Last week, the oil company Chevron took out a full-page ad in the Atlantic Monthly to say – seemingly innocuously – that hydraulic fracturing, better known as fracking, needs to be "good for everyone". It was a part of Chevron's ubiquitous "Human Energy Campaign", which uses "real people" to soften its corporate image and argue its case.

The multinational is currently ramping up the PR to coincide with the release (also last week) of Promised Land, a controversial new film directed by Gus Van Sant and starring Matt Damon, which highlights the tactics used by drillers to buy up farmland that sits atop the vast Marcellus shale gas fields.

Chevron's ad in the Atlantic is co-signed by Bruce Niemeyer, a vice-president of the corporation and Radisav Vidic, a professor of environmental engineering at the University of Pittsburgh. Professor Vidic's office sits a stone's throw from the Chevron Science Center, a 15-storey state-of-the-art chemistry laboratory and teaching facility made possible by the philanthropically-minded corporation. I asked him if he saw any conflict in interest in signing an ad paid for by an energy company, when academics are expected to be impartial arbiters. He replied by email:

"I don't since I agree that the shale gas should be good for everyone or not developed at all."

Vidic believes that fracking is safe and says that there are only two scientifically documented incidents where underground water was contaminated. He told me that neither he nor the Swanson school of engineering (a division of the University of Pittsburgh) has received any compensation for his participation in the Chevron ad.

In addition to endowing science halls, Chevron and other energy companies have been sponsoring research on fracking at some of the nation's leading universities, including several in Pennsylvania, a hotbed of natural gas drilling. But the question is increasingly being asked: can these industry-funded studies be trusted?

Academia has typically been regarded as a "neutral umpire", according to Tyson Slocum the director of the Public Citizen Energy Program. He told me:

"Policy-makers have traditionally depended on university research to make tough decisions. But in the last two decades, we've seen an increasing advocacy role for corporations that try to sway regulators and public opinion with research of their own design."

A case in point. Last September, the Pittsburgh-based industry group, the Marcellus Shale Coalition, cancelled its funding of a Pennsylvania State University research project after two faculty members bowed out, citing bias in the study. An earlier Penn State report, also paid for by the natural gas industry, was used by Pennsylvania legislators in 2009 to kill a state tax on gas drillers. Sadly for the Keystone State, fracking created fewer than half the jobs that the industry-bankrolled study had predicted it would.

Big energy companies have always had a large presence on campus, sponsoring conferences and scholarships and funding research. But nowadays, this influence has been extended below the campus as well. In Pennsylvania, Governor Tom Corbett signed a bill recently that would allow drilling to take place on state university property. Not to be left behind, Ohio, Colorado and West Virginia have also begun leasing out their own hallowed educational ground for drilling (Texas has been doing so for years).

The organization Campus Progress reports that many universities see fracking as an opportunity to make up for budget cuts that have left the schools chronically strapped for cash. Drilling on campus gives a whole new meaning to "frackademia", a term coined to underscore the cozy ties between Big Gas and institutions of higher learning.

Most of the collusion between industry and our nation's universities, however, still takes place above the ground – albeit usually under cover. When that cover gets blown, heads roll.

Dr Charles "Chip" Groat took early retirement from the University of Texas at Austin after his financial ties to the industry became public. The researcher, whose study had concluded that there is "no link between hydraulic fracturing and water contamination", sits on the board of Plains Exploration and Production Company, a Houston-based fracker. Groat has received over $2m in cash and stock options from the company since 2007.

The State University of New York at Buffalo shut down its shale resources and society institute in November after "extensive ties" were revealed between its researchers and the gas industry. Kevin Connor, the director of the Public Accountability Initiative, a Buffalo-based nonprofit, said the closing of the institute "sends a strong message to the oil and gas industry that our universities are not for sale".

But the fact is, big corporations that can afford to pay for it have always pretty much dictated how research dollars get spent. Amy Mall, a senior policy analyst at the Natural Resources Defense Council, told me that this means that almost all of the scientific work on fracking is directed toward finding more efficient and cheaper ways of getting the gas out of the ground. Virtually none of the studies focuses on the critical environmental and public health effects.

Mall insists that we need truly independent research on all aspects of fracking's impact. But with fracking technology now largely unregulated, industry has little incentive to demonstrate scientifically that their drilling is safe. As she says:

"We just don't have the data."

One critical area where the data is inadequate is in assessing leakage rates. Natural gas is largely composed of methane, which is a greenhouse gas with 25 times the global warming potential of CO2.

The problem is that a significant amount of methane escapes into the atmosphere during the fracking process, and also later due to leaks from pipelines and from storage facilities. The journal Nature reported last week that studies in Colorado and Utah conducted jointly by scientists affiliated with the National Oceanic and Atmospheric Administration (NOAA) and the University of Colorado at Boulder, found leakage rates ranging from 4% and 9% – far more than the current Environment Protection Agency estimate of 2.3%.

If methane loss turns out to be as high as the initial NOAA studies suggest, it could mean that fracking is as bad, or possibly even worse, for the climate than burning conventional fossil fuels. It is too early right now to make that determination. The Environmental Defense Fund has partnered with academic and industry scientists to assess leak rates in other parts of the country. The first of three reports is due out in February.

The natural gas boom has been fabulously lucrative, injecting new life into the nation's flagging fossil fuel industry, and reviving rural communities with seemingly miraculous infusions of cash. The glut of cheap natural gas has also helped to cut US CO2 emissions to their lowest level in 20 years, as scores of coal-fueled power plants have switched over to the cleaner burning gas.

These clear benefits have made fracking a tough call for some mainstream environmental groups. Environmentalists are split between those who would like to see the natural gas drilling continue – albeit strictly regulated and restricted to safe zones – and others who see the gas boom as a disaster for the air and water, as well as a distraction of the real work of switching over to renewable energy sources like wind, biofuels and solar.

Public Citizen's Tyson Slocum calls the boom "a mirage", which will vanish once gas prices start rising above their current bargain-basement levels, as he says is sure to happen in the years ahead. With untold billions of dollars yet to be made from fracking, however, it is not going away any time soon.

What we can do, in the meantime, is make fracking safer and limit it to places where it won't poison vital aquifers. We will also need to cut harmful methane leaks to a minimum. To accomplish these goals, our universities will have to start conducting some demonstrably impartial research – for a change.