Scott Baker’s investigations of whale and dolphin DNA have taken him from Alaska’s humpback feeding grounds to the illegal marine mammal trade in Asia and an Academy Award-winning documentary. (Photo: David Baker)

For most Americans, eating a relative of Flipper or Keiko would be as unthinkable as dining on Lassie or Smokey Bear. But in some seafaring cultures, dolphins and whales are traditional foods, sold in supermarkets right alongside the fish fillets and beef cutlets.

The sale of meat from whales and dolphins accidentally drowned in fishing nets or left over from “scientific” whaling operations is allowed in some countries as “exceptions” to the international moratorium on commercial whaling. Trouble is, neither customers nor enforcers eyeing the packages of fresh or frozen steaks or stew meat can distinguish a minke whale taken in the scientific whaling program from, say, an illegally killed gray or humpback whale.

That’s where Scott Baker comes in.

The OSU conservation geneticist is one of the world’s foremost experts in using DNA to identify specific populations of cetaceans — whales, dolphins and porpoises — and thereby detect the unlawful sale of protected species. Baker travels frequently to Japan and South Korea, where he holes up in cramped hotel rooms in Tokyo or Seoul with his portable genetics lab, listening for a knock at the door. When the secret code is tapped out, he cracks open the door and a local collaborator, who has been covertly trolling grocery stores and sushi bars, furtively passes him a bagful of bloody meat for analysis.

This cloak-and-dagger science was documented in the Academy Award winning eco-thriller The Cove, in which Baker was cast (see sidebar).

“No scientist has contributed more to our understanding of cetacean genetics than Scott,” says Phillip Clapham, a cetacean scientist with the National Oceanic and Atmospheric Administration. “In particular, his innovative use of genetic analysis to detect and track illegal or unreported trade in whales and other wildlife has given scientists and managers a powerful tool to assess the extent of this traffic and its impact on populations. He’s been one of the major players in the field of whale biology worldwide.”

Catcher in the Bay

Height, as everyone knows, is an advantage in basketball games and presidential elections. But in marine science? Surprisingly, it can be — at least at New College of Sarasota, Florida. For a pioneering dolphin study launched while he was a student there, Baker’s 6-foot-4-inch stature gave him an edge over his shorter classmates. That’s because he could stand in the shallow waters of Sarasota Bay, his head well above the surface, while helping to use a seine net for the capture and release of wild dolphins.

“The researchers tended to enlist tall undergraduates for the hard work,” Baker says, laughing.

As a kid in Alabama, Baker vacationed on the Gulf Coast every summer with his dad (an electrical engineer and decorated veteran of Omaha Beach and the Battle of the Bulge) and his mom (an activist and humanitarian in the nuclear freeze movement and many other causes). “When you live in a place like Birmingham, the Gulf of Mexico is sort of like paradise — except for the mosquitoes and sand flies and jellyfish,” he says, grinning. The Gulf was where he first became intrigued by dolphins. But it was in that shallow Florida bay as he wrapped his arms around individual bottlenoses to process them for the study — weighing, measuring, tagging, drawing blood, taking tissue samples — where the animals etched a deeper impression on his psyche.

“Those kinds of things change your life,” says Baker, who left New Zealand’s University of Auckland in 2006 to become associate director of OSU’s Marine Mammal Institute. “How many people get to have an experience like that — capturing and releasing wild dolphins for a groundbreaking scientific study?” He adds, “We caught a lot of dolphins.”

Describing himself as “not terribly sentimental,” Baker nevertheless admits to being charmed by the joie de vivre of dolphins. Whales, on the other hand, are hard to relate to. He calls them “extremophiles,” a term borrowed from deep-ocean biologists who apply it to such exotic creatures as cold-seep tubeworms and giant hydrothermal vent clams — organisms that live in Earth’s most extreme environments. Not only have whales shed such basic mammalian characteristics as hind limbs during their evolutionary history, they can dive as deep as 5,000 feet, live as long as 200 years and travel as far as 6,000 miles during annual migrations.

“Whales are so alien,” Baker says. “They’re fascinating and magnificent animals, but it’s hard for us to imagine their world. Dolphins are much more like humans.”

