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Thought Exercises in Deciding Whether to Stay in PhD Program or Leave?
TL;DR: Thinking about leaving my PhD program after 6 months.
1.) The program is not what I imagined it would be.
2.) I'm not positive I need a PhD to do what I want to do.
3.) I've been offered a pretty great opportunity that would put me back on a track that I was happy with prior to my program.
4.) However, I do not want to burn bridges with faculty/people that have invested time and resources in me.
I would love to hear any thought exercises or lines of self-inquiry that people have found useful in making a decision of this nature! tl;dr/close

I will keep details in the following fairly vague to avoid identifiers.
I am a 1st year PhD Student (6 months in). I've spent several years in "the real world" in between my Masters and my current position. I was achieving just about everything I wanted to during this time, but felt that a little more access to independence and/or creative discretion in designing projects would be nice.  I decided to pursue a PhD, visualizing 4-5 years of independent research in a free-thinking environment, and then returning to an applied position outside of the academic arena.
Without getting stuck in the weeds, I'll just say that my program, and academia in general, is not what I had built up in my mind, and I am now incredibly disillusioned with the work of my cohort.  I feel as though the end result of my research ideas will simply be research products that remain one or two steps removed from being applied in practice, whereas prior to this work I was taking ideas and just implementing. Creativity realized. I'm not sure a PhD is necessary for what I ultimately want to do. In the end I'd rather share my ideas with a broad audience of practitioners, researchers, as well as lay communities. No textbooks. "Regular books" with complex ideas distilled into elegant simplicity that even the public could ponder.
I have recently been offered a pretty great position that would place me back in an applied position and on the track I was on previously.  My intuition tells me to find a graceful way to exit my program, but I also know that I am new. I would give the decision more time, but the external opportunity requires fairly immediate action, and I'd hate to become more ingrained in a current team project and have folks invest more resources in me.
I would love to hear any thought exercises or lines of self-inquiry that people have found useful in making a decision of this nature!
Thanks in advance!

I would love to hear any thought exercises or lines of self-inquiry that people have found useful in making a decision of this nature. I would ask myself: 1. How many lives do I have? 2. Which do I care more about, my own long-term happiness and ability to contribute to the world in the best way I think I can, or what some random group of people I happen to be working with at the moment thinks about me?

When the usenet group alt.grad-student.tenured was active they had a heutristic rule: if you would rather scrub the toilet than work on your dissertation you are in trouble. You're not quite that far along yet, but the same principle applies. If there is something most people consider a dreary chore that you would rather do than work on your studies, maybe grad school isn't for you (or not at this time).

Been to similar situation. Here couple of points:
Decision and Responsibility: You have enough personal reasons to leave. In fact, I'm impressed you figured it out in the first 6 months, which is a good thing. Here is the thing: You need to make a decision, and take the full responsibility for it. Other people in your research group, might have different agendas, and therefore might give you the answer which is good for them. Probably your supervisor spent decades in research and does not get you, or doesn't want you to leave, because he/she spent time and energy in the last couple of months to guide you through your early PhD stage. you see what I'm trying to say here?
Burning Bridges: If you decide to leave, this is your answer to your current situation, and other side effects are out of your hands. They are not your wife/husband that you need to take to your consideration. It is a professional decision you made for yourself. Good thing is, you are a PhD student and not a supervisor to leave number of students and their future behind.
Interaction To Your Supervisor: First have a meeting with your supervisor, and tell him/her, your decision. Tell him/her sorry for the situation created but you have to do what you have to do.
Interaction With Friends: You can also let others know about this, and wish them best of luck.

I'm in a PhD and I absolutely love it, and I fully appreciate how fortunate that is. It's not for everyone, and you've given very good reasons why it's not for you. There's absolutely nothing wrong with that!
Regarding burning bridges, just be open and honest. They'll understand, and they'll appreciate that you won't spend the next 4 years wasting their time and money.
The important thing is you tried, and your decision is based on your experience rather than assumption or hearsay.

