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I've already got a little experience doing self-led research but not in doing setup for the domain in which I work. I really enjoy talking with my supervisor about actual research topics, but I don't enjoy the workflow he suggests.

For example, there is a particular software development toolkit I've been told to use, but it's constructed in such an unorthodox way as to be unusable outside of a certain development environment in a very specific way (in Eclipse IDE) and isn't compatible with development conventions which are nearly ten years old (Maven). I only found this out when it was too late and have had to jury-rig everything as I go, and now, due to having thrown together a bunch of weird stuff together without testing it properly (having been given the green light by my supervisor, respecting his decision that it would work fine), I've spent six months collecting data which is messed up to the point of being unusable. My supervisor was also surprised, admitting that he didn't expect any sort of problem like that (which is why he recommended throwing the said things together).

I like and respect my supervisor but can't help but feel the whole project has gone sour thanks to "just doing it the simple way" which has turned out to be unbelievably complicated and now it's very likely I spent all that effort for nothing. What can I do when I respect my supervisor's research advice but don't like doing things the way he does? — What kind of "workflow" can I form where I take his research advice but still do things "my" way... or at least to know what implementation advice I should take with a grain of salt? Obviously it works well for him, so I feel even more disillusioned that I'm the one with all these problems. I feel that just saying "no, your software doesn't work" would not be constructive, because it does seem to work... for him.


Being more sure of the nature of the working relationships at the department, I now feel that I could have politely declined at the time without offending said person as long as I was confident and produced results.

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    Welcome to adulthood, where not everyone will do things the way we'd like them to. – Mad Jack Apr 30 '17 at 19:16
  • Are you trying to decide whether to ignore your advisor's advice in future? Whether to pretend to follow it, but then ignore it in practice? Whether to switch advisors? Or are you trying to decide how much to kick yourself for having followed your advisor's advice? // I'd like to hear your thoughts regarding what you learned from this experience and how you hope to avoid these pitfalls in future. – aparente001 Apr 30 '17 at 21:20
  • @aparente001 I really have no idea what to do. I could post a ton of related questions right now, e.g. "should I throw everything away and start from scratch?", "how can I convince my supervisor that doing stuff his way might not be best?", "I just wasted six months of my PhD; What do I do now?"... – errantlinguist Apr 30 '17 at 22:13
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    What can I do when I respect my supervisor's research advice but don't like doing things the way he does? -- You can say no. But you already know that, so I don't think that's your real question. I suspect your real question is "How do I move forward from here?" I recommend editing your question accordingly. (I would seriously suggest restarting the coding project from scratch, lessons learned.) – JeffE May 1 '17 at 10:13
  • I apologize if I expressed myself in a hurtful way. I'm going to delete the offending comment now, because it really wasn't my intention. I do hope, though, that when you're ready, you'll consider my list of options, cross out the ones that are non-starters for you, and add some more that may occur to you. I find that brainstorming is often the best first step when one is feeling stuck. – aparente001 May 1 '17 at 14:37
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One important part of being supervised is to learn to know when you are likely to know better than your professor. You can expect him to know the broad field better than you, and be a good judge of whether a broad strategy is likely to work, or if it has been tried before and failed.

You should be the better expert in your particular dataset, instrument, etc. You are the one working with it, you know the problems and the technologies, you are the one that calls the shots.

I have had to reject all sorts of ideas of my supervisors because the data was too noisy, too biased, the idea would solve the wrong problem, or they misunderstood something. Sometimes, this lead to a second round of ideas that corrected the original problem, or me ignoring the idea and going on with my choice. (In fairness, I have also rejected ideas that were actually good, but that is the cost of learning). With time, we all learned what each other is better at, my supervisor gives me more advise on the areas that I need, and I can judge better when the ideas are applicable.

There is one sentence that raises a concern:

having been given the green light by my supervisor, respecting his decision that it would work fine

I don't know how your workflow is, but I know that my supervisor is not familiar with the details of my code. His way of finding bugs is by looking at the results, and comparing with what he would expect. If there is a mismatch, he will ask for further analysis to either bound the problem, or convince himself that the results are correct.

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First, research doesn't come with a specification with all details ironed out. In most cases, many things are undefined and unknown; hence, it is called research. We could change direction at any time, especially when we realize there is a better problem or the problem at hand is rubbish. Consequently, the code in academia is pretty bad, poorly designed, and ad-hoc as compared to what you find in the industry; although codes in the industry can be one bowl of spaghetti too.

On your question, think about the problems at hand. Try to plan them out as best as you can. Collect evidence to justify the strength and weakness of a given tool/solution. Bring these pieces of evidence to your supervisor. If he/she is rational, he/she will either side with you or give you better reasons to not go a certain way.

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Supervisors are not superhumans. Their knowledge and experience might fail them like yours does you. If you are doing a PhD, now is the time to start being an independent researcher. I tend to expect more independence from bachelor students than I probably should, but I still give them way more guidance than I receive myself.

Yes, sometimes you would need more guidance. But in a PhD thesis it is not your supervisors job to know beforehand how exactly everything has to be done. It might be for a bachelor thesis (but leave a good student freedom, if you trust they can handle it). It is to some extend for a master thesis (but already here is normally some venturing in the unknown included). But definitely not for a PhD.

In a healthy environment it should be perfectly fine for you to go to you supervisor (regularly) saying something like "I tried/researched what you suggested but it is not a good option because of A, B and C. I did some more research and here are options D and E that I found. I would prefer to start with D, because it sounds more promising and Someone et al. used it in a comparable setting. Are you okay with that?" This behaviour should be a strong positive in your supervisors eyes, not a thread against their "supervisorness".

It did not sound like your supervisor brought you in this situation knowingly, neither did they so far say anything blaming you on it, as I understand from your post. The blame and the possibility they will (knowingly?) fail you again is something you seem to suggest yourself. If that is not the case and there has been fighting and name calling, the situation is of course rather different.

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Sounds like you feel your contributions are not valued, which very well may be true. When we look at how our actions are or are not being addressed it can be easy to loose sight of your true goals. If you feel the situation is unhealthy have a face to face conversation away from any snooping coworkers and break down how you really feel. He will respect you more for it.

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