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I have been working on a certain paper for about two years, the first year funded and the other one pro bono.

The data and methods were fixed during the first year. The data has high quality, the sample size is three times larger than in a typical study, and the papers that describe the methods I am using have been cited thousands of times.

Now one of my senior co-authors, for some reason that I do not know, is saying that the methods are essentially junk, and refuses to allow me to submit the paper to a good journal, though he would find low-rank journals just fine! I have rewritten the paper once already but it still does not satisfy him. The other seven authors have given generally positive feedback with good suggestions on how to improve it.

I will soon finish my studies, so I have little incentive to remake everything for a third time. However, it would be wasteful to discard the paper entirely. I don't know. I am very angry about this but I do not know what to do. My supervisors have been helpful but I feel I am not getting anywhere.

I could perhaps file a formal complaint and burn some bridges but then I would only lose more time in that. Any suggestions for further action?

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    There is nothing you can efficiently do about that, speaking realistically. The described situation is a frequent enough consequence of working in large teams. What about applying the same method to a different problem, so that you will be able to publish on your own? The major product of your studies is that you know how to produce research, not a particular set of data or a manuscript. Once you have solid skills, you can prepare 10 times more papers in a relatively short period of time, instead of negotiating with your senior colleague. – phys_chem_prof Dec 3 '15 at 20:41
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    What worries me most is that according to the coauthor, the method is flawed, but he's willing to submit to a lesser journal nonetheless. If the method is flawed but salvageable by adding a paragraph about its restrictions or something like that, then he should suggest the edit before publishing to whatever journal. If the method is so flawed that it's not salvageable, he should refuse to have his name on the paper at all. Submitting an unedited version to a lesser journal in the hope that they won't catch the flaw in the method is a disservice to academia and possibly fraud. – Sumyrda Dec 4 '15 at 6:02
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    @Sumyrda: It depends on whether "essentially junk" was really the senior coauthor's phrasing (which would indeed be troubling, since it's not worth publishing junk at all). It's plausible that the method gives some information but just isn't conclusive or exciting, in which case recording it in a lower-prestige journal could make sense. – Anonymous Mathematician Dec 4 '15 at 14:59
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I suggest that you get all of the co-authors together to have a discussion. When you organise the meeting, say something neutral like "let's get together to figure out what to with this paper".

If your senior co-author has a good point about the methodology being flawed, then the other co-authors may suggest a way to salvage the paper. They also have an incentive to get the paper published, if possible.

If the other co-authors don't agree with the senior co-author, then they can put forward their arguments, and hopefully a resolution will be reached.

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Now one of my senior co-authors, for some reason that I do not know, is saying that the methods are essentially junk, and refuses me to submit the paper to a good journal.

I would work to understand what his objections to the methods are. Presumably they are in good faith. Perhaps recruit one or more of your other supportive coauthors (especially if they are peers of the senior coauthor) to mediate if you feel that his objections are not in good faith.

could perhaps file a formal complaint and burn some bridges but then I would only lose more time in that.

Unless you have compelling evidence that your disagreement isn't just academic (like say, your difficult coauthor plans to use your work and publish without giving you credit; very unlikely) a formal complaint would probably not even work. Disagreements like this are common in academia (and professional life in general) and I don't think any department would step in on your behalf. Unless of course you have evidence of something more sinister in which case it's a totally different conversation.

Hope that helps!

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    An acquaintance of mine actually had a co-author who expressed undefined concerns about the methodology of their paper and asked to be removed from the paper. It ultimately turned out that the co-author was planning to publish on the same data separately with a different collaborator. This case did go to academic mediation, but I agree that in general this is very unusual. – Cecilia Dec 3 '15 at 23:25
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    @Cecilia, I also have a similar story which is why the example came to mind. It's rare but sadly not rare enough. – Sumedh Joshi Dec 4 '15 at 0:35
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If they have unresolvable objections to the paper, ask them if they want their name removed from it. This will show whether they are genuinely objecting to the paper or have some other agenda.

mhwombat suggests calling a meeting. That would be a good place to ask this question.

If they agree, ask if they want to be acknowledged. They may or may not want their name connected to the paper in this manner.

Then, work with the remaining authors to get it published as soon as possible.

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