text:
Unsure of Convention for In-Text Citations
I'm writing a longer paper for a course as part of a final project. The paper is on a topic we didn't cover in class and is obviously intended as a way to let me teach myself something we didn't have time for. As such, I'm using other people's ideas for my paper nearly every single sentence. I'm unsure of the convention for determining exactly what bits I need to cite and how often I should cite it, but I'm pretty sure it's not that I need to cite something every sentence. Is there some sort of convention for this sort of thing?

Generally, you cite a paper in the first occurrence of its matter and in occurrences where the matter is significant.
For instance, suppose you are explaining about a method that is proposed in a paper. You cite it when you first state the method. After which it is understood that whenever you use the term, it refers to the one cited initially. If you are discussing two are more methods, explain each one separately by citing them and you also ought to cite at a tabulation during result comparison. Same goes for citing concepts; cite only when the concept is first introduced.
Other than that, citing for every sentence would be only be redundant and doesn't make the manuscript look neat either. If you do feel that you are in a position to have to cite nearly every sentence, then your content is probably largely of matter covered in your reference and not of your own. You ought to make appropriate edits in that case.

In every sentence where you present other people's ideas, you must cite those people. If several sentences stem from the same source, then begin with 'According to Jones(1992)..' or similar.
In an Introduction you cite a lot. Use your own words to structure the Introduction, e.g. to motivate and frame the topic. In a Discussion, citations will also be prevalent where you reflect upon existing ideas.
How you stand out as a person in the text, is in your disposition of the topic. You must learn how to use references dynamically. You must convey ideas of the past as an interesting story while adding your own little share of original thoughts.


text:
Is it okay to typeset someone’s to-be-graded assignment for them?
I have a friend who’s an undergraduate at university. I believe myself to be fairly proficient in TeX/LaTeX; I’ve seen some of the assignments that he’s received back, and we both agree they could look more professional.
Is it ethical for me to typeset his work to look more like a paper before it's submitted for grading? I would not be adding any new information to the assignment and I would not correct any mistakes that I think I see, but it still seems to me that perhaps it could be against the rules.

You say the assignment has already been graded?  Is it going to be handed back in for regrading, or submitted for some other academic purpose?  If not, I don't see how there could possibly be any problem.

No, I mean the assignment is to be graded (it will directly impact his grade).

I would have them ask the instructor if its ok, he is the ultimate authority in this case.  If this was a class on how to use LaTeX its clearly not ok.  However, in other cases it might be ok.

If it affects his grade, it is clearly a violation

Back in the old days (pre-ominipresent computers, my experience is early 1980's) a fair number of students made good money typing other people's essays (the alternative was handing in a hand-written essay or typing it slowly oneself if you weren't a good typist). And there were a good number of people in the community who advertised as well. If you are not editing as you go, I really do not see the problem. If the professor is swayed by how it looks, that is a different problem.

You're so innocent! How would you typeset this? :-) (exaggerating obviously, but hopefully you can see the point underneath)

Different idea: write a pandoc latex template for your friend and teach him how to use markdown + pandoc.  Won't cover all cases where latex code is necessary, but hopefully most.

There was a very good student in my department, a couple years ahead of me, who had trouble with handwriting growing up.  He coped by training himself to write big.  His submissions were twice as many pages as the average, because he wrote so big. It takes practice to write that big! Alternatively, it would be a big asset for your friend if he knew how to use math word processing or typesetting or speech to text software.  You could teach him.

Tell your friend to buy a copy of Grind EQ if his professor objects.  Back in the day (as Jon Custer mentioned) these services were widely used and advertised.

Back when dinosaurs roamed the Earth it was commonplace to employ a typist for theses and papers. I don't see any problem with simply typesetting an assignment.

"Student... look professional." This is a category error.

Show him how. It's obviously something he could stand to learn.

Related: https://academia.stackexchange.com/questions/81082/should-formatting-affect-grades-of-student-essays

Publishing? Absolutely! Classwork? Where are your priorities for what matters in the world?

I think this is probably not appropriate.  You could ask the professor, but if it were me I would say no.
An important part of learning math at the undergraduate level is being able to write math clearly, and this includes the low-level yet essential skill of being able to handwrite or typeset math notation.  If you're typesetting the assignments for your friend, the professor is not getting an accurate view of their proficiency at this skill, which could factor into the grade.
There could be an exception if your friend has a disability that makes it unusually difficult for him to write clearly by hand.  But again, you would need the consent of the professor (and possibly also of some university disability service office).
(If your friend doesn't have a disability but just has particularly atrocious handwriting, the professor might agree to this, simply out of self-preservation; reading bad handwriting can be really frustrating.)
I agree with Massimo Ortolano that in the long run, the best thing would be to help your friend learn to typeset the assignments himself.  You could of course typeset some of his previous assignments for him as an example.

i was once asked to submit a handwritten math assignment.from that teacher's point of view, atrocious is an underreaction.

Furthermore even if the person doing the typesetting honestly intends it to be "just typesetting" it is difficult to rule out them either adding (because they made a typo) tor removing (because their brain read what it thought should be there rather than what was actually there) errors.

I think that the best favour you can do to your friend is to teach him how to use LaTeX, so that he can improve the look of his work by himself.
In this way, you won't go against any rule and you'll teach your friend a new skill.

Excellent advice, which otherwise doesn't answer the question.

Rather than teaching LaTeX, you could suggest LyX (or similar), which is easier. (Whether it is worth learning LaTeX depends on a person's career plan.)

@Orion - from the help center: What, specifically, is the question asking for? Make sure your answer provides that – or a viable alternative. The answer can be “don’t do that”, but it should also include “try this instead”. Any answer that gets the asker going in the right direction is helpful

@Kimball I personally like and encourage such useful "alternative" answers. I simple noted that it doesn't answer the question about whether x is ethical.

In my department, any homework/assignment etc. ends with a declaration which includes the claim that the author(s) did all of the work themselves unless mentioned otherwise.
My opinion is that typesetting is a process that is included in the assignment and while not explicitly stated is work you should do yourself.
I do agree with Massimo Ortolano that showing someone the ropes with a typesetting system is a good way to handle the situation though.

I did not notice this answer until I saw there was a Low Quality Post flag raised against it. After I read the answer, I decided to give it an upvote because it's a good answer.

I agree with a lot of the other answers and comments: I think ultimately it should be the professor who makes this decision.
That said, I've occasionally had students ask me if it was acceptable to do similar things. Many times – assuming I didn't feel it was a matter of academic integrity – I've answered by saying it would be okay if the student got formatting help, but I wanted them to acknowledge the help openly in the assignment.
In other words, an assignment such as the one you are describing could include footnote with an acknowledgement, something to the effect of:

This assignment was typeset in LaTeX by J. Smith

That way, everything is above board, and the student isn't passing off someone else's work as their own.
One other idea that might be considered or proposed is handing in a copy of original work along with the LaTeX document, so the professor can get an idea of what the original work looked like before the improvements.

How much the look of the assignment/paper affects the result?
If the key value is the content (proof, research results, etc.) and the look is just the icing on a cake I dare to say your help is acceptable. At least your friend realized that the outcome he produced can be improved and you showed them how it can be improved.
If the graphic outcome is the key value, your friend's topic is graphics, for example, then your help - typesetting it for them - is unethical. Teaching them to use (XxLa)TeX is, on the other hand, completely different case.

As pointed out in the comments, back when dinosaurs roamed the earth, students (and others) routinely hired typists to type their papers. There was nothing wrong with this then, and there's nothing wrong with it now, although I haven't heard of anyone hiring a typist in decades (except in the case of disability).
LaTeX, unfortunately, tends to occupy a different place in many professors' minds than typing does. In principle, having someone else TeX your work is no different from hiring a typist, and in fact in the early days of TeX the only people using it were professional technical typists. However, many professors, especially in mathematics, believe that "learning TeX" is an integral part of the course if they specify that assignments need to be LaTeXed. So it is probably not acceptable to typeset your friend's assignment if the professor requires LaTeX.

I just think the OP will have trouble copying the document without also doing some formatting...especially since they say that the students work looks unprofessional, and they want to make it look more professional.