...perhaps this might serve you as well as it does me:
Imagine that you have arrived at the end of your life, and are on your deathbed.  Looking back upon your life, enumerate that which you would like to have accomplished in life.
If any of those accomplishments necessitate as consequence the PhD which you currently pursue, then perhaps you might reasonably bear out the current course.
Wise would be remembering a simple truth: that each of us is infinite at the core of our conscious awareness.  Infinite possibilities we each might at any moment enact, conjure, attract, or cause to precipitate in reality, within the external illusion of the physical world.
Best of luck,
F.

Perhaps more a comment on @MercedesSchrödinger's answer, take into consideration that your advisor/school did commit resources to you (a place in the research group, some founding, time, a potential thesis thema, ...). Don't believe that you just walking away will go over just like that.
Taking such a step is burning some bridges. It is not something to be taken lightly. You might consider putting your PhD on temporary hold (but not for too long!) until your sort out your dilemma.
In any case, if you rummage around here (and also by personal experience, both undergraduate and more acutely during the PhD), you'll see that doubting if you are on the right track is quite common. Sit down, clear your mind, and work through the issues. Write down pros and contras, weight them carefully with a cool head, and lay out your future path.
Whatever you decide, good luck.


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What is the principal investigator’s responsibility regarding data authenticity?
Every now and then, you hear stories of data being fabricated by a graduate student (or post-doc) who felt the pressure to publish groundbreaking results was too much. This unethical behavior makes me wonder: What can a PhD advisor (or group leader, or project principal investigator) actually do to avoid that in her own group? What are her ethical duties in ensuring that all published data is genuine?
Please note: I'm not singling out graduate students or post-docs because I think they are statistically responsible for more ethical misconducts than others… only because it gives a good case of when the PI would have only indirect access to the data (meaning: she didn't actually do the experiments herself, but was only presented the data by others in her group).

The opposite also happens, where PhD students suffer from a supervisor that fabricates data...

@gerrit that was the point of my “please note”… I am not implying that the opposite doesn't happen, but I am merely interested in that particular case.

I didn't mean to correct you, just to provide an interesting read on the opposite — PhD students almost lost their PhD because they were suddenly without any publications, and it's even more difficult for a PhD student to question his supervisor than vice-versa. The PhD student who finally flagged the situation is very brave (imagine making this accusation and being wrong; bye-bye academia)

@gerrit indeed, sometimes it isn't even black/white, as in the advisor telling which data to omit because it would not be of interest or would make the story inconsistent

The PI is responsible for the output of the scientific employees under them, while they are doing work for the PI. (I think it would be unfair to hold a PI responsible, for instance, for quality control on the work done by a post-doc on a paper submitted with his or her former group.)
From an ethics standpoint, however, the PI is responsible for encouraging an atmosphere in which errors are caught and corrected, rather than tolerated. If errors are "innocent" in nature, then no guilt or punishment should really follow from catching and fixing those errors. However, a PI is responsible for not sanctioning deliberate lapses. If the PI sets up a culture in which such behavior is viewed as expected or necessary, such failures do lie on the PI.
I would argue that the PI's responsibilities extend to ensuring that the work claimed has been performed, and that the data has been correctly analyzed. Some places I've worked at have instituted quality control procedures for doing so, to varying degrees of formality. While I don't think a full review of all of the data is often required in academic settings, I think most groups would benefit from some implementation of such measures. As Ana suggests, if you do "random" sampling of the work produced, then it makes it that much harder to falsify anything, since you don't know if that will be the work that will be checked.
A PI shouldn't be expected to fall on her sword for a single incident involving an underling. The PI could perhaps be castigated for making a poor personnel decision, but it shouldn't be a career-ender unless the PI is aware of and condones the unethical behavior. Cases such as the Bhrigu tampering case at Michigan, in which a postdoc tampered with the work of a graduate student in the same group, and which led to the PI moving to another university, are unfortunate, and only serve to make things more difficult for everyone. But the aversion should not have been cast upon the PI—which seems to have happened here.

