How to deal with disagreement with advisor regarding research proposal and direction? 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


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.  
There has been no evidence that any method X
has performed better than method Y for any related problems.   
In fact,
some instances of method X is the same as method Y. So the problem is ill-posed. 
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?
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.