The bike lane on the Golden Gate Bridge was a Sunday-morning celebration of spandex, speed, and bulging quads, so I was the only one looking at the dead whale. I had paused to press myself and my bike into one of the shallow cutouts in the railing to scan the Pacific side for wildlife, while other cyclists whizzed by. A congregation of gulls drew my eye to a small, rocky cove some 220 meters below, in the Golden Gate National Recreation Area. They had just discovered a buffet worth telling their grandchildren about.

The gulls claimed territories on the body and pecked desultorily, while many others sat still around it. Maybe they were already full, or maybe they were waiting for the flesh to break down a little more before the real party would begin. Vultures circled. Low tide was two hours off; the white water charged the beach and foamed back. The whale lay still, on its side, mostly intact. It was dark-gray with white patches where skin had peeled off. I checked my phone for recent whale death news and wondered how long it had been there. Saturday had been a king tide, so maybe the ocean wouldn’t carry it away until the next moon.

One thing I knew: This whale would not be buried, like two that washed ashore in April at Muir Beach on the Pacific coast. (Or exploded—we don’t do that anymore.) This body had washed up into one of those neverland nooks of real wilderness that have managed to avoid civilization by being too dangerous to approach: sheer cliffs above, famously fretful waters around it. I called the hotline for the Marine Mammal Center (TMMC), a Sausalito-based nonprofit, and texted my photos over. 

The hotline is mainly for animals that are in distress, but you can use it to report those beyond pain too. Nine dead whales, seven of them gray whales, have now been seen in San Francisco Bay since February—which is a lot. Since 2016, the eastern Pacific population of gray whales, which migrates up and down the West Coast of North America every year, has dropped by about one-quarter, according to the US National Oceanographic and Atmospheric Administration. In 2019, the agency declared the steep drop to be an Unusual Mortality Event, triggering an immediate scientific investigation, which researchers from Mexico to Alaska are collaborating on. 

The rise in the number of dead whales has taken its toll, said Tim Markowitz, Cetacean Field Research Coordinator for TMMC: “The biologists are exhausted right now.” In the San Francisco Bay, TMMC works with the local science museum, the California Academy of Sciences, to examine any deceased marine mammals that appear in the area for signs of what might have killed them. TMMC has the expertise in soft stuff, like tissues and parasites. The Cal Academy specializes in bones and has the dead animal collection permit. In the US, a person or institution needs to be federally authorized to even touch a whale, alive or dead. But lots of people end up getting in on it, when a whale dies. Literally up on it, since a ladder may be involved. A whale necropsy is an extremely hands-on affair.

A dead whale has many stakeholders

Moe Flannery, bird and marine mammal collections manager at the Cal Academy of Sciences, is one of the first to get the call when a dead whale is spotted in the bay. Her first actions depend on whether the whale is accessible—as “my” whale wasn’t—and if the whale looks like it will stay put in a sensible location (though the tides giveth, they may also taketh before a team can even assemble). If both are true, Flannery and team then track down the relevant land manager for permission to do a necropsy. Technically, if a dead whale washes up on a beach, whether private or public, it’s up to the landowner or agency in charge to decide how to deal with it. (But again, don’t touch it, unless the feds say you can.) Usually owners are OK with a necropsy, which can hasten the decomposition process because it airs things out, as it were. But, in the short term, a necropsy can also exacerbate the smell, so some opt out.

“It’s a big, stinky business,” Markowitz said.

How to conduct a whale necropsy

A whale’s “peculiar and not very pleasant smell,” as Herman Melville described it in Moby-Dick, is a domineering factor on the necropsy stage. It is why a carcass may be buried, despite the food it would provide to local wildlife. It is why some may prefer to view a whale necropsy from afar, and why some local boat companies refuse to shuttle researchers to boat-in necropsies. One salvage company has a craft that local researchers have depended on in the past, but it is in the yard right now, which is unfortunate considering all the whale deaths that need investigating. 

If a whale has washed up in a reasonably convenient spot, like a juvenile male fin whale did recently on Fort Funston, a beach to the south of San Francisco, a crew of about five to 15, depending on the size of the whale, accessibility and who’s around, arrives on the scene. They’ve already checked whether they will have to work carefully around endangered snowy plovers, whose nests could be put at risk by a large beachside necropsy. If any beachgoers are watching, a few docents may peel off from the group to engage them in this teachable moment. 

The whale necropsy begins with a barrage of morphometric measurements—flipper lengths, snout-to-eye, and so forth. They sex the carcass and take photos from every angle Then a two-person team works to open up the whale: one cutting into the carcass with a knife and the other peeling back the blubber with a hook. They separate the blubber from the muscle (as the gulls could not do alone) and try to collect samples from every organ they can identify as well as gut contents, feces, urine, blubber, tissue, and skin. All told, they may leave with several bags and a cooler’s worth of tissues. 

A whole whale skeleton is too big to archive, but the Cal Academy will grab the pelvic bone and anything broken, since it may be evidence of trauma. Flannery describes herself as a librarian. Once done, she and the rest of the team go home and scrub off the stench and preserve samples for the future researchers of five or five hundred years from now.

One of the most valuable historical records a necropsy can reveal, Flannery said, are a whale’s waxy earplugs—mostly keratin and lipids that have built up in layers inside the ear canals, like tree rings. Earplugs can reveal how old the whale is, where it has been, what contaminants it encountered, what its hormone levels were, when it was pregnant or nursing. But since dead whales heat up from the inside, earplugs often disappear before researchers can get to them. The Smithsonian National Museum of Natural History has an impressive earplug collection going back 50 years. The Cal Academy hasn’t got any yet, but Flannery is keen to find some.