Why do you want to do this work for him?
Is it because he is your friend and you want to help him?  Why don't you help him learn LaTeX then instead of doing all the work of typesetting yourself? (Give a man a fish...) You can help him learn by guiding him through typesetting a non-graded homework assignment.
Is it because you believe that he is likely to get a better grade if the typesetting is better?  If your work directly influences his grade, the answer is clear: it's inappropriate. He should be graded solely on his own work.

From personal experience in the UK, both the Undergraduate course (completed in 2013) and my current Masters programme have had various stipulations on submission presentation.
I can recall a particular assignment in the final year of my undergraduate degree where the marking scheme required submission in IEEE format with appropriate referencing. It was constructed such that if you followed the format and referenced correctly you would attain 30% of the marks, regardless of content.
The module leader allowed us to peer review the submissions as it was his (rather clever) way of teaching us to critique. You would be amazed how many failed to read the marking scheme and didn't submit in a format that you can download from the internet.
Your friend needs to learn that in the real world presentation, together with spelling and grammar are often as important as said content. If you can proficiently enable him and have the time and patience, he can go away and do it for a lifetime.

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How to politely respond to a PhD offer follow-up email from potential supervisor?
I received an official PhD offer from University A on Jan 30 (15 days ago).
In an interview with the faculty from University A, they asked me where A stands among my applications. I honestly replied that A was among the top 3 universities and said that I need to hear from the other two schools before making any decision. I also expressed that it would be hard for me to make the decision before hearing from the other two schools from my top 3 shortlist. The offer from A arrived soon after the interview (obviously).
Today a professor from University A sent me a very short email asking if I had questions or I was close to making decisions.
Is he implying that I should hurry up?
I have not sent them any email since the offer as I had nothing to update. The offer follows the rule of April 15, but the school would offer me a small amount of fellowship (which I don't care) if I accept before late February. The other two schools just interviewed me several days ago and I would expect to hear from them soon.
How should I politely respond?
Thanks!

the school would offer me a small amount of fellowship (which I don't care) if I accept before late February - Uh, this is certainly against the spirit of the April 15 Resolution, though I don't know enough about the specifics of the agreement to definitively say it's disallowed. The whole point of the resolution is to not make financial offers of any sort contingent on making a hasty decision, to keep a level playing field across institutions and in the best interest of the students.

@BryanKrause Ironically I just found A on the list of the April 15 Resolution.

I have a hard time coming up with a US university that is not; it's quite a sensible resolution.

I don't think the professor is necessarily implying that you should hurry up, they are simply putting pressure on you and hoping that you accept their offer, keeping open a channel for communication if you have questions (like a salesperson asking if you need any help as you are browsing a store), and trying to politely test whether you may have accepted another offer.
If you choose to go elsewhere, they likely want to know as soon as possible so they can extend an offer to another candidate.
I would say it is sufficient to respond with a brief, polite note that you decided before applying to wait for all offers before making a decision, and that you promise to inform them immediately once you have made a decision.

Dr. Professor,
I appreciate the email, I will certainly ask you if any questions come up. My plan when applying was to wait until I hear back from all institutions I interviewed at before making a decision.
I will inform Impatient University immediately once I have made a decision, either way.
Best,
Prospective Student

Your responsibility is to inform them as quickly as is reasonable once you have made a decision, but you shouldn't be pressured to respond more quickly than you are ready.
You mention "the school would offer me a small amount of fellowship (which I don't care) if I accept before late February" - this is certainly against the spirit of the April 15 Resolution, though I don't know enough about the specifics of the agreement to definitively say it's disallowed. The whole point of the resolution is to not make financial offers of any sort contingent on making a hasty decision, to keep a level playing field across institutions and in the best interest of the students. That said, I wouldn't suggest bringing this up at all or making an issue of it, unless it makes you uncomfortable in which case you could certainly consider it in your decision-making process.

I think that the only thing this professor is doing is "cultivating" you.  And I mean that in a nice way.  He's just showing that University A remains interested in you and keeping communication open.  I would just thank him and maybe take advantage of his offer.  The way I would take advantage of the offer is to ask if there were current grad students in program whom he could put me in contact with, so that I could chat with someone on the inside.

I would say you are right about your guess and he is indeed implying that you should hurry up.
If you still wait for the other responses, something like below may be a proper answer:

Dear Professor Smith,
Thank you for your kind reminder. However, as I have mentioned, I can
  only inform you about my decision after I have answers from other
  universities.
I do apologize if this situation gives you inconvenience. Please feel
  free to proceed further with your other applicants in case you need an
  answer from me immideately.
Best,   John.

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Is it right to cite a retracted research article?
I was doing literature review and I came across a paper which is in the area of my interest but has been retracted because of duplicating the figures (technical drawings) of other papers.
Can I cite this paper in my literature review?
Also, is it ethical to work on the topic of this retracted paper?

Related: How to correctly cite a retracted paper?

According to your description, the retraction might be more about copyright violation than about research misconduct. A journal would be legally liable if it let an article remain that violates the copyright of other journals, so of course they could not leave it in their journal. My point is that, going on nothing more than the details you've given here, the article might have been retracted mainly for copyright violation, rather than for plagiarism of the text contents. (Of course, it seems that perhaps they plagiarized the figures that you mention.)

You Absolutely Can Cite a Retracted Paper
Research is about telling the truth about facts of reality.  You can cite any fact of reality you want if it is relevant to your research; if someone says something, you can report that they said it.  You can cite a published academic paper; you can cite a newspaper article; you can cite a letter; you can cite a Post-It note or a tweet; you can cite that thing your neighbour said to you over the back fence when he got really drunk that time.
Generally researchers cite claims/information from academic papers as a source of authoritative information that has been through the process of peer review.  However, there is certainly no rule that confines academics from citing information from other sources, including sources that have not been through peer review, or have been through it, but have later been retracted.  There are many cases where it might be useful to cite a paper that has been retracted.  There may be cases where you want to cite something from a retracted paper, where the part you are citing is undisputed, and the cause of the retraction had nothing to do with the part you are citing.  There may be cases where you want to cite a claim that has been retracted, but you still think the claim is relevant despite its retraction.  There may even be cases where you want to cite a retracted paper because you want to talk specifically about it having been retracted (e.g., if you are doing research on how often and why academic papers in some field are retracted).
Now, if you cite a retracted paper, it is proper practice to disclose to your reader that it is a retracted paper, and this should be done in your bibliography where you list the citation details, and should probably also be done in your main body text (e.g., Johnson 2011 - retracted).  If you are citing something from the paper that is a reason for the retraction, you should make it clear to your reader that you are citing a claim that has been retracted (and hence has not passed peer review).
The notion that retraction of a paper precludes you from citing it has several obvious absurdities.  First, it would make research on retracted publications extremely awkward, if not impossible.  Secondly, it would implicitly require that other sources of material that have not passed peer-review could also not be cited.  Thirdly, it is tantamount to claiming that writers/editors have the prerogative to preclude you from reporting what they have written.  If a politician says something scandalous, and then says "retracted!" does that mean you're not allowed to report it in your research?

Absolutely correct. It sounds like in the OP's case he'll want to avoid it most likely (although using it to find other citations could prove fruitful nonetheless), but papers get cited for more than just their conclusions. Heck, if you cite important paper A from Dr. X, but you know that papers B and C also by Dr. X have been retracted for some reason, it may be a good idea (if not necessary) to evaluate A in light of B and C, which requires citing them.

Absolutely - add this to the many reasons you might have to cite a retracted paper.

