In the first moments of José Padilha's Secrets of the Tribe, about the anthropologists who study the Yanomami, we learn exactly what the observed think of the observer: "You Nabäs are always such liars," says one tribesman. "I don't like to believe anything you say because you always lie." After watching this 96-minute film that documents a "he said-he said" war of egos fought among ethically dubious anthropologists on opposing sides of a theoretical debate that includes accusations of genocide and pederasty, it's hard to disagree.

Insulated by the dense rain forests along the border of Venezuela and Brazil, the Yanomami became known to the outside world as vicious and fearsome after the publication of American anthropologist Napoleon Chagnon's groundbreaking study, Yanomamö: The Fierce People. Released in 1968, it describes the tribe, thought to have descended from the Asians who first crossed the Bering Strait, as warring over women and celebrating in hallucinogenic frenzies.

The data Chagnon collected for his book and the films he made with Timothy Asch seemed definitive evidence in support of biological determinism, which purports that genes and the evolutionary imperative to pass them on are the primary forces that shape human culture. Chagnon had made his career, and his rise in academia only cemented the Yanomami's reputation as "Fierce People." The book became de rigueur in Anthro 101 courses on campuses around the world and has since been reissued in five editions, selling more than four million copies. It was also a herald to other anthropologists and scientists who beat a path to the jungle in order to gather their own data among the last unacculturated peoples in the world--data that paint radically different pictures of the Yanomami.

In Secrets of the Tribe, Padilha interviews an entire roster of Who's Who in American Anthropology to explore the controversy that first entered the mainstream with Patrick Tierney's November 2006 New Yorker article, "Fierce Anthropologist." Tierney's book Darkness in El Dorado: How Scientists and Journalists Devastated the Amazon, published that same year, is a dense catalogue of unethical and illegal actions perpetrated not only by Chagnon, but also by his colleagues: Dr. James Neel, a geneticist doing research for the Atomic Energy Commission; Venezuelan naturalist Charles Brewer Carías, who had ties to gold-mining interests; and Collège de France's respected linguist Jacques Lizot, who traded goods for sex with Yanomami boys. Also revealing how governments, fellow academics and missionaries cast a blind eye toward these atrocities, the book landed like a bomb and blew up an entire discipline.

 "Mike Chamberlain [of Britain's Stampede Films] took Tierney's article to Nick Fraser at BBC, and Nicky called me," says Padilha, whose Bus 174 was a big success for BBC Storyville back in 2002. When I spoke with the Brazilian filmmaker in April 2010, he was fresh from the opening-night screening of Secrets of the Tribe at the Rio version of It's All True, Brazil's 15-year-old documentary festival. He was also in the midst of post-production on his sequel to Tropa de Elite (Elite Squad), a fiction feature about the take-no-prisoners police force that is attempting to wrest control of Rio's slums from entrenched drug lords. When I ask why he chose to make Secrets, his answer is surprising: "Because I love science."

A student of math and physics, Padilha turned to filmmaking after a brief, unsatisfying career in banking. Since producing 1999's The Charcoal People under the wing of Oscar-winning documentarian Nigel Noble, Padilha and his production partner Marcos Prado have made several films together, acting as producer on each other's projects. In his documentaries, Padilha takes an aesthetic approach called for by the material. To reconstruct the tragic life story of the hijacker of a Rio city bus in Bus 174, he used the plentiful news and amateur footage taken at the scene, which was badly managed by local authorities. Garapa, his 2009 documentary about the effects of chronic hunger on three families in Brazil's arid northeast, was shot cinema vérité style on black-and-white 35mm film and finished without music. The Golden Bear-winning Tropa de Elite would have been a documentary, if, as Padilha told me in a 2009 interview, he didn't fear for his life. For Secrets of the Tribe, Padilha knew immediately it would primarily consist of talking heads, with each scientist and the surviving Yanomami having their say.

To interview the Yanomami, Padilha did what those before him had done: He paid them. "Everything is trade with the Yanomami," he explains. How did he get Chagnon to willingly revisit the allegations that forced the embattled anthropologist into early retirement? "I say I am making a film about science," Padilha explains. "Everyone thinks they are the good scientists and everyone else is doing bad science.