With whale buffet zone comes great responsibility

Before the Unusual Mortality Event, gray whales were doing pretty well. Since the Marine Mammal Act passed in 1972, the eastern Pacific population has grown in number. Though they no longer swim the whole Northern Hemisphere, as they did before we humans went on a several-century whale-killing spree, they got off the endangered list in 1994. Most gray whales travel up and down the coast, about 10,000 to 14,000 miles round trip, from breeding in Baja California to feeding grounds in the Arctic. And they don’t generally stop to feed along the way—with the exception of a few groups like the Sounders, a dozen gray whales who detour into Puget Sound for three months a year to hoover up ghost shrimp.

Forty years ago, a single whale wandering into San Francisco Bay made news. (That was Wrong-Way Humphrey, the Los Angeles Times–dubbed humpback, who wandered up the Sacramento River and attracted a crowd of hundreds in 1985 before being herded back to sea by a rescue crew playing tape-recorded whale sounds and banging pipes underwater.) Twenty years ago, gray whales were sometimes seen outside the bay. 

Today, times are changing. Pit stops are being made.

In 2019, TMMC biologists noticed that a few of the gray whales passing through stayed for four or five weeks inside the bay, mostly between Angel Island, Treasure Island, and Alcatraz. This year they spotted the characteristic mud plumes that gray whales create while eating. Gray whales are filter-feeders, like humpbacks, but instead of feeding near the surface, they dive to muddy seabeds about 50 feet down, roll onto their sides, and swim slowly along. As they go, they scoop up mud and strain it through their sieve-like baleen for shrimp, crabs, and other tasty invertebrates. Flannery and Markowitz suspect the new whale visits are a sign that the bay is no longer too disgusting for them. “That’s amazing news, ecologically,” said Markowitz. 

But more whales around also means more risk of whales being killed by port traffic or getting entangled in fishing nets and other boat gear. Of the 24 dead whales that researchers have responded to in the Bay Area since 2019, nine died or were suspected to have died of ship strikes and two of entanglements. “This is all new,” Markowitz said. “A new situation for the commercial shipping industry, folks in fishing, recreational boaters, for everyone. So right now we’re trying to get the word out.” 

That word is please slow down. A whale has to notice you to move out of the way, and it tunes out noise pollution, just like you do. The Bay Area has a modest “exclusion zone” with a voluntary 10-knot speed limit; TMMC is advocating to expand that area and working on a system to warn boaters in real-time of whales in the area.

Not every necropsy is a dream necropsy

I wanted to see the whale up close, but friends persuaded me that kayaking under the bridge alone was a bad idea. Instead, I hitched a ride with a Sausalito fisherman who was on his way out to find halibut. It was too dangerous to attempt a landing, but we bobbed as close as we could, and I could see that the waves had shoved the carcass up against the cove’s steep wall. It lay almost incognito in a deep shadow, while the water in front sparkled and glowed a brilliant turquoise. Even a whale can be swallowed up by the ocean.

The Marine Mammal Center biologists later confirmed that what I saw was a roughly 32-foot gray whale they were already acquainted with. TMMC had photographed it foraging in the area four times, beginning on March 13. Forty-seven days later it washed up dead on the Tiburon peninsula. A dream necropsy, for research purposes, is a whale that dies in sight on an accessible beach (though of course, no one wants that for the whale). This whale had not obliged. In that tricky location, the biologists hadn’t been able to do much, necropsywise—even the sex was unknown, since its position didn’t offer a good genitalia-viewing angle. Now that the tide had moved it again, it seemed likely this whale would remain anonymous, since the spot under the bridge was even less accessible. 

Exact cause of death, even with a full necropsy, isn’t always knowable, but according to Flannery, the whale I saw was “severely emaciated.” In 2019, a good year for necropsies, TMMC found that seven of the 12 whales that it was able to dissect had died of starvation. (In 2020, a bad year for necropsies because of the pandemic, the team managed just one full necropsy of the five dead gray whales spotted.)

Why the whales are starving is unclear, said Flannery. Some disease could be at work. So could climate change. It’s possible that the loss of Arctic sea ice is reducing the population of amphipods in the Arctic mud, where whales feed.

Or it could be that these fluctuations are normal. About 20 years ago, gray whales experienced a similar Unusual Mortality Event, then bounced back to pre–Unusual Event levels.

Wallow not, whale worriers

While Flannery tries to figure out what’s happening, she said, she cannot afford to get too upset about all the whales that die. One must get the science done, and she has a 150,000-specimen collection to manage. “It is sad when you think overall of the effects that humans on this planet are having on animals such as large whales,” she said. “Especially if it’s a human-caused death, it really does make you think and want to make changes in your own life.”

If you are melancholy about the gray whales, think of the bounty they represent. Alive, they churn through the muck and produce enormous clouds of poop that are a crucial part of an ecosystem’s biochemistry. Dead, they feed the masses. Markowitz, noting that the California condor was once one of the major scavengers of whales along our coastline, wondered if condors will feast on whales again soon, since the birds are on the rebound.

“They are part of the ecosystem, as we all are,” Markowitz said of the whales. “And, you might say, they are a very large part.”