text:
How to handle Co-author who is not listening the suggestions to improve the paper quality
Assume I am involved with a work and the lead author is writing a paper. However, after every draft version, I see that not all my comments are well addressed in the revised version. I expect that if the comments or major suggestions are not addressed, then some explanation must be given.  During the previous conversation, the coauthor did not raise any doubts or concerns about my suggestions. Thus I pointed out these issues in the paper again and they again fell on deaf ears  this loop continues.

As I already spent a huge amount of time on this paper and made a significant contribution, I don't want to withdraw my coauthorship.
Topic is relatively new, in addition the current version is good enough to have a decent chance of getting accepted into a medium level conference.
Some minor issues (may be major) are bother me. I am not sure whether I am wrong. However, there is no discussion on on my concerns even after they are explicitly highlighted.

Should I just let the paper go? or make some statement? I don't want to burn bridges with any of my coauthors.

I can't allow myself to see these issues with the paper. — What does this mean? (In fact, I'm unclear on the first three sentences of your third bullet point.)

@Mad Jack Edited.

but I found there is no proper response for some issues in the revised version Would you please clarify what you mean by proper response? You mean no response? Or some response that you are not satisfied with? In other words, what kind of responses you think are proper responses? Or Improper responses?

@scaaahu By 'proper', I mean to say 1) if the issue was addressed, or 2) if not, give some explanation why was it not addressed in the manuscript. I didn't find neither of them.

Have you tried asking your coauthor directly why they did not accept your suggestions?

I have had this problem on a few occasions. Usually I got ignored over suggestions on points the lead author did not want to discuss directly because (i) s(he) felt (s)he was on the right side; (ii) s(he) felt (s)he was on the wrong side but wanted to push their version nonetheless; (iii) s(he) felt I was not in a position to criticise that part.
In all cases I demanded for an explanation, and this is why I can answer your question here. So, my first suggestion is that you contact this person demanding an explanation. (Mind that most people don't do these actions -- questioning parts of manuscripts where they are co-authors, and later seek to understand why they got ignored -- and that most lead authors prefer having passive "co-authors".)
How did I react in such situations described above? I will briefly explain:
(i) I tried to make my point clearer, which subtly meant I was trying to prove the lead author wrong. The lead author always insisted on their point without seeming to listen to what I said, while emphasising on how they took my suggestions on other points. I had to let these issues go, and they got published, and as a result I do not fully agree with some of the papers I participated in.
(ii) I insisted. This will make the lead author uncomfortable, and you will have to make sure this person understands you're not cornering him/her. Typically there is a clear mismatch with data or logic that the lead author doesn't want to hear aloud. Usually I got the problem fixed, usually the lead author wasn't happy and is now unlikely to collaborate with me in the future. I think that is OK, given the circumstances. Once I had to let it go.
(iii) This is the most common situation. Typically it involves a collaborator from a different field under strong influence of their bossy PI, where you're not sure which of the two is doing the writing or even answering to your emails. They do not appreciate being questioned "on their turf". You have to consider the possibility you're wrong there. Which I think is irrelevant, because if you are wrong then there's all the more reason you deserve a clear, logical answer. In such cases I insisted, and was authoritatively told to "keep to my business". I insisted again, and got ignored, and had to let it go. Usually the lead author apparently did see my point but was told by their PI (i.e. the last author) what to do. As a result the lead authors in these cases made sure to communicate they were open to collaborate with me in the future, while their boss cut communication.
Anyway, hope that helps. In the long run you're selecting whom you can work with.

In every scientific paper that I have been involved in, there has been opportunity for co-authors to directly edit the manuscript themselves, if they wish to make a contribution.  If you feel that you have suggestions that are not being taken up, I would advise you to ask something like:

Would you mind if I did a pass on the paper to edit in some of the suggestions I've made?

If your co-author hasn't been editing in your suggestions because they are unclear, overloaded, or not able to do so, this will give you a chance to adjust the paper in the ways that you want.  If, on the other hand, they actually disagree with your suggestions, then they may not want you to edit them in, and you can then actually have a discussion about whether and why the proposed edits should occur.
In short: I believe that you need to shift from being a passive critic to being an active contributor who provides actual text that accomplishes what you want to have accomplished.

I like the way that you suggest. By the way, in all of my previous work with coauthor went very smoothly. Sometimes, I am surprised to see the quality in final version compared to the first draft. This is due to the active involvement of all coauthors, no matter how much they write the actual text. For example, a good suggestion in motivation section can put the paper in different level, however, the actual text may come from another coauthor.

"If I were a reviewer"
I think a nice way to get people to step outside of their rigid viewpoints is to explicitly ask them to take the point of view of a peer reviewer.  By saying something like "if I were a reviewer, I might wonder if X" (where X is your point).  or "If I were your reviewer, I might want more evidence on this, considering XYZ".
This also has the advantage of putting you and your co-author on the same team, anticipating the concerns of a sometimes adversarial anonymous reviewer.

I shall adopt this one myself!

There are at least three possibilities here:

The quality of your feedback is low.  You might be wrong, incomprehensible, or nitpicky.  Ask for feedback on your feedback.
The lead author is unable or unwilling to do a good job.  In this case you should do more for them or withdraw your coauthorship.
There is a third author who is giving advice which contradicts yours.  It might be important to the lead author not to upset this third person, so they might not admit this to you.  The solution is to talk to other authors.

I totally agree with your first two. For the third, I say that I always send the comments to all authors. Further, I also try to make comments on comments by others if I found anything to mention. I agree that there might be a contradiction that is very true in every research, however,  can be solved with an 'open discussion' among all coauthor.


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Why are "discretionary" desk rejections generally implemented when they are an obvious bias loophole?
To be clear I am not referring to out of scope, incorrect formatting or language quality rejections which are mostly detected by junior editing staff and a reasonable explanation is usually supplied in the rejection letter. I am referring to desk rejections by the editor in chief after a paper has passed all quality checks. These are performed under the sole discretion of the editor in chief who may reject any paper providing a conclusion s/he does not like. It culminates with a standard form letter which provides no valid information to the author as to how they might improve their work.
This is a clear and obvious bias loophole (unconscious or otherwise). It is extremely unfair towards the author who has spent many hours developing an argument which is simply overlooked and a burden on the progress of science because it poses a severe disability to any paper with a controversial conclusion. Controversy is the breeding ground of scientific progress.
This practise is censorship by prejudice. i.e., Really bad science.
My understanding is that a paper was published which proved that desk rejections saved time and since then, they have been generally accepted and implemented throughout scientific publishing.
One of the main purposes of peer review is quality control aimed at overcoming bias.
It does not take a genius to figure out that circumventing quality controls is a sure fire method of saving time.
In all forms of endeavour, this has been the cause of many disasters. People have lost their lives from this type of behaviour. Whenever it is exposed, we view the perpetrators with deserved contempt.
I would be surprised if there were no academic suicide deaths which could be attributed directly to this behaviour of journal editors in chief.
It should be stopped.

This is a rant rather than a genuine question.

My apologies. I have edited the "rant" out of my question.

Ended up voting to close.  And, honestly, I feel for ya.  It sounds like you're having a huge problem that's really getting you down, and that's a sad thing.  The problem's that there's just not anything anyone else can do.  You're basically saying that something that works for us all of the time in our own projects isn't working perfectly for you when you try to use it.  And that sounds like it's a problem on your end, ya know?  I mean, angular momentum's still going to be conserved when I do my stuff in the lab later.  So if I get your paper, I'd have to reject it too.  What else can one do?

The fact that you believe it's working perfectly does not make it so. There is no scientific experiment which confirms that angular momentum is conserved in a variable radii system. Please go and actually try it in your lab before making false claims?

@Nat, The fact is that if you were to receive any of my papers for review, you would have to address the proof contained within it before you could validly reject it.

@John Definitely, I'd read it before rejecting it, but that'd take all of 10 seconds.  Were you under the impression that, if your paper were sent to peer reviewers, they'd be forced to argue with your about your ideas?  Because that's not how it works.  If anything, they're the jury and the editor's the judge; you'll be found guilty despite your pleas.  I really don't think you'd enjoy it.

@Nat, In order to reject a logical proof, it is necessary to show the premisses false, or the deduction flawed. It is irrational to proceed any other way. That is how it works.

@John The reviewers aren't obligated to formally disprove you, and they certainly aren't obligated to disprove you in a way that you'd find agreeable.  If they think your work's not worth publishing, they'll just tell the editor so, and that's kinda it.

@Nat, I would be provided with a reviewers report and have an opportunity to rebut it. And pointing out that the rejection is irrational would be a valid rebuttal.

