I am currently writing a proposal for a new research topic in my field of system biology. This proposal will determine what I will be working on for the next couple of years.

However, I am running into disagreement with my advisor on the viability of the research proposal. I think he is completely in the wrong on this one and I cannot convince him otherwise (after talking to him), and the research proposal is due soon.

Essentially, his vision is that a new method X (of a class of methods) might work "better" than exisiting method Y on our problem. So I should do research on method X for the next two-three years. I should put into my proposal that method X could work "better" than Y.

However, I am convinced that there is no evidence that method X will perform better than method Y on our problem.

My argument is that

  1. Comparing method X and method Y is like comparing apple with oranges. Method Z is the one that should be compared with method Y. But it is already known that method Z does not yield benefits as compared to method Y. In fact, they are the same, just different order of execution.
  2. There has been no evidence that any method X has performed better than method Y for any related problems.
  3. In fact, some instances of method X is the same as method Y. So the problem is ill-posed.
  4. Other researchers are already aware of method X, but they do not use it. We can all guess why.

I think the line of research is fundamentally wrong and I cannot convince myself to write up a research proposal on something I disagree with and imagine spending the rest of my research career on. I almost feel like he is trying to fail me, because I read his rationale for pursuing this problem (benefits of method X) and the rationales were wrong or very hard to arrive at a conclusion at the present moment. Plus he is definitely not an expert in method X in any sense.

I am lost as to what to do. The proposal is due in 5 days and I cannot bring myself to write a single word. To be honest it feels like I am writing utter bullshit. I do not have time to quickly check method X (because it is an entire class of methods with some variations) and to compare with method Y in order to come up with evidence that it is indeed better.

Is there anyone out there who had these sorts of disagreement with their advisor on a research direction and how did you solve it?

  • 3
    spending the rest of my research career on — This is at most a proposal for what to work on "for the next couple of years". With luck, your research career will last several decades.
    – JeffE
    May 11, 2019 at 5:54

4 Answers 4


This is general advice and may or may not help in your current situation. Especially since time is short.

But mostly it is a warning that fighting with your advisor is not often a path to success. Ideally you want to graduate and make your own career untethered to your advisors and their ideas. You want to make your own way. But the realities of being a doctoral student are that the advisor has a lot of influence over and impact on your future - at least initially. Most places, they need to affirm the quality of your work, which means, generally, that they agree with it. Fighting with them doesn't get you there.

There are ways to avoid fights that may be open to you. One is to just go along with the advisor's view until you have the opportunity to substitute your own. Many do this successfully. Others cannot for various reasons. Another way is to find a more compatible advisor, even if it means changing universities, perhaps even starting over. This is an extreme step, of course, and causes disruption. But sometimes it needs to be done for ethical or even psychological reasons. If you are so strong in your views and will not yield, then you are probably better off finding a different path to success as it may not lead through this advisor. Whether yielding in the short term to enable long term success is at all attractive only you can say.

I'd suggest also, that making it a formal fight - going to higher authorities to impose your will over that of your advisor is probably the least safe option. You may win the battle, but be sabotaged for the rest of your career if the advisor also has a personality that will not yield. Try not to get into such a situation. It isn't likely to end well for anyone.

It is possible, for some students and in some institutions, to work completely independently of an advisor.

Finally, I suggest that you look for what seems to you to be the least disruptive path. You know the situation better than anyone here, but beware of the career destroying actions that might lie along the path.


I have regularly had problems with my supervisor regarding scientific direction. I have always known that I write much better than I speak. About 6 months into my PhD I reached the conclusion that its possible that I am not able to coherently convince my supervisor regarding my ideas and reasoning.

This has in fact been pointed out to me by my PhD advisors and also the examination board. In their words, I have an extremely unstructured, abstract and convoluted line of thought. Although, I may reach at the same conclusion, my process is not easy to understand for other people.

So what did I do?

I adopted the show them before telling them process. So whenever I wanted to introduce new ideas to my supervisor, I would generate data for the same, create a presentation and then speak to them. This mostly meant that my supervisor got the point.

In you case, that may not be possible because your application is due in 5 days.

In that case, I would suggest you write up an alternative draft containing your vision of the proposal. Do this, but also complete the proposal your advisor wants you to write. Before submission, when reviewing the drafts send both proposals to him in a politely worded e-mail asking him to review both.


Talk to your advisor - either you submit a proposal or you don’t.

Between you, if you both agree to submit, you need to work out a plan of X or Y or even a comparison of X to Y.

So four options: 1. No submission

  1. X

  2. Y

  3. Some combination

Until you two find an agreed path and with time running out, if you don’t then you may well miss this proposal opportunity.


The best advice is to talk to the Program Officer. You didn't mention which agency you are submitting to. They have published goals about what they want to fund in addition to individual solicitations. Have you looked into any of this? Aside from any ethical decision about how to spend your time, your program officer may just say flat out they aren't interested in a type of work and can save you a lot of conversation and angst.

As a research administrator, I can tell you that hastily written proposals are not likely to get funded to begin with. There is a lot of administration involved on top of your own writing, and in general you need the administration to align with your project. If you don't know what your science is, you probably haven't done much with the administration, and that will cost you as well.

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