I have two papers. In the acknowledgment of the first one I thanked my adviser for his mentorship and there was no problem. When I finished my second paper and I sent it to him to review, he replied back with bunch of comments, mostly reasonable. But one of the comments was that he asked to be removed from acknowledgments where I thanked him again for his mentorship. He wrote, "I am not happy that you never listen to advice! please remove this", where by "this," he meant the part in which I thanked him. Why would he do that? What is the meaning of this? What are the possible reasons for such a comment? After several years of hard work and collaboration I am somewhat hurt by this, please help me to get better perspective.
The meaning seems pretty clear as far as it goes: he thinks that you do not listen to the advice he gives you on your papers. If you are a student and you acknowledge your advisor, that makes it look like the advisor has "endorsed" or "signed off" on the results of the paper. It seems that your advisor thinks that the version of the paper you will submit is not one that he would have endorsed in this way.
This sounds like a nontrivial breakdown of the student/advisor relationship, so I suggest that you meet with your advisor in person and try to smooth things out. If applicable, tell him that you thought you were pretty receptive to his advice, and ask for specific avenues for improvement.
Ask the advisor. I could image different things:
- He is angry with you, as you might have published stuff with his name attached and he did not consent.
- He might think that he asked you to remove the acknowledgement last time (I would always do so, so I would assume similar in such a situation) but it remained.
- He thinks that the acknowledgement section is not the right spot to have a general thank you for your advisor. I would share this view. Either he has contributed enough to become a co-author or he is out.
- It was meant as a joke you are just not getting it.
Make sure to clarify this, as it might be or become a strain to your relationship.
Edit and disclaimer: As was explained to me in the comments, the practices described below are not acceptable in the math community.
Why are you not listing your PhD supervisor as the last author of your paper? I am in physics, and last authorship is a big thing. The last author is traditionally designated for the supervisor or the group leader.
The number of last author publications is also separately tracked and plays an important role in obtaining tenure, permanent positions etc. as it is a measure of how well you have supervised your students. Even second-last authors are tracked by our library system, often daily advisors are listed as second-last authors.
If you had any serious discussions with your supervisor about the content of the paper at all, he should be in the author list. Maybe the math community has different standards, but a PhD student putting their supervisor into the acknowledgements would be considered something between a faux pas and an insult in my community.