FORTUNE -- In the early 1990s, when Michael Mann was at Yale working on his Ph.D. in the geology and geophysics department, he became fascinated with theoretical climate modeling. By studying data inferred from ancient sources like tree rings and coral and ice cores, he could understand natural fluctuations in climate over the eons. Mann envisioned a quiet career in the halls of academe. In 1995 he made a big splash in paleoclimatology with his co-publication in Nature of -- wow! -- "Global Interdecadal and Century-Scale Climate Oscillations During the Past Five Centuries." So what's a nerd like him doing at the center of a raging debate over academic freedom? "I had absolutely no idea what I was bargaining for," Mann told Fortune.
Based on his research, Mann, 44, became a leading global-warming scholar, first at the University of Virginia and now at Penn State. The data, he declared, were irrefutable: Human activity has caused rising temperatures -- particularly in recent decades -- and could one day imperil life. Fossil-fuel companies and other doubters have long challenged the certitude of such conclusions, and global-warming deniers often single out Mann as a scientist with a political agenda.
The skepticism gained widespread media attention last November when hackers publicized hundreds of e-mails among prominent climatologists, including Mann. Global-warming deniers said the stolen e-mails demonstrated climatologists were willing to manipulate evidence. CLIMATEGATE! proclaimed uncreative headline writers. Yet despite the smug, petty opinions expressed in some e-mail, five review panels cleared the climatologists of unethical conduct. In Mann's case, the attorney general of Virginia had even charged that he'd defrauded taxpayers in obtaining nearly a half-million dollars in grants while at UVA. Several weeks ago a judge dismissed those civil charges, which the state plans to refile.
Mann says the AG's investigation represents a "witch hunt" that is the predictable culmination of efforts by "vested interests" to attack not only science but scientists. He says the threat to the academy isn't theoretical and knows of graduate students who've decided to steer clear of research in global studies for fear of controversy. Others in climatology never list their home addresses and have bodyguards at public-speaking events. Mann himself says he's had to contact law enforcement over harassing e-mail and snail mail; read one: "I was hoping I would see the news that you'd committed suicide. Do it, freak."
There's no excuse for that kind of implicit threat. It's hard to forget that the acts of the Unabomber maimed professors. And McCarthyism proved that mere words could jeopardize academic freedom. But it's wise to remember that demonizing scientists is nothing new. Charles Darwin published On the Origin of Species 151 years ago. Six decades later the Scopes trial was a national spectacle, and evolution remains a target for opportunists who can't distinguish between religion and fact. Even so, most of us are wise enough to recognize that creationism isn't a danger to science. "I used to believe that truth would prevail in the public discourse over climate change," says a frustrated Mann. He ought to have a bit more faith.