away from them."
The work is done amid constant noise and bombardment from the 300,000 seabirds flying overhead, prompting some biologists to wear ear plugs and hardhats. Bond said elephant seals make a metallic drumming sound at night, while the endangered stellar sea lions growl like bears, a combined cacophony that can make sleep difficult.
"I love it," Lee said after another long day counting and monitoring animals. "It's a living spectacle of nature every day."
E-mail Peter Fimrite at pfimrite@sfchronicle.com.
As the month of February comes to a close, the winds are howling, massive waves are crashing against the beach, rain and hail pound the Farallones, and the thermometer has dropped to 8 degrees Celsius. But the chilly weather is no problem for an elephant seal weaner, wrapped in its thick layer of blubber. Some of the heftier pups are made up of 50 percent fat just after weaning, “much like the consistency of a fine camembert” as noted by one biologist with a sense of humor. Elephant seals are built to withstand extremely cold conditions deep below the surface of the sea, and in fact it is the warm rather than cold weather that makes them uncomfortable. 
eaving their pups to fend for themselves. The beaches and gulches of the Farallones have been turned over to the elephant seal weaners. The 2007 crop of over 100 weaners is scattered all over the marine terrace, Sand Flat, 
