I am a postdoc in math who defended his Ph.D. a year ago. I have 4 papers where three of them were written by me(only author). From time to time, when I don't understand some part of a paper, I send an email to the author and ask them about it. I have been told since I was a student that I should not be ashamed to ask questions, but sometimes I have a bad feeling after asking questions that why I asked questions or I was so stupid that I didn't think about it. I have always tried to think a lot of my questions before I asked them, but I still have this feeling when I was pointed out the answer.
It sounds like you may be experiencing impostor syndrome. It's the feeling that you don't really deserve your accomplishments and that you could at any moment be exposed. Most people will experience it sometime in their lives but high-achieving individuals are especially predisposed by their inclination to compare themselves unfavorably to even more high-achieving people.
You've achieved a PhD and you're published. Think of how many kids you knew in high school that have achieved that. It's possible you're the only one. You should feel great but you don't because you compare yourself to other researchers you assume are better. Still, there's every possibility that when they see your questions, it may race through their minds to wonder if you've discovered their papers weren't that good after all. The impostor syndrome can happen to anyone but high-achieving people are especially susceptible.
If this continues to bother you and your access to healthcare allows, you might ask your primary care provider for a referral for some counseling or perhaps a support group. Good luck on this but I suspect you're doing great and having trouble giving yourself credit for having earned your achievements.
While asking questions should never be discouraged, there are good questions and there are bad questions.
For your case in particular, reading a paper and not understanding part of it, there is a due diligence involved in trying to find the answer on your own, or asking for help from a more appropriate person, than to just write off a note and ask the author.
Your first pass should be to go to the papers cited by the paper you're having trouble with, and see if that clears things up. Next, it might be wise to ask local colleagues, peers you have an established working relationship with, or your postdoc mentor, before asking the author. Indeed, the exercise will almost invariably result in a better formulated question for the author by the time you get around to asking it.
Other times, your experience may tell you that there is no person you can go to other than the author to get your answer -- then, by all means, go to the author.
If this is a frequent issue for you, I suggest forming a journal club that meets periodically to discuss agreed-upon papers might be a valuable thing for you to organize. It might help you develop some more insight for how you approach papers. These can be valuable forums for everyone from advanced undergrads to expert emeriti. It would be very appropriate for a post doc to try to form such a group.
As author, I'm usually happy to be asked questions about my work. So I do encourage it, and people who do it shouldn't feel bad. Generally I feel that I'd be fine with more people asking me something than actually do. It gives me a good feeling that somebody reads my work and really tries to work through it, and occasionally people point out mistakes (or a question leads to my finding a mistake), so that I can also learn from this.
However people need to understand that my time is limited. Very occasionally people have overdone it, and asked things where I felt that (a) questions were asked that reveal that basic understanding of the field is missing that would be required before reading specialist papers, or (b) people think that because I wrote something about a method that they use, I would give them detailed support applying it in their specific application, or (c) people read only the first 5 pages and ask something that is explained later, or (d) people start with a good question and when I answer they start to think they can ask me all kinds of stuff that is only loosely related to the paper.
I think that's a fairly exhaustive list of questions I'm not so keen on.
I should also say that both answers by Nicole Hamilton and Scott Seidman are really good and show you two very different ways of thinking about the issue that both make sense and complement each other. Many people are too ashamed about asking questions and tend to feel bad about it when they really shouldn't. On the other hand it is worthwhile to make good efforts to clarify things for yourself or with people with whom you talk more regularly before asking the author.
Others have made the point that you shouldn't feel bad. I would like to add that if you do feel bad, you can use those bad feelings to increase your empathy with your students (assuming that your position involves teaching). Once you have a Ph.D., it is easy to fall under the curse of knowledge and forget what it is like to not know something which you suspect might be basic. To combat this, it is a healthy thing to be regularly confronted with evidence of your own continued ignorance of areas outside of your domain of expertise (or even within that domain).
I find that asking a good question sometimes helps to actually understand what you are asking.
I have this a lot on SE (especially SO) where I am building my question with the explanation of what I understood and what I did not. Often I would end mid-question with an epiphany (I actually can answer the question myself), or realize that my question does not make sense, or realize that I do not even know what I want to ask.
So yes, ask the question, but make sure to elaborate on what you understand and what not, in details.
Yes it's normal and I'll explain your (flawed) logic for feeling bad, because it is likely the same as my (flawed) logic.
When I ask a question, my question is either:
- Stupid, or
- Not stupid
If it is stupid (and my inner imposter says this is likely), then I have just made a fool of myself and displayed my stupidity to "everyone". I will feel bad about that.
But if it is not stupid, then maybe I have made a fool of the authors. I have found a flaw in their work and they will feel bad. A major social faux pas. I will feel bad about that (even if it ultimately results in better science).
So to save time, and in the knowledge that I will inevitably feel bad in the future, I start to feel bad as soon as I've asked the question. From that logic, all questions are bad.
