The museum is perhaps best known as the place where Ishi, California's last "wild" Indian, lived for five years until his death in 1916. Ishi was a living exhibit at the museum, which was then in San Francisco. The Hearst sent his brain to the Smithsonian Institution, where it sat in a jar until 2000, when it was returned to California for burial.
The early Berkeley archaeologists viewed themselves as preserving the last fragments of a disappearing culture. They and their students went out collecting, digging up old villages and burial sites.
Berkeley began housing the bones in the gymnasium basement under the outdoor pool in the 1940s. Rows of yellow metal cabinets and wooden drawers hold the remains, some consisting of just a few bones, others complete skeletons, according to people familiar with the collection.
Many bones are kept in plastic bags; a few are wrapped in old newspapers. Soil still clings to some, making it appear that they haven't been touched since they were brought to the basement.
To maximize storage space, most skulls are kept in one set of drawers and the skeletons in another, a practice that offends Indians. Access to the basement is restricted to museum staff, a handful of researchers and tribal representatives. The university declined to let a Times reporter into the storage area, saying it was "too sensitive."
Some Native Americans complain that scientists view their ancestors as "research materials."
The university acknowledges that one researcher was recently allowed to take a small Ohlone bone and destroy it in a test to analyze the individual's diet. The Ohlone, once numerous in the Bay Area, are not eligible to receive remains because their tribe is not federally recognized. A similar test was performed on a second bone. Both fragments weighed less than 2 ounces, the university said.
At least one professor, archaeologist Tim White, uses bones from the basement in his teaching. As curator of the human remains collection, he also has a major say in which items are returned to the tribes.
White is a star at Berkeley because of his discovery of fossils in Ethiopia that have helped redefine human evolution. But some Native Americans view him as an obstacle in repatriating remains. Even among colleagues he is known as a "hard-liner" on returning bones.
"In many ways these collections are irreplaceable," he said. "And had they not been recovered and curated and placed in a museum, they would have been lost forever for everybody."
White said he supports the federal repatriation law and sees it as an opportunity to persuade tribes to let the museum continue caring for tribal objects.
"Part of the intent of Congress," White said, "was to set up this process so that people like me could explain to people who didn't have my perspective" that preserving remains could help the tribes, for example, in proving land and water rights.
Under the law, the Hearst was supposed to inventory its Native American bones and artifacts by 1995 and determine which items were associated with certain tribes and which were "culturally unaffiliated."
The museum completed the job in 2000 but designated about 80% of the remains as unaffiliated -- despite archaeological records showing where nearly all the bones were excavated.
White says the number of culturally unaffiliated items is so large because many California tribes lack federal recognition. The state has passed its own version of the law that would allow the return of items to non-recognized tribes, but it has yet to take effect.
Even for federally recognized tribes, the process of getting bones back from Berkeley is time-consuming and rigorous. Some say the deck is stacked against them and that Native Americans too often have little input in the process.
At the center of the museum dispute is Fredericks, the ousted interim coordinator of the repatriation unit. A member of the Athabascan tribe from Alaska, she has a doctorate from Berkeley in medical anthropology and two master's degrees.
She has worked at the museum since 1999 and began heading the unit in March 2006. Some tribal leaders say she was the first museum representative to deal honestly with them and to willingly provide information about what items were in the collection.
"I understand science and appreciate it," she said. "But even if you are a scientist, you should also have fairness, and if there is a law you should follow it."
In May, UC officials created a two-member panel to review museum operations and rebuffed Fredericks' repeated calls to add a Native American to the committee.
Robert M. Price, the associate vice chancellor for research, said later in an interview that the tribes were excluded because they have no experience in museum operations.