Daniel Everett looks and talks very much like the middle-aged American academic he is - until he drops a strange word into the conversation. An exceptionally melodic noise tumbles from his mouth. It doesn't sound like speaking at all. Apart from his ex-wife and two ageing missionaries, Everett is the only person in the world beyond the sweeping banks of the Maici river in the Amazon basin who can speak Pirahã.

Just 350 Pirahã (pronounced Pee-da-HAN) hunt and gather from their simple homes in the Brazilian rainforest. Linguists believe their language is unrelated to any other; racist Brazilian traders say the Pirahã talk like chickens. This obscure Amazonian people speak using only three vowels and eight consonants (including the glottal stop) but their language is far from simple. Like Chinese, for example, Pirahã is tonal and speaking in a different pitch transforms the meaning of a word. Unlike other tonal languages, Pirahã can also be hummed and sung.

The Pirahã have no socially lubricating "hello" and "thank you" and "sorry". They have no words for colours, no words for numbers and no way of expressing any history beyond that experienced in their lifetimes. And, in the late 70s, Everett was dispatched to the Amazon to learn their language, translate the Bible and convert them to Christianity.

The idea that we can be enlightened or destroyed by living with exotic people has transfixed western societies since before Joseph Conrad's rogue trader Kurtz was corrupted in the Congo. Yet Everett's life could be a more dramatic example of enlightenment and destruction than any fictional encounter with a drastically different culture. Thirty years living with the Pirahã destroyed his evangelical faith in God, wrecked his marriage and estranged him from two of his three children. It also dismantled his intellectual framework and set him on a collision course with one of the most influential intellectuals in the world. Today, he is continuing his fight with Noam Chomsky in a debate that could transform our understanding of human language.

Everett is taking a working break from his professorial duties at Illinois State University when we meet in London. He grew up in a "redneck" home on the Mexican border. His father was a cowboy but Everett developed an interest in language after mixing with Spanish speakers at school. He was "pretty heavily into drugs" in 60s California, he says, until he met Keren Graham at high school. She had spent her childhood with her missionary parents in the Amazon; Everett was converted. "I credit religion with getting me out of drug culture," he says.

He and Graham were married at 18 and had three children. After joining a missionary organisation and studying linguistics, Everett and his young family were dispatched to the Pirahã, where two other missionaries had spent two decades struggling to pick up the language and failing to convert any Pirahã. Everett's first visit ended when his wife and daughter nearly died from malaria, but he persevered, spending all of 1980 with the Pirahã and returning to live with them for four months or so every year for the next two decades. Despite close encounters with snakes and Brazilian traders who incited the Pirahã to kill Everett, the missionary/linguist befriended the Pirahã and painstakingly picked up their extraordinary language.

Everett's discovery of the elegant linguistic theories of Chomsky was his second conversion experience. At the time, Chomsky was not merely known for his trenchant, left-leaning political activism but was revered as the father of modern linguistics for his theory of "universal grammar". Following Chomsky's idea that humans are innately programmed to produce language according to a fixed and finite set of rules, Everett studied for a doctorate in the 80s and took advice from Chomsky. Gradually, however, as he spent more time with the Pirahã, he came to doubt Chomsky's claims of universality.

These doubts exploded three years ago, like "a bomb thrown into the party" in the words of psychologist and linguist Steven Pinker, who initially welcomed Everett's findings against Chomsky before becoming more critical. In 2005, Everett published a paper about the Pirahã that rocked the foundations of universal grammar. Chomsky had recently refined his theory to argue that recursion - the linguistic practice of inserting phrases inside others - was the cornerstone of all languages. (An example of recursion is extending the sentence "Daniel Everett talked about the story of his life" to read, "Daniel Everett flew to London and talked about the story of his life".) Everett argued that he could find no evidence of recursion in Pirahã. This was deeply troubling for Chomsky's theory. If the Pirahã didn't use recursion, then how could it be a fundamental part of a universal grammar embedded in our genes? And if the Pirahã didn't use recursion, then is their language - and, by implication, other languages - determined not by biology but by culture?

Thirty years of living with the Pirahã has taught Everett that they exist almost completely in the present. Absorbed by the daily struggle to survive, they do not plan ahead, store food, build houses or canoes to last, maintain tools or talk of things beyond those that they, or people they know, have experienced. They are the "ultimate empiricists", he argues, and this culture of living in the present has shaped their language.

Everett's claims created a furore. Chomskyites rushed to defend universal grammar and academics cast doubt on Everett's view of the Pirahã. Nineteenth-century anthropologists had judged exotic peoples similarly, saying they had no creation myths and apparently crude languages that could not count or convey abstract thought, before it was proved it was our erroneous understanding of these "primitive" societies that was primitive. "By framing his observations as an anti-Chomsky discovery rather than as un-PC Eurocentric condescension, Everett was able to get away with claims that would have aroused the fury of anthropologists in any other context," wrote the increasingly sceptical Pinker, who argued that even if there was "a grain of truth" in the Pirahã's preoccupation with the here-and-now, it was by no means unique to their society. In other words, Everett was an almost racist throwback to the days of, well, missionaries.

Yet Everett's life with the Pirahã didn't just cause a gradual disenchantment with the Chomskyan intellectual framework he had once cherished: it also triggered another, even more dramatic, de-conversion.

