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I'm a first year PhD student in the life sciences. So far, my PhD has been going well. I meet my supervisor regularly and he is interested in the project and generally supportive.

A couple of months ago my supervisor encouraged me to start writing a draft for a paper, incorporating the results I have so far. We regularly meet to discuss parts of the draft, mainly figures and main statements.

The problem I noticed once we started working on the draft is that my supervisor has a different attitude towards the project. Very often I try to emphasize that I am uncertain about a statement, a method or whatever but I feel unheard and ignored. I feel as if my doubts are not taken into account when we work on the draft at all. It appears as if my supervisor has this grand idea already fleshed out in his head and appears unwilling to hear that some statements might have to be toned down a bit. I feel uncomfortable and depressed as of late, as it is me who is ultimately responsible for producing a piece of scientific work that adheres to the standards of scientific rigor that I think are correct. I feel pushed into doing something that is wrong.

Could it be that I overthink this? Are there different shades of scientific rigor? 'Selling your story' is part of the modern scientific world, right? Do young PhD students tend to be overly defensive and critical of their own work? Is this just 'how the game works'? Should I just trust my supervisor?

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From on your key statement "It appears (...) my supervisor has this grand idea already fleshed out (...)[and is] unwilling to hear that some statements might have to be toned down a bit" my understanding is that you are perceiving potential flaws in your supervisor's thinking.

Firstly, my congratulations, as you seem to be maturing as an independent thinker, ie. a scientist. You are probably what I would call a 'true' PhD student, which (I am afraid) might be not so common nowadays.

I believe being skeptical towards colleagues' ideas is fundamental to healthy scientific logic. This is discussed in the invaluable books from Bachelard, Popper, among many others. The problem is, this is not in line with the practice and expectations of modern academia, where a sense of "collegiality" and smooth political connections are valued over traditional logical and scientific rigor. A main message here is: a maturing PhD student ought to understand the dividing line between scientific practice from academic practice. Contrary to what ivory tower inhabitants preach, science is not contained within its walls. I discuss the two sides of this coin below.

Side 1: Questioning your colleagues and being skeptical until convinced otherwise is healthy for your scientific formation. Constantly debating with your peers should be an essential part of your formation as a PhD student, towards becoming an expert in your field. In this line, I encourage you to politely push your advisor into discussing your project with you in open terms. Bring in papers, seek the opinion of others in the field. Come up with your own hypotheses and encourage others to question you.

Side 2: It is common practice in today's academia that institutions compete for available resources within a logic akin to the corporate environment of companies in the real-world market. Departments try to impress an internal sense of political unity focused at short-term materialistic goals (e.g. authorships, grant proposals, equipment, etc) for institutional survival. This favours a mentality where criticism and judicious thinking are counter-productive. Disagreement becomes an impediment to fast publication instead of the origin of new ideas. Advisors are seen as office heads and staff managers, and students/technicians/postdocs jointly regarded as employees to generate quickly the assets. Questioning an advisor equals insubordination which in corporate logic leads to micromanaging and firing (i.e. alienating the student and failing his degree).

My personal experience furthermore suggests your advisor (others here might say "your boss") has quite personal ambitions regarding your line of research that he would like to see published on paper. Under his name. However, unable to achieve this personally from his bureaucratic seat, the supervisor expect "his staff" to produce in his behalf. That would explain why you're not allowed to question his will, against any logical thinking. Because this person wishes his ideas published as such.

Finally, my advice is that you weigh inside yourself whether you value science over academia or vice-versa, and what is the current tradition in your institution and among workmates. Prioritise your objectives as strategically as possible to minimise conflicts of interests. Stay aware that successfully acquiring PhD training does not equate to successfully earning a title. Consider postponing the open reasoning and publication of your ideas if you wish to work as a true scientist inside the academia, while already being conscious of the necessity of finding the best like-minded colleagues and collaborators.

Sorry for an intricate answer, and good luck!

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    Very insightful – SSimon Jul 26 '18 at 14:14
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I think you may be attempting perfection (though you may not define it as such), but the reality of research is that it is constantly evolving, and may never mature into perfection.

Conflict, rejection and skepticism are all indeed 'part of the game'. If not your guide, then an editor, a reviewer or a fellow-researcher will (almost certainly) at some point refute your ideas. Many times they will not (and may not need to) justify themselves, which will add to the discomfort.

If an idea is wrong, it will be pointed out at some stage, maybe before submission, or during review (and sometimes after publication). Even if this happens, it will not blot your career as a researcher (unless the mistake is very fundamental, targets other researchers wrongly or involves some kind of trickery). So you should do your due diligence and rest assured after. By due diligence, I mean being thorough, verifying and re-verifying until you are satisfied that your work is technically and logically sound, in all aspects.