@John Well, kinda - it's the judge-and-jury thing here again.  As the jury, they'll provide their recommendation to the editor, who's the judge.  In principle, if you can convince the editor, they might choose to publish your work even if the reviewers disagree.  But since you're getting desk-rejected, the judge is so confident that you're guilty that they're not even bothering to summon the jury first.  Then even if they do summon the jury and they find you guilty, then the judge will be like "Yup, that's what I thought!  Sorry for wasting your time.", then reject your paper again.

@Nat, I believe that if the reviewers are requested to review my work then they might actually do that properly. If they do then they will overcome their prejudice because the fact is that I am right. They are denied this opportunity because of the bias loophole provided by the editor having an option to desk reject.

I edit the Journal of Widgets. We only publish papers about widgets. You send me a paper about sprockets. Why should I not desk reject?

@John I’ve already told you this, but pages and pages of rambling words is not a tight logical argument in physics no matter how good your grammar is. It’s simply too easy to “cheat” when using only words. If you want your work to be read at all, replace the words with real mathematics.

@aeismail, that is not a desk rejection, it is an out of scope rejection.

@knzhou, Your comments are completely out of scope here.

@aeismail: A "desk rejection" is supposed to be any rejection that occurs before the article goes to peer review. The reasons can vary. But that doesn't change the fact that there are many articles that shouldn't make it to peer review.

@aeismail, As I understand it, a desk rejection is that once a submission has passed all the quality checks an lands on the desk of the editor in chief s/he rejects it based on nothing but his/her personal feelings about the work. Other rejections are acceptable because they are accompanied by a reasonable explanation. Desk rejections are a standard form letter that give no valid explanation and no information which might be used to improve the work. If I am wrong fine, but those are the rejections I am referring to here. Do you have a different name for them?

I'd call that a discretionary rejection.

@knzhou, My claims are correct. Your "problems" are nothing but the avoidance of addressing my argument. It is yourself who is ignorant. The desk rejections I have received are also simply an avoidance of addressing my infallible arguments due to unconscious bias. The fact is that there is a bias loophole in the system and it should be addressed and not avoided.

(Only dealing with poor submissions, since the text of the question indicates John is not interested in e.g. poor English or out-of-scope reasons for desk rejections.)
If a paper has no real chance of passing peer review, why not desk reject it and save everyone's time - from the peer reviewers to the editors to the authors?
For example, suppose a paper claims to prove that angular momentum is not conserved. For such a paper to be credible, it needs to not only provide exquisite experimental data, it needs to find flaws in the experiments that generated the already-available experimental evidence. It needs to explain why Kepler's laws are obeyed in a world that doesn't have this conservation, it needs to explain why generations of physicists have not noticed a violation of rotational symmetry (equivalent to angular momentum conservation by Noether's theorem), and so on. If the author does not provide these, the paper has no chance of passing peer review. At that point, one might as well desk reject it, save everyone's time, and move on to the next paper.

Incorrect. All of your reasoning here amounts to an appeal to tradition logical fallacy. All a paper needs to do is provide a single proof of it's claims. Peer review would require that proof to be addressed. A desk rejection allows logical fallacy to have effect.

@user109420 Academics should never be OK with logical fallacy.

The review system is not perfect; even when papers make it to peer review, and even assuming good faith on everybody's part, there is a huge amount of randomness in the process. One aspect of that is that an initial assessment of the paper is made by an editor who is probably not sufficiently specialized to fairly judge all of the contents.
Think about it from the perspective of editors and reviewers, though, rather than authors[1]. If a reviewer is to do a good job with a paper, they must give a significant amount of their time for free. If they receive a lot of work that is clearly rubbish, they (a) will have less time for reviewing work which may be worth their time; (b) will be less likely to agree to review future work. Hence, the editor has to make an initial judgement as to whether a manuscript is worth sending for review. Undoubtedly, sometimes they are wrong.
[1] While also remembering that those editors and reviewers are also authors; they know what it's like.

If there are no obvious quality or scope issues with a paper then it should be passed for peer review. A judgement based solely upon whether the editor in chief believes or want's to believe the conclusion or not should not be allowed.

@john be reminded, once again, that everybody involved here is a volunteer, giving up their time for free to review and (often) to edit. http://www.baur-research.com/Physics/rejections.txt is a rather breathtaking demonstration of how much of such volunteers' time you have wasted. Before continuing to tell everybody they are wrong, may I suggest going over to Physics.se and asking humbly for help in understanding your mistake? If they can't find one, then perhaps have some confidence that you might be right...

I have not wasted anybody's time. Everybody's time is being wasted by the fact that there is a bias loophole in the system. If I am wrong, then it should be a simple process to review my work and prove that rather than assuming it as you and the journal editors have done. Then there will be no more time wasted. The fact is that I am right and therefore have no option but to continue to submit my work until such time that it is properly addressed. Veritas omnia vincit. Refusing to address the truth merely causes delays (wasted time).

@alephzero, You cannot address a theoretical paper by "reading the titles". You must show false premiss or illogic, or you must accept the conclusion drawn whether you like it or not.

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Reading Projects Listing in CV
So I'm a Physics undergrad about to apply for my master's. I'm currently making my CV and I was listing out the reading projects that I've done and was confused if I should:
List out all the books I used for the project
OR
Link in a website which has the books + all the resources (i.e. lectures and notes) I made for the project
Which is preferable and why?
Clarifications

What is a reading project? A project in which I undertake guided reading under a faculty. After reading certain sections we discuss the contents after which I'll be asked to deliver a short talk about it. I may or may not make notes dependent on time constraints.
Where am I applying? I'm applying to universities in Germany for an MSc degree in Physics
What resources am I trying to list? I'm trying to list the books/papers I used to study it. At the max, it has 4 entries.

Maybe an answer to your specific situation could depend on how long that list of resources is.

Could you please specify what's a reading project and which country you are applying? If I understand the meaning correctly, I'd consider highly unusual to list such thing in a CV, at least for my country.

Thank you! I've made edits, do let me know if there are any more clarifications

As a rule of thumb, don't rely on linking to things in a CV/research statement/other document. Inevitably, someone will print it out to read, and the link is then useless. Better just to explain in words where you can.

Thanks for the insight! Makes sense

If I were looking at your CV in the US I would expect a line for each project, like

supervised study of quantum electrodynamics

or

reading project on quantum electrodynamics

I would not expect a list of sources any more than I would expect a list of texts for a course you took.

Understood, thank you!

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Does IEEE accept a previously rejected paper for peer review?
A few months before, I have submitted a manuscript to an IEEE journal. But, unfortunately, it has been desk-rejected (because the manuscript is written like a report). The editor has mentioned in an email not to submit this manuscript again in the same journal.
However, I am planning to submit it again in the same IEEE journal because, I have made so much modifications and believe that this time the manuscript is up to the mark.
I have mentioned the above issue in the cover letter.
Is this a good idea? I mean does IEEE accept a previously rejected paper for publication? Because, the editor has explicitly stated not to submit the manuscript again. Does the editor consider the fact that we have modified the manuscript a lot?

I have submitted a manuscript to an IEEE journal Was it the first time you submitted the manuscript to that journal?

"The editor has mentioned not to submit this manuscript again in the same journal, however, I am planning to submit it again in the same journal."

@scaaahu, yes. This time if I submit then it will be my second submission of the same manuscript.

@DirkLiebhold, because, I feel that I have changed the manuscript considerably.

@user1838343 so "you feel" - what do you think the editor will feel?

@SolarMike, thats why I am asking for opinion/suggestion before submission, not after.

If it has sufficient changes and answers the concerns of the editor you will probably get a new hearing.
However, if you think of it as the same manuscript then perhaps you haven't made sufficient changes that it will be considers as new, rather than a resubmission.
However, if you have done the necessary work, I think your note accompanying the manuscript (NEW manuscript) should be sufficient. It is a courtesy to them so that they can be reminded of the history.
And of course, make sure it doesn't read like a "report". You may be able to get some local advice on that.

I agree with your main point here, but “if you think of it as the same manuscript then perhaps you haven't made sufficient changes” seems misleading to me.  Even if I revise or expand a submission quite substantially, I’d still often think of it as (a revised version of) the same manuscript, unless I’ve literally scrapped the original and rewritten starting from a blank document.  The relevant thing is not “do you feel this is the same manuscript?”, but “do you think you’ve revised it thoroughly enough to address the editor’s concerns?”