I see at least two aspects to your question: can a retracted article, in general, be cited in other research; and can a literature review include a retracted article in its review?
Can a retracted article, in general, be cited in other research? YES. On this point, I have little to add beyond Ben's excellent answer. I disagree with those that think that only scholarly or only peer-reviewed articles should be cited in scholarly work. Anything can be cited, but especially if what is cited is not peer-reviewed, then the citing author is responsible to verify the validity of what they cite. (We should even be responsible to verify the validity of the peer-reviewed work that we cite, but because there is so much research out there, it is understandable that we generally trust the peer-review process to do this validation for us.)
Can a literature review include a retracted article in its review? YES. I want to be very clear that such an article is NOT part of the scholarly body of peer-reviewed literature--it has been retracted, so does not have that quality stamp. However, I strongly believe that a literature review should include grey literature--the body of scholarly research that is not peer-reviewed, and even when meaningful, high-quality practitioner articles or books. However, you need to be clear that if you cite grey literature (including retracted articles, in your case), you should bear the responsibility to appraise and validate the quality of such work that has not been peer-reviewed. For your readers, it would be irresponsible of you not to verify that the work you cite is valid, particularly if other scholars have not already done so (that is, through peer-review). In particular for a retracted article, you should definitely explicitly mention to your readers that it was retracted and that you are knowingly citing it anyways.
Finally, you asked, "is it ethical to work on the topic of this retracted paper"? You are free to work on the topic of any article, whether published or not, retracted or not. As long as you cite and acknowledge the source of original ideas, then you are fulfilling your ethical responsibility. If your concern is that the retracted article no longer has a standard scholarly citation, well there is a good question and answer on how to correctly cite a retracted article.

You should not cite a retracted paper
Retracted papers are no longer part of the scientific record. Their original publication was in error. If there was a small fix required, a correction could be issued, but in this case it seems that the journal editors deemed it necessary to retract it. You don't know for sure the details behind their decision, but if you trust their judgement in deciding which papers ought to be published (which you implicitly do, in citing published papers), then you have no rational reason not to trust their judgement in deciding which papers ought to be retracted.
You can work on the topic of a retracted paper
Assuming here you mean the same general area, I don't see a problem with this ethically. For example, a paper on learning in cotton-top tamarin monkeys was retracted due to mistakes (or possibly misconduct?) in data coding. It is in no way unethical for other scientists to continue to work on how cotton-top tamarin monkeys learn things.

"Retracted papers are no longer part of the scientific record." I would contest this. Retracted papers remain on record, and usually (unless due to double publication/copyright issues) downloadable and consultable; any pre-retraction citations still exist. It's more that it's had a massive red flag attached to its record. Granted, you don't want to trust/cite like a regular paper, but I can envisage times when it would be appropriate to mention/cite either the paper or the retraction notice. (e.g. if a high-profile retraction provided impetus/context for a piece of work)

Science is no religion. If you can give a reasoning, or reference to it, you can write it. Stealing ideas from a (possible) thief is just as contemptible and illegal as any other theft.

@WanderingChemist The example in the question sounds like it is a copyright violation, actually, so that particular paper might no longer be available. But I agree with your point in general.

Why not cite the paper it was retracted for duplicating?
The retraction isn't a reason not to work on the same topic as that paper, but if it's retracted for plagiarism, then there are likely better papers that will fit its functional need.

It was retracted for duplicating the figures (sketches) only and not the entire work. Rest of the paper is of good quality.

The fact that the authors demonstrated misconduct (whether willfully or through carelessness) casts doubt on whether the rest of the paper is indeed good quality. The safe answer is no, it isn't.

@phimac If you think the rest of the paper is original, and trustworthy, you cite it. If you think otherwise, why would you even think about it? And if there are numerous papers available to cite for sth., you take the oldest, and the best one. The latter is again at your conception.

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Intellectual Property Rights When Moving University
I am considering moving institutions (from a one UK University to another), but I am concerned about what Intellectual Property (IP) rights my current institution may retain. Some of my PhD students, one of whom has been funded by my university directly, would move with me, or at least I would like them to. I am also unclear about the rights they/I would have to the research they have already done. Their projects would naturally remain similar, but I see no obvious commercial potential, and have no intention of trying to find some.
My questions are:

The University's policy is clear that they own all Intellectual Property I produce during my employment. I assume this can't apply to projects that have not got to the point of being protectable/tradeable but where one project begins and another ends is not always clear. Many of these projects naturally build on work I have published, or is in the process of being published. How can I tell/establish what exactly they have rights to?
How do I 'leave' them with what they own so that I can make a clean break.

There is a policy, which states that all IP created whilst employed is owned by the University. However, the policy also makes it clear that I am expected to make them aware of anything that potentially commercializable. Given I don't think I have anything, and haven't made them aware of it, it's not clear where that leaves me. The policy is also very clear about my responsibilities as an employee, but not what happens if I am not. I will edit to clarify.

This sounds like the sort of thing that should be discussed with the department. You don't want problems years down the road when it turns out that research you have already started does have commercial value.

There are two reasons why asking these questions from eg your uni is much better idea than here: 1) details always depend on university AND often on negotiation, 2) details may depend on very specifics of your research - if you are an engineer you most probably have other problems than a mathematician.

My issue is that I would not want to alert my department to the fact that I am considering leaving and so was hoping to obtain some general advice.

Go consult a lawyer who does IP law. This is going to be very fact specific and contract specific.

In general you should be fine:

Your research is published, so everyone (including you) can build upon it.
You do not have any patents (which would remain at the university)

The only thing might be software written at your institution or hardware built during your work. Those remain at the university as long as you do not agree on otherwise. But usually, one becomes smarter over time so this might be a good point in time to re-implement some stuff...
On the other hand, your work might be worthless for your university when you are not there - e.g. no one will digg into foreign research code... So you should have a good position for negotiations.

You seem to be giving a legal opinion. I don't think that is proper here. Are you a qualified UK lawyer?

@Buffy: There is nothing definite in the answer (everything has shoulds, mights, and similar). Also, the entire concept of giving opinion on legal questions being illegal is limited to the US, as far as I know, and even there this is probably far from problematic. (If not, please cite a respective law that says otherwise.)

@Wrzlprmft, I don't claim it is illegal, just unwise. If the advice is taken and turns out to be wrong, the OP will be the one that suffers, not the person giving the bad advice.

@Buffy: Can you tell me one statement of which you think it might be unvalid? And as Wrzlprmft already noted: There are enough should in the text to indicate that the real situation might be different since we do not know the specifics of this university and the work involved. I'm sure the OP can put the answer in the right context and will ask a lawyer if needed.

You leave the impression that there are few issues. I disagree. The OP says the university claims rights. Depending on the level of insistence they have it could be a serious issue. Work in progress? Courseware? Lab procedures? There are a lot of things potentially other than already published papers, patents, and software. My first line would be "In general, you need to know more, both from the university and their lawyers." and NOT, "you should be fine."

I think the point Buffy is making is that if you wish to offer an opinion that a particular course of action "should be fine" then it would be useful to know if you are a lawyer yourself, and what is the legal basis for the asserted opinion.  I don't think it's incumbent on Buffy to point out errors in the assertion --- he just wants to know if there is any legal training/experience/reasoning behind those assertions.

Read the contracts and policies.  If the existing contracts and policies are not answering your questions, then this is something you cannot resolve.  It is up to the universities to work out between them how to divide intellectual property.
If the intellectual property is very valuable, the lawyers of the two universities will negotiate a deal.  Nobody will want to license something if the owner of the rights is uncertain.  As a result, the universities will be motivated to cooperate.  Arranging this is not the author/inventor's responsibility.
If the intellectual property is not valuable, then so long as you are honest and open about what is going on I doubt you will have any problems.

Beware that the contracts and policies may contridict each other and in the case of the policies, themselves. It may need a lawyer to work out what the actual grant is in that case if you are unwilling to talk to the university.

I think regarding publications, as soon as you include the affiliation of the old uni on publications whose work has started during your employment there it should be fine.
If there are patents involved things might get more complicated.
What other issues were you thinking about?

I wonder, can the people who voted negative in this answer please explain what is wrong with what is stated here?

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On the definition of research - are 'what' and 'how' questions also considered as research?
In Philips and Pugh's How to get a PhD, the authors describe the general philosophical concept of research 'in all disciplines'. I have two questions in this context.
A. They said that an activity that tries to answer a question like

'What are the age, sex and subject distributions of doctoral students in
  British higher education?'

is considered descriptive, intelligence-gathering activity, but not research. This is pretty clear and agreed upon. However, they attribute that to the 'what' nature of the question.
Later, they said:

Research goes beyond description and requires analysis. It looks for explanations,
  relationships, comparisons, predictions, generalizations and theories. These are the ‘why’ questions. Why are there so many fewer women doctoral students in physics than in biology? ...
All these questions require good intelligence-gathering, just as decisionmaking and policy formulation do. But the information is used for the purpose of developing understanding – by comparison, by relating to other factors, by theorizing and testing the theories.

