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Depending on your politics, Virginia Attorney General Ken Cuccinelli II’s “fraud investigation” involving the climate-change research of the former University of Virginia assistant professor Michael Mann is either a witch hunt or a long-overdue assault on the Ivory Tower.

But Mr. Cuccinelli’s demand last month for a decade’s worth of e-mails and scientific work papers from Professor Mann’s former employer, UVa, should give comfort to none of us. A fundamental principle is at stake, often described in shorthand as academic freedom. More to the point, it’s the understanding that government will not without extraordinarily compelling reasons intrude on the process of scientific discovery. It’s a principle on which liberals and conservatives alike can agree.

The ill-advised investigation in Charlottesville transgresses a long-honored boundary, with implications that extend far beyond the Albemarle County courthouse where the university has filed a petition to block the subpoena. That is why I, along with other higher education leaders, scientists and scholars (including even some of Professor Mann’s scientific detractors), support the university’s legal battle.

The stakes are high. Academic freedom protects scholars of every stripe from government repression or retaliation, especially when they take on controversial topics and espouse unpopular theories. Throughout history, nations that protect academic freedom have strong institutions of higher education. Where academic freedom is weak, governmental power goes unchecked.

The matter concerns not just the academy but all of us as citizens. We know that a thriving, independent, intellectually diverse higher education sector is best able to produce the scientific discoveries and advances in knowledge that make society better. The process that leads to innovation involves dialogue. Scholars debate hypotheses, examine data, and scrutinize each other’s ideas.

At their best, the exchanges are blunt and unstinting: thus theories are criticized, refuted, honed, and improved. The free marketplace of ideas in which this exchange takes place is the best engine known to mankind for producing innovation while weeding out discredited hypotheses. Society has a strong interest in ensuring that scholars can engage in dialogue without the chilling threat of government intrusion.

History shows that when governments interfere, science is stifled, and society suffers. For his theory that the sun was but one of an infinite number of stars, the 17th century astronomer Giordano Bruno was burned at the stake -- setting back astronomical discovery by perhaps centuries. The Soviet government persecuted the plant geneticist Nikolai Vavilov for his contention that principles of genetics, not Marxist ideology, should inform agricultural policy -- while the Russian people starved. Here in the United States, McCarthy-era persecution chilled scholarship to the detriment of all.

Mr. Cuccinelli argues that he is trying to protect Virginia taxpayers from fraud. No doubt inquiry is appropriate in cases where there is real evidence of financial wrongdoing. But Professor Mann has been cleared of wrongdoing by numerous scientific and governmental bodies that have investigated Climategate. And the exceedingly broad “civil investigative demand” served on UVa sweeps in scientific papers and scholarly exchanges between colleagues -- exactly the kinds of exchanges that prosecutors should be chary to disturb.

What’s more, Mr. Cuccinelli, who is separately suing the EPA to block regulation of carbon emissions, has a legal stake in the climate change debate: he seeks to make the scientific validity of research like Professor Mann’s an issue in the EPA case. The attorney general’s positions, and the subpoenas themselves, have led many to question whether his investigation of Professor Mann is really about financial misfeasance, or whether it is about the politics of climate change.

Next month, an Albemarle County court is scheduled to hear the UVa subpoena case. If the attorney general’s request is granted, the chilling effect on important academic research will be felt at Thomas Jefferson’s university, throughout Virginia, and beyond. That prospect should give all of us pause, no matter whether our politics are blue, red or green.

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