Brain Train

During discussions of cetacean genetics, Scott Baker’s train of thought passes through a hundred switches, side rails and branch lines, diverging down one surprising aside after another. For him, everything in biology is connected to cetacean genetics.

Ask him about genetic diversity among whales, for instance, and he’ll tell you a story about cheetahs — a story with an Oregon angle, no less — from a Scientific American article that strongly influenced his early career. At Southern Oregon’s zoological park, Wildlife Safari, cheetahs were mysteriously dying of a common feline virus that causes only sniffles in housecats, suggesting a weakness in the big cats’ immune systems. The resulting gene-pool study by U.S. National Cancer Institute scientist Stephen O’Brien piqued Baker’s curiosity about the impact of genetic “bottlenecks” (large die-offs in a population caused by natural or human forces, such as the intensive whaling during the 19th and 20th centuries) on long-term species survival among the great whales.

Ask Baker about the human bond with wild animals, and he’ll engage you in an exploration ranging from the philosophy of Descartes to the methods of Jane Goodall to the quantifiable self-awareness of pigs, chimps, crows and (of course) dolphins. If you venture into the topic of evolution, you’ll dive with him into the Eve Hypothesis (the theory that all humans share DNA traceable to the emergence of Homo sapiens sapiens in Africa about 200,000 years ago), take a detour into Mendel’s peas, then veer from Darwin’s (mistaken) hunch that whales evolved from bears to the current scientific thinking: Today’s oceanic behemoths had a hoofed, hippo-like ancestor. If you’re still with him, you’ll careen around a hairpin turn, returning to the origins of modern humans to look in on the late pioneer of molecular evolution Allan Wilson of UC Berkeley, who discovered the “molecular clock” (using genetic mutations to date evolutionary changes).

Genes on Screen

By this point in the conversation, your brain will probably verge on overload. But Baker is just getting warmed up. As he talks, he frequently jumps up from his seat to scan his bookcase for a relevant article, or swivels to his computer screen to pull up a DNA barcode or digital map showing worldwide distribution of humpbacks, which he has studied since his years as a Ph.D. student at the University of Hawaii.

He’s at his most animated when talking about those early discoveries — such as one stunning, predawn revelation in a darkroom where he was developing “autoradiographic” images of humpback whale DNA. These were some of the first “DNA fingerprints” derived from small skin samples, which Baker had collected with a biopsy dart fired from an inflatable research boat in Southeast Alaska’s Inside Passage and Central California’s coastal waters, as well as in Hawaii and the Gulf of Maine. (Previously, whales and dolphins had been ID’d photographically by natural markings on their fins, flukes and flippers.) The finding he made that night in 1988 was a breakthrough in the just-emerging field of molecular ecology — using molecular markers for clues to relationships among individual whales and the ancestry of populations.

“I remember pulling out the first autorad that showed samples from feeding grounds in Southeast Alaska side-by-side with samples from California, and there was no overlap between the two populations,” he says. “All individuals from Southeast Alaska had one pattern, and not one individual from California had that pattern. It was like, wow!”

These population-level variations in DNA, which geneticists call “fixed differences,” pointed to ancient migration pathways swum again and again and again over tens of thousands of years. The black-and-white barcode he stared at that night supported his hypothesis that migratory routes from winter calving to summer feeding grounds had persisted for hundreds of generations — in other words, across evolutionary time. Biologists call this enduring continuity “maternally directed fidelity,” that is, patterns taught from mother to calf and reflected over eons in mitochondrial (maternally inherited) DNA, which scientists denote as mtDNA.

“This was one of the first discoveries we made using molecular methods,” he says. “What we were seeing in whales was a very distinct population substructure. The markers showed that despite their mobility, despite their ability to travel 12,000 miles roundtrip on each migration, these animals keep returning to the same place year after year, generation after generation. They don’t wander around. It was puzzling, because these aren’t terrestrial animals isolated by canyons and rivers and mountains — they’re out there in the ocean with no obvious barriers. Who would have thought the ocean would be so subdivided? Who would have thought whales would treat the ocean the same way bears treat their habitat, inheriting their mothers’ home range and returning there each year?”