Is it sound to consider only 'why' questions as research? How about some 'what' and 'how' questions?
B. In the same text:

All research questions have comparisons in them, as the words ‘fewer’, ‘different’ and ‘less’ in the examples above illustrate.

Should all real research questions really contain comparison (explicitly or implicitly)?

This definitely seems overly restrictive to me. I don't think that "all research questions have comparisons in them" is at all true. In my area (pure mathematics), probably quite a few research questions are phrased as 'what' questions, although answering these questions will also involve explaining 'why'.

the general philosophical concept of research in all disciplines — All disciplines?  Oh, please.

@JeffE: This is what the authors of that book said, not me. Please.

@Orion:  I'm pretty sure JeffE understood that.

Language side note: every why-question is a what-quesion as well: what is the reason for ...

It's important to keep in mind that nobody is in charge of what is or isn't research, and nobody has universal perspective or expertise across all disciplines.  (Not just no person, but also no organization.)  In my experience, the term "research" is used incredibly broadly: for any topic you can imagine might be considered research, there are communities of thousands of people who think it's obviously research and who would be offended if anyone questioned this.

According to the Belmont Report (1979):  "the term 'research' designates an activity designed to test an hypothesis, permit conclusions to be drawn, and thereby to develop or contribute to generalizable knowledge (expressed, for example, in theories, principles, and statements of relationships). Research is usually described in a formal protocol that sets forth an objective and a set of procedures designed to reach that objective." I think the idea that its aim is to contribute to generalizable knowledge is central to the question of what does or does not constitute research.

In biology, what questions are extremely popular, even though they can be largely descriptive. The point is, that knowing descriptive details of a system is the first step in understanding how it works, and can often raise many interesting hypotheses. In fact, this trend of questions is increasing as high-throughput experimental methods are used to collect more and more data (which by itself is only descriptive).
Some famous examples of such what questions are "what is the structure of DNA?" and "what is the sequence of the human genome?".

There are lots of different types of research. Some research is hypothesis driven other research is not. What questions generally are not hypothesis driven while why questions usually have a related hypothesis. Comparison words are useful to indicate both sides of the hypothesis (i.e., the null hypothesis which you are often attempting to reject and the alternative hypothesis which you are often attempting to provide support for). Hypothesis testing is the basis of the scientific method. Typically doctoral research leads to a thesis/dissertation which historically has been about hypothesis driven research. Things like design based research in the sciences and performance based research in the arts, however, are now often being submitted as dissertations. Whether this is a bastardization of the term dissertation is not clear to me.
Within the wider realm of research, the quoted material is wrong. Within the realm of getting a PhD the quoted material may be historically and technically/etymologically correct, but it is clearly a dated view.

The Australian Higher Education Research Data Collection specification (2012)[1] (ie: HERDC) defines research as

the creation of new knowledge and/or the use of existing
  knowledge in a new and creative way so as to generate new concepts,
  methodologies and understandings. This could include synthesis and analysis of
  previous research to the extent that it leads to new and creative outcomes.

and uses the OECD Frascati Manual[2][3] to support that definition as:

consistent with a broad notion of research and
  experimental development (R&D) as comprising of creative work undertaken on a
  systematic basis in order to increase the stock of knowledge, including knowledge of
  humanity, culture and society, and the use of this stock of knowledge to devise new
  applications

HERDC and the Frascati Manual focus on the generation of new understandings, of new knowledges.  There's a commonly agreed purposive utility to knowledge that is lacking in the generation of data and information.[4]  I would suggest that as knowledge lies in a network of other knowledges, that any production of knowledge is implicitly or explicitly comparative to the existing body of literature.  HERDC goes on to suggest that apart from "increasing the stock of knowledge" and being in a form suitable for the dissemination of knowledge, that research publications must "evidenced by discussion of the relevant literature,
an awareness of the history and antecedents of work described, and provided in a
format which allows a reader to trace sources of the work, including through
citations and footnotes."  This explicit comparison between the production of understandings as knowledge and the past production of understandings as knowledge would be the basic comparison at the heart of scholarship and research.
While the HERDC specifications are normative, and punative (they're about divvying up a pot of government research money), there has at least been an attempt to cover them with a fig leaf of collegiality, and for them to reflect academic practices.  The absence of protest over their unfairness is an indication that they "work" as a punative practice.
[1]: HERDC (2012) http://www.innovation.gov.au/Research/ResearchBlockGrants/Documents/2012HERDCSpecifications.pdf at page 7-8, 1.3.10
[2]: OECD (2002), Frascati Manual: Proposed Standard Practice for Surveys on Research and Experimental Development, OECD: Paris.
[3]: Cited in HERDC (2012)
[4]: DIKW models, Zins, Chaim (2007). "Conceptual Approaches for Defining Data, Information, and Knowledge" Journal of the American Society for Information Science and Technology 58 (4): 479–493. doi:10.1002/asi.20508 cited in Wiki.

I agree with the other responders and commenters that it's silly to generalize over all disciplines like this. What makes it particularly funny to me as someone in physics, is that it is often said that physics is concerned with the 'how', not the 'why'. I guess we, along with people in other hard sciences, don't do research at all then... At least philosophically, we're in the business of describing how nature behaves, how a particle moves and interacts, but can't really tell you why our models work, only that they more or less "fit the data". (Then there's the problem of model-dependent realism - do our models actually reflect what's going on in nature, or just happen to predict the same outcomes?)
For example, in the words of Feynman

While I am describing to you how Nature works, you won't understand why Nature works that way. But you see, nobody understands that.

Sometimes you can ask 'why' questions that lead to unifying principles, with better explanatory power. For example, "why do these properties share property X?" rather than "what properties do these materials have?", but generally, you don't get one without the other, and both are considered research. Even if you manage to answer this 'why' question, however, you'll be left with a more fundamental 'why' question that we don't know how to begin to answer. And many levels of the more accessible 'why' questions are beyond the scope and time frame of most PhD studies.
As for the statement that all research questions should have comparisons in them, I don't even know where to begin. Consider e.g. the 2017 Nobel prize in physics for the observation of gravitational waves. The LIGO project attempted to answer questions like "do gravitational waves exist?", "can we see them?", and "can we use them for new kinds of astronomy?". If you really want to twist things, I guess they could be rephrased "are there more than zero gravitational waves in the universe?" and so on. It still wouldn't be a 'why' question as described above though.


text:
How do traveller academics get reimbursed for accommodation shared with families?
I will travel to a conference at which I will present my work. My funder usually reimburses me for fees of conference registration, travel, and accommodation.
However, since my wife and kids will accompany me, I will book separate travel tickets for them, and a family room, which is usually more expensive than a single one.
I will ask the funder whether/how they would reimburse me for the accommodation.
I guess many other academics around the world travel for work with their partners, friends, or families, and I am wondering how they usually/ideally get fair reimbursement for accommodation shared with other non-funded travellers.

Usually, you will explain the specifics of your travel and provide some documentation about

the actual expenses for travelling with your family
the expenses you would have had, had you travelled alone

You should then be able to make a case for getting reimbursed for the (lower) expenses listed in item #2, even though all your bills show the (higher) expenses from item #1.
If there was anything that cost the same, or even less, for the whole family compared to what you would have paid alone, make sure to provide good proof of the hypothetical 1-person-price and you might even get reimbursed some of what was used by the entire family :)

@dan1111: This may work, but it may also be that the funder will say that you'll only get the part of the expenses that would have been necessary to fund you at this particular place, i.e. if you book a double room you only get what a single room would have been and sometimes you even get 50% of the price of a double room.

Dirk: That is true, although I'd probably try and protest in the case of getting only 50% of a double room (if that is less than the cost of a single room). I consider the requirement to not have a single room questionable to begin with (in particular if I already picked a place where a single room rate is lower than 50% of a double room in the official conference hotel), and when I don't know anyone else who will attend, I consider it inacceptable to be put into a room with a total stranger.

