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We are currently writing a first article with my PhD advisor. The research was mainly designed by him; I performed all the experiments and found a model to explain the results.

The article is soon to be finished. I am supposed to be the first author of the paper but at this point, I am more and more considering to ask my advisor to put me as the second author or maybe even ask to have my name removed.

My advisor wrote most of the article, which I already find weird given that I am the first author. This is not due to my lack of initiative, I've been explicitly told not to write some parts. It really feels that I am simply a secretary asked to check for typos, formatting issues, and to make graphs and figures as he sees fit. When I correct some of his writing, he sometimes takes into account what I propose/correct, sometimes he disagrees and explains why, but sometimes completely ignores it (my comment is deleted and not addressed). Some of these ignored comments are not fundamental, but I find some others very important and I am really not comfortable with some parts of the manuscript (he knows this given that I wrote it in the comments).

As an example, my advisor is very excited by a small theoretical model I proposed to him once that could roughly explain the experimental results. Yet there are still gaps and unsupported hypothesis. He knows that I am very reluctant to make this modeling an important part of the paper (which otherwise present both qualitative and quantitative experimental evidence of phenomena not previously reported), but this is now becoming more and more important and is almost the central part of the article. We discussed that once, his answer was simply that I should be proud of myself to have explained something rather than be too critical.

Other examples include him writing something along the line of "when XX was observed, we systematically found that this was due to YY". Something I actually only observed once and I am not confident that it can be so easily generalized.

My question is simply how to deal with that. My relation with my advisor was great but it is becoming more and more strained (especially from my side) as this article evolves. Is this a regular flow between a student and its advisor during the writing process? This is a long, in-depth >30-page article, if this information can be useful. With my Master advisor I had written and published a short-letter (4 pages), and I was completely leading the writing.

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    On the 'systematically found....' comment, perhaps your supervisor already knows it to be true. This is usually the case if your supervisor is experienced and hence he/she can safely make a claim stronger even though you may have only seen it once. – Prof. Santa Claus Jul 28 '17 at 22:21
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    consider yourself lucky. most phds have advisors who don't give any help – giò Jul 29 '17 at 16:46
  • No. It is not a normal flow. At least it is not a good flow. Perhaps I was extremely lucky and or good during my phd. I suggest you to be patient, show that you care a lot of the current paper, and perhaps things will go smoothly when you will write the second one. I wish you so. – Alchimista Jul 30 '17 at 1:47
  • I want to add that indeed writing "systematically" when the student say basically "once", well, doesn't have justification of sort. An experienced one shall write the paper so that won't be easy for a stupid referee to bother with details which are not the point, but without inventing even a single word as "systematically".. (if they're the points, then the paper shouldn't be written at all, but experiments repeated). – Alchimista Jul 30 '17 at 1:56
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I do not know whether this could be an answer to your question or not.

I find it completely normal, especially because it is your first paper. My advised changed 99% of the first version of my first article, and when I read now what I wrote, I laugh about it because it was really low quality. Of course, this is normal because I was new in writing papers. My advisor did not even explain the changes. Instead, he said: "check my revision, and you will learn how to write papers". Now his revision does not exceed 1%.

Back to your case, I think, your advised found that this paper has a high potential to be accepted, and he wants to increase the chances. Even if a scholar did the experiments by himself, the adviser has an experience of many years in writing papers. In the first paper, we usually try to write all the details, believing that they are all important. In most cases, what is important for a scholar is a part, which took more time. On the contrary, an experienced researcher knows what is important and what is redundant.

Overall, It is too early to disagree with your adviser about what to write, where his experience makes the difference. Try to follow him and if you are right, the reviewers will prove it. Otherwise, you will learn from your mistakes.

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    This answer gives good advice in general but I'm not sure how it applies to the specific situation. The advisor is claiming that something that was seen once is a systematic finding: that seems to be a straight-up lie, not a more experienced author knowing how to write better. – David Richerby Jul 28 '17 at 17:32
  • @DavidRicherby As far as I understood the description of the OP, I would not call it a lie. Rather, jumping to a quick conclusion. May be it is a weak point from the scientific point of view, but still OK, and they can indirectly discuss with the reviewers (in case it is submitted to a journal). Calling it a lie is an exaggeration in my opinion. – Younes Jul 28 '17 at 17:40
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    If something is "systematic", it must, by definition, happen almost every time. The only thing I can think of that's worse than describing something that happened once as "systematic" is claiming that something that never happened at all is "systematic". It's so egregiously untrue that "lie" seems to be the only possible description. It is claiming something as a conclusion that is completely unsupported by the experimental data. – David Richerby Jul 28 '17 at 17:47
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    No, it is the obligation of the authors to make sure their paper is correct, not the referee's job to expose untruthfulness and overstatements. – Gregor Botero Jul 28 '17 at 19:14
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    This mainly depends on how you interpret what is correct and what is not. I do not see at all that the OP's description indicates something about a deliberate mistake. It is more about the belief that this conclusion is correct. Therefore, this is the job of the referees. Otherwise, we accept papers directly because everything in their content is assumed to be correct. The question in my understanding is about thee agreement between the student and his adviser. – Younes Jul 28 '17 at 19:28
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This does not seem like the "regular flow" from my experience, contrary to what other answers state. Whether it is normal may depend on your field, country, and institution. Most PhDs I know or knew wrote their first articles with more help from their supervisor than latter articles, but ultimately they wrote the articles themselves. There are benefits to writing an article yourself, such as learning.

