Earlier this week, documents were passed to the news media, including Nature, that link the global-warming sceptic Willie Soon, a researcher at the Harvard-Smithsonian Center for Astrophysics (CfA) in Cambridge, Massachusetts, to funders in the energy industry and conservative circles.

The files include research contracts and year-end reports, and provide new details on the kind of“deliverables” that Soon was providing for his funders. The group that released them, the Climate Investigations Center in Alexandria, Virginia, raised legitimate questions about whether Soon had properly disclosed this funding to journals that published his work. The CfA has responded by launching an investigation.

Willie Soon has been a poster child for the small community of climate-change sceptics for more than a decade. Environmentalists and other watchdogs have examined and exposed his industry funding countless times. Unknown until now were the explicit details of the strings that come with such funding. In some cases, these strings included requirements that Soon show copies of proposed publications to Southern Company, a major electric utility that has given him nearly US$410,000 since 2006, for input before publication. The company did not have the right to require changes, but another provision prevented Soon and the CfA from revealing its involvement without prior notification. This is troubling indeed.

Many scientists receive funding from industry as well as from foundations. Private money for science can often have an agenda, and this is why transparency matters so much. (Global-warming sceptics say that government funding has the same taint, but this comes with an assumption of disclosure.)

CfA director Charles Alcock said that agreeing to provisions to limit disclosure was a mistake, and one that the centre will not repeat. Although it has no explicit rules on disclosure, the centre does expect scientists to follow the publishing rules that journals set out.

One thing does not add up. The CfA, after all, is launching an investigation into one of its own staff members on the basis of the evidence of its own documents, but only after it was forced to hand them to an environmental group under a Freedom of Information Act request. Whether or not Soon fully disclosed the source of his funding to all of the journals remains unclear, but the basic facts were always there.

Alcock says that his job is to protect academic freedom at all costs. Fair enough. But freedom comes with responsibilities.