I have always eaten these cost differences. My family is small (me and wife), and I always get a room with a king bed anyway. We pay the cost for my wife's flights, the university (maybe through grants) pays for my flights, per diem, and hotel. If there is a rental car required, it doesn't change size, so the university pays that as well.
I don't think that the university would pay the difference for anything I chose to make different for my work travel (extra stops, room for children, etc.), because I think there are either university rules or granting agency rules that prevent it. These are my choices to travel with family, I must make up the differences.

It's simpler if you can claim on a per diem basis, but that's often not possible and you have to submit receipts (this has tax implications for example).  At that stage you could technically claim only for your own share of the bill.  Recognising the absurdity of this, many places will pay for the bigger room on the understanding that you don't claim for food etc.

@ChrisH, many places, in what countries? My university pays a per diem without receipts based on a table of median/average costs for every city or region. Hotels/rental cars/taxis require receipts. Each country/region/nation has different practices. Some are more or less flexible than you suggest. Mine university doesn't really look at room size unless you book something outrageous.

In both industry and academia I've never come across more than rumours of per diem arrangements in the UK. They used to happen but were clamped down on as taxable income. In industry the maximum daily amount claimable for certain categories of whoever claim with receipts was set on a per-country basis.

@ChrisH, the US IRS (PDF) has a method for this. Either the per diem is for lodging, meals, and incidentals, or it excludes lodging. They set acceptable rates for each locale. That per diem is not taxable income if what is paid is less than or equal to the posted rate.


text:
Can co-authors disagree in their own paper?
Co-authors are increasingly required to report their individual contributions to a research paper. But can they report their (internal) disagreement?
Co-authors may disagree on parts of a final draft. Each may have own interpretation of (parts of) the results or view of their implications.
The different views can be of course expressed in the publication without attribution, e.g.:

Our results may mean x, but they may also mean y.

But some co-authors may find others' interpretations/views controversial, or they may wish to get "exclusive" credit for their own ideas.
In such cases, is it appropriate for co-authors to explicitly attribute certain interpretations/views in a paper to their owners? Should they do that?

Co-author A thinks results mean x, whereas co-author B thinks they mean y but not x.

Is this a hypothetical question or do you have a real reason for asking?  If you have a serious need, at least say which field you are working in.

It's hypothetical, but it applies to many fields.

Maybe this is something you can add to a "discussion" section of the paper.

If it's a fundamental disagreement, you might consider splitting the paper or splitting a companion paper (Part I and Part II, with separate authors). I've seen it done albeit rarely. If it's a minor matter of interpretation, I've often seen authors write "One of us is inclined to believe that...", without actually naming who thinks what.

Do you mean: agree on the methodology but disagree on the (numerical) results? or agree on the numbers but disagree on their statistical interpretation? Or agree on both of those but disagree on the implications? It seriously helps if you can give a specific example. (Is this economics?)

I'm hoping for someone to post an example of a single-author paper in which they disagree with themselves.

It is rather unusual, but it has occurred before. In the paper

Piccione, Michele, and Ariel Rubinstein. "Equilibrium in the Jungle." The Economic Journal 117.522 (2007): 883-896.

each of the authors has their own conclusions, marked "4.1. Concluding Comments by MP" and "4.2. Concluding Comments by AR." It should be noted though that the writing in economics tends to be less structured (no such thing as a "method section") and this is a somewhat unconventional paper to begin with.

I, too, have seen it on occasion.

@GEdgar - Could you possibly bring any references to where you've seen it? Feel free to post as your own answer.

Very interesting! I hadn't see this before. I would like to be able to read different interpretations of work in my field using an approach like this.

And Ariel Rubinstein is not your conventional genius...

This might not perfectly fit your bill, but the paper Trialogue on the number of fundamental constants
 by Michael J. Duff, Lev B. Okun, and Gabriele Veneziano
basically consists of three co-authors disagreeing.
Abstract:

This paper consists of three separate articles on the number of fundamental dimensionful constants in physics. We started our debate in summer 1992 on the terrace of the famous CERN cafeteria. In the summer of 2001 we returned to the subject to find that our views still diverged and decided to explain our current positions. LBO develops the traditional approach with three constants, GV argues in favor of at most two (within superstring theory), while MJD advocates zero.

In theoretical cryptography, we have a major paper by Canetti, Goldreich, and Halevi, showing that in general cryptographic systems which are proven secure in the so-called random oracle model are not necessarily secure in the real world. At the end, they each offer different opinions about what this means regarding the usefulness of ROM proofs. (Basically, Goldreich says they offer no evidence whatsoever of real-world security, while the other two say they're not ideal but better than nothing.)

Yes, but I guess that this would usually set the tone of the paper, i.e. the paper would focus on a debate between the co-authors. For instance:
https://www.nature.com/news/does-evolutionary-theory-need-a-rethink-1.16080
But that is something different.
I don't think mentioning author names in the manuscript is a solution. All authors should take responsibility for everything that is written in the manuscript. So I would say present both interpretations as possibilities without committing to either.
An alternative solution (and one which I try to use) is to avoid views/interpretations that your co-authors don't agree with, and instead write your interpretations in a follow-up opinion paper. This looks much better than the authors disagreeing with each other, I believe, especially if this is a basic research paper.


text:
Risk to academic reputation by publicly requesting pay-walled articles
The Twitter hashtag #ICanHazPDF has been popular among academics as a method for peer-to-peer exchange of pay-walled articles. Some people call this practice "piracy", and it could be illegal depending on the publisher policies.
Apparently, many users use it with real names and real profile pictures.
What are real risks to academic reputation and career of people by publicly requesting pay-walled articles?
I'm looking for an objective assessment.

It will be news to me the first time someone points to a case of a hashtag, or anything on Twitter, having an impact on academic reputation.

@LaurentDuval Risk to reputation of individuals and organizations can be objectively assessed and managed. #UseGoogleBeforePostingNiceComments

@DanielR.Collins I edited the question to make it clearer that it's about requesting PDFs on Twitter, which is a "dubious" practice, rather than merely using the hashtag.

Risk to reputation of individuals and organizations can be objectively assessed and managed — [citation needed]

@JeffE Here we go:
http://dx.doi.org/10.1108/09513570810863932
http://dx.doi.org/10.1258/cr.2009.090045
http://dx.doi.org/10.1287/orsc.1050.0127
http://dx.doi.org/10.1007/978-3-662-04008-9_2
https://books.google.com/books?id=rjuBTqZPS_EC
https://books.google.com/books?id=aaeLF_3VPJEC
https://books.google.com/books?id=TWqUAgAAQBAJ
http://www.criticaleye.com/insights-servfile.cfm?id=409

@Orion I agree that your citations support assessed and managed, but they do not support your claim of objectivity.

@JeffE They do. Reputation management implicitly involves objective assessment! Objective measures of corporate reputation may include client satisfaction.

@DanielR.Collins Here's something on twitter having effect on reputation! https://www.insidehighered.com/news/2013/08/07/fat-shaming-professor-faces-censure-university

Probably very little unless they're very pro-copyright or lawsuits start to happen. In the former case, they'd look hypocritical. In the latter, a University might be less likely to hire the academic to protect themselves from future liability issues.


text:
Using well-established abbreviations for new concepts in the same field
Should a researcher try her best to avoid using existing abbreviations (such as IEEE, WHO, DNA, ANOVA, BMI, CERN, NASA, UNESCO, OPCW, NHS, CDC ...) that are (well-)known in her fields, when creating abbreviations for new concepts (methods, substances, studies ...) in the same field?
Or is it OK if the abbreviation for the new concept is just defined where it is used (e.g., in a publication)?

This is not good practice : global search algorithms will find "results" that are not relevant... engineers have to use letters for things and use an upper case letter with descriptive subscripts to focus the meaning ie Cf (coefficient of friction), Cd (coefficient of drag), Cl (coefficient of lift, could be confused with the symbol for chlorine, but these are subscripts not lower case...

You should avoid using abbreviations entirely.  Give your new concept a mnemonic name.

"You should avoid using abbreviations entirely." "– JeffE". *cough*

@DavidRicherby I'm going to assume Jeff has taken his own advice, and from now on will pronounce that name in my head as "jeffy" rather than Jeff E. There's also a mod over at Biology and Psych/Neuro AliceD, who is indeed not Alice D. but intended to be read as an entire phrase.