We've talked about this at the institute where I'm doing my PhD, and the best solution seemed the following:
First, make a central database for all raw data, that can be accessed per request. Upload/copy data to it as soon as it's collected, including noisy data that might not enter the final analysis. This ensures that any excluded data has to be properly justified.
Second, let everybody know that every so often a random dataset will be pulled out and some basic checks run on it.
Third, run those basic checks. For this you need someone with knowledge of statistics who can tell you what is appropriate for your type of data. A lot of basic aspects of normal data are difficult to simulate without a lot of knowledge on statistics. To give an example, if you take data that have a normal distribution, split it into quintiles, then plot the mean against the variance in each quintile, they should roughly fall on an inverted U-shaped curve. I know of a case where this relationship was perfectly linear, which raised alarm bells. In any case, these checks should be simple and easy to run.
Fourth, decide who will do these checks, because it takes time and effort.
Fifth, make sure you have some idea of what types of mistakes are honest mistakes, and what constitutes actual fraud. Make sure you discuss mechanisms of dealing with these mistakes (and fraud) beforehand, i.e. don't leave this decision in the hands of the supervisor at the moment it happens.
Edit: I guess the main question was what's the PI's responsibility. My reply reflects my opinion that the responsibility should be more institutionalized, and not left just to the PI. On the other hand, the PI could run some of these steps internally if needed / if there is no other help available. But then it might be too elaborate, so perhaps you will get some better answers from other people.

While it quite doesn't answer my question, it is an interesting suggestion for dealing with the issue. Thanks!

I agree. There is no excuse for the current status quo in many fields where data is passed around via emails with poor documentation of its history. (Not that I think this extent is required, but it would be nice.

It's a sad reality. That is why research group leaders should be so deeply involved in their post-graduate students' research that they can detect fabrication of data easily. It is unfortunate when research group leaders only sit in their room and expect the student to do everything for them and put their name for the paper. It is the duty of the leader to scrutinize and question the results and ask for repeats when necessary and go carry out a few experiments too to authenticate results before accepting them.

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Face-saving way of asking whether audience is familiar with specific topic
Sometimes I give a talk for a limited number of persons (typically well below 15). Here, the audience consists of persons from different subfields of the same fields. Consequently, I am often not familiar with the background of all persons in the audience. In the past, I sometimes was unsure whether all the attending persons are familiar with a specific topic that is considered basic in my subfield but might not in theirs. I then asked directly, whether they are familiar with the specific topic. The answer was almost always "yes" although later it turned out that the topic was not so clear to everybody.
How can I rephrase this question in order to get an honest answer?

Your question title and body are asking two different questions. To your final question in the question body, "How can I rephrase this question in order to get an honest answer?", I would suggest never asking whether everyone knows X (the audience cannot know whether "everyone" does), but always about who doesn't know X. That can be quite effective, but it certainly isn't face-saving (other than making the audience used to seeing lots of raised hands and thereby getting the feeling that not knowing is normal and does not mean losing face).

For a small audience, it may be worth asking them to briefly introduce themselves and say what they do (maximum 30 seconds per person). If you want to have interaction during the rest of the talk, define the "rules of engagement" right from the start.  If the audience members also don't know each other, the introductions will probably be of interest to them as well as to you. This is more likely to get them interacting than asking the whole group a question - after all, almost everybody's favourite topic of conversation is talking about themselves!

Don't expect to get honest (verbal) admissions of ignorance.  Egos are fragile, especially in academia.  Instead, watch and listen, and be prepared to adapt your presentation to what you see and hear.  More details in my answer below.

Just to comment, I find asking "raise your hand if you have no experience with ..." tends to catch people from flying under the radar more than "raise your hand if you have experience with ...". Plus, IMHO, it's a more important count for the speaker than the number of people who are familiar with what you are discussing.

