I thought I would write about a very touchy subject tonight! That topic is politics. What I include in the term politics are things like authorship, how to deal with disagreements, and what to publish and when (especially when someone disagrees with you or works on a similar or even the same topic). Of course, being a PhD candidate and not a seasoned professor, I am far from an expert but I have some opinions that may or may not be the same ones that others hold.
I'll start with the subject of authorship. Who should be included on your papers, in what order, and why? These are difficult questions, especially when you're a budding scientist. I definitely want to collaborate and share authorship with people that I admire. For me, it has always been a relatively easy process but I usually have a frank discussion with collaborators about who should be included and in what order. It might seem like a subject that is uncomfortable to talk about, especially if you're worried about upsetting someone. But I guarantee that it is less uncomfortable than having a disagreement when it comes time to submit a publication or even after the paper has been published.
It is important to determine what the contributions of individuals will be to the paper. In my opinion, all authors must make an intellectual contribution. Acceptable contributions usually include analyses, writing, or data collection (or all of the above). There are some cases, however, when it is unclear if someone should be included on the paper. For example, if an individual has given you advice or ideas, do you include them on the paper? I think this depends on the gravity of the advice. Did they simply suggest you use a particular analysis? I would not include this person as an author. Did they come up with the idea? I would include this person. Whenever you feel an individual's contribution might merit inclusion on the paper, you should always proceed by asking them if they wish to be. If they decline, then you've done your political duty and made sure that there will be no hurt feelings. If they say yes, the next step is to determine the order of authorship.
For me, author order has always been obvious. The person who writes the paper and does most of the analyses is first author, the person who did some of the analyses or contributed some data is second author and so on. But I have never been involved in a project with more than three or four authors. Once the number of authors starts to grow, I think an explicit agreement should be made prior to any paper submission. Don't leave the discussion until it is too late or until someone is put off. Ask them outright! "Shall I include you as second/third/fourth/fifth author?"
The situation is a bit different when it comes to your supervisor. Different supervisors have different policies when it comes to authorship. Some prefer to be included on all papers and others make this judgement on a case by case basis. Sometimes supervisors prefer to be included as the last author (this is sometimes reserved for the PI) while others are open to any position depending on their contribution. Regardless, when you move on to a new supervisor you should always ask! That way no one will have any excuse to be angry. You'll also avoid pissing off the person that controls your funding!
I have only heard of people having major problems with authorship. I can imagine there have been situations when someone originally agreed to contribute but then failed to uphold their obligation. This can be politically difficult if this person is an office or lab mate but especially if they are a seasoned professor or famous researcher. I can't offer solid advice on this front but if you have made every effort to elicit a contribution, I think you would be justified in excluding them. A well worded email or phone call is likely to smooth things over.
Unfortunately, graduate students are often afraid to have these conversations or exclude authors that haven't contributed. All I can say is that, you're not at the bottom of the ladder. If you're going to put the effort into a project then you should be satisfied with everyone's contribution.