Here we are, in 2015 debating the safety and efficacy of vaccines. I've always shied away from writing about vaccines because there's so many people out there who can write about it so much better, and with a much bigger audience. But here we are, in 2015, and I guess every little bit can help.
What non-scientists tend to not usually grasp about science is that it's not just a collection of facts you read in a book. It's the only process of gaining information about the universe that is willing, and in fact actively desires to prove itself wrong. You all know that the process starts with a hypothesis that needs to be tested, and that the results of the test then may lead to peer-review, but where I think the understanding diverges is that this peer-review process absolutely does not stop at publication.
Authors have to defend their studies and their data to a collective body of tens of thousands of people around the world who have spent millions of cumulative hours studying the same field, subjecting themselves to some of the harshest criticism in any human endeavor. Sometimes they do this for decades, and if you're only casually paying attention, it seems like it goes back and forth and nobody knows anything, but that's almost never really the case. Sometimes conflicts of interest and fraudulent data are exposed that immediately discredit a study. Sometimes good ideas and compelling data really are suppressed, but the key is that this cannot be done by an entire field. Fifty years ago, scientists were certain that lead in gasoline was an environmental and human health disaster unfolding in slow motion. They knew that tobacco exponentially increased the risk of lung cancer. The "debate" was not scientific, it was entirely political. If a researcher is claiming persecution by some industry or another, see how that researcher's field overall sees it before you assume anything. The power dynamic alone tells you little, and if you're like me, that's a very difficult thing to accept, but it's true.
So yes, the process is messy, but not so messy to make cynicism and nihilism the appropriate response. If this process eventually results in a consensus among all of these people that is completely overwhelming, then if you "disagree", the problem is your understanding of the topic. It's not Big Pharma. It's not Big Ag. It's not Big Government. It's you. You don't get to bypass this process because you can make a fancy webpage about "toxins". You don't get to bypass this process with superficial catchphrases like "treat the cause, not the symptoms", or lobbing around terms like "reductionist" or "scientism" that are often just catch-all terms to dismiss empirical evidence out of hand. You don't need to know how a vaccine works on a molecular level to know it works. A randomized control trial doesn't depend on a detailed understanding of biochemistry, it depends on simply comparing the final outcomes of two or more options. That's not reductionism, that's not arrogance, that's just the way we can tell if something works. If a new measles prevention therapy continually and undeniably works better than the MMR vaccine, and it's determined at some point that the reason has to do with chi or chakras or praying to Odin, then I guess it's time to unlearn everything I know.
If you watch things like "Cosmos" meant to communicate how various fields coalesce into an overall understanding of how the universe works, virtually every single fact ever mentioned in the show has gone through some version of this process, whether it was physics, chemistry, biology, or whatever. Whenever a finding revolutionized a field, it was the result of years of build-up, and years of sometimes bitter debate. People have always tried to bypass this process, but they are always forgotten over time, because the process wins every time.
You'll find a crank in every corner of every field that has the kind of credentials to adequately assess this same evidence, but for one reason or another decides to go against the grain. You might even find a Rand Paul or a Chris Christie to elevate these cranks and force dumbass pundits on cable news to debate things that have been settled for decades. But you'll know better, because now you understand the real meaning behind the phrase "extraordinary claims require extraordinary evidence."