@alephzero interesting approach. However, the audience is familiar with each other in my specific case. The problem is that even that I know that a person is in subfield X doing Y, I do not know if the person is familiar with the concept of Z that is used in my subfield.

If it's a question of whether a discipline is familiar with a topic, I'd suggest more informal discussions with individual people from that discipline. While talking about the topic you see whether they are familiar with it or how they see it (or which name they use for it). However, even between people in the same discipline there might be huge knowledge differences. So, essentially, I'd suggest to follow "Dan C"'s suggestions in any case.

When I give talks in similar situations, I typically assume that at least some of the audience members will be unfamiliar with much of what I think of as basic.  Your job is to "remind" them, without spending excessive time on the topic.  A good place to use this technique is with definitions.  For instance: "... a polynomial, for example 3x4-5x2+2x+6."  (The best way to teach most things, particularly definitions and algorithms, is with examples.)  You can do this fairly unobtrusively, so that those who don't recall the definition are reminded, while those who do are still not offended.
Another point to remember is that generally, it's good for some of your talk to be a refresher.  You might say something like "most of you are probably familiar with this, but just to make sure we're all on the same page..."  This material shouldn't be the majority of your talk, but 5 or 10 minutes of this is often very appropriate, say in a 25 minute talk.
In most talks I start by saying: "If you have questions as we go along, please ask."  If you get many questions on material that you think of as basic, be ready to slow your pace.  A variation on this is to have some worked examples early in your talk.  Give the audience time to think about a question, then ask audience members for the answer before revealing it on your slides.  Their responses (especially nonverbal) can give you a good sense of who knows what.  Typically, I talk with slides, but answer miscellaneous questions on a whiteboard.
A final option is to get to the room early, and try to talk one-on-one with the audience members, as they arrive.  If you ask them then, you may be more likely to get an honest answer.  Another version of this is to ask the seminar organizer (or whoever schedule you to give the talk) what knowledge they think is reasonable to assume of the audience.
To summarize,

Make educated guesses beforehand about what your audience knows (typically less than you would think), asking them (or the organizer) if possible.
Make liberal use of examples and "parenthetical explanations".
Plan for 20-30% of your talk to be review.
Adapt the speed of your presentation based on the feedback you get during the talk.

In particle physics people often allege that the mini-lesson at the start is there to "establish notation and conventions". And because we have a lot of subjects that do have varied conventions and notations it sounds perfectly natural. I've learned quite a bit from that part of talks that then promptly took off through my hair and only gained altitude from there.

@dmckee, And yet I still never have any idea what the particle physicists are talking about  after slide 4.

@user1717828 You should try general relativity physicists then :-D

I'm not generally a big fan of speakers asking non-rhetorical questions in research talks.  It always makes me feel like I'm back in middle school and was just asked a question by the teacher, only I wasn't really listening and don't even know what the question was.

Great answer. A quick refresher not only helps clue-in those with less experience in the area, it also helps orient the minds of the other folks who walk in to your talk thinking about getting cat food on the way home tonight and whether they should pit-stop at the restroom before or after your talk.

Some of the earlier comments remind me of this

In talks I have given, I simply over-exaggerate the question.  Then I tone it down and re-ask it until I see a majority of hands.
Example:
"Show of hands, please: How many people here feel they have an excellent, clear and thorough understanding of Graph Theory?"  (1 out of 20)
"Okay, how many of you have a good, decent familiarity with Graph Theory?"  (6 out of 20)
"All right.  How many of you have heard of Graph Theory?"  (18 out of 20)
The first question is so exaggerated in the thorough grasp being asked about that no one feels embarrassed to not raise their hand, so I get pretty honest answers.

However, I agree with Dan C's answer: it is absolutely crucial that you define the terms that you use.  You may cover the definitions extremely rapidly—and should, if the majority of your audience is already familiar with them to some degree—or you may cover the definitions thoroughly and in detail, if it is a totally new subject for all of your audience.  But you need to define your terms.  (Even if you don't plan to argue with me.  Or Voltaire.)  ;)

Good advise. But I personally prefer the opposite order: First ask about trivial understanding and then raise the bar until most hands go down. This first activates the audience to give you feedback but then puts them back into a "I don't know everything so I might learn something here" mindset. But I don't want to claim that one way to do this is inherently superior to the other.