@PLL, no argument from me. It is just a psychological cue as to whether it is sufficiently different. A "wake up call" if you like.


text:
Verb plurality when citing paper with multiple authors
I already wrote a paper draft using inline citations like the following:

However, [12] argues that ...

Here I use "argues" instead of "argue" because the citation "[12]" acts as a singular noun (i.e., the paper), regardless of how many authors that paper has.
Now, I must change my citation style to the following format:

However, Smith et al. [2018] argues that ...

Must I change "argues" to "argue", since the subject is plural (i.e., multiple authors)? Or can the phrase "Smith et al. [2018]" still refer to a singular paper, meaning "argues" is still correct? Is it better to be consistent and always use a singular verb (I have many such constructions with single and multiple authors), or should the verb plurality depend on the number of authors?

Please take a look at this and this, I believe between the two you will find your answer. If not, please mention why you feel your question is different.


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My main research advisor refuses to give me a letter (to help for apply US physics program). What should I do?
By "main" research advisor I mean: with him, I got my most valuable research experience, greatest results and of course I invested most of my research time. Our field is Physics and I am making some achievements, but when I asked him for a recommendation letter for my PhD application, he refused and said I would not want his letter if he really writes one. I'll give his reason at the end, but I want to state my own question here first.
Will it be weird that I state my research experience with him very clearly (I think it will make a strong part) in my SoP but without his recommendation? Will the admission committee wonder where this advisor's recommendation is? If this is not a problem, does it even help that I merely mention this experience in SoP without the support of a letter? I have another piece of research experience from a very prestigious place and I have the LoR from my supervisor there, but that one doesn't have strong results as this main piece of experience and I am counting on this experience to make my application strong.
Here is his reason why he doesn't want to recommend me which might be trivial to my question but I guess you would want to know.
First, my undergrad major is an engineering field that has almost nothing to do with Physics. My advisor said if he is recruiting graduate students, he would only consider Physics Bachelors to be graduate students because it will be very hard and even impossible for students trained in other majors to shape their thinking to be suitable to do research in Physics. I am no exception, although I am doing part-time research with him and have taught myself most Physics core coursework (Damn, another equally prestigious Physics Professor in the neighbouring office just holds the opposite view). For me, his suggestion is that I should treat Physics as a hobby but forget about going to graduate school. (We encountered a nasty math problem which was important for logical completeness of our work some time ago, and he got around it with a trick which to me was "ridiculous" by then. I proposed my own alternative method, but in his view my method is rigid, and he then used my failure of understanding his trick to tell me that my thinking is already not suitable for Physics.)
Second, he is really really an "idealist" in doing research. Since I am applying for grad school, I want to speed up a little bit to revise our work to have a presentable draft (I had already derived the results by then, we were polishing the writing and dealing the above-mentioned math problem). He said I was appearing to be like a "pragmatist" because I was not acting or thinking slowly and calmly like an idealist. He even got a bit unhappy with me when I was arguing with him, wanting him to explain his trick (mentioned in the first reason) more clearly, when I was so desperate to understand it.
As a result, he said I would not want his letter since his opinion is just he won't recommend me to a graduate program although I did research with him.

You should stop spending your time on research with someone who doesn't consider your contribution important.

Do you mean "but in his view my method is rigid" part?

In fact I am not taking his reaction as such. He isexpressing that although I am working, I am still not suitable for graduate school. We are working to publish our work in fact. But my application is now making me worrying :(

Long text, I recommend to shorten it and to make it clearer what's your point.

Its a bit hard to judge or suggest where to look without knowing more about the subject you are working in or the math trick that was used (though its probably better to mention in the comments than in the question itself, unless of course this revels their identity). I am a physicist who has a number of engineers as friends/family and could imagine scenarios where this comment makes sense, since I know their thought process tends to be different to my thought process (build something that functions vs deep understanding). Though part of a PhD/masters is to learn how to think.

I sympathize with the "two algorithms" story because I've been there myself. I have a math degree and have worked mostly on developing software for mech eng applications. Once, there was an issue proving that an algorithm would never fail in practical situations. Mathematically, that was equivalent to a statement for matrices with a certain mathematical property, there was always a sequence of submatrices such that factorization of each one had no zero diagonal terms. It was hard to even formulate the problem mathematically without getting lost in a mass of notation.

... But from an engineering point of view, it was easy to see that the algorithm was equivalent to saying that it was always possible to physically construct the object which was modelled by the matrix, piece by piece, without the need for any temporary supports during the construction process. Professional engineers (and probably most people who had played with LEGO!) could easily understand why the algorithm always worked. In my case, luckily there was no need to provide a formal mathematical proof, so we just got on with using the algorithm in practice!

I have worked in a situation like yours (no respect for engineers). I got out of that lab, started over somewhere else and finished my PhD in 3.5 years and incorporated aspects of comp. engineering in my thesis. The world needs more people who are multi-disciplinary, not less.

Could you re-phrase that? Does "My main research advisor refuses to give me a letter (for whatever)…" mean your advisor won't give you a reference, or what?

@RobbieGoodwin yes, he refuses to give me a reference.

If it causes a problem on your side, you could ask him for that letter anyway. Whether it is "bad" depends on the context. It is possible that you come in a situation where the bad point is not a problem. For example, if I would need an employee, and, after talking with you a while, or showing you the work with you joining the work for half a day, I could possibly decide just by intuition. And in this case, I'm basically not interested in reading the letter, and will probably not do it. But also in a formal situation, I may have only you, or just like you mor than others, I may not read it.

@VolkerSiegel Ignoring reference letters can have legal implications. If a letter anti-recommends someone and you  hire them, and it turns out the letter was right, you may not be able to easily get rid of them, despite underperformance, because they can claim you knew what you were getting.

It is always possible that the employer does not find the "bad" part relevant enough that it causes a problem, if at all.
Also, there can be lucky situations where the letter is not read at all - it is always possible. All the above is equally possible with no letter at all - that for some reason nobody ever thinks about it or at least not cares enough to actually. ask you. It applies also for the letter being read only partially.  (Do you think this should be an answer?)

@CaptainEmacs Of course, pessimistic cases are possible too, on both sides. It could be just something unexpected randomly. That means the probability for an optimistic case is higher than I could estimate. From general life experience, I would say the probability is high enough to be relevant. There are more unexpected cases than one expects by intuition.

@VolkerSiegel The question is as always how costly can the pessimistic case be? There is a reason why bureaucracies are risk-averse, because when something goes wrong, it can go very badly wrong. If you have excellent people skills, and you can trust your personal judgement, then you might be able to afford to ignore the letters. If your judgement is not so reliable, probably not.

Here, we are only interested in the probabilities for the employees side! On this side, the pessimistic probability is quite high, but the cost for a pessimistic outcome are very low.

Yes, it might look a bit weird, but you don't have control over that. And he is giving you good advice that he shouldn't write you a letter. Not every advisor is willing to be so honest.
But, I don't think it is an absolute block to your plans. Find others to write you strong letters and (US perspective) you should be ok.
What you need are letters from people who can confidently and honestly predict your future success based on their experiences with you. This advisor is not that person.
And FWIW, it is his problem, not a problem with your work mode. And no admissions committee should make any decisions based on guesses or suppositions. They should take your materials as they stand.

Do not press for a recommendation letter of someone who is reluctant to give you one. Nothing good is coming out of that.
You have a different approach to things. It's very dangerous of you to label him as "idealist", maybe what happened is that he considers you an strong pragmatist and if you let through that you see him in the opposite side of things, this simply escalates to the point where he sees you both not to have common ground.
Engineering and Physics have a lot in common, but they are quite distinct in the way of thinking. Physics is about finding out how things work, Engineering is about how to use these rules to create something that you want to do specific things. The way people think in both areas is quite distinct and you can sometimes recognize whether the education background of someone in a 3rd field comes from physics, engineering, math, or something else. Thinking style is almost like a signature.
You ended up in a situation where your prof sees only the outcome-oriented aspect of your work. [As an aside: The rigidity he accuses your trick of is a bit of an accusation that he may have leveled against a mathematician rather than an engineer (assuming your trick is really rigorous), which is unwise, because usually it is better to use the more solid mathematician's "trick" than a handwaving one. The latter may be justified to get an insight, but not because it is better.]
That being said, that's not a bad thing. Different backgrounds can bring in different fresh ideas into a field. However, if someone holds prejudices against you, there's not much you can do. You could of course try to kick off a social movement against the discrimination of engineers by physicists (and I am only partially joking here, because this is a form of discrimination, a suitably named -ism).
But, as long as you are on your own, your best bet is to look for a different recommender. You will not get a good recommendation from him, and better to answer questions about that discrepancy during your interview once that happens.

