Conflict of interest: My research reflects badly on my PhD supervisor Post Q2 2016

I am in the final stages of writing-up my thesis. Unfortunately, my findings don't seem to reflect well on my supervisor. I have just had a key chapter returned with many comments like "rubbish", "full of mistakes", etc. I don't think they are justified.

I am reporting on the quality control of a trial for which she was PI. There is clear evidence of QC problems and it seems to me that there is a conflict of interest which is preventing objectivity in the feedback I'm getting. I feel that I'm being pressurized into coming to conclusions in my thesis that I don't agree with - i.e. the trial didn't have any significant QC problems.

My relationship with my supervisor was amicable enough before I sent her this chapter. In order to complete my conclusion I need to reach some sort of agreement, but after her recent outburst I feel this will be difficult.

My University doesn't seem to have any policy about this type of conflict of interest, yet it must be common enough. What should I do?

UPDATE (June 2017):

The good news is that I submitted my thesis and it was accepted with minor changes at my viva. My examiners were kind and described it as a 'tour-de-force', though after five hours of argument I suspect they just wanted me to go home ;-) Therefore I have my PhD. 

The bad news is that the papers derived from two of my PhD chapters which detail the quality failings in the trial have yet to be published. This is despite significant support from my examiners who both felt it was very important for the information to be published. At present there is a big row going-on at the highest levels of the University with good scholarship being pitted against the medical school's desire to avoid reputational damage and potential loss of future grant income.  

I sincerely hope that no other PhD student is going through this sort of debacle, but just in case I give the following advice:


Don't give-up. Just keep on writing the best thesis you can. Let the pages become chapters and the chapters become a finished thesis. Save worrying about your viva until after its been submitted.
Don't keep quiet about problems with your supervisor. Stand-up for yourself and keep in the light. In my case I made sure senior management knew was going on and also that I was documenting everything. This wasn't something that they could easily sweep under the carpet. In the end it became very much in everyone's interests that I got my PhD.
Try to maintain a relationship with your supervisor and keep the arguments on a professional than a personal level. You want your supervisor to congratulate you on getting your PhD and write-off the arguments over your thesis as healthy academic disagreement.  


I must thank the >1,000 people who have viewed my original posting. Good luck to all PhD students and remember that careers are built on results not methods ;-)

UPDATE (March 2018):

My main paper was accepted by the key journal in the field in August 2017 and finally appeared in print, March 2018. I'm still working on getting the second paper accepted.
I had interesting situations during the final stages of my PhD career, and I found that my dissertation committee was an incredible resource. If you are in the final stages of writing your thesis, that means you have a dissertation committee (or have otherwise established a collegiate network of professional academics that support your PhD training). Now is the time to use this resource. Ask to speak to them in person about the problem. Specifically, you should approach your committee chair (who should be different than your supervisor). If your chair is your supervisor, then just speak to the most senior person in your committee. 

The way that I understand the power dynamics / vested interests of the whole PhD situation is that your supervisor has inherent conflicts of interest - they want you to do research that supports them. Thus, they 1) are better off keeping you as long as possible (but not too long) and 2) want your research to support their research. Your committee chair, on the other hand, wants to see you graduate. Your department chair also wants to see you graduate. Your supervisor wants to see you graduate, sure, but as I mentioned, they have other motives. 

Ultimately the goal is to keep everyone happy, and especially your supervisor. Having your PhD supervisor on your side is key to a successful career in Academia (or at least makes getting recommendation letters are lot easier). 

Use this situation as a learning experience (one of the many tangential learning experiences associated with a PhD) for how to navigate the people problem of science. So in conclusion- 

1.) Give your supervisor the benefit of the doubt. Try to understand their points and try to actually discuss it with them - IN PERSON. Abandon email for this interaction - you need the full spectrum of our human communication abilities. 

2.) If #1 fails, engage your dissertation committee. This exact situation is a fine example of why dissertation committees exist.

3.) If #2 fails (or you're in a program that doesn't have dissertation committees), engage another trusted senior investigator if you've created relationships with other investigators.

4.) If you get to here, go to the department.