I recently re-read an one-page article by Martin A. Schwartz with the topic: “The importance of stupidity in scientific research“. I can only highly recommend it. Many PhD students feel very stupid and unqualified for the scientific world when they start working on their PhD projects, their dissertation theses.
And yes, this works makes you feel stupid — because it is science. Prior to doing science yourself your main task was learning what other people had found out, perhaps criticizing it, perhaps imagining other ways to do things, but not doing it yourself. Now you are wading in swamp-water, not knowing where the potholes are. And sometimes you fall in, sometimes you find them first, but you cannot ask anyone for the solution, only for ideas for possible ways — you are doing the exploring yourself.
So, don’t be discouraged when you feel stupid, that’s normal. You get used to it — and with time, it’s even fun. It’s the riddle, the exploration, and the finding out what makes science great.
You can find Martin A. Schwartz article here on the website of the Journal of Cell Science (it’s an universal problem every (real) scientist has). There’s also a link to the PDF on the same page.