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This month, National Institutes of Health Director Francis Collins seemed to shut down a noxious ethical problem. The agency released a 165-page internal investigation of an alcohol consumption study that had been funded mostly by beer and liquor companies. The study’s lead investigator and NIH officials were in frequent contact with the alcohol industry while designing the study, which, according to the postmortem, seemed predetermined to find alcohol’s benefits but not potential harms, such as cancer. In several email exchanges published in the report, NIH scientists seemed to joke about taking a drink every time somebody said “cheers,” which was a proposed acronym for their study. Collins ended the trial and promised to create new ethical boundaries for how NIH officials deal with industry.

But the intellectual corruption at our government research agencies runs much deeper, and this was only the latest scandal involving hidden corporate influence. I spent 3 1 / 2 years as a Senate investigator studying conflict-of-interest problems at the NIH and the research universities it funds. During that time, I found that the agency often ignored obvious conflicts. Even worse, its industry ties go back decades and are never really addressed unless the agency faces media scrutiny and demands from the public and Congress for change.

We know how corrosive financial conflicts of interest can be for scientific research. Tobacco companies famously funded studies to downplay the dangers of smoking, and similar bias has been found in research funded by pharmaceutical, chemical and pesticide companies. In early 2015, the New York Times reported that a scientist at the Harvard-Smithsonian Center for Astrophysics whom politicians cited to undermine arguments about climate change had been secretly paid by the fossil fuel industry. Two recent studies found that Coca-Cola sought to fund scientists who would shift discussion away from sodas’ role in obesity and instead blame lack of exercise.

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Officials with the NIH’s National Institute on Alcohol Abuse and Alcoholism (NIAAA) courted alcohol-makers for several years to fund the study now in the news. According to media accounts, the NIAAA’s director, George Koob, declined to fund research critical of alcohol advertising, and he appeared in a promotional video about company-sponsored research for Anheuser-Busch InBev, one of the study funders, according to several reports. Collins told The Washington Post that Koob had changed NIAAA priorities to focus on preventing underage drinking.

This is the second time this year that Collins has been forced to distance his agency from corporate funding. In April, the NIH announced that it would decline money from drugmakers to support a proposed $400 million research program to discover opioid alternatives or new medicines to treat addiction. Because the NIH cannot receive cash directly from industry, the money would have been routed through the FNIH, which Congress set up in 1990 as a firewall between NIH officials and corporate donors seeking to influence the research they fund.

But the foundation’s ability to protect the NIH against corporate influence is in doubt. In 2016, the House Energy and Commerce Committee’s minority staff found that the NFL had waged a campaign to influence NIH research on the link between football concussions and brain disease. The report concluded that the NIH “may have gone too far in attempting to accommodate the NFL” but generally praised the agency for not buckling to the league’s pressure. Instead, House investigators trained their ire on the foundation, saying it had “failed” in its congressionally mandated role to act as an intermediary. An FNIH spokesman disputed the Democrats’ report and said the foundation had strengthened its protocols to prevent inappropriate contact between companies and scientists.

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My first job on the Hill as a congressional investigator in 2007 for Sen. Charles Grassley (R-Iowa) was looking into problems at the NIH’s National Institute of Environmental Health Sciences. After receiving several phone calls from scientists complaining about management problems there, we began poring over documents. The Post eventually reported that the environmental institute’s leader was ignoring conflict-of-interest guidelines and trying to hide it.

Over the next three years, I spent hundreds of hours examining other problems at the NIH, sending dozens of letters to the director and generating close to 100 stories in the press about the agency’s lack of oversight regarding its grants. About 80 percent of the NIH budget is spent on grants to universities across the country; its rules require professors receiving these grants to disclose their ties to corporations. But we found that universities were flouting these rules and that the NIH seemed to not care. In one instance, the director came to Grassley’s office and said there was little he could do if academics broke the rules. I was ready for this argument and handed him a legal ruling noting that the NIH had the authority to halt grants.

Grassley had become interested in the topic in the 2000s after investigating Merck’s drug Vioxx — a painkiller tied to tens of thousands of heart attacks — and discovering that the Food and Drug Administration panel that approved it had been stacked with physicians with links to pharmaceutical companies. After the drug was removed from the market, the Journal of the American Medical Association published a study noting that Merck transformed peer-reviewed research into marketing brochures by ghostwriting studies for academics.

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When President Barack Obama picked Collins in 2009 to run the NIH, Collins met with me and two other committee staffers as part of his nomination process. But whenever I pressed him about the ethics matters we were investigating, he shifted the conversation back to all the great science he wanted to do if the Senate confirmed him. (Collins says that he has always taken conflicts of interest seriously and that the agency upholds high standards for publicly funded research.)

Indeed, it took many more months of committee pressure before the NIH began to work on new rules that would force academics and their institutions to post financial conflicts on a publicly accessible website. Then, weeks before the rules were finalized, leaders at several universities met with White House officials to weaken the requirements; to this day, universities do not have to post their professors’ ties to companies online.

It took a four-year journey with constant congressional pressure and negative stories in the press to get the NIH to reform rules that were potentially putting public health at risk. Halfway through the process, leaders at the Institute of Medicine briefed us about a new report finding that financial conflicts of interest were a huge problem in biomedicine that threatened the integrity of research, patient care and public trust in science.

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The NIH has always needed congressional pressure to deal with conflicts of interest. When the institutes first proposed conflict provisions in 1989, academics protested them as an undue burden, forcing officials to pass rules that were greatly watered down. (In one example, universities would self-report and police their own conflicts.) Then the NIH eased its ethics policies in 1995, allowing workers to consult with industry, supposedly to help the agency recruit top scientists. This led to a 2003 Los Angeles Times investigation that uncovered senior NIH scientists consulting for pharmaceutical companies; one researcher pleaded guilty to violating federal conflict-of-interest rules. After embarrassing congressional hearings led by Rep. Joe Barton (R-Tex.), the NIH was again forced to ban federal scientists from consulting for corporations.

A 2009 report by the National Academies of Sciences, Engineering and Medicine, a body that advises the federal government, was clear about the costs of financial conflicts to biomedical research. Still, corporate money continues to funnel through government bodies. Half the members of an NAS panel that produced a 2011 report on pain management had ties to companies that manufacture narcotics, including opioids, according to an investigation by the Milwaukee Journal Sentinel. A separate New York Times investigation in 2016 discovered that a National Academies staffer who helped choose the members of a committee on regulating biotech was simultaneously applying to work for a biotech nonprofit — and three people he suggested for the panel were on that nonprofit’s board. Many of the committee members he picked had undisclosed conflicts of interest with the biotech companies. The National Academies has revised its conflict-of-interest policies.

At the heart of the matter is money. As Congress has declined to spend more on research, many academics have been forced to collaborate with companies. At a 2012 Harvard Law School symposium, several university leaders and NIH officials discussed financial conflicts of interest. Harvard President Emeritus Derek Bok hinted at the problem: Financial conflicts have grown more pervasive, but university administrators avoid discussing how to deal with them, because they fear losing revenue. Only continued scrutiny of the NIH, by the public and Congress, will result in better transparency. Without it, we’ll reap more scandals, plummeting confidence in public science and potential harm to citizens.

Twitter: @thackerpd

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