Get a job.
He is trying to tell you that you have no future in Physics at a uni.
You could try to see if someone else would write a letter but I doubt that would be productive.

"I doubt it would be productive" - how do you come to that conclusion?


text:
When do I say I can only start PhD late
I am applying for a PhD position in computer science in Europe. They specify a start date but say that it can be negotiated. Due to other circumstances, it is not possible for me to start until a month and a half after their given start date.
I see two options on what to do now. Either I say so at the end of the motivation letter potentially putting myself at a disadvantage, or I start negotiating once (/if) I get an offer, risking that someone will be annoyed at me because "I was supposed to tell them earlier" (which would clearly not be a good way to start a PhD if that someone would be the supervisor).
Which option should I choose? Would it be advisable to wait until I have an offer?

(European professor with hiring experience here.)
A month and a half is not a significant delay, but a quite moderate one. If the professor wants to hire you, it's rather likely that they would be happy to have you already one and a half months after the planned start date! So I recommend to not address it before you have an offer or they ask.
More generally, it's understood that people take a few months to start a new position, even more so in academia, where people typically move between countries for a job. That applies even stronger in the times of a global pandemic, where visa issues alone can defer the start date by many months.


text:
Starting PhD, university says I don't have to sign contract
I am starting my PhD in three weeks in Denmark. In Denmark, it is usual that PhD students are formally employees of the university but also have student status. I have received recently my employee contract electronically through a trusted website (not email, but a governmental portal, with verified identity of the sender). There was no way to sign it, so I asked how to sign it. To my surprise, I was told that I don't have to sign it.
What is that? The contract states some of my obligations as well as my pay. How can anyone enforce a contract that I have not signed? I have not even explicitly stated that I agree with the contract. (I would have some understanding if they told me to reply that I agree with the contract through the trusted website.)
Can there be any negative consequences for me if I don't sign it? I don't think I would be being unreasonable if I ask firmly that I want to get it signed. For example, the contract specifies several-months-long notice in case they want to fire me. Even though it is unlikely that would be ever a problem, I am worried that it may not apply if I don't sign the contract. Or am I just overreacting?
My supervisor is a very reasonable person and I am sure he would understand if I tell him I want to sign (and get signed) the contract.
If it matters, there is no signature on the contract I have received but it was provably sent by the university's HR.

Update: While it was not necessary for me to sign the contract, I did need the signed contract from them. I needed this for my residence permit (even though I have an EU citizenship) as well as for my "tax card" (a document that determines my tax bracket (without it, one pays the maximum tax)).

I don't know the law, of course, but there may be provisions for "implied consent" to the terms if you show up. A signature only makes consent explicit.

Does the e-contract website serve as a long-term reference that can be accessed later? Having proof of the date and content of the contract the university submitted to you would make it difficult for them to later claim that you actually had a different contract or no contract at all.

@NuclearHoagie, excellent point. You could also make a copy and have it notarized by some legal authority.

@NuclearHoagie, yes, it will stay there forever.

Forget it. Both sides know they have exchanged the contract, when you show up for work and they let you in, that's a perfectly clear sign of mutual agreement. The audit trail of that government portal and your email exchange with it is another one.

Duplicate of https://law.stackexchange.com/questions/31715/what-is-the-point-of-signatures

https://law.stackexchange.com/questions/18875/is-signing-a-document-useless-if-no-one-checks-the-signature

In Switzerland one does not have to sign the contract as a PhD. That is due to some strange law we have. Maybe in Denmark this is the same.

Very interesting question (highlights variation in academic practices) -- I'm in the U.S. at CUNY, our "contract" is something formally negotiated between university & union, not something individuals sign. I get a letter of appointment from the college President, stating I should be aware of college bylaws & collective bargaining agreement, and sign I've accepted that, but don't personally receive or sign the "contract" itself. PSC-CUNY Contract

FYI, the links further up are definitely not duplicates of this question: those ask what good is signing, whereas this asks what's the state of not signing.

Here is a video explaining contracts according to Marx. No, not Karl, Groucho.

Also in Germany, a work contract by mutual consent is valid but the employee has a right to a written contract. Fixed term contracts require written form, though, incl. signatures. This is why you'll never find such a one-sided proceeding for a PhD employment contract in Germany - the contract by mutual consent would be permanent and there are few things that scare German university administration as much as permanent contracts... (AFAIK, conditions for ending employment contracts differ a lot between DK and D). (side note: you can do a PhD in Germany without being employed by the university)

Besides that, again I hope DK is less burocratic than Germany, but over here, there will be things you have to sign but they are not part of the employment contract. E.g. that you read and understood the anti-corruption rules etc.

According to these Danish labor union websites, it is correct that you don’t need to sign:
https://www.detfagligehus.dk/faa-hjaelp/loenmodtager/i-arbejde/ansaettelse/ansaettelseskontrakt/
“The law doesn’t say that an employment contract has to be signed. The contract is valid without a signature. What matters is that it has been given to you.”
https://krifa.dk/fs/ansaettelsesvilkaar/ansaettelseskontrakt-og-vilkaar
“Did you know that … there is no requirement that your contract has to be signed? If it has been given to you and/or you work according to the contract, it is already valid.”

Can you elaborate? So what happens if you do an interview, they just send you a contract but you don't like the terms you still have to use these terms? What if you send contracts to random people?

I will let it go, based on this answer, but I still agree with @lalala. For example, I have been coming to the university for the past couple of months for free because I enjoyed it. This would, for example, make the implicit consent noted by Buffy more complicated, I would expect.

@lalala: It’s implicit that the employee is not bound by the contract before giving their consent (it’s just that that consent can be given simply by showing up for work). The quotes are from informal Q&A texts – they authors have not been super careful with their formulations.

@lalala, while I this is from a German perspective, I wouldn't be surprised if the same holds for Denmark: these contracts are subject to collective agreements (unionized) - there's hardly anything to negotiate. The full terms are publicly available in the internet. I've had a single page employment contract at a university with plenty line spacing, basically stating who's employed, on which project, for which (fixed) term,  and basically a #include statement for the collective agreement. For postdoc positions, there may be a little wiggle room to negotiate on step on the wage scale ...

...(which would correspond to you conducting the work without the need for academic supervision/supervising yourself) and the years of work experience they count towards this job. A PhD student would almost always be supervised and start without academic work experience.

@lalala Legally, this is called acceptance by performance.

In US law at least, a "contract" doesn't necessarily mean a piece of paper that two parties have signed. Any agreement, whether or not it's in writing, can be enforceable. If you are attending the program, that's pretty good evidence that you and the university have made an agreement.
But it's still a good idea to get a signed copy since it's a lot easier to point to a piece of paper than it is to argue that the contract was valid in the extremely unlikely event that the university disputes it.

it's not only US law, but almost every jurisdiction in the world. The principle goes back to at least Roman times, and it probably precedes it. Any jurisdiction that was even a bit in touch with the Romans (roughly everyone) has a clear separation between consent and formalities, and the primacy of consent.

And indeed if you had to draw up a written signed contract every time you popped into a shop to buy a newspaper, or engaged someone to clean your windows, or the vast vast vast majority of other contracts we enter into on a daily basis, life would pretty quickly become unliveable!!

Here while it is generally true (for work contract oral agreement is enough) some agreements have to be in writing (termination of work contract for example) and some have to be notarized (like real estate purchases), otherwise they wouldn't be valid.

Employment contracts without signatures are less common in Academia, but most academics would consider them acceptable.  In my experience, university purchasing is conducted entirely with unsigned contracts, but employment contracts often have a digital image of a signature on them.  The image is just there because it is traditional, not because it is important.
If you want an answer based on law, consult the Law Stack Exchange.


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How to handle a case of unpublished plagiarism?
I am a Master's student in a field of the humanities. Half a year ago I was invited to an informal colloquium of mostly doctorands and post-docs who work at the institute I'm studying at. One participant's draft for an essay was the topic of the first meeting.
On working through that draft the evening before, I found five sentences in total that were obviously copied from online sources (blogs, wikis, etc.) without any citation. Due to stress I decided to postpone the decision on what to do with my findings and did not attend the colloquium at all.
To date, I can find no evidence online that the essay has been made available to the public and I do not know if it was ever supposed to be. Its form though is clearly that of an essay (not a sketch or an unstructured gathering of ideas), so that I can not think of any circumstance under which this would not qualify as straight-out plagiarism.
The author is still working at the institute and holding classes.
What is the professional way to handle my findings?

In the form in which you read it, did the essay have any citations?

@PatriciaShanahan Yes, it did.

You have no findings at all.

