One of the biggest misconceptions people seem to have about science is that anybody who does not hold a PhD is ignorant. This is not the case. While a doctorate does confer a status of knowledge about a particular subject, it does not mean that the PhD becomes super-human. There many things people with little experience in the field can point out as flaws in even the best papers published in the top journals.
As a case-in-point, take a look at "Innate immunity and transcription of MGAT-III and Toll-like receptors in Alzheimer’s disease patients are improved by bisdemethoxycurcumin" by Fiala et al. If you can read that and completely agree with it, finding no loopholes in the logic, no flaws, then I concede my point. Any thinking person who reads that paper will come out with a great many questions about its validity. I did not specifically pick this paper because it was bad - it was simply one of the papers we've read in one of my seminars. I am also a chemist and have no in-depth knowledge of the molecular biology field. So if you read this and actually do believe that stuffing your face with curry will cure Alzheimer's, then I really have nothing more to say.
Sounds like you should go to more lab meetings or read the literature more. I've been in this particular lab for about that amount of time and I know exactly what the lab does - from lab group meetings and from reading the recent literature. My project is also in computational chemistry, but more on the inorganic side of it. During your research, you should seek to gain an intuitive feeling for chemistry such that when somebody presents you with data, your intuition can tell you if something's fishy. I know that when doing work with a grad student, you might find your tasks to be repetitive and have no understanding behind why you're doing it (why am I running extractions, why do I have to use a nitrogen atmosphere, how does the rotovap work, etc.). For example, if someone shows you an NMR spectrum showing that they've achieved a synthesis at room temp (without a catalyst) that your calculations have shown has an obscenely high activation energy, you should be questioning their work. Unless there's some other kind of energy input, there's no way that reaction will go at room temp. They might have accidentally heated it at some point or maybe there is another species with a similar NMR spectrum.
One more minor point - I don't know if you just unintentionally said this, but if you go into research with the mindset of finding an "ultimate solution," then of course you'll think that you don't have enough experience in the field to make a qualified argument. If your PI or any other researcher can find the "ultimate solution," then he/she will likely win the Nobel Prize. No, research is about making a tiny step towards a solution for a real problem. Not only that, but with every step forward, you take ten steps back and discover something new that you never thought about before. There is no ultimate answer in science - only ones that research makes more likely to be true.