Yes, you should avoid using well-established acronyms to mean something else. I would especially avoid those like the ones you present as examples that are likely more recognizable as the acronym than what the acronym stands for: they are effectively words by themselves with a specific meaning.

Yes. But then again, no. Depends.
If you can easily avoid it, sure - avoid it. It will only cause confusion in the long run. But this confusion is dependent of the previous acronym being relevant (as opposed to known) in that specific field. So if you are creating a new modular iterating algorithm (stupid example, but you catch my drift), and your last name is Brown, it is OK to call it the Brown Modular Iterator (BMI). No one, in context, will think this is the Body Mass Index.
A slightly different example of when it is OK (not, mind you, optimal) to use an existing acronym which can actually cause confusion, is when there are specific naming conventions. This is how we have the American Sociological Association (ASA), the American Statistical Association (ASA), and the American Society of Anesthesiologists (ASA) - with most societies holding the convention of country_societyname_association, and medical societies to the country_societyof_societyname.

On the other hand, it's going to be really hard to Google for BMI because Google will be convinced you mean body mass index. So, really, re-using existing common abbreviations seems like a pretty bad idea.

@DavidRicherby To be fair, Google tends to do well if you add context clues, at least when there's little overlap between the fields. E.g. "BMI airport" finds the airport just fine, but "BMI burger" probably won't find the Big Mac Index.

@Anyon  Actually, “BMI burger” (without the quotes) in a Google search gave me the Big Mac Index as the third search result. (The first link was to a burger event at Broadcast Music Inc. in Nashville, and the second link was about the Body Mass Index. YMMV since Google’s results are personalized, but it seems to do a decent job, even with overloaded abbreviations.)

OP specified that are (well-)known in their fields which I suppose is a bit grammatically ambiguous but I took to mean "their" field to relate to the researcher, rather than the acronyms. The Brown Modular Iterator would probably not be used in the same field as the Body Mass Index, but perhaps should be avoided since BMI is used as such a popularly known acronym, alongside others like NASA. I think the ASA examples are a better counter example. Working as a statistician in an anesthesiology department has me in a bit of a bind personally, however...


text:
Rights of authors who withdraw peer reviewed manuscript due to refusal to transfer copyright
Many (traditional) journals request copyright transfer upon acceptance.
A group of librarians suggested that authors negotiate the copyright transfer and prepare to walk away if the journal insists on full copyright transfer.
Suppose the authors refused but the journal insisted on the transfer, and therefore the authors decided to publish elsewhere.
Generally, what are authors' and journals rights in such a case?
What happens to the peer review the authors received from the first  journal? Can or should they present it when submitting to another journal?

Surely, authors can access journal's copyright transfer form and study it thoroughly before they submit to this journal.

Surely. But they can also negotiate after acceptance.

What would be the benefits of doing it after?

If the editor/journal finds the article important, e.g., of potentially high impact, they may ask for less restrictive terms or even allow authors to retain ownership.

For some journals, submitting the manuscript entails transferring copyright, see for instance http://www.ma.huji.ac.il/~ijmath/instructions.html

The authors should check when the journal transfers copyright. As mentioned by Andrés E. Caicedo in the comments, some journals assume the authors transfer copyright once a paper is submitted, not after acceptance.
If the authors withdraw a paper because they do not want to transfer the copyright, the journal's likely reaction would be to remind the author about the possibility of publishing open access. If the authors decline that too, then the journal will probably think, "why did you submit it to us then?" Getting the paper reviewed involves a nontrivial amount of effort. If the journal decides the authors submitted the paper knowing that they will withdraw it if it's accepted, effectively wasting the journal's time, they might blacklist the authors.
As for what happens to the peer reviews, from the journal's perspective, nothing. The reviews are left on the manuscript's record, of course, but nothing beyond that. The authors will still have access to them, and they can do whatever they want with them (such as use it to improve their manuscript). They should not, however, present them to another journal. As I wrote in an answer to another question, these reviews don't help the new journal:

We can't use the original journal's reviewer comments & your responses. We don't know who the reviewers are. We can't tell if the reports are legitimate. We can't see if confidential comments were submitted.

If you do not transfer copyright to the journal (or in some way provide them permission), the journal has no rights to reproduce the manuscript. If you do not transfer copyright to the journal, your rights are not limited.

What happens to the peer review the authors received from the first journal? Can or should they present it when submitting to another journal?

I am not sure if this has anything to do with why you withdraw the manuscript from the first journal. You clearly do not hold copyright on the reviews (e.g., the reveiwer probably does, but maybe not), so forwarding them on is probably a no-no. That said, there are likely no damages, so if you did, it probably is not a big deal. More importantly, if the new journal wants the reviews they would probably go through a portable peer review system (although that does not seem to be very popular).

Transferring copyright is not necessary for a journal to print an article. All the journal needs is a license. My impression is that they ask for full copyright for their convenience. My experience suggests that not all journals are willing to merely license articles, unfortunately.

@BenTrettel yes it is possible the OP gave the journal a license but not copyright, but I think this is splitting hairs based on the question.

I was just commenting on your first sentence, not saying that the OP gave the journal a license. Your first sentence reads to me that journals can only publish a paper if they own copyright.

@StrongBad "I am not sure if this has anything to do with why you withdraw the manuscript from the first journal." The withdrawal is purely due to disagreement with the journal on copyright.

I doubt you should ever forward the reviews.  Irrespective of this copyright gambit.  You can summarize that reviews were done and the general positive/negative and evolution of the paper (in succinct fashion).  But the reviews themselves were in confidence.
I would also mention your copyright issue with the second journal.  Otherwise you are wasting everyone's time.  Probably wasting people's time at first journal too.  If you want the rights, find a journal that does this or just self publish.
Academic journals are different than paid authored content (stories, novels, freelance articles and photos) where some negotiation dance is tolerated.


text:
Does examiner's own PhD outcome influence decision?
PhD examination outcomes, depending on country/university, may include unconditional pass, pass subject to minor or major corrections, and resubmission among others.
Is there any evidence or analysis (in any country) on whether an examiner's decision can in some way be influenced by their own PhD outcomes?
For instance, is an academic who himself/herself got a lower PhD outcome, e.g., major correction or resubmission, more likely to give lower outcomes when acting as an examiner?

I doubt that there is any significant data to show one way or the other...

I'm curious to know where you think this might be an issue. In my experience, if a candidate didn't do well in the defense, they were just given some ideas about what they needed to do to improve the work or presentation. There was no record left until success was obtained or the candidate gave up. Minor corrections, especially were treated as more of a clerical issue than substantial. Moreover, we treated it as the advisors responsibility not to let bad things happen.

@Buffy I'm curious to know how your comment relates to the question. Could you please clarify?

@Orion, the first sentence is my puzzlement. The rest is why it is a puzzlement. With clarification, an answer might be provided, but I wouldn't know how to approach it without more from the OP.

@Buffy I think you misunderstood the question. It is about factors related to examiners rather than the student or the student's work.

Which question are you asking? Limit it to one clear question...

@SolarMike There is one clear question: Is there any evidence or analysis (in any country) on whether an examiner's decision can in some way be influenced by their own PhD outcomes?

What about the last para then...

@SolarMike This is an explanation of the question, I guess.


text:
Grad school and pregnancy
I 'm planning to apply for Masters in Computer Science (Non-thesis). I 'm wondering if both, pregnancy and school, can be managed at the same time. Or is better to wait until I get my baby and then apply for the school. I 'm trying to learn from others experiences.

Are you asking only about being pregnant while studying (i.e., you would time it so that you give birth after graduating), or also about giving birth mid-course?

One of my professors gave birth to her daughter during her PhD. She's pretty successful now. Not that much to worry I guess.

Since I'm not female, I can't give direct evidence. However, there are a couple of things you might think about.
The first is your general health. If it is good, then the stress of pregnancy will most likely be manageable. Then your studies will also be manageable. Note that the stress can be both physical and mental.
The second, is stress itself. Both a pregnancy and a graduate education can add to your stress. If you have other stresses in your life (financial, ...) it can get pretty high. That isn't a recommendation against it, however, but a recommendation that you will need ways to manage stress. If you do this well already, then there is likely no problem, otherwise, find active stress reducing activities.
In fact, having something to think about other than your studies can actually be a help because of the way the mind works. If you do nothing but try to force your mind to action it can stall.
Also, it is probably a mistake to delay your dreams unnecessarily, either for a child or an education.