Scott Baker was featured in "The Cove"

In the seaside village of Taiji, Japan, there’s a jarring juxtaposition: Jolly-looking tour buses shaped like happy dolphins putter up and down the streets by day, while by night fishermen secretly slaughter hundreds of panic-stricken dolphins in a nearby inlet and sell them as meat.

This sinister irony permeates the Academy Award-winning movie, The Cove, produced by the Ocean Preservation Society. Scientific adviser and cast member Scott Baker is delighted by the accolades, not because they widen his fame outside science circles but because recognition from the Critics’ Choice Movie Awards and the Sundance Film Festival means broader exposure for the movie, which critics have characterized as an “eco-thriller.” That, in turn, means more international pressure to end the carnage.

“There has been tremendous resistance to the movie in Japan,” says Baker, a leader in international efforts to uncover black-market trade in products from protected species of whales and dolphins. “The Tokyo International Film Festival initially turned down the film, but under pressure from American actors like Ben Stiller, they agreed to allow one showing outside the formal festival. The international press was relegated to the back of the auditorium.”

Baker, associate director of OSU’s Marine Mammal Institute, acts as the film’s scientific voice on dolphin biology and the health risks to humans who eat dolphin meat, which is high in mercury (mercury levels are concentrated in organisms that are, like dolphins, high up in the food chain). As the world’s first scientist to use DNA to identify whale species being butchered for human consumption, Baker appears in the movie both as an expert “talking head” and as a DNA detective, hunkered over a portable genetics lab in a Tokyo hotel testing samples purchased, covertly, in Japanese fish markets.

“We spent days filming in that hotel room — a room not much bigger than my office,” recalls Baker. He describes director Louie Psihoyos as “visionary but meticulous,” shooting “tons of film” to tell the story of the annual killing of more than 1,200 dolphins in Taiji.

Baker’s science-based scenes of DNA identification and his comments on the threat of mercury contamination in dolphin meat are a counterpoint to the movie’s main storyline: An intrepid team of cinematographers and activists (including the dolphin trainer of the 1960s TV series Flipper), wearing camouflage and night-vision goggles, risk arrest and even death to capture video and underwater acoustics during the slaughter.

Besides being a gripping piece of filmmaking, the movie highlights a heartbreaking issue of massive proportions: the international black market in wildlife. From elephant tusks and rhino horns to bighorn sheep antlers and panther pelts, the illegal trade in endangered animals is worth an estimated $5 billion to $8 billion a year worldwide. Cetaceans are lucrative commodities in that grisly enterprise. In Japan or Korea, for instance, a whale killed in coastal fishing nets can sell for more than $100,000 wholesale. Dolphins, too, bring in fat cash: Aquariums pay $150,000 for a live animal.

But it’s the dead ones that most worry Baker, a longtime delegate to the International Whaling Commission (IWC). Despite the IWC’s 1986 moratorium on whaling, Japan, Korea, Iceland and Norway continue the hunt, either under the guise of science or under an “objection” (basically, a rejection of the commission’s authority to regulate whaling). Loopholes in the commission’s 1986 moratorium, it turns out, are big enough for a whale to swim through — and die in. A “scientific whaling” loophole allows a limited number of whales to be killed for research and the remains to be sold. A “bycatch whaling” loophole allows fishermen to sell whales and dolphins that become entangled in fishing nets. Hundreds of protected animals die unreported each year because of the laxity of IWC rules and regs, Baker says. “The continued sale of ‘legal’ whale products acts as a cover for other illegal, unreported and undocumented hunting,” he argues.

Still, whales are afforded at least some measure of protection by the IWC. Dolphins, on the other hand, have none at all from the IWC or other international conventions (although many individual nations have outlawed dolphin killing).

Forensic genetics is a potent weapon in the fight to save wildlife. Baker’s technique — a method of quickly amplifying segments of DNA called a polymerase chain reaction (PCR) — is the same one used by crime-scene investigators to match “perps” to body fluids, hair and other tissue they leave behind. PCR is used for all sorts of investigations, from nabbing moose poachers to detecting cystic fibrosis in eight-celled human embryos. Indeed, Baker and his Ph.D. student Merel Dalebout were using PCR in 2002 when they discovered a new species of beaked whale, the first new whale species in 15 years and the first to be described primarily by DNA.