Also, never forget that the work is a partnership between you and your guide. Any responsibility for mistakes is held jointly between both. The more junior you are, the greater is the guide's responsibility.

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    Yes, if this disagreement is about tone of he paper and it’s claims, a peer reviewer is likely to catch it. Just make sure the tables and numbers are accurate. – Dawn Jul 18 '18 at 15:38
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You may be overthinking it. Or not. Certainly your supervisor has more knowledge and experience than you. (One sincerely hopes, anyway.) On the other hand you are right to be skeptical and cautious. After all it is your reputation that is at stake here.

If your supervisor is correct he may be willing to provide you with some references that have led him to his conclusions. I hope your relationship is good enough that you can ask for that.

Your dissertation gives you a chance to say many things in support of your theses. In particular you can have a section listing non-supporting evidence. That is, things that seem contrary to your main ideas. You also can, properly, rebut these - with appropriate evidence.

Skepticism is an excellent trait at your stage of development. In fact, for a scientist, at any stage.

If time and effort permit, consider, at least mentally, two versions of your paper, one in which you accept the assurance of the professor and one in which you don't. You needn't contradict the prof, but you may be able to simply sidestep the issue. I don't suggest completely developing these two versions. It is just a mental experiment. See where it takes you.

However, a solution that angers your supervisor won't help you, but you understand that already, of course.

  • I think this answer is on the right track, but I would like more discussion of the role of peer review in this dispute. – Dawn Jul 18 '18 at 14:06
  • @Dawn, Say more. I don't understand. Where does peer review come in at this point? After submission, certainly. – Buffy Jul 18 '18 at 14:22
  • If the advisor is overly optimistic about the importance of the results, a reviewer will likely point this out. So it does not need to be only on the judgement of the student. – Dawn Jul 18 '18 at 15:36
  • @Dawn. Perhaps. I worry, though, that if the advisor is actually going beyond what is really known and accepted that the paper will simply be rejected. And the rejection will come to the OP, not the advisor. Your comment, though, made me think about "peer" review as coming from a more local source: other students or faculty. The might be impossible, of course, and likely risky. – Buffy Jul 18 '18 at 15:40
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In my experience the attitude towards expressing uncertainty and hyperbole in manuscripts varies a lot between disciplines. Some fields (notably math, as far as I know) tend to be extremely conservative, while in other fields a certain level of confidence in your own experimental design and results is basically expected by peers and reviewers. In my field (applied CS), uncertainty about methods is virtually never explicitly mentioned in papers (that is, it is very rare that an author would write a variation of "we used method A, but method B would be promising as well but we did not try it"). Expressing a certain caution about results is common, though ("the results appear to support hypothesis C, but further research may be required"). My community is also very big on describing limitations of experimental design in a dedicated section, but many other CS fields don't do this either.

It is very honorable that you try to be truthful and conservative, but I suggest that you trust your advisor's experience on the expectations of the life science community on how manuscripts are typically written. Note that this does not mean that you need or should throw scientific rigor out of the window, but as a PhD student, you are most likely not in a position to change the general culture of how the community likes to write papers. Frankly, it's also not like a lot of harm is done by not describing obvious alternative methods or limitations. A qualified reader will typically be able to read between the lines - if you don't write anything about alternative method B, they will infer that you did not do B and judge your results accordingly.

If you are really unsure about this, you can get feedback from a trusted second senior person in the community, but in general, in the context of a PhD study, it is correct to trust your advisor's experience more often than not, and learn what you can until you have your own lab. This is the time to enact larger changes that you would like to see in your community.

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As assistant editor in the journal related to life science, what your advisor is doing, is to sell the manuscript to an editor. Unfortunately, many papers are relying on the strongly elaborated idea. This is something that you as for the first-time author, cannot understand yet. Usually, it takes time and routine to get accommodated with such routine. Professor as expected to publish several publications in one year. Do you think they would succeed to do that in a timely matter if they would doubt about the content of the manuscript?

So main point is to pursue editor to send your manuscript to external referees.

As SE member @scientist said:

your advisor (others here might say "your boss") has quite personal ambitions regarding your line of research that he would like to see published on paper.

and I agree with him, it is all about "publish or perish".

as about your other questions

Do young PhD students tend to be overly defensive and critical of their own work? Is this just 'how the game works'?

yes, but over the time this disappear. What should you actually do is to be critical toward peer review comments.

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