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When a whale shows up dead on the beach or afloat at sea off Cape Cod, Massachusetts, biologist and veterinarian Michael Moore is one of the first on the scene. Armed with rubber boots, foul-weather clothes and an assortment of knives, he digs in to determine the cause of death before gulls, sharks and other scavengers destroy the evidence. Moore has conducted field necropsies on more than 55 whales, from a 2.5-metre beluga to a 17-metre immature blue whale, sometimes climbing into the body as it floats way out to sea. He’s even done it surrounded by dozens of blue sharks.

It’s a messy job, but someone needs to do it: the northern right whales that migrate along the east coast of the US are among the most endangered large whales in the world. There are fewer than 350 left, so when one dies, it’s important to know why. Moore’s research is helping to shape plans to address the whales’ two biggest killers: collisions with ships and entanglement with fishing gear. As he tells Carolyn Malkin, he is also working on new technologies for helping injured whales at sea.

What does a dead whale smell like?

It’s unique, and the different species smell different, depending on their mixture of oils. But I wouldn’t know, I lost my sense of smell in vet school. We were always leaning over tubs of animal carcasses preserved in formaldehyde. The more assiduous you were in sticking your face in to get a closer look, the more your nose got burnt by it. I burned out the sensory epithelium in my nose.

What happens to a whale’s body when it dies?

There’s a lot of bacterial decomposition inside, which produces gas. Very often the organs get rearranged. The largest orifice is the oral cavity, so most times the whale will decompress by way of an eruption of both the chest and then the abdomen through the mouth. Quite often you’ll find abdominal parts in the chest. At one time, we thought that was a sign that the whale had been hit by a ship, but it’s just from the pressure of the gas. We saw one right whale expel a fetus out of its mouth. It gets quite gruesome sometimes.

What’s the most challenging whale necropsy you’ve had to do?

A whale had washed ashore and travelled 16 kilometres down the beach. We stopped it with an anchor and line, and I had to climb down a cliff to get to it. I was trimming down the sample in the surf and was trying to get the peduncle, the muscular junction between the tail and the body, but the surf kept sucking this peduncle – which weighed 150 pounds – back out to sea while I was trying to get it onto the beach.

Most of the necropsies you do are on the beach, but you’ve also done some at sea. How is this different?

Those are samplings, rather than necropsies. Once, I went to look at 17 dead humpbacks out on Georges Bank. It was 35 °C and I landed on a whale in swimming shorts: you have to get onto them because a humpback is about 3 metres wide and all the organs are in the midline. Also in a swell it’s much easier to be moving in the same cycle as your target. People think I’m crazy, but you can’t do it any other way. I get on and cut it open from sternum to anus. It forms a sort of dugout canoe into which you can climb. The organs pop up at you.

Half of all right-whale deaths are caused by collisions with ships. How do you know whether this is what happened to a whale you’re studying?

We see fractured jaws, smashed skulls, broken vertebrae, broken ribs, bruised chests. It’s a random thing. Why right whales fail to get out of the way of ships is a mystery. They seem to be oblivious and may roll out of the way at the last minute. A graduate student in our lab is modelling the blunt force required to fracture a whale’s jaw. This should allow us to get a sense of what speeds, theoretically at least, are going to be lethal. It looks like the breaking point is a ship speed of 10 to 14 knots (18 to 25 kilometres per hour). Many long-distance cargo vessels and cruise ships are doing 20 knots (37 km/h).

Conservationists agree that if the deaths of just two females could be avoided each year, the northern right whales could begin to recover. How is it going so far?

Four right whales have already died this year: one adult that was too decomposed to examine and three calves. One was caught in a gill net, another had its fluke chopped off by a ship, and a third was struck by a ship. An unregulated fishery off Jacksonville, Florida, was closed down because of our necropsy of the one-month-old whale calf caught in a gill net. This was the first time a fishery was closed down as a result of a whale getting entangled in a net. It gave me a sort of grim satisfaction, but I didn’t feel good about putting 10 guys out of making a living.

How common is it for whales to get entangled in fishing lines and nets?

Seventy per cent of right whales exhibit scars from fishing gear. Most of them get out of the entanglement, but those that don’t suffer a horrible death. A whale hit by a ship is often killed within seconds, but a right whale entangled in fishing line can take up to six months to die. The most dangerous gear is any anchored to the bottom with rope in the water column: lobster traps, hagfish traps, crab traps, gill nets. The fundamental problem with fishing gear is there is so much of it. Fishermen can help by doing things such as avoiding floating loops between traps by using sinking rope.

Five years ago, I administered a sedative to a right whale at sea for the first time, when it had fishing gear deeply embedded in its flesh. Despite five attempts to disentangle it the whale, which we called Churchill, died three months later. Churchill was the first case of attempted chemical sedation, a method that could make it easier and safer for people to rescue whales from nets. We are talking with a ballistics company to develop a better, long-range drug delivery system.

Do you get any trouble from sharks?

I’ve had a couple of experiences with sharks. One was with a fin whale floating off Nantucket island. When the aerial survey found the animal, it was surrounded by hundreds of blue sharks 3 metres long. We tied the boat up to the whale like a raft and I used a flensing knife to pop it so it would flatten out and I could climb on. The sharks basically ignored me – there were no great whites, which might just jump out and grab me. There’s a definite risk here, but I guess it wouldn’t be such a bad way to go.

What has been your greatest contribution to whale conservation?

Probably the development of a 12-metre cantilevered pole that I first used with an ultrasound probe to measure a living whale’s blubber at sea. I had learned that if you stay at least 6 metres away, the whales appear to be less bothered, so I needed to invent a very long pole. The pole started with the blubber question, and it opened the door to delivering drugs, attaching digital tags to whales, and collecting blowhole discharge.