Yes, it’s OK to second guess experts. At your peril, of course. Scientists, doctors, plumbers, roofers, auto mechanics. To reduce the “at you peril” part, you should have an understanding of the issues involved.
I’m not an auto mechanic, but I’m engineer, and I understand how things work in general. I took my car to the shop and told them to replace a fuel pump relay, which I had concluded was intermittent (it would die randomly, the maybe a minute later I could restart my car). I thought about the behavior a lot, and in an internet search mentioning an issue with the fuel relay in my vehicle model, I realized that was a failure mode that would precisely result in the behavior I suffered. The mechanic replaced the PCV valve instead, without consulting me. I went through weeks of a new fuel issue with my car, in and out of the shop as they redid their work trying to figure out the problem. Ultimately, they realized they had used a non OEM part, replaced it again and I got the car back. But it was still dying randomly, as before. I dig inside the dash and removed and repaired the fuel relay board myself—it was a poor solder joint. The car has run for years since, without issue. No, I’m not going to ever rebuild an engine, I’m in awe of the knowledge of mechanics, I don’t even think this guy was a poor mechanic. But I knew the nature of the problem, and I knew it wasn’t the PCV valve.
Same with doctors. I could tell lots of stories of misdiagnoses. The doctor who told me my stomach pain was due to my drinking and taking drugs? Me, a guy who took no drugs at all and rarely drank because it detracted for the work I put in at the gym—and couldn't stand to drink if I wanted to, due to the pain it would cause. He refused to send me to a specialist. I went to a new doctor, who in a few minutes of chatting diagnosed it as h. pylori, subsequently confirmed by tests.
Specialists? Like the dermatologist who looked at my right lower jaw area and said it was severe sun damage. I'm not a dermatologist, but that kind of damage usually falls on surfaced angled towards the sun (forehead, ears, cheeks, nose). I voice a little surprise, he barked angrily at me. I went to another dematologist, who basically said the guy was an idiot, and of course the angle is not conducive to sun damage—he said it was clearly a case of rosacia, and treated it.
I herniated disks in my neck years ago, in weight training. I was sent to a physical therapist—a good one, I had been to years before for a rear-ender accident. He had me stretching my neck by touching chin to chest. I told him I didn't think this was the right thing to do, he chuckled and said yes it was and we needed to do this, I complied. I mentioned it to the nerve doctor, who was horrified and said to stop doing it immediately (it was making the herniation worse).
Sorry for the boring personal stories. But I hope you see my point is not just that experts aren't always right, but if you have a reason that you think they might be wrong in a particular case,
do not let anyone tell you to keep your mouth shut because you are not the expert.
It should go without saying that if you're an idiot and simply hunt for a doctor that agrees with what you want to hear, then you're an idiot. Personally I believe the idiot quotient on this board is low.
Scientific research: Some of it is very good, some of it is well done but the researchers get tricked by looking at the wrong thing, some of it is flawed, some of it is influenced by wanting a certain outcome too badly, occasionally to the point of fraud. If you read a lot of research papers, you know that many papers on the same topic will have opposing conclusions, and also conclusions that shift over time. For instance, there was a time when people wanted margarine (hydrogenated vegetable oils) to be healthier than butter a little too much. There were scientists from the start who disagreed, but they were either considered wrong, or pawns of the diary industry. Until it was concluded that they were right, and trans fats were in fact a health threat, and butter really did not correlate well with heart disease after all.
My opinion: Do question scientific research, as you see fit. Be disciplined enough to understand why, be able to present your case. If someone can argue why your case is flawed, that's a discussion. If they are right, accept it and think it over. If someone argues that you don't have the credentials to make an argument, ignore them politely.
Don't apologize for being a thinker.
PS—I'm presenting this respectfully, to those who might have implied otherwise. Just a little different viewpoint that I hope they might consider.