The same reason you should not accept the TSA's opinion on security, or the FED's opinion on economics, or the DEA's opinion on marijuana, or the NSA's opinion on information security, or the SEC's opinion on market manipulation.
They are not working for you; while they try to avoid uprising, and that often does correlate with what is good for you - they generally care more about the profits/benefits to themselves/supporters/friends/industry.
Somehow, it is clear to almost everyone on this forum about the TSA and the DEA, to many (but not all) about the SEC - but almost everyone believes the FDA and FED are "the good guys". (The NSA switched sides from good to bad recently thanks to Snowden, I believe).
But there's no difference. Regulatory Capture has happened in all of these. Follow the money trail and the revolving door with the industry.
I haven't been following them recently, perhaps they are a little more dependable now - but in the late 80s they had reports saying a lot of coastal cities will be flooded by 2000 if we don't do anything. We didn't do anything. Nothing happened - but in 2008 I looked and those early reports mysteriously disappeared.
Yes, climate does change, for sure, and it's probably bad - but so many of the climate scientists were wrong in their predictions from 30 years ago, that they need to do more to be convincing with their predictions for 30 years from now. And the data crunching they are doing, every time I looked at it, is not convincing.
I agree with you - I hate the "the science is decided" or the "economics is decided" argument for any of the examples you mentioned. Whether it is saturated fat, sea level rise, or quantitative easing, one should maintain a healthy skepticism.
Should we listen to the government bodies and medical organizations that give us nutritional guidelines? This is a hard question to answer. I don't think anyone doubts that these bodies have good intentions and have our best interests at heart. But there is an obesity epidemic going on in America and spreading to the world, which has lead many people to question common nutritional teachings. Some people think we're just exercising less and eating more potato chips. However, those who are truly curious and go out hunting for information find evidence that contradicts the advice of these organizations.
We can see that slowly people are agreeing with the other side. They aren't doubting for no reason, evidence is coming from science and analysis of history. Really, you have to read studies. Science reporting is rarely accurate. Once you find the bad science that has lead to our current common knowledge nutrition, and how we got our current recommendations, you may doubt the advice of these organizations.
I am not saying don't trust them. They are working in the name of science for a good cause. But you have to be informed, and if your informing leads you to find doubting evidence (like it already has for me, some doctors, and many laypeople), then you can make your own decisions.
I'd there any reason we shouldn't just accept the opinion of the FDA or AMA