@Philipp, true.  The example above takes advantage of the inherent humor in the situation for the I.T. world, where the first question usually gets a chuckle and helps build rapport.  Hardly anyone in I.T. has a deep, thorough grasp of Graph Theory, but nearly everyone has heard of it.  (Come to think of it, actually, I believe ending the questions on the "win" that they have at least heard of the subject may in fact be inherently better just as it gives a success rather than a failure.)  :)

I usually ask in the negative. "I assume that not everybody is familiar with woffles. However, I could skip over this part if you feel bored." Then look at their faces, usually several people will slightly shake their head. In this way nobody has to state that they do not know something.

I agree that asking in negative might keep you in the safe side. However, often the problem is a shy or unresponsive audience that doesn't give you a good clue even if you ask both whether they know about the subject and whether they don't know about it.

Tell them this one: "The saying goes that in any talk, the first twenty minutes are for the audience, the next twenty for the speaker, and the last twenty for God.  Pay attention, now; this part's for you."

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Acknowledge grants (which may indicate conflict of interest) in double blind review?
I have run into a bit of a double-bind for double-blind reviews as an editor. In short, the problem comes down to if reviewers should see an author's Acknowledgements section which cites the grants that supported the work. Either way has problems:

If you let the authors acknowledge their grant during the review process, it is often trivial to find out who is involved in authoring the paper (since the awardees for many grants are published online).
On the converse, if you do not let authors acknowledge funding sources, it is not possible for reviewers to identify potential conflicts of interest or biases in the manuscript.

In general, at least in my core topics, conflicts of interest due to funding is rare, so I am leaning strongly toward having such funding sources omitted. However, I could see it being a significant problem for other disciplines that I collaborate with. Does anyone know of any good rules of thumb, other than "use your judgement, case by case"?
Note: My general stance has been "No Acknowledgements during review" up to this point. However, on considering the issue in light of allowing reviewers to be aware of funding sources, there seem like very rational reasons why you should have this information available to reviewers, provided it could be done without identifying the authors or unfairly biasing the reviewers.

Can you just blur out the grant number and leave the funding agent in the paper?

Very good point, actually.  That might be a good compromise.  Post as an answer?

@Drecate: Does that help much? In my experience, funding agents are often something very unspecific like "National Agency of ..." or "Research Society ...". Chances to give away one's approximate geographical region or even specific country like this are high, but chances to find an actual conflict of interest (unless one adopts a very wide definition here) seem to be comparably low.

In general, the conflict of interest angle is not touched upon in the linked question, which is why I vote for reopening this question.

if you do not let authors acknowledge funding sources, it is not possible for reviewers to identify potential conflicts of interest — That's the editor's job, not the reviewers'.

If this reopens I'll add this as an answer, but the American Journal of Epidemiology, which requires submitted manuscripts to be anonymous, does not allow the inclusion of an acknowledgements section until after review.

This really should not be marked as a duplicate.  It is a completely different situation than just omitting self-cites and acknowledgements in general as an author (which is standard practice).  This is from an editor's standpoint and addresses funding sources (which is an edge case).

@JeffE While in practice this might have historically been the editor's job, I am not convinced that reviewers (who, in aggregate, spend more time with a paper) should not be aware of funding sources when reviewing. The editor is then a single point of failure. On the converse, it could be argued that knowing what organizations were willing to fund the research might bias reviewers, but honestly I would think that reviewers are not likely to be swayed positively by funding sources (unless it is perhaps "This research was funded by my multiple Nobel Prize and MacArthur awards...")