It can absolutely be done but you should be realistic up front with yourself regarding the challenges. You know yourself best.
Anecdotally, in my graduate school there was a PhD student who ended up pregnant and gave birth at the end of her second year. She had to make some adjustments such as working from home more, video and voice conferencing with her advisors, but she made it work. One of the strongest students in the program.
I think this is a question that you decide the answer to.

I think that anyone is capable of going to school even while having a kid. All the more power to you and pride you would have! It could be hard but any person knows what they're capable of and if you think you are, why wait on having a kid or getting the degree/why choose between school and parenthood?

You should / could check in advance how open your university actually is. We are very supportive and try to help wherever possible, since many of our professors are young(er) parents as well, and sometimes we are stretching rules a bit which makes it much easier and reduces stress.
In general, having a kid during grad school might be wise, because when it comes o employment questions afterwards, you can always declare that you already have a kid ;-). (yes, I know that you should not be asked about it, but I know of several companies which are not employing younger women because of the risk of them becoming pregnant).
So in short: Do whatever feels good to you!


text:
How to deal with unnecessary stress introduced by the supervisor?
I am doing my PhD in a high prestige UK university.
I am finishing my second year and I have funding for three years in total.
I have already two papers finished (pending to be published) and working on two more.
I like research and I like being pushed to achieve the best I can. What I don't like however is introducing unnecessary stress into my daily life. With this I mean the following:
I think that it is totally acceptable and expected of me to work overtime when nearing a deadline. Usually the month before a deadline I work 12 hours per day, 6-7 days a week. This is totally fine and to some extent I enjoy it.
My supervisor is a brilliant researcher. Young and successful in his field with many publications in high prestige venues. However, he's also the classic stereotype of the super-workaholic academic who works 7 days a week, from early in the morning until late at night.
It's common for him to send messages or emails at 23.00 or during weekends asking for something. This could range from asking to complete a certain task or a simple "What is the status of X?".
I find this exhausting. To work hard during the week I need to have a "safe space" where I know that I can relax without worrying about work. Otherwise I feel demotivated to work hard. Due to this behavior I have anxiety issues. Recently, after a very stressful period mostly due to work, my hair started falling. This was identified by my GP as "Telogen effluvium". It can happen after very stressful periods. Thankfully it stopped but it's a clear sign that I've been stressing too much.
Ignoring my emails and messages is not an option for me. The reason is that I know that he genuinely cares about my PhD and many times his messages may be about the changes he has done on my paper. Ignoring this makes me feel ungrateful.
My most important problem is that, looking back, 70% of the stress introduced by supervisor could have been totally avoided if he could relax a bit. He's micromanaging me and wants to know everything. And many times we could have taken a month more on a project instead of rushing things.
Moreover, because he's always pressuring me to do as many things as possible as fast as possible, I feel that I cannot do any quality work. I prefer quality for quantity. He's the opposite.
I have tried to convey my feelings to him multiple times already. He does not seem to get it. Or he may back off for 2-3 weeks and then resumes his previous behavior. In a recent confrontation I mentioned the words "unnecessary stress" and he didn't take it very well.
Many colleagues have told me that I should be thankful because he's actively working on my PhD while other supervisors are totally absent. I find this unfair. None of the two should be OK.
Overall I feel burned-out and demotivated. This saddens me because I really like my PhD and research in general.
However, I don't think I can take this for one more year.
Question: How to deal with a workaholic supervisor who is introducing unnecessary stress into my daily life?
p.s. It's important to mention that my supervisor probably suffers from anxiety as well. This is somewhat known by his PhD students and he has implied it one or two times.

Have you tried not answering an email until the morning? Was he mad? If yes, he has unreasonable expectations and this should be addressed. If no, you need to work on your own mindset (i.e., you are stressing yourself first and foremost - your supervisor is at best the trigger) and let your supervisor work whenever he feels productive.

@xLeitix He isn't mad but if I repeat this behavior he gets passive aggressive. Other than that, I totally agree I must work on my own mindset.

Answer emails only once, perhaps twice a day. The rest of your working time is for actual work. If he asks why you have not responded earlier, just say "I was busy working on X, so I could only check my emails so often".

I think the primary problem here is conflating leaving a reply until the next working hour, and ignoring that email. They're not the same thing.

How do you receive emails at 11 PM at night? Are you at a desktop with an email client open? Did they come through your smartphone with an alert? Something else?

If the supervisor asks why you didn't respond to the 11 PM email, the answer should be "I was asleep".  Likewise, most weekend emails can be answered by "I was out hiking (or whatever) where there's no service".

"I think that it is totally acceptable and expected of me to work overtime when nearing a deadline."
I disagree. Routinely expecting overtime near a deadline (rather than occasionally when something has gone wrong) - whether in academia or anywhere else - indicates either too much work, or poor planning.
In academia the first will almost certainly apply, and the second may too, but that doesn't mean that academics should be inflicting this on PhD students, for whom the workload does not have to be more than a full-time job.

@Flyto I wish things were like that.

I know people who will send me a little quickie question at odd hours. Then after suckering me into outing myself with a quick and easy reply, they follow up immediately with a big hassle email requiring a lot of my focus and time. And it would now be clear I'm knowingly ignoring their email. Luckily I take joy in doing so, rather than stressing about it.

Learning to deal with stress is kind of part of the education. The more prestigeous it is, the more so.

It is not unreasonable for a supervisor to write emails in the middle of the night. I do it myself, and frequently at that (sometimes because I am honestly just working late, sometimes because I am in a different time zone). However, it is unreasonable to expect immediate response when you do so (more accurately, it is unreasonable to expect immediate response for basically any email, as the medium is fundamentally asynchronous and nobody should expect you to have your email open all the time).
That said, a significant part of the problem also appears to be your own mindset. You can't realistically change when your supervisor sends you work, but you can definitely change when you read it, and when and how you react to it. Just not reading emails in the night is a big start. Many people do it, and you do not need to have a bad conscience when you do it as well. A second part of this is also to not interpret every email as implicitly highest-priority. Try to assess what a realistic timeline for any given work task is - if your supervisor does not specify you don't need to assume it needs to be done next thing in the morning.
One problem that you may face is that you have by now trained your supervisor that you read and react to every email at any point in time. Even if it's unreasonable, it is somewhat understandable that this is by now how your supervisor thinks you work. The most pragmatic way is to change things gradually over time, combined with a non-accusory one-on-one talk with your supervisor that you are unable to deal with your current work mode. Don't use the words "you are stressing me out" or anything else that puts the token and blame on him. Say that you are stressed out and need to change how you work. The goal is not to elicit a different behavior from him (although this may also come out of the meeting as a sideeffect), but to communicate to him how you plan to address your stress-related issues going forward.

+1 though it’s not uncommon in academia for managers to expect fairly immediate replies. Pushing back against this can itself be draining.

You had my +1 already at " it is unreasonable to expect immediate response for basically any email, as the medium is fundamentally asynchronous" and I'm sad I can't add a couple +1 for the other paragraphs.

Excellent answer. OP says "Ignoring my emails and messages is not an option for me," but needs to see and use the wide range of possibilities in between ignoring and replying immediately.

The focus on email in most of the answers is a little odd to me. I agree that the email situation is a problem to be addressed, but I think there is a broader problem of a stressful, controlling supervisor. You say to not put blame on the supervisor in talks with him (good advice), but we should seriously acknowledge that the blame is majorly on the supervisor. This is a motivated, extremely hardworking student, who produces good output, and the supervisor is micromanaging them and always expecting more, and even acts passive-aggressively if the student does not respond to email immediately.

Overall, I feel this answer is a bit optimistic. This approach may not work. It is possible that the supervisor is a bad apple. Such a stressful environment may have no other solution than either (i) finding a way to endure the stress or (ii) finding a new supervisor.

@6005 We are focussing on the email thing because that is what OP wrote concretely. The rest (micromanagement, passive-agressive) are just side remarks, which I have learned to not take much stock in.

