Behind the Scenes at the California Academy of Sciences

By Erin Bank

At the California Academy of Sciences, visitors can stand underneath the skeleton of a blue whale the length of two Muni buses. The whale is hard to miss, extending the length of the massive room that showcases the museum’s Giants of Land and Sea exhibit. Looking up, it is hard to picture how bones of this size made it from the sea to the ceiling. 

When whale bones wash up on Bay Area coastlines, there is a special stop along their journey: the roof of the Academy of Sciences.

How did they get there?

The Pacific Ocean along the Northern California coastline is a major migration route for many species of whales, and home to even more species of marine mammals, like seals, sea lions, otters and dolphins. When a dead animal washes up onto the beach (termed a “stranding”), a team of Academy scientists go to the site and collect material that is useful for research. 

Senior Collections Manager Maureen (Moe) Flannery oversees all bird and mammal specimens at the Academy and oversees the process by which the museum obtains samples and prepares them for preservation and research. 

Senior Collections Manager Moe Flannery shows the skull of the northern elephant seal, part of a vast research collection of the California Academy of Sciences. Photo by Michael Durand.

“We take measurements, we identify the specimen, we look for any signs of human interaction – gunshot wounds, entanglements in fishing nets or lines – and we will sometimes, not always, collect the skull,” said Flannery. 

The Academy’s scientists pay special attention when a whale washes up on the beach. The Academy is part of the Marine Mammal Health and Stranding Response Program, a federal research program run by the National Marine Fisheries Service. This program monitors strandings, and if there is a high rate of death, it becomes an Unusual Mortality Event that warrants additional research. 

Dion Lim, a reporter for ABC 7 News, and a camerman cover the story of a whale that washed up onto Ocean Beach on May 6, 2019. Photo by Michael Durand.

Starting in 2019, there has been a large increase in the number of strandings of gray whales, which migrate between Mexico, where they give birth, to Alaska, where they feed– enough to classify it as an Unusual Mortality Event. By collecting samples from the stranded animals, researchers can learn about how the animal may have lived, what the animal ate, and the cause of death. The information Academy samples provides is paired with research being conducted by other scientists to create a full picture of the habitat and ecosystem of gray whales. The goal is to determine what is causing the Unusual Mortality Event, how climate change may play a role by creating food shortages, and what can possibly be done to help whale populations survive.

The Academy often partners with the Marine Mammal Center in Sausalito to perform necropsies and collect samples. Teams try to move quickly to preserve samples, but also to protect the animal from human scavenging.

“Marine mammals are protected under the Marine Mammal Protection Act, so it’s completely illegal to collect anything,” Flannery said. Instead, people who encounter a dead animal should contact the Academy of Sciences to report it.

It sometimes can take several days and dozens of people for whale samples to be collected and transported away, often requiring heavy machinery to dissect and move the heavy bones. Sunset and Richmond district residents may remember the beaching of a large gray whale on Ocean Beach earlier in 2021: it was detected in the early morning but was quickly covered with sand by mid-day. Flannery had seen a unique opportunity to collect the skull and brain: nearby, backhoes and bulldozers were moving sand as part of the seasonal beach maintenance. She flagged them down and asked them to help turn the whale, weighing more than ten tons, so she could access its head to get brain samples, which can reveal the presence of disease. The machinery could then move sand on top of the animal right away to protect it.

After being hauled from the beach, the massive bones are brought to the museum for preservation. Because of limited space for such huge samples, many of the bones are transported to the museum’s Living Roof, where nature can help with the process.

Senior Collections Manager Maureen (Moe) Flannery at California Academy of Sciences displays a bone that was left outside on the Living Roof atop the Academy building in Golden Gate Park. Flannery is in charge of the bird and mammal specimens. The bones of whales and other animals are left outside on the roof to allow nature to help clean them of any living matter. Photo by Michael Durand.

Tucked away among wildflowers and grasses, under mounds of soil, Flannery points out what look like pointed rocks. They are, in fact, vertebrae, a rib, a fin. They are covered with crawling pill bugs and beetles, and even more invisible microbes that eat away at the flesh which cleans the bones. After six to 12 months, they are brought back inside to be catalogued and stored. 

The whale bones currently on the roof will eventually join the huge collection of other mammalian specimens – more than 32,000 of them from all over the world – that are kept on shelves in library-like stacks in the bowels of the Academy of Sciences building, behind locked doors. Flannery moved among them with obvious familiarity, showing off whale teeth larger than her hand. There are slender penis bones, collected to confirm the gender of an animal, and drapes of moss-like baleens.

In addition to bones, there is another unique part of whales that is important for researchers.

“Whales have ear wax, just like we do,” Flannery said. Researchers can use the wax plugs to determine the age and habitat of a whale, due to the various layers that build up over time.

Collecting and preserving specimens from the unique underwater ecosystem is incredibly important, Flannery explained. 

“Instead of books at a library, we loan out specimens,” she said. Scientists can take samples from extinct animals, or from individuals who lived in the past, to understand changes in diet or behavior, for example.

One researcher from UC Santa Cruz received permission to cut a tooth from a sperm whale in half, which is layered like the rings of a tree. From each layer, she could determine where the whale lived and what it would have eaten, and how that changed over time.

“It’s my job to make sure that all of these specimens are here for the next 100, 500 years, so that whatever research technologies come up, people have their resources to study them in the future,” Flannery said.

To report dead marine mammals, call the California Academy of Sciences’ department of Ornithology and Mammalogy at (415) 379-5381, or email

Photos by Michael Durand

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