Not all instances of plagiarism are equally severe. So, while your assessment that this is plagiarism may be correct, it looks like at most a fairly mild case of it.
And it may not be plagiarism at all: you say the document being read was a “draft for an essay”. Well, drafts are understood to be incomplete works-in-progress, so having some missing citations (or factually incorrect statements, bad grammar, or any number of other problems we try to avoid in finished documents) is in general acceptable. If the document was explicitly marked “draft”, I don’t see how a plagiarism accusation could make sense. If it wasn’t, then it would depend on additional contextual details - I guess we’d need to know what your description of the document as a draft is based on.
A related question is, what benefit would come to the writer of the essay from passing off the quoted sentences as their own? Was the work read in that meeting graded, or was there some other material benefit they could have hoped to gain? If there was, that could make an intentional deception more likely as a possible explanation.
At the end of the day, what you’re describing sounds sufficiently mild that I don’t think you should get too alarmed that the person is “still working at the institute and holding classes”. You can complain to their adviser or some other person in charge if you are genuinely concerned, but I would expect that this person would, at most, be told to be more careful in the future, but would not suffer (and do not sound like they deserve to suffer) any more severe career consequences.


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Dealing with the inevitable presence of mistakes in paper submissions
When writing a paper, there are inevitably mistakes. Many of these can be caught by careful revision, and the more time spend revising, the more mistakes which will be caught. However, clearly a draft should be submitted at some point.
How should one determine this cutoff point? How much does it vary by field, individual, etc?
As a concrete example, I recently submitted a paper to a big ML conference where one of our results was off by a factor of two. While we fortunately caught this error before the camera ready version, the experience has caused me to question whether I am spending sufficient time on revising my work before submission. I have heard that such errors repeatedly occurring in published work can seriously damage your reputation in math.
On the other hand, I wonder if the standard for errors like this differ across disciplines. For instance, if we had submitted the paper to a journal in applied math, then I believe such an error would have been caught by the referees since the review process there is more fine grained. Thus, it also seems possible that fields in CS, where conferences with short review processes (relative to math journals) are standard, have a lower threshold on what what kind of errors are acceptable to the community.
I've already discussed this with my advisor. However, I am also interested in hearing the thoughts of others on the issue.

Edit: Thanks everyone for the responses! I'd also be interested in the second part of the question about how these standards vary across disciplines, individuals, etc.

ML conferences may indeed be a special case, reviewing there tends to be superficial, and the number of completely wrong theorems (not just by a factor of 2) is depressing.

Getting some other eyes on the manuscript is pretty essential, especially if you are starting out.  Maybe the first person you could ask is supervisor, or friends who are mathematicians who can glance over the manuscript and spot obvious flaws.

@MarcGlisse I am even more depressed by the general quality of the English text in ML-based papers.

Do other areas of CS not have the same issues?

I believe Terry Tao has probably the most ideal model.  He has a popular blog and his works are reviewed by many people before submission; i.e., he capitalizes on his fame to further improve the quality of his work.

@MarcGlisse well, often rather not even wrong. And yeah, the review process seem to be mostly about rating how exciting results a paper presents.

Ideally, the desired error number is zero. But as you observe, it is difficult to achieve. One problem is that the author of a paper is probably the least able to proofread it. (Maybe not literally "least", but I hope you get the point.) The reason is that when reading your own work what you "see" on the page is too often what you thought your wrote, not what you did write. Your brain glosses over errors.
What you need to stamp out errors is a set of fresh eyes of people with enough background to find any errors. They aren't influenced by what you were thinking when you wrote the paper. This is one of the main benefits of the reviewer system, actually.
An important author in CS (Don Knuth) has the practice of funding bounties for errors found in his book. He will send a check to the first person to catch any error. (He is so renowned, however, that few cash the checks anymore.)
So, you do what you can, being as careful as you can, for as long as is reasonable. But get some new "eyes" on your work.

Note also that some important errors in important papers have gone uncaught for decades. I once found an error in a paper by a renowned mathematician about 40 years after the paper was published. I don't claim to be the first to notice, of course.
I'm working on a long term project and have, after a few versions, still seen some incredibly bone-headed errors. The biggest thing holding me back is the lack of those "other" eyes.

Thanks for your response, it makes a lot of sense. I'd be interested in further details about the difference between disciplines if you have any thoughts. In particular, about the difference in expectations for review.

https://en.wikipedia.org/wiki/Knuth_reward_check

In my field, the main journal's guidelines simply states that accepted submissions should be "as far as is reasonably practical, completely free from error". They still employ sub-editors, however, who do change things (grammatical, almost never mathematical) in the proofs.

In addition to typos-versus-flawed-proofs, there is another distinction worth making, I think. Namely, some proofs really are (perhaps) delicate computations (or other intensely symbolic lines of reasoning), and thus their persuasiveness and believability is already somewhat fragile. For example, here typos are terrible.
In some contrast, some written arguments are more "narratives" of a procedure/process that could be carried out, with many details visibly dictated by "the plan". If/when the details are determined in a more top-down fashion (or can be made to seem so), the argument is much less sensitive to typos (or even larger blunders...)
I'm not claiming that there's a dichotomy of innate nature of arguments. Rather, I'm advocating more-narrative approaches to what might otherwise invite fairly fragile, long computations without a good accompanying narrative. More-narrative approaches can be more robust, and less sensitive to typos and other errors.

If you have a long fragile computation, please for the love of your favorite mathematical deity copy-paste it into a computer algebra system, substitute generic values for enough variables to make it tractable, and have the computer algebra system check every step.  Chances are you've made a nonzero (but hopefully even) number of sign errors.

@JoelReyesNoche: I think that "her " should be "here" (as we're talking typos... :-) ).

@AlexanderWoo While I agree that CAS systems can be beneficial for spotting odd mistakes in calculations and programs alike, normally they do not provide a reliable way to “check” a calculation/program: https://www21.in.tum.de/~ballarin/publications/thesis.ps.gz. This is what the proof assistants are for (of course, nowadays there exist a variety of interfaces that allow combining the power of the traditional CAS systems and proof assistants).

@AlexanderWoo When I make an even number of sign errors, I make them far enough apart that they fail to cancel out.

Here is my approach (pure math):

I consider a paper ready for submission when I personally am completely convinced of it's correctness.  If I only think, "it's probably okay", that's not good enough.  That said, I do put more effort into verifying central statements than tangential asides.

When possible, I try to cross-check my results in different ways (do they contradict other approaches or heursitics) and compute examples.  For me, computing examples and comparing with related results in the literature is very important for finding errors and convincing myself my finalized version is correct.

Explain the work to others, and ask others for feedback.

After I finish writing the paper, I put it aside for a couple of weeks, and then reread it as carefully as I have the energy to.  If there were significant changes, repeat this.  Do this again after referee reports.

This doesn't mean all of my papers are error free, but as far as I know there are no major errors in the final versions of my papers.

Typos: "it's correctness", "heursitics", "error free".

@YuvalFilmus I don't try to make sure my SE posts are error-free!

My response to this, with an amount of seriousness safely bounded away from both 0 and 1, is: depending upon my mood / psychological / metaphysical state, I may not be completely convinced of the correctness of anything.  (But, with over 50 published papers, I only know of one result that is really faulty: the proof is correct but doesn't prove as strong a result as claimed in the statement.)

@PeteL.Clark I agree that it's subjective, and "completely convinced" might be a slight hyperbole, but I think the main thing I was trying to add to the existing answers was the computational aspect.  I realize I am error-prone, and actually checking sufficiently diverse examples (when possible) is often what convinces me that the results are okay.

+1 for sanity checking with other people's results, examples, test cases, comparisons against earlier versions, looking at intermediate results etc. and taking as much time as it takes. Especially in complex algorithmic analyses it's so easy to incorporate mistakes. Please don't add more irreproducible papers with loads of mistakes in the details to the already huge pile.

Depends on mistakes. If these are crucial mistakes in arguments, you should correct them before submitting the paper. It is doable. Misprints, on the other hand, are not that important and you do not need to catch them all. So to submit your paper you need to be absolutely sure that the arguments are correct. Recently I edited a paper submitted to "my" journal. The referee found that all proofs are correct. Then I found lots of small misprints and gave the authors a few weeks to proofread the text. When they do that, I intend to recommend the paper for acceptance.

Well, some mathematical misprints can be troublesome...