And, if you are that supervisor who sends emails at any hour, it would be "enlightened" of you to make it clear at the beginning of your relationship that you don't expect immediate response to every email unless you add some particular signal to an individual mail. And, any email from my (former) employer that was flagged as high priority went to the bottom of the stack since it rarely was.

As someone who has had to handle some significant health-related issues, let me begin by saying

Your health is more important than any project!

If your health is being impacted negatively by the stress you feel and by other concerns, then this is something that you have to deal with, and you need to make it clear to your supervisor that this is starting to become an issue. Phrase it as a health issue, not a stress issue, and you should see a change in behavior.
That said, one of the things that you can do is to make time for yourself to decompress. Even if your boss is a workaholic, that does not obligate you to be one as well. You should schedule time for yourself to do whatever it is that allows you to “unwind”: maybe it’s work out, or do something artistic, or maybe it’s just cooking dinner for yourself. But whatever it is that you do should be added into your schedule, just as if it were a group meeting or a class: it’s time that you don’t let others infringe upon.
Also, you need not answer an email as soon as the professor sends it—indeed, in many ways, there are studies showing that you’re more productive only dealing with email a few times a day rather than all day long because you’ll spend less time on “task switching,” which costs you the focus and attention you need to do well. A few hours’ or a day’s delay in answering an email is perfectly acceptable if it leads to a more thoughtful and fruitful discussion.
But the most important thing is to keep an open line of communication with your advisor. Clearly he’s interested in your work and in your success, and you should try to use that to your advantage. Keep working with him, but do it in a way that doesn’t assign blame to either of you. Make it a collaborative rather than adversarial conversation.

+1 for Your health is more important than any project! It's ok if sometimes project things don't get done as fast as they might because you're spending time looking after yourself by resting or doing something fun. Don't let that little guilty voice in your head force you to work all the time....

You will have to differentiate between the stress put on you by your supervisor and the stress you are accepting. E.g. even noticing that you received an e-mail around midnight is unnecessary. Just switch off your phone (seriously!) or stop message transmission during sleep times. If you feel better, you can offer an "emergency channel" for important tasks (e.g. allow for chat messages in urgent cases), so you can rest assured that the world will still be rotating after you woke up ;-).
It is part of a PhD process o learn about your own working style and preferences, and how to interact with other people who are not doing it the same way you prefer things to be done. I assume your mindset is close to the one of your supervisor, so you don't want to disappoint him, but you still have to draw your borderlines. And you can only draw your borderlines, you can not change your supervisor.

This answer will be orthogonal to the question and might help or not.
In some ways you have an ideal situation with an advisor invested in you, your work, and your future. He also seems to trust you greatly. Be glad of that. Contrast that with the situation of many others asking questions here who have advisors too busy or disinterested to help them at all.
But stress can kill you.
While this will take time, I suggest that you find some activity that you can do for an hour or less each day that is know to be a stress reducer. Yoga comes to mind. My solution is Tai Chi, which is a mind-body melding exercise. It is very difficult to be stressed when doing Tai Chi.
However, you must, then find a way to compensate for the time spent. But this is not a good way to think about it. Your mind will work without you consciously "pushing" it. Many people wake up from a period of rest knowing the solution to a difficult problem that eluded them before they let it "gestate". An hour of calming exercise can have this effect also.
Far better this, IMO, than trying to change your supervisor, especially if he treats it as criticism and separates from you and your work. You could even get him to join you in Tai Chi. (Pipe dream, I know.)

Exactly the same situation with you...
Sometimes I received 10 more emails one day with shouting...
But I survived because I tried to think like he was not trying to destroy me but help me. I hope you can cooperate with this, try to reduce the times reading emails late at night, or simply don't reply to it until next morning.
What can be done tomorrow should be done tomorrow.
Hope you the best.

This sounds like a pretty typical problem in many workplaces. Regardless of when your supervisor sends his emails, the stress is generated by you reading them in the middle of the night or over the weekend. If the supervisor explicitly follows up during office hours to state that he is unhappy with your lack of response then that's something that needs to be addressed with him since it's unreasonable. But to begin with I suggest you stop checking emails outside of office hours. Most email clients can be set to only update during business hours. Failing that just switch it off.

To add to the excellent existing answers, you may be able to induce a change in your supervisor's behaviour by being more proactive in your communication. One reason that supervisors may feel the need to micromanage is if they feel out of touch with what you are up to. So, if your supervisor regularly sends you messages asking "What is the status of X?", perhaps this is a sign that you need to be updating him more frequently. If you take the initiative and send the first email, it has several advantages.

You feel less nagged.
Your supervisor may start to feel more confident in your ability to manage yourself, as they can clearly see that you are making progress
without the need for constant prodding.
If you are the one sending the email, you can do it at a time that suits you.

I don't think the existing answers have sufficiently dealt with HOW you should approach your supervisor about this.
I suggest framing the change in your work habits as a positive for something he cares about - which is (apparently, frustratingly) not your stress level. I would say that you are making a change either because you are trying to work more efficiently or because you are trying to do more high-quality work. Or choose another goal he cares about (more creatively, etc.)
You could frame this as: One of my goals is to work more [efficiently]. I have noticed that when I do work past X pm, it tends to have a lot more errors than work I am doing earlier in the day. Then I have to redo this later. So I am trying a new work pattern where I only do analyses before X.
The goal is to frame the change as being in service of something that the supervisor values so it is not seen as a change in your work ethic. Likely the supervisor views hours worked as an indicator of dedication etc. so you want to make it clear you value these things, too.
You might begin the conversation as a discussion of work strategies, how to be the most efficient, what work habits your supervisor has experimented with, etc. to get him into the mindset that each person needs to find their own best work style. You may also want to drop into the conversation that you admire his work style, and you are hoping you can mesh your two work styles well.

This is not much different from industry.
I have taken the habit to consciously disconnect and make sure I cannot connect.
The "cannot connect" part is important : I leave my laptop at the office and I use a separate app for work emails. When on vacation I even change the password so that it does not fire up by mistake.
This way my brain knows that even if this is the end of the world and président Macron is trying to mail me, he will have to wait until tomorrow or Monday.

Set a vacation message that says you will respond at certain times.
Before you do this, tell your advisor you need to normalize your sleep patterns, on the orders of your doctor, in order to work more effectively (you did see the doctor about this, yes?).

I disagree with your premise that the stress is introduced by the supervisor, let me explain:
There are two types of communication: synchronous and asychronous.
Syncronous communication relies on everyone participating at the same, for example a meeting or a telephone call. It is unreasonable to do these outside of normal working hours except in emergencies, that is urgent but very rare occasions.
Asynchronous communication, like email, does not rely on everyone participating at the same time, so people understand that you don't need to answer those immediately but only when you have time. It is not even productive to do so because getting back to a concentrated state takes a long time. I propose that you check and answer your email only once a day at a set time.


text:
Applying for job while 3/4 done with MS program
I am currently a MS student finishing my last (2nd) year. I have just applied to a top company of my field in my city (perhaps the nation as well). I did a video, phone, and on-site interview. They understand that I have just 1 class left next semester, but also need to finish my thesis (which is maybe 25% done?). I have informed them that I can work a full 40hrs a week (I am actually currently working about 35 hrs on top of 2 classes, TAing, thesis work). I have received an offer to start in January that is generally quite high for a new MS grad in my field. To be honest, I am much more interested in the work I would be doing at this company.
Should I take the offer and start working while taking the class/work on thesis? Or don't take it ?

Usually a masters thesis is a full time job, especially closer to the end of the thesis. Honestly, I would not recommend working 40h/week on top of working on a masters thesis, as long as the fields are not closely related. But of course this depends on individual factors which we can not appraise without knowing you and your thesis / course work.
Some questions which might help:

How much of your thesis can be finished before January?
Will it be possible to reduce the working hours to complete your studies if necessary (without being paid during that time)?
How well can you handle stress?
Would it be possible to start with 20-30h/week whilst you have to study?

In the long run, it is not a good idea to screw your thesis for a job. It is the most important grade! When people apply for a position at my lab, I am mainly looking at their thesis topic and grade - the rest is less important.
Maybe you can twist it another way: At our university it is common that students are doing their thesis in cooperation with a company - maybe you could switch your thesis topic and combine job and thesis.