Total skepticism about all research results based on funding links: worse.
One-sided skepticism about any research you don't like because of funding links: worst of all.
Conflict-of-interest accusations have historically been used selectively to marginalize dissenting opinions, as Gary Taubes nicely illustrates in his book, “Good Calories, Bad Calories.” Scientists who disagreed with the accepted wisdom on the evils of fat in the diet were accused of being corrupted by industry grants even if they had received most of their money from government agencies that were looking — unsuccessfully — for evidence to back the fat-is-bad theory. Meanwhile, scientists who went along with the conventional wisdom on fat weren’t criticized for the corporate money they’d received from food companies.When Matt and I were writing on alcohol, we'd often be accused (woefully incorrectly) of having been funded by the alcohol lobby; by contrast, nobody much worried about the money paid to the consultancy firm that seemed to have been directed to come up with a very large number on the costs of alcohol.
Mr. Taubes has also found some wonderful examples of selective journalism in the dispute over sugar’s health effect: An article stressing the harms of sugar would make dissenting scientists look bad by stressing their connections to the sugar industry, whereas an article exonerating sugar would make the other side’s scientists look bad by stressing the money they received from companies making sugar substitutes.
Meanwhile, Mr. Taubes writes, journalists have paid too little attention to the scientific questions or to other types of bias: “Scientists were believed to be free of conflicts if their only source of funding was a federal agency, but all nutritionists knew that if their research failed to support the government position on a particular subject, the funding would go instead to someone whose research did.” David Kritchevsky, a a member of the federal advisory board that issued dietary guidelines in the 1980s, summed up the pressure on researchers: “The U.S. government is as big a pusher as industry. If you say what the government says, then it’s okay. If you say something that isn’t what the government says, or that may be parallel to what industry says, that makes you suspect.”
Anther journalistic blind spot, Mr. Taubes argues, concerns not-for-profit advocacy groups like the Center for Science in the Public Interest, which campaigned for more regulation of the food industry and denounced scientists who accepted money from it. Such advocacy groups, Mr. Taubes writes, “are rarely if ever accused of conflicts of interest, even though their entire reason for existence is to argue one side of a controversy as though it were indisputable. Should that viewpoint turn out to be incorrect, it would negate any justification for the existence of the advocacy group and, with it, the paychecks of its employees.”
The sad state of affairs is that anybody suggesting that alcohol or tobacco is anything less than completely evil will have all of his work entirely discounted if he's funded by industry, government won't fund anything that isn't likely to show alcohol and tobacco as being completely evil, and folks funded by government agencies or NGOs that demand findings of "EVIL EVIL EVIL!" are never thought to have anything but the most benign and non-pecuniary of motivations. Guess what that does to the level of debate over time when researchers also have to pay their bills?
Aim for two-sided moderate skepticism. If you're worried about the corrupting influence of big oil on some climate scientists, worry also about the corrupting influence of competing for research grants from pro-warming governments. Put more faith in results where the authors set things up for easy replication and less where they bury the data.