Sometimes the bodies show up floating in the ocean, other times they wash ashore. Then it's up to investigators to figure out what happened.

Whales, like humans, can meet unnatural ends. The bodies they leave behind can tell a story about what killed them, sometimes revealing evidence of a prolonged, painful death.

Michael Moore, director of the Woods Hole Oceanographic Institution's Marine Mammal Center, is among those who lead examinations, known as necropsies, on dead whales.

Whales, because of their enormous size and weight, present a unique challenge when they wash up on a beach or appear floating at sea. [In Photos: The World's Biggest Animals]

A plan & tools

"I don't get involved unless I have a plan, because as soon as I am involved, I am committed to disposing of it," Moore said of a dead whale's body. "So essentially you work backwards from the end stage, whether it be digging a hole in the beach, or trucking it off or towing it back out to sea or whatever."

Moore's tools include a camera, knives (kept in a box marked with a note for airport security), chest waders, rubber gloves, hooks, chains and heavy machinery with trained operators. The heavy machinery ideally includes an excavator, for pulling the animal apart and digging a hole, and a front-end loader, for moving the animal and parts of it around, as well as filling the hole.

"If you don't have the machinery it can take days and days, you may never finish," the necropsy and bury the whale, he said.

Overall, his crew typically includes eight or nine people.

A 1-year-old female right whale was spotted in July 2002 near Nova Scotia with lobster gear caught just above her flukes. After she was later found dead, an investigation concluded that a deep laceration by the gear had killed her. (Image credit: From Diseases of Aquatic Organisms 96:175–185, 2011, used by permission of the publishers.)The suspects

The deaths that most concern Moore are those caused by humans, specifically, by collisions with boats or fishing gear that entangles the whale.

Sometimes the cause is obvious. A ship's propeller can leave slices on a whale's body. In one case, a whale found floating near Jacksonville, Fla., had obvious propeller cuts down one side of its body, including into its chest.

"When the animal was pulled up the beach, you could hear gas coming out of the chest," Moore said.

The blunt trauma of a collision with a boat can be less obvious, while entanglement in fishing gear can be more obvious, or not.

Information about why whales die matters because many whale populations are small and vulnerable.

Right whales, a species of particular interest to Moore, were estimated in 2007 to number at least 396 in the western North Atlantic; they are one of the most endangered large whales in the world. Ship strikes and entanglements with fishing gear are believed to be holding back the right whale population's growth and recovery, according to the U.S. National Oceanic and Atmospheric Administration's 2011 stock assessment.

The necropsy

After inspecting the whale externally and taking measurements, Moore and his crew measure the thickness of its insulating fat, or blubber, which they strip off by hooking the blubber to a chain attached to the bucket of an excavator, to "unpeel it like a banana," he said.

Once the blubber is off, the team peels away the now-exposed muscle, getting down to the chest and abdomen, where they remove ribs and examine the animal's organs — if they haven't already decomposed.

Moore can't explain what a decaying whale smells like; he lost his sense of smell in veterinary school, because of exposure to formalin, a preservative made with formaldehyde. But rather than an advantage, this is a problem, he said: "I think a good sense of smell is a valuable diagnostic tool, so I regret not having my sense of smell." [The 10 Weirdest Animal Discoveries of 2012]

During this process, the investigators are looking for abnormalities, such as bruising, often accompanied by fractured bones. These are common signs of a boat collision.

Evidence of a fishing gear entanglement may be obvious — for instance rope, net or other gear still attached to the animal — but sometimes these are gone.

The whale may have lost the gear over time or fishermen may have removed it in the hopes of salvaging the gear, Moore said.

One humpback whale he examined had obviously been in a trawl net, yet only a small knot of twine in its mouth remained.

A male right whale, at least 19 years old, was found in Quebec with nearly its entire body entangled in filament rope. Investigators suspect the whale drowned because of the extent of the entanglement. (Image credit: From Diseases of Aquatic Organisms 96:175–185, 2011, used by permission of the publishers.)A slow death

Particularly agonizing stories can show up in the entanglement deaths.

Right whales that pick up gear meant for lobsters or humpbacks that catch herring trawl nets can survive for months. The gear — depending on where it has become attached — can kill in a variety of ways, Moore and colleagues describe in a review article published in the Journal of Marine Biology earlier this year. It can drown a whale; if caught in the whale's mouth, the gear can starve the animal; it can exhaust them by creating drag; it can cause injuries that can lead to infection and loss of blood.

In the review, Moore and graduate student Julie van der Hoop label these long-lasting whale entanglements "cruel" in their article.

"I think any animal on this planet, especially the more cognitive, higher sentient beings have a right to be as pain-free as possible, and when human activities cause wild animals to be in pain I object to that," Moore said.

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