Assume the perspective of a Reviewer.
As a Reviewer, I will never reject a paper because of "mere" typos unless:

they make the paper unreadable. But this happens when the author(s) spend no time in spellchecking, or have very little English writing expertise (and both of these are different problems)

they are still widely present after the first round of review. I can tolerate some typos in the first submission, but my acceptance level decreases for subsequent rounds, especially if I made it clear that the paper required revisions in the English text (but this is also a different circumstance than what you are likely referring to)

the typo affects a crucial claim. These are the most crucial offenders, because these "mistakes" undermine the credibility of the paper and can be the ground for rejection. I once rejected a paper because the authors stated "X" as the main contribution of the paper in the Introduction, and then stated "not X" as the main contribution of the paper in Section 2; the rest of the text did not allow me to determine which was right, and most of the remaining paper was too complex for my expertise, so I suggested a rejection. Note that this was explicitly due to the usage of the word "not", which can single handedly flip the table around.

the typo affects Proofs. This is self explanatory and is strictly related to the previous point, but it demanded a dedicated entry.

the typo affects the Results (numbers, tables, figures). The result section is arguably (depending on the field) very important and usually the source of many significant mistakes - which may or may not be considered as typos. Consider a 2d plot where you have two horizontal lines, a red at y=3 and a blue at y=6: if in the text you say that "the blue line is clearly lower" that is a big problem. Was the mistake due to (i) the incorrect use of the "black/red" color, (ii) incorrect use of the "lower/higher" term, or (iii) maybe it was a problem in the plot? As a Reviewer I do not know, and hence I can use this issue to reject the paper.

In summary, my recommendation is to try to point out the key areas in your paper that are likely to be read by Reviewers and focus on having those completely free of mistakes. Perfection is difficult to guarantee, so at least focus on the big picture.
As a final suggestion, make the Abstract error free: abstract with typos are a red flag.

When making the abstract error free, also check the title (and author names)

s/redable/readable? Ironic given the context

@D. Ben Knoble, that's another suggestion: don't write a paper with your smartphone.

Perspective of a recent PhD student here:
You learn to make papers "better" by writing papers. And by "better" here I mean useful to your audience. The goal of academic writing is not to create perfect piece of text that will stay valid forever, but to help others and to move the scientific discussion forward. You can do it even when you have mistakes and typos.
By writing and submitting more work you will improve your work process (for me it was learning to slow down and letting papers "marinate" for a few weeks without me working on them). You will also see your mistakes published, which will remind you to try harder next time.
However, typos (not critical logic/math mistakes) and other blemishes are not disqualifiers for an academic piece to be useful.

Definitely agree with marinating. Forgetting what you wrote, and then reading what you actually wrote, versus what you thought you wrote, is a good method of making a better paper.


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What steps could universities take to reduce Ph.D. drop-outs?
One of the major issues in universities with respect to PhD is the high dropout factor. Demotivated students cause a big loss to the university - a lot is spent on assistantships, but in the end, the students quit without making any meaningful contribution.
What steps do/should universities and faculty members take to reduce alarming drop-out rates? One step is obviously to choose the right person for the job, which we expect the admissions committee to do anyway. PhD involves years of wading through uncertainty and possibly it is in these years that students get distracted and unfocused. How should universities ensure the students remain unwavering in their efforts during these uncertain years?

If they did assistantships, then they have contributed something (and probably at quite low wages!), even if they never make a novel contribution with their dissertation.

One difficulty is that it's far from clear what the ideal dropout rate should be.  Probably not zero, for two reasons:

Even the best students sometimes find that their interests change over time, in ways nobody could have predicted.  Dropping out may become a quite sensible choice, in which case it's harmful for the university to discourage it.
It's reasonable for a university to give someone a chance even if it's not certain that they will succeed.  The only way to get a really low drop-out rate is to admit just the applicants that are obviously destined for success.  The top few schools can get away with this, but if everyone tried it, then many talented candidates would be shut out from graduate school.

So some attrition is OK, and some is bad but may be a necessary consequence of policies that are on the whole good.  The question then becomes how you distinguish these kinds from needless and damaging attrition, and then how you minimize that kind.
Advisors play a key role here, because some are much better than others at being supportive or motivational.  However, at least in mathematics, most advisors don't supervise very many students, so the numbers often aren't large enough to see patterns clearly.
I'm sure people have studied this problem, and perhaps identified best practices for addressing it.  However, in my experience any studies or solutions are not especially influential (at least in the few math departments I've been in).  Most discussions are at the stage of trying to figure out whether there is a real problem and if so why, rather than what to do about it.

It's not enough for advisors to be supportive and motivational; they also have to be aware of their student's progress or lack thereof and willing to offer appropriate feedback/guidance/advice.  My department's dropout rate (especially the late dropout rate) went down significantly when we started doing annual reviews of all PhD students.  Also, I'd be surprised if one couldn't see patterns at the department level, even in fields like math where each advisor has few students.

@JeffE: Interesting, what do the annual reviews consist of (and how are they carried out)?  As for seeing patterns, that's part of what makes this contentious.  You can definitely see patterns, sometime even at an individual level, but the sample sizes are small enough that some faculty always argue that it's not statistically significant and therefore not fair to them.  The net effect is that it's very difficult to target anything, even advice or guidance, to particular advisors, no matter how justified.  These annual reviews sound appealing because they'd treat everyone on an equal footing.

Every spring, students submit an online self-evaluation form, which includes classes taken, admin hurdles jumped, talks given, papers submitted/published, funding used, etc. since last year; a summary of ongoing work; and a few advising questions. Then advisors submit comments/feedback on the student's self-evaluation.  Then (in principle) each research area meets to discuss all its students, and the area chair submits comments/feedback on each student's self-evaluation.  Feedback is collected and sent to the students; other comments are saved for reference in future years.

And yes, this is also implicitly an advisor self-evaluation, with feedback from our peers.  Mostly what we want to avoid is the answer "I don't know." (or worse, an unjustified "Just fine!") when asking an advisor "So how's your student X doing"?

I think this is asking the wrong question. To me, the right question is, what are the main reasons that students drop out, and what steps can be taken to address those reasons? To properly examine this data would need to be gathered, but anecdotally I can think of a few reasons:

Student gets bored/loses interest/experiences major life changes (marriage, death in family, midlife crisis, etc.). This will happen in any profession, and are essentially unavoidable. It can be mitigated somewhat by stressing at the outset the time commitment necessary to complete a PhD, but that can only do so much... a lot can happen in four (or five, or six, or...) years.
Student has major fallout with advisor. Again, this happens in every profession... people have personality conflicts with their bosses all the time. Communication, and lots of it, is often cited as the best tonic for this problem.
Students become disillusioned with academia. This problem often manifests later on in the career, as papers are rejected, grant applications are rejected, and/or the student has difficulty with his or her research. I would venture that this is simultaneously the most treatable problem and the most difficult to treat correctly; the advisor has to work very closely with the student and give them good academic and professional advice. From my experience, the success of the advisor in this task is often the main factor in whether the student remains in academia.

There are likely other reasons students drop out; if I think of more I'll add them, and please list others in the comments.

Barbara Lovitts' book Leaving the Ivory Tower presents a lot of interesting research on this topic.  Your anacdotal summary does a good job covering several major findings in her research.

I think that the problem is that often many professors underestimate the PhD student's will and personal scientific aims.
Often it happens that a perspective PhD student apply for PhD admission to work on a project X, and then, once he/she starts the doctorate program, professors say to him or her "Surely you will work on X some day, but now you have to work on Y".
But, effectively, that "some day" never arrives. So the PhD student looses motivations, gets sick, and finally quits...
To answer the question, I would sat that PhD student supervisors should take more care of the PhD student will and expectations, and understand that letting him/her work on the topic he/she prefers will make him/her more motivated and finally get better results than working on someone's else objectives.

Possibly universities should be more careful about hiring PhD students in the first place.  It's not enough that they are smart.  Students need to be persistent and motivated and their motivations should be realistic.  I think it helps a lot of if the students have had some time out of academia so they know early whether this really is what they want to do with their time.  I've seen a lot of faculty try to talk smart students into staying when if anything we should be trying to talk them out of staying to make sure they really want to be here.  (And "staying" is a bad idea anyway, it's better to change institution so it really does feel like you aren't at school anymore, because a PhD is a lot different from a college degree.)
I think the worst thing is students that hang around forever neither quitting nor working hard.  It is the student's life and career and time, and they need to take it in hand and change supervisor if they need to, or change project, or leave.  But wasting everyone's time including their own is almost criminal.

"I think the worst thing is students that hang around forever neither quitting nor working hard." – I'm one of those and I'm neither proud nor happy about it. My first project didn't go well (I'm still finishing it) and the increasing frustration end up tanking my motivation and productivity. I started working on something else two months ago and it felt like a breath of fresh air.

