The annual meeting for the National Association of Science Writers got off to a heated start last October in Cambridge, Massachusetts. The first session centered on the knotty issue of ethics. According to several reporters in attendance, many in the audience voiced concerns about whether it is ethical for a reporter to take money from outside interests for travel, hotel expenses, or honorarium. Some attendees grumbled that fees for freelancers have remained stagnant for decades and when media companies don’t pay expenses, reporters miss out on stories. So what should be allowed.

Toward the end of the session, a veteran journalist went to the microphone and posed the following scenario: You’re reporting on a new paper finding that doctors think they can’t be swayed by gifts from pharmaceutical representatives, even though research shows physicians are in fact influenced by small gratuities such as pens. As part of your reporting, you go to lunch with a pharma representative, who then offers to pick up the tab. Is that okay?

Almost everyone in the room agreed that it was not.

While issues of journalistic ethics aren’t new, the debate has become contentious recently in the world of science journalism. One key reason is a push by industry to combat the labeling of foods made with genetically modified organisms (GMO). Advocates for labeling, who think coverage has been too favorable toward industry, have fought back by questioning the independence of journalists covering GMOs. In some cases, they’re using FOIA to expose scientists whose ties to Monsanto have not been disclosed by the media.

In recent months, several outlets, including the Washington Post and the magazines Science and Nature, have faced complaints from labeling proponents arguing that journalists have had their expenses or speaking fees paid by parties with a financial or ideological interest in pushing GMO technology. In each case, the outlets batted back complaints and stand behind the reporting.

Reporter Brooke Borel freelanced a piece for Buzzfeed on GMOs, focusing on a professor who had his financial ties to Monsanto exposed by a FOIA filed by a pro-labeling organization. In that piece, she wrote about her attendance at a biotech conference, adding a parenthetical disclosure that the conference organizers paid her travel expenses. Borel followed this piece with another at Popular Science, where she delved into the ethics of this disclosure. Because the funding came in part from industry, she decided to allow her expenses to be paid but declined the honorarium after consulting with several journalists and her editor at Popular Science.

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Distilling the range of opinions she received, Borel wrote: “Don’t take the honorarium. Do consider the travel money. It isn’t money going into your pocket, which limits the potential COI, and you can do some good by being there, both to present your views on the panels you sit on and to bring back valuable information for your readers. And if you ever write about the conference: Disclose that money clearly.”

To get some sense of how widely standards vary across news outlets, CJR emailed 18 media organizations that cover science to describe their disclosure standards for both journalists and the sources they use in their stories. Fourteen of those outlets replied. The responses present a jumbled mix of policies. Some draw a bright line—preventing journalists from having financial ties to any outside sources. Others allow some expenses and speaking fees. To complicate matters further, some organizations have written rules, while others consider incidents on a case-by-case basis.

Standards advocated by professional societies also seem to differ. For instance, the National Association of Science Writers (NASW) advises that members should “attempt to avoid” financial conflicts of interest, while the Society of Professional Journalists (SPJ) draws a much brighter line: Refuse gifts, favors, fees, free travel and special treatment, and avoid political and other outside activities that may compromise integrity or impartiality, or may damage credibility.

Many outlets say they follow SPJ guidelines and refuse to allow reporters to accept speaking fees or have their expenses paid by outside sources. “Bloomberg News pays its own way and assumes the cost of travel and meals,” wrote a Bloomberg spokesperson. “Bloomberg News journalists may not accept speaking fees or honoraria.”

Reuters also stated in an email that they don’t allow staff or freelancers to accept expenses or speaking fees. The Wall Street Journal wrote that they make exceptions on speaking fees and expenses only when a reporter is teaching or speaking at an educational institution, and a spokeswoman for The New York Times referred CJR to their guidelines, which allow staff to accept speaking fees and expense reimbursements under certain limited conditions.

Even when standards are straightforward, says Science magazine managing editor John Travis, conflicts can crop up. His staff isn’t allowed to have their expenses paid by sources they cover, but he said in an email, “If for some reason Science cannot directly pay an expense, we ascertain the expense as best we can and reimburse the source/industry. In rare cases where that’s impossible—[National Science Foundation] providing plane access to the Arctic and refusing reimbursement, for example—we typically note that in any stories that are produced.”