"The methodology of anthropology is flawed," Padilha continues. "Each anthropologist finds exactly the evidence to fit his paradigm. To destroy the data you have to destroy the person. Who cares how you feel about Einstein? Take his data to the lab and see if what he says holds up. No one ever said that about Einstein, but you get my point...Chagnon doesn't agree with Ken Good, so he says, ‘Oh, he married a teenager.'"

The cavalcade of bickering eggheads that Padilha created in the editing room is riveting, sometimes even funny. The interviews with the Yanomami, who describe entire villages of people dying, sexual abuse and the havoc wrought by anthropologists who traded information for steel axes and machetes, create a cumulative effect that can only be described as heartbreak. Watching archival footage of Yanomami: A Multidisciplinary Study (1968) and The Feast (1970), both shot by Asch during the joint Neel-Chagnon study on a measles vaccine, we learn that most of the people on film died shortly thereafter.

Pieces of Jean-Pierre Marchand's collaboration with Jacques Lizot, Les indiens Yanomami (1968), stands in for Lizot, who declined Padilha's request for an interview. (He is now sought by French police on an unrelated molestation charge and is thought to be in Morocco.) "The film is very candid on Lizot, yet I did not touch the surface of what he did," says Padilha. "The French injected the Yanomami with radioactive isotopes. The French side is much uglier than it looks in the film."

The French arm of ARTE is one of the co-production partners on Secrets of the Tribe and, it turns out, protective of Jacques Lizot and the Collège de France, where Lizot's mentor Claude Lévi-Strauss was chair of social anthropology. ARTE asked Padilha to put Lizot's pederasty in context. "Many of these [commissioning] editors come from liberal arts, anthropology backgrounds," says the filmmaker. "No one thinks about the kids." For his part, he sent the filmed testimony to Interpol in Brazil, which sent it on to France. "Lizot can be active somewhere right now," he notes. "When I showed [the footage] to the French, they didn't even consider this. If Lizot had molested French boys? Yanomami kids are far away. They intellectualize it as somehow excusable."

Anthropologists behaving badly is nothing new. Franz Boas, the father of American anthropology, asked Arctic explorer Robert Peary to bring him back "a middle-aged Eskimo, preferably from Greenland," for the American Museum of Natural History's live dioramas. Within eight months, four of the six Inuits Peary delivered had died of tuberculosis. Congolese pygmy Ota Benga lived at the museum and later at New York's Bronx Zoo before killing himself. Ishi, the last of the California Yahi Indians, lived at the University of California's Museum of Anthropology, and some of his remains were shipped off to the Smithsonian. Robert Flaherty--whose Nanook of the North unleashed a controversy in ethnographic filmmaking that continues today--fathered an Inuit son he later refused to acknowledge, or help. Even the ethically meticulous Margaret Mead admitted to having considered a sexual affair with one of the Samoans she was studying.

Today, anthropology is going through another round of soul-searching. Barbara Rose Johnston, who saw Secrets when it premiered at the 2010 Sundance Film Festival, invited Padilha and his film to the American Anthropological Association's annual meeting, held in November in New Orleans. "I think it is a trap," Padilha joked back in April. "Maybe they will try to kill me." The film, minus its director, became part of a panel exploring the ethics of the discipline and, in a move that cannot be coincidental, the AAA decided to drop the word "science" from its statement on long-range plans. "The thing is, I think that biology has a lot to do with behavior," Padilha says." But the science is clumsy. Chagnon is an embarrassment to sociobiology. This film will help that."

No matter how anthropology decides to settle its debates, it is clear from the film that the Yanomami reached a verdict long ago. "Look here, they are taking my picture again," one man points at Padilha's camera. "You should be ignorant of us."

Secrets of the Tribes airs March 2 on HBO. The film is distributed in the international broadcast market through Sideways Film, and in the worldwide educational market through Documentary Educational Resources, which also distributes Timothy Asch and Napoleon Chagnon's Yanamamö Series, including The Feast and Yanomami: A Multidisciplinary Study.

Shari Kizirian currently lives in Rio de Janeiro.