Pay, if you paid me what I would make working on an industry project I would have been a lot more compelled to stay.
At the moment, even looking purely at GRA hourly rate it's almost half the hourly rate of a junior engineer. The way current PhD system works is basically projects get subcontracted out to universities who then pay the people involved a fraction of their real worth in hopes of getting a degree afterwards.

As a person who dropped out from a part-time PhD programme in Engineering in the UK. I can add my reasons for dropping out.

Family - being a father and husband changes worldview and sometimes it becomes apparent that there are more effective ways to further one's career than PhD if your aim is not to be an academic. But a university can't do much about this
Lack of proper academic knowledge in the area of PhD project. For example my professional experience  and academic background was in electronics, audio and acoustical engineering whereas PhD turned out to be be essentially a theoretical physics. Any physics  bachelor would have easier time than me.
Supervisor is  not an expert in the area of PhD project. Especially difficult if also the situation in point 2. is present. The lack of appropriate guidance in this case is harmful.
The experimental part is  not within control of your department/unit in my case it was not possible to just pop down to the lab to do experiments. It was a cross faculty project and it was  difficult to communicate  with the other people from outside you faculty
Lack of community support. As a part time student it was difficult to have other PhD students available as you colleagues. Also the project  was so removed from anything that the other PhD student were doing so it was quite alienating project.
If your goal is just to further your knowledge it actually may not be the best way to do it. As rigour required to prove your method would steal your learning time.
Topic, it is true that even if you love the topic you will hate, but is also true you can grow into the topic and will start be passionate about it. But if your project has no purpose to you it will be extremely difficult to  finish. You need to believe in it. In this case supervisor should at the beginning talk about possible applications or importance of the problem. But there is only so much they can do.

I need to add that the University and my supervisors were really helpful and nice, but the hurdles were just too much for me.

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Ethics of/rules regarding submitting multiple presubmission inquiries
It is well-established (and typically spelled-out in journals' instructions to authors) that is unacceptable to submit a single manuscript to multiple journals for peer review simultaneously. However, the rules for presubmission inquiries (which are essentially cover letters asking whether the journal would be interested in reviewing a given paper) are not clear to me; a presubmission inquiry does not constitute a formal submission.
Is it permissible to submit a presubmission inquiry regarding a single manuscript to more than one scientific journal?
Is it unethical to do so?

Further details on what presubmission inquiries are:
Presubmission inquiries are relatively common in genetics and biology. From the Nature website:

Presubmission enquiries are provided purely as a service to authors
  (for example, to see if a manuscript is likely to be of interest to
  the journal) and are not compulsory... Presubmission enquiries are not
  required for Articles or Letters, and can be difficult to assess
  reliably; Nature editors cannot make an absolute commitment to have a
  contribution refereed before seeing the entire paper. Entire papers
  should not be sent as presubmission enquiries, but should be formally
  submitted through our online submission system.

What is a a presubmission inquiry? Is this practice common in your field?

As an author I have done two presubmissions in the past. I do not know how they are handled by editors, but as an associate editor myself I gather they are informally skimmed by 1-2 editors within hours after submission. This means it is unlikely some "multiple presubmission" would be detected and I have never seen specific rules about priorities in presubmissions.
Thus I think one is safe from editorial action if "caught" in multiple presubmission enquiries. However I believe it will not be seen with good eyes by a handling editor, and might leave a bad impression.
Thus I would not recommend doing it. Particularly as an editorial answer usually comes in less than 48h.


text:
How do I modify the abstract in Arxiv (without changing the paper)
I recently changed the location of a link to be in the abstract part. While it works perfectly in the paper, the link doesn't work of Arxiv (the main page) because it's in the end of a sentence and they added the "." to the link instead of realizing that it's the end of the sentence.
Do I need to resubmit even though i'm not changing the actual paper? How terrible is increasing the version of a  paper (I'll probably have to change it again in a month or two)?

I guess up to 5 times revisions are allowed for a one submission. If the submission is online, you cannot make any changes rather than v2.

It's going to be v3. How bad is it? does anybody cares (it's under review)?

All the versions will be available online, however your arxiv link to title refers to the latest version. I guess it’s alright.

The only changes that do not generate a new version number are adding a journal reference or DOI. Changing the abstract will generate a new version. As far as I am aware there are no limitations to the number of updates, but at some point arXiv will stop including udpates in the daily mailings (I believe after version 5). Making many new versions with minor changes might give the impression though that you have not carefully checked your manuscript before submitting, so generally I would recommend to save such small updates for after the paper is accepted or revised. This would also be less work for yourself and for the arXiv moderators.
Personally, in the case you mention, I would not bother to update it now. Most people are smart enough to try to remove the period at the end of the URL.


text:
Is it okay to modify the LaTeX template for article submission with additional packages?
I want to start writing on an article that is probably going to be published in one of the IOP journals. There is a template for their publications, but it lacks some (for me) essential packages. Since I've never submitted an article myself, I want to be sure the editing process goes as smooth as possible by eliminating problems early. So here's the question:
Can I add all the packages I like to the template without pissing off the editor? I talk about things like inputenc, fontenc, biblatex, microtype, etc. Nothing fancy, but very basic LaTeX stuff. I also prefer to have a separate .bib file for my bibliography, since I have them already organized that way and do not want to manually copy the info into the bibliography as suggested in the template.
I already read the guidelines for authors and there was no mention of modifying the template, only that its use is highly appreciated.
If anyone could provide any (preferrably inside info) on how editors work with submitted LaTeX files, that would help a lot! Thanks.

You can add packages, but you should maintain their template. You can also read various papers in the journal to see the presentation style. However, what is more important is the content of the paper itself, with less emphasis on the presentation.

I have never met (or heard of) an editor that cares about the Latex journal templates. Or guidelines for authors. At least in my field, I would say that you can safely ignore them. Just give them a pdf, and it's fine. If there is anything that may have an impact, it's packages that may alter the page limit (if there is one). But definitely not inputenc, fontenc, biblatex.

fontenc and mircotype are essential? They just alter the output (and will probably removed for the final publication anway…).

@Dirk well, they are of course not essential, they are just packages that I use in every document by default, so I gave them as an example. I realize that the actual typesetting is out of my hand in the final release.

@FedericoPoloni Yes, with my first papers, I tried to follow the submission guidelines exactly including bibliography style, and then I discovered for the initial submission (almost?) no one cares (at least in math).

In mathematics, this is only relevant AFTER acceptance, not before.

Unless explicitly forbidden, adding packages is usually ok and fully expected - e.g. in order to add support for listings, tables, symbols, encodings, operational utilities (extended macro/logic support), or specific features thereof. This should, however, never mean a general change in the appearance of the paper. Therefore, packages that globally alter fonts or font sizes are usually not allowed.
As for using a separate .bib file, you can usually work with that and (if explicitly requested by the guidelines - this varies a lot by publisher) copy the formatted information into the .tex file as late as for the camera-ready version (when nothing changes any more).

As for the last point: No need to copy something - just hand in the automatically generated .bbl-file together with the other documents of the paper.

@Dirk: Ah, probably true for IOP. I have come across some other publishers who insisted to have the bibliography right in the .tex file (and also some who were ok with getting a .bib file). I'll clarify this is publisher-dependent.

I've seen some specifications about the bibliography like you mention and restrictions about certain packages, but out of curiosity, do you know of any journals that don't allow any packages? (or any besides a small explicit subset?)

That said, add packages only when your paper requiers it. I have seen too many papers loading 20+ packages when all they needed was amsmath, which was loaded by the document class. A lot of package do thing in the backstage and can make the class not do what it should, like enumerate and enumitem (which change the typography of all counters in {enumerate}) or inputenc and fontenc (which can render the paper unreadable if you're not using the same setting as the journal and write in other language than english).

I usually publish in IOP journals and I can confirm O. R. Mapper's remarks.
As an example, these are the packages included in a recent paper of mine:
\documentclass[10pt,a4paper]{iopart}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{iopams}
\usepackage{amsopn}
\usepackage{graphicx}
\usepackage{cite}
\usepackage{siunitx}
\usepackage{tikz}
\usepackage{array}
\usepackage{subfigure}
\usepackage{longtable}
\usepackage{listings}

Notice that for what concerns mathematics, there are a few idiosyncrasies related to the iopart class: e.g., this class is incompatible with the amsmath package, and it is suggested to use the eqnarray environment, which is otherwise deprecated. I thus suggest a careful reading of the IOP LaTeX guidelines, which can be found here.
A few notes on the example above:

The package iopams is an extension for amssymb to provide
predefined names for bold greek letters (thanks to Barbara Beeton for
pointing out this and Canageek for reporting it here).
The package subfigure is obsolete but the the newer subfig package seems to be incompatible with iopart because it includes the caption package.

