An excerpt from Newsweek:

it’s hard to grasp how much of science is subjective, and especially how much leeway there is in choosing how to conduct a study. No one is alleging that scientists stack the deck on purpose. Let’s just say that depending on how you design a study you can practically preordain the outcome. “There is an amazing array of things people do to botch a study,” says Rebecca Maynard of the University of Pennsylvania.

For instance, 153 out of 167 government-funded studies of bisphenol-A, a chemical used to make plastic, find toxic effects in animals, such as low sperm counts. No industry-funded studies find any problem. It’s not that the taxpayer-funded scientists are hallucinating, or that the industry scientists are blind. But here’s a clue: many industry studies tested this estrogenlike chemical on a strain of rat that is insensitive to estrogen. That’s like trying to measure how stress affects lactation … using males.

Choosing the wrong methodology can lead science, and the public, astray. Early studies of hormone therapy compared women who chose to take estrogen pills and women who did not. The studies concluded that the pills prevent heart disease. Wrong. Women who chose to take hormones after menopause were healthier and more plugged into the medical system than women who did not. Differences in the women, not the effect of hormones, explained the difference in heart disease.