Soon after he first arrived in the Amazon, Everett was nearly killed when the Pirahã discovered he was ordering passing river traders not to give them whisky. The Pirahã were rarely violent, but intensely rejected any kind of coercion. Crucially, Everett came to see his religion as fundamentally coercive. His academic studies were ultimately designed to help him translate the Bible into Pirahã. When they heard the word of God, his evangelic mission believed, they would be converted. Everett translated the Book of Luke, read it to the Pirahã and they were utterly unmoved. By 1985, he had privately lost his faith.

"It's wrong to try and convert tribal societies," he says. "What should the empirical evidence for religion be? It should produce peaceful, strong, secure people who are right with God and right with the world. I don't see that evidence very often. So then I find myself with the Pirahã. They have all these qualities that I am trying to tell them they could have. They are the ones who are living life the way I'm saying it ought to be lived, they just don't fear heaven and hell."

His wife, Keren, and three children were all "committed" Christians. Extraordinarily, Everett couldn't tell them of his loss of faith until the late 90s. "I kept hoping that I might get my faith back," he says. He likens telling his wife to coming out as gay. "I said, 'I just can't do this any more, I can't pretend, I don't believe this stuff.' So she immediately called the kids to tell them. It was just such utter shock and revulsion." Did they feel betrayed? "Yes, they felt betrayed. My youngest daughter said, 'Were you a hypocrite the whole time you were raising us? Did you teach us to believe one way, which you never believed?' I did believe. I had a genuine, sincere conversion experience. I was quite a successful evangelist. I've had people write to me and say, 'Gee, I'm a Christian because of you and I hear you're not a Christian, that's shocking to me.' I don't take these things lightly but that's who I am. I can't change it."

Murder is rare among the Pirahã. The only punishment they regularly practice is ostracising members of their society. It seems a bitter irony that Everett's loss of faith caused his ostracism not from the Pirahã, but from his own family. His marriage broke up. "After a couple of months I tried to get us back together and she said, 'Only when you come back to religion will I even consider it', and I said, 'Well, then it's over.'" Two of his grown-up children, Shannon, a missionary like her mother, and Caleb, an anthropologist like his father, cut off all contact. Three weeks ago, after the death of a close friend, they got back in touch for the first time in years. "Now they are coming around." An almost imperceptible tremor registers in Everett's voice. "Maybe I'm coming around. We're approaching one another and realising the most important thing is love."

Everett, who has remarried, has not visited the Pirahã since January 2007. It has been his longest period apart from them. Occasionally, his ex-wife, who is still pursuing her missionary work on the banks of the Maici, will put them on the satellite phone. "I know they are not understanding why I haven't been there," he says. But it is difficult to return with his ex-wife there. "There will always be tension," he says. "She believes that if the Pirahãs reject the gospel it's because it hasn't been communicated clearly. I believe it has been communicated clearly and they reject it because it's utterly irrelevant." It's almost tragic: Keren's beliefs impugn Everett's competence; Everett's findings attack her entire belief system.

For academics rushing to the defence of the Chomskyan model there is another problem: Everett is the only linguist in the world who is fluent in Pirahã and virtually the only academic to have gathered data on the language. It must be hard not to feel possessive over the Pirahã, but Everett claims he wants academics to go there and test his theories. He just doesn't want to be dragged along to do translation work for them.

Despite challenging the linguistic theories he once followed, Everett insists he still has "tremendous respect" for Chomsky. "I'm not denigrating his intelligence or his honesty but I do think he is wrong about this and he is unprepared to accept that he is wrong."

Everett hopes his story of his life with the Pirahã will demolish charges that his account of their society is crude and politically incorrect. "If you can find evidence that I am making 19th-century claims, I will be shocked and disappointed in myself," he says. "If anything, they are superior in many ways to us. Thinking too much about the future or worrying too much about the past is really unhealthy. The Pirahã taught me that very lesson. Living in the moment is a sophisticated way to live. I don't see depression. I don't see some of the things that afflict our society - and that's not because they don't face pressures. People who claim that I'm Eurocentric and putting these people down need to read the book and decide for themselves."

The Pirahã population has climbed back to 350 after a measles epidemic is believed to have reduced it to around 100 in the 50s. They have had contact with traders and missionaries for 200 years and have proved remarkably resistant to change. They live on a 300,000 hectare reservation, which is reasonably secure, says Everett. So far, at least, no precious minerals have been found in the area as has happened elsewhere in the Amazon, bringing miners, deforestation, pollution and disease.

Everett, however, is pessimistic about their future. Missionaries and government officials see Pirahã society as poor and seek to help by giving them money and modern technology. "The Pirahã aren't poor. They don't see themselves as poor," he says. He believes capitalism and religion are manufacturing desires. "One of the saddest things I've seen in Amazonian cultures is people who were self-sufficient and happy that now think of themselves as poor and become dissatisfied with their lives. What worries me is outsiders trying to impose their values and materialism on the Pirahã."

I wonder whether Everett feels grateful for his life with the Pirahã or scarred by it. "It has been a traumatic experience," he says. "There is a lot of good and there has been a lot of pain. There are times when I think of the Pirahã with great nostalgia and want to be with them and there are other times I think I am really tired."

He hopes to return next summer to help a BBC/HBO documentary and continue his research, but only on the condition that the visitors do not disrupt the Pirahã. What does he miss the most? "I miss the evenings. After I've gone down to the river to have a bath, I would make coffee for everyone in the village. We'd sit around on logs out in the open and wait until the night fell, and talk. They are just an incredibly peaceful, sweet people to be with. The time spent talking to them, these will always be the best memories I have".

• Don't Sleep, There Are Snakes by Daniel Everett is published by Profile Books, price £15. To order a copy for £14 with free UK p&p go to theguardian.com/bookshop or call 0870 836 0875.