My answer probably can't just give another side to other answers, so my advice would be:

Discuss with others in your group, is this normal for them?

Discuss with your supervisor, explain that you want to learn to write a paper and this involves undertaking the writing.

Taking the lead is also a skill, which involves taking initiative in a way that does not create confrontation (although with some people, this may be impossible). One thing you can do for next time is simply to start writing yourself, then in meetings control what advice you are given, ask for the supervisor to look at specific definitions or how you have phrased a hypothesis. This way, you are in control but you are not in confrontation with your supervisor, in fact you are doing exactly what many supervisors want (becoming an independent researcher).

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or maybe even ask to have my name removed.

You did the experiments you have to be an author, everything else would be wrong.

At least in chemistry this authorship assignment is also quite common, the PhD who did the experimental work is first author, the supervisor (who oftend eveloped the idea behind the research) is last author and corresponding.

As for the other concerns, I guess there's a lot of field specific details here so I cannot really comment on that but you have to keep in mind that your supervisor has much more experience on writing paper and might see it differently on what is important and what not. I also don't see a problem in reporting unknown phenomena without having some kind of model that explains this in detail. This could also be a follow up paper.

but sometimes completely ignores it (my comment is deleted and not addressed).

From my experience if you write paper together the lead author just has to do this, otherwise you will end up spending more time on commenting on comments than everything else. If there are specific things he ignored then ask specifically why he did this.

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Yes, this is a regular flow, especially of this is one of the first papers you are writing together.

Consider that your advisor is much more experienced than you are and likely has a better idea of what shouldn't an of what should be on the paper. Your advisor is also more experienced in academic writing and probably knows the field from a more professional standpoint.

Also consider that s/he may not trust you entirely and hence is rewritting everything to make sure there is no possible cause for plagiarism.

None of those points are bad signs or mean that your advisor thinks badly of you.

Please use this opportunity to learn from her/him. That's your role as the mentee. As you publish more papers together, it is likely thar your role in the writing process will increase.

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    What? The professor writing most of the text is one thing, but ignoring serious doubts a co-author has (whether a junior co-author or not) about whether some scientific claims in the paper are really justified is not "a regular flow" and definitely is a "bad sign". – ff524 Jul 28 '17 at 4:09
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    I agree not addressing his/her questions is strange and marginally suspicious, but it seems more likely to be a communication issue. Maybe ask the advisor personally about possible issues? Honestly, some things are not easily responded on a Word comment pop up. – user63725 Jul 28 '17 at 4:16
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If you have good relationship with the advisor this is probably the most important thing. Make you best to preserve this asset! The concerns that you describe indeed seem like issues related to the work, but not to his negligence or lack of respect to you. As people said before, your advisor is much more experienced than you. Writing and ultimately publishing the paper is very different from a seminar work. You will understand it, particularly, when you get your first reject from reviewers. Do not even think about changing your authors position in this paper. This is pretty usual that for the first paper the advisor makes a lot of work. If there are really conceptual issues that are red lines for you, try to explain and convince your advisor, to soften the phrase. Do it gently and keep in mind that you might not understand many things. If you now make all the editing by Email, ask to meet your advisor personally. You might be furious by Email, but when you meet, this probably can be resolved in several minutes.

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This is totally aberrant. I am a Professor (even when I was a student) and currently with my students, I take the time and effort to sit down with them and explain every single change. A student is not a photocopy machine and he/she should understand the writing process, not just memorize phrases and regurgitate them in following papers.

Keep in mind that this PhD student will become a Professor and a mentor one day and being currently a student is his/her only time to learn basics.

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    I think it answers whether it is normal, which the original poster asked. I think it's a good anewer, multiple perspectives are useful. – Dr. Thomas C. King Jul 29 '17 at 13:59

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