I was looking for a group project for a new investigative reporting class for undergraduates that I would teach in spring 2011. I had already begun looking at the pharmaceutical industry's influence on clinical trials when ProPublica published its "Dollars for Docs" database.

Thanks to a series of court cases around the nation, a handful of drug companies were being forced to reveal payments they were making to physicians. ProPublica collected the drug company's publications—which were hard to find and even harder to extract data from—and put them in an easy-to-search database. It was meant not only to be a consumer resource (you can look up your doctors to see if they're on the take) but also to be a resource for investigative journalists looking into physicians' practices.

I realized that the database could be used to find direct payments from drug companies to scientists; as most clinical researchers are physicians, payments to researchers from certain big pharmaceutical manufacturers should be listed in the database.

In my journalism class at New York University we decided to use the database in two ways: First, we would look for payees on the list who happened to be National Institutes of Health advisory committee members. This would give us a little insight into money flowing to decision-makers at NIH. Secondly, we would join a small section of the database (payees in New York State; the whole database was too much for us to handle) with a publicly available database of NIH grantees. This would give a sense of how much money was flowing to individuals who were also taking government money to perform biomedical research.

My students—including Hoon Bae, Randy Kreider, Allan Kustanovich, Veronika LaRocque, and Farzana Zaman—did the heavy lifting of joining and cleaning up the databases.

People on these lists haven't necessarily done anything wrong. Many of these payments don't pose conflicts of interest. For instance, if someone takes money from a company yet doesn't do research related to that company's interests, then it might not be a problem. Also, if people are open and up front about whom they're taking money from—if they're telling their institutions or NIH about their consulting arrangements—they've done everything that they're obliged to do. But an essential job of watchdog journalism is to make sure that everybody's playing by the rules.

When looking through the list of NIH grantees, my eye was drawn almost immediately to Felicia Cosman and Robert Lindsay. Here were two researchers taking enough money from Eli Lilly to put them near the top of the list and who were working at the same institution, Helen Hayes Hospital, and publishing papers together. A quick look at their NIH grants showed that they were doing research on teriparatide, which is marketed by Lilly. Here was the appearance of a possible conflict of interest.

When applying for an NIH grant, an institution is required by federal regulations to ask investigators about financial entanglements—and when a conflict is identified, the institution had to reduce, manage or eliminate the conflict. (The wording of the regulations changed slightly as the investigation was underway.) I set out to find whether the law was being followed as required.

The obvious question was whether Lindsay or Cosman had told Helen Hayes about their conflicts, and if so, whether Helen Hayes had told NIH and reduced, managed or eliminated that conflict as required. Answering this was difficult. I called Lindsay first, but didn't get a clear answer. Cosman refused to speak to me. Officials at Helen Hayes would not agree to speak to me either, nor would those at the grant management agency, Health Research, Inc. (HRI), after my initial contact. Working the other end, at NIH, I got an elliptical answer.

I next turned to the federal Freedom of Information Act (FOIA) and its New York State equivalent, the Freedom of Information Law. From NIH, I requested copies of the conflict of interest paperwork for three of Lindsay's and Cosman's NIH grants. From the New York State Department of Health, I requested the same paperwork as well as the researchers' financial disclosure statements and a number of other records.

NIH processed the FOIA relatively quickly. The results are hard to understand, but they gave me confidence—although not certainty—that HRI and Helen Hayes had not told NIH about any potential conflict of interest with those grants. New York State, however, was not forthcoming. It gave a substantial response a year later, and then only after I had sent a strongly worded appeal, which would have been my precursor to a lawsuit. The documents they sent confirmed that there were no conflicts of interest declared with the grants in question. They also revealed the institutional review board meeting that my investigation had apparently triggered.

NIH advisory committees
I suspected that NIH was not obeying federal regulations when it came to conflicts of interest on its advisory committees. Proving this would be difficult, however.

In the law prohibiting government officials from participating in matters in which they have conflicts of interest, there's a special provision for advisory committee members: If an agency official certifies in writing that the need for an individual's services is so great that it outweighs the potential for a conflict, then the member can serve on the committee in a limited capacity. These certifications, known as 208(b)(3) waivers, are supposed to be made available to the public. But when I used FOIA to request these documents (as well as several other documents related to how NIH manages conflicts of interest), NIH refused to turn them over—not even redacted versions—as they're required to do by law. I appealed, and when the agency didn't respond in a timely manner, I sued in federal court.

In the decision, which came in June, the judge, Gabriel Gorenstein, ordered NIH to turn over the waivers, but allowed the agency to protect other documents, known as recusal lists, from public scrutiny (although they had to turn over redacted versions of the lists during the course of the litigation). This was a bittersweet victory.

The waivers showed that the vast majority of financial entanglements my class and I identified were not declared on the waivers I obtained, which suggested that NIH was being less than diligent about identifying conflicts of interest. NIH insisted, however, that the missing entanglements had been declared on the recusal lists that it refused to reveal. In the course of trying to convince me of the truth of that statement, an NIH official revealed that it had not released several of the recusal lists I had requested.

Although the documents were highly suggestive (as was the lack of waivers for a number of individuals who probably should have gotten them) on their own, they did not constitute proof that NIH had been overlooking conflicts of interest.

The Office of Government Ethics is the agency in charge of setting the ethical standards of executive branch personnel. Every time an agency like NIH issues a 208(b)(3) waiver—except under "all but the most exigent circumstances"—it is required by federal regulations to consult with OGE about the waiver. I put in a FOIA request for records of any such consultations from NIH. Despite producing a number of consultation records, including one with NIH about a different kind of waiver, OGE was unable to substantiate a single instance between 2005 and late 2011 where NIH consulted with OGE regarding a 208(b)(3) waiver as required. When I asked NIH to provide evidence that it was consulting with OGE, NIH refused to do so.

Investigative journalists are familiar with all the techniques my class and I used to write this story. We figured out how to use existing data in new ways, as we did with the Dollars for Docs dataset, to generate leads for story ideas. Then, once we had those leads—the list of grantees and advisory committee members taking money from big pharma—we chased down documents that could help us figure out what was really going on. The answers we got were worth the effort.