Correction from the TeX stack exchange, via Barbara Beeton (The expert on AMS packages): http://chat.stackexchange.com/transcript/message/31170810#31170810 "there's an inaccuracy in one of the answers. iopams is stated to be an iop adaptation of amsmath. it is not. what it is, is an extension for amssymb to provide predefined names for bold greek letters. amsmath is not used at all; iop has an entirely different style for math displays."

subfigure is obsolete, by the way.

Thanks for your answer! Do you happen to know which font exactly IOP usually uses? I want to use the same font in my plots. The guidelines say one should stick to Helvetica, Arial and such, but I think the CM font family is more appropiate.

@cfr I know, but the newer subfig package seems to be incompatible with the iopart class because it includes the caption package. Thus, we used the obsolete subfigure.

@mwormser Unfortunately, I don't know which font they use. Notice that iopart, even in twocolumn mode yields only a lousy representation of the true article format.

@MassimoOrtolano Well, then I guess I will use LM Sans for my figures and see if the journal has any issues when I submit it (someday far away in the future... :)).

Why do they suggest eqnarray? Isn't it all kinds of awful?

@tomasz Probably they are used to it. For a publisher, it may be easier to deal with awfulness you are familiar with than new non-awfulness.

@tomasz Moreover, as I said in a previous comment, iopart  yields only a lousy representation of the true article format: thus, the publisher might not be willing to keep it up to date with LaTeX developments.

As someone who moonlights as a type-setter for a mathematical journal let me tell you something about bibliography.
Bibliography styles are different from one journal to another. There is nothing more terrible than having to reformat 60 entries by hand, and there aren't many things worse than having to reconstruct the .bib file in order to use the journal bibliography style more easily.
Sending the .bib file to the publisher is not a bad idea. If they can handle LaTeX, they can handle bibtex as well. I never worked with biblatex personally, so I can't quite tell you about that. But I do recommend that you submit you .bib file separately, and save the hassle to the type-setter.
Of course, this assumes that your .bib file wasn't hand-made. When you add an entry by hand, it has a high percentage of chance not being up to standards. Always use MathSciNet, if not then ZBMath, and if not, then Google Scholar as a last resort.

Thanks for the tip! My citations are all automatically generated/scraped, so they should be fine.

Always use MathSciNet, if not then ZBMath, and if not, then Google Scholar as a last resort. — ...but assume that the MathSciNet / ZBMath / Google Scholar .bib entries have errors, double-check everything against the primary sources, and fix the errors.  Especially Google Scholar.

Not in math, but the same holds for acm bibtex entries. Some publishers provide their own bibtex entries for their papers (but even then verify)

If these packages do not interfere with the paper layout than it is completely OK. However you should follow the instructions for authors style guidelines. For instance, if the template uses a specific package for generating tables, then you shouldn't change it.
Regarding the bibliography I think that it is allowed to use bibtex and derivatives as long as the paper references style is preserved.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
How to take leaves as a Visiting Researcher?
I am a PhD student employed by a German university, and I am in the middle of a six-month J1 visa in the US as a visiting researcher in another university, still paid by my German employer.
Those six months are considered as a business trip, which means that I get daily allowances to cover for the difference of life price between Germany and the US. This also means that I can not take days off officially for six months (although I have plenty of days off left to take).
I want to travel home to Germany for 10 days to visit a sick relative, see family I couldn't see because of COVID, and handle the apartment I sublet.
I brought this up to my German supervisor in an email but he did not react to this specific point. I can just ask my advisor in the host university but I can not go without telling anything to my German supervisor...
Edit:

My visa allows me to go back to Germany for a couple of days.
German federal reimbursement rules typically forbid business travel being combined with vacations longer than 3 day.

My Question:
The administration told me I can not take vacation because it is a business trip. But not letting me take vacations for 6 months although I earned them is quite a precarious situation. Is it legitimate for me to require some vacations and with what lever can I negociate?

Isn't this more of a visa question than anything? Would the Workplace be a better place to ask? https://workplace.stackexchange.com/

A J1 visa does not allow you to take vacation days?

Is the daily allowance relevant?

Are you asking about the implications for your visa of returning to Germany from the US while on a J1 visa, or are you asking about the interpersonal aspect of informing/getting permission from your German and US supervisors? And on what basis/whose authority do you state that you "can not take days off officially for six months"?

@Buffy Most J1 visitors are going to be in academic settings, I don't see a connection to Workplace. Possibly https://expatriates.stackexchange.com/ would be appropriate for visa issues.

I suggest the travel stack.

Who's rule is it that you can't take days off for a while??  Since you'd like to take days off when the terms (I can't tell whether those terms come from your home Uni, your host uni, or your visa) tell you that you can't, I'd start with whoever that rule came from

As long as the J-1 visa isn't restricted to single entry or otherwise expired it seems the immigration part should be straight-forward. As for the reimbursement issues that's something to discussed with your home institution.

I suppose the problem is that the visit is being financed as a business trip by the German employer. German federal reimbursement rules typically forbid business travel being combined with vacations longer than 3 days. If this is the case the OP should clarify this.

@TimRias Indeed. It is not a visa problem, as my visa allows me to go home. It is more of an administrative problem. I think my advisors don't mind if I take days off, but if it goes through the German university administration, they will forbid it.

@MaiKar Are you getting your per diem in advance, or will you be claiming it afterwards?

@MaiKar Can you please update your question to be what you are specifically asking this site for help with? If your supervisors are fine with your vacation, your visa is fine for you to leave and re-enter the country, but your German university will forbid it no matter what (for reasons still unclear to me), what's the problem you want help with?

Can't you just formally interrupt the business trip? Just have the German university handle it as two 3-month trips with a gap in between instead of a 6-month one. I assume that should be perfectly legal even in Germany.

I realize that rules in Germany can be pretty strict, but isn't there a humanitarian exception for such things? I would guess that there must be.

@TooTea Maybe this is an option actually. But if they split my business trip in two, they are theoretically supposed to pay for my flight back and forth.
Maybe I can negociate on this base: split my trip but no need to pay for the flight for my week off.

In my experience it's all a matter of a gentleman's agreement between you, your supervisor from the home institution and your supervisor from the host institution.
Usually they only want you to get the job done. If you do everything in one month, you can have a five months holiday. I exaggerate just a bit.
Best answer is to just ask both your bosses.

Indeed, I finally did that. US boss agrees, I'm waiting to see what German boss says as this is the tricky side.


text:
Is it good to publish a research paper with many partially answered questions with sub-optimal results?
I work in abstract mathematics and I'm currently in the mid stage of my PhD. I try to get bounds on computational aspects of mathematics. I have been working on one problem for almost half a year and I have got four/five really challenging questions in this way. I am trying to solve these new questions but some of them seem to be very tough. I have been able to solve some of these new questions partially, but did not obtain the optimal results.
Question:  Is it good to publish a research paper with many partially answered questions with sub-optimal results?

Just go for it. Best of luck

In your other question here you describe yourself as a post-doc. Here as a pre-doc. I've seemed to answer both questions in different ways, but largely on what you have said about yourself. Different things are more appropriate at different stages of your career. If you were a junior professor, up for tenure, I'd think publishing a lot would help. Don't misinterpret the two answers.

This depends on many things. Most important is the significance of the questions themselves and whether the partial solutions add anything beyond standard techniques. The questions can be "challenging" without being significant, of course. Do they lead to other things, for example.
If your solution techniques are standard, then they won't add much either, but if you have developed a new way of looking at such problems, then it could be very important.
"Almost half a year" doesn't sound very long, actually, for the stage you are at.
Your advisor should give you good advice here. He or she is more familiar with your problem and your attack and degree of attainment.
However, I come down a bit on the side of waiting to publish. For one thing, if you publish partial results it may lead others to join the search for solutions in competition with you, perhaps denying you a more significant publication (or even a dissertation) in the future.
If it makes sense to separate them, having four or five papers, each with a complete solution would be much better for you than rushing now. The publishing venue is likely to be more prestigious, and also more likely to accept complete results.
Carry on.

@sade, yes, that makes a difference. However, a full year on the research leading up to writing the dissertation is not excessive. I earned the doctorate in the (very) old days where it was uncommon for students to publish before finishing. I agree that the world has changed. If your research problem is significant it may just be in the nature of things that solutions are hard to find. This is true in maths certainly.