Rosie Mestel, Chief Magazine Editor at Nature, noted similar rare cases where a reporter’s only viable option is government-funded travel—Antarctica, for instance.

Tracy Grant, deputy managing editor at The Washington Post, wrote that reporters can’t accept payments from organizations that “try to influence issues the newspaper covers.” Some media and educational organizations may fall outside this exclusion, unless the reporter is involved in coverage of them. “Obviously, it is harder to impose such strict guidelines on freelancers, but we have a very thorough system for vetting freelancers,” she wrote.

Indeed, freelancers open up a whole different set of problems. Like the scientists they cover, many have streams of money that can create conflicts of interest. A spokesperson for National Public Radio wrote that it has turned down pieces from freelancers who had “some of their reporting expenses paid by groups or organizations with interests in the subjects they were covering.”

Nature ran a story by a reporter who received funding from the European Geosciences Union to write about any topic involving geoscience. The story noted the funding source at the bottom. “Freelancers are writing individual stories for us,” Mestel wrote. “We do not own (and again, cannot police) the rest of their lives, which can be financially insecure. Unlike staff, they do not have a budget that enables them to travel and that otherwise supports their work.”

She said that Nature is reviewing its conflict of interest policies for both staff and freelancers, and pointed to some instances where her publication chose to not run pieces over concerns of conflicts of interest. For instance, Nature declined a story written by a journalist whose fellowship was underwritten by an organization invested in a particular product.

An Editor at Discover, who declined to be named, wrote that if a freelancer or staff writer has any expenses paid by an outside source—a fellowship for instance—it will be noted in the story. But the editor added that the NASW standards should be strengthened, especially as more freelancers combine journalism with contract writing work for universities and industry. “Writers must maintain professional credibility by keeping those two arenas completely separate, i.e., they can’t be writing about a specific scientist for an industry publication and turn around and sell a similar story to a consumer science magazine, all based on the reporting of that initial industry assignment.”

It is not just conflicts of interest with writers that challenges news organizations, it’s also identifying sources with potential conflicts of interest. Here too, policies appear somewhat haphazard.

“We don’t have a uniform standard for disclosing COI for sources in stories,” wrote an editor at Discover. “It would depend on the story whether that came into play, and if it did, we’d note it in the story.” Bloomberg added that it discloses conflicts “when relevant” a point echoed by Travis of Science who wrote, “We disclose the conflicts we deem relevant but don’t have a blanket policy that every disclosure is noted in a story—judgment does come into play.”

Adam Rogers, editor at Wired, said in a phone interview that his publication doesn’t work hard enough to ensure that sources’ conflicts are disclosed in Wired stories. “We don’t regularly ask the people we quote and I think we should.” However, uncovering a scientists’ ties to industry can be difficult, unless they appear in the Open Payments website, which CJR covered last February.

“One of the things that is most difficult to understand is when a story is based on a journal manuscript and the manuscript includes some disclosure and still the story doesn’t even nod in that direction,” wrote Gary Schwitzer, Publisher of HealthNewsReview.org. “It’s almost willful ignorance.”

He pointed to a recent Bloomberg story on a Merck drug that failed to disclose that one of the study authors was a Merck employee and that several other authors also had Merck ties. He added that in a review of 2,100 stories written over a decade, his organization graded 45 percent as unsatisfactory for not using independent sources or for not identifying the source’s financial relationships.

Schwitzer applauded science journalists who take that extra step and identify the financial conflicts in stories, saying it educates readers helps them read the news in a more critical manner. But he said this appears to the exception, not the norm.

“It’s often a sad state of affairs,” he wrote. “The blind – or willfully blind (journalists) – leading the blind (news consumers).”

Correction: An earlier version of this piece misspelled the last name of Rosie Mestel, chief magazine editor at Nature, on second reference.

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Paul D. Thacker is a journalist and consultant to nonprofits. He’s periodically had expenses paid by universities for speaking on investigations of corruption in medicine and science. He also helped write the Open Payments Act, which discloses the name of physicians, including journalists and their sources, who have received compensation from the pharmaceutical and medical industry. He has no ties to the GMO industry.