If I consider myself as the answerer rather than the questioner...
If the question is a basic question, then maybe I didn't communicate my ideas effectively. This asker should not feel bad because they've helped me communicate better, or they've given me an opportunity to talk about my research. If I have time, I'll respond and provide them with some resources and add their question to my mental "Ways my research might be misunderstood" list so that I can communicate better in future.
If the question is not basic, they've given me something to think about. Maybe it's a flaw I'm already aware of, maybe not. If it's an in-person question, I don't think there's anything wrong with saying "I didn't think of that". If it's an email, I might think about it for a while and respond or act on it if I have time.
If I don't have time, I will likely do nothing. But I'd like the asker to trust me to make that decision and forgive me if I don't respond. I don't want them to feel bad about asking the question.
The question means that someone has read my output and thought about it long enough to ask (and hopefully try to answer) a question. The worse reception is a large round of indifference - even controversy brings acknowledgement. Ergo, questions are good.
A simple reason you may feel bad is because Academia is both collaborative and competitive. Working with others is encouraged, but it's also about "pecking order" and "survival of the fittest". And the further you go, the stronger the competition. The stakes (and the dynamics of the relationships) are not the same for a student and a post-doc. In fact an established academic may be happier to answer the same question from a student (potentially, a future recruit for their research lab) than from a post-doc (potentially, a competitor for their next research grant).
Bearing that in mind... By asking a question, you're making yourself vulnerable to criticism. You are highlighting your weaknesses. It is however an opportunity to learn. What you need to balance here is your thirst for knowledge (good!), and your (perceived) social standing within your community (important, but can conflict with the former).
Every question you ask is an opportunity to learn, but also a source of fear (not just a "childish" fear of looking foolish, but the very rational fear that negative perceptions from your peers may affect your career in the future). You have to learn to manage that fear. It's part of "growing up" as an academic. By becoming a post-doc, you are entering new territory. It's quite normal to feel cautious. However, I do find that keeping a youthful enthusiasm about asking questions can be a good long-term survival strategy. Seeming "harmless" is not necessarily a bad thing. It's actually a good filter for forming future collaborations. You don't want to work with people who sneer at "stupid questions".
Yes, it is normal. Many people have this problem; the assumed logic is that by asking a question you demonstrate that you are lacking knowledge or the mental resources to come to your own conclusions. Together with the fact that the whole point of being in academia (and maybe to a lesser part businesses) is to build a lot of knowledge, one might feel that one is inferiour for asking questions.
Also, some people with less than optimal social skills then may turn this around and mention your question specifically in a way which throws salt into the wound. Some people with less insight may actually think that you're a lesser person for it.
All of this is true from a psychological standpoint, and still, objectively, being able to ask question is almost always a great ability. Obviously, first, you may get an answer and learn something much quicker than figuring it out yourself. Secondly, there are things that you simply cannot know without asking (for example, about predilections or opinions of other people). Third, asking questions and actually thinking about the answers is great for general conversations - it avoids those kinds of discussions where everybody is just spewing facts and trying to "win".
As to how to do it... of course you can spend time on wording your question right - this may be worthwhile in an asynchronous setting, i.e. when asking by mail. Try to ask in a way which makes it easy for the other person to understand what you actually mean. Avoid too much verbosity or vagueness. If you have multiple questions, either separate them clearly, maybe through bullet points, or ask them serially (after you get the answer).
When asking questions in a social setting, i.e. in a meeting or discussion, just do it. There often is no time to think long and hard, and overthinking can lead to weird things being said. If it is a group setting, and you think the question is interesting for others, ask in front of the group; if instead you think there's really nobody else who could possibly be interested in it, maybe try to catch the other person later.
As to the bad feeling - at least for me, it still crops up occasionally, when I ask a particularly "stupid" question in front of a particularly important (to me) person, but I have a lot of practice meanwhile, so the feeling now goes away very quickly. I recommend to practice this skill - both the asking, and then being able to live with it.
Something that one of my lecturers at university first said, to a class that I was taking, has always stuck in my mind, and that was:
If you are thinking about asking a question about something that you don't quite understand, don't feel shy about sticking your hand up and asking because you can be sure that at least someone else is wondering the exact same thing!
This has stood me in good stead and by always remembering that, I have never hesitated in asking for clarification of an issue.
Conversely, from the point of view of the lecturer, this feedback also indicates that (at least part of) the audience is actually engaged in the discourse and are not just dumbly letting it waft over them.
There are already many great answers, and I would just add that in my opinion and experience low self-esteem leads easily to this type of problem. If you frequently end up self-criticizing yourself and your actions (even the good ones) also in other parts of life, then low self-esteem could be also affecting you. There may be no quick fix, but over long term things can get better. In the meantime if this would be truly the cause of your "problem", then acknowledging it can already help a bit.