I think the best approach is, as recommended in the comments, to cite the funding organization but not the particular grant.  In fact, I have recently encountered some journals that request this information explicitly as part of the submission meta-data, which I think is very wise.
Citing only the funding organization may, indeed, be extremely vague information: for example, "US National Science Foundation" tells you pretty much nothing.  In general, however, this is already enough information to determine potential conflicts of interest:

If the funder is a broad-mission government agency, there there is generally no meaningful conflict of interest to consider.
When funding comes from a private organization, such as a company or a foundation, that information is generally enough to identify potential conflicts of interest.  It doesn't matter which division of an oil or pharmaceutical company is funding a project---all of their research projects will still be expected to relate to their bottom line somehow.

This does seem to be the most reasonable solution.


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Are references with indication of page number uncommon in computer science?
I am writing a computer science paper in which I cite several lengthy sources (text books and standard specifications). Whenever I cite such a source, I add the page numbers of the subsection to which I refer, e.g.:

Bla bla is considered very important [52, pp. 210-214].

One of the reviewers of the paper remarks the following:

Do not use references with indication of page numbers (e.g., [52, pp. 210-214]), this is very uncommon.

Is this really true (in computer science)?
Am I wrong to include the page numbers in the reference?
The reference in question is a 400+ page book that broadly covers a whole subject area and I thought knowing which pages I actually refer to might help the reader. There are several other (and longer) sources, such as technical standards, which I cite in the same fashion.

I can't address how common citing page numbers in books is in computer science, but it certainly ought to be standard.  I'd recommend ignoring the reviewer's comment.

Yes, it's uncommon; no, you're not wrong to do it.

It seems like a practical issue as well: Many CS textbooks that I've read were digital copies with no page numbers at all!

This is uncommon for a reason. You should not reference by page number unless there is really no better way to reference the part you need (which means that the book is badly organized). The book might grow by a couple pages in a new edition and your page-number references are screwed.

@darijgrinberg: Based on the answers, I'm not sure this question is particularly asking for page numbers as such, rather than for any kind of further specification where to find the particular cited statement in the referenced work.

@darijgrinberg - So long as you're careful to cite the edition in your references, that shouldn't be a problem. If the author says "pp 210-214" in the citation, and the reference says "3rd edition," then I can figure out that all bets may be off for page numbers in later editions. Plus, the page numbers may still be helpful; if I have the fifth edition on my bookshelf, I might still be able to find the relevant passage if I can just get a table of contents for the earier edition.

Many computer science venues are fairly picky about their citation styles and also use highly abbreviated citation styles that don't give any option for including additional information like a page number.
If page numbers are critical to your citation, then you have two options for how to include them while conforming to the required style:

If you only use one narrow set of pages in the book, use an "in-book" style citation (@inbook in BibTeX) that includes the page numbers in the reference.
Alternately, or if you refer to more than one set of pages, you can include the pages in the text rather than the citation:

Bla bla is considered very important, as described on page 210--214 of [52].

ACM, for example, does not include page numbers in the in-text reference style.

Thanks @jakebeal and @bill-barth! This seems to be a good solution for my problem. Interestingly, the IEEE style guide uses the "in-book" style, but also [52, pp. 210-214] (see page 7).

@joergl That passage in page 7 of the style guide refers to "references within a reference", which is probably not your case.

@federico-poloni: Are you sure? The IEEE style guide talks about "ibid. or op. cit.". As far as I understand, this refers to, e.g., different sections in the same book.

The best way to conform to computer science citation styles is to use the LaTeX packages supplied by pretty much every venue (including IEEE and ACM) as their preferred format.

@joergl No, I am not sure. :) That point seems very unclear in the guide.

-1, bad advice. Do not use @inbook. Do not use numeric citations as part of a sentence ("page 210-214 of [52]"); they are similar to footnotes.

@JukkaSuomela I've happily used inbook for a long time.  Perhaps you can provide a reason that it should not be used, beyond the ad populum fallacy in the linked post?

"The best way to conform to computer science citation styles is to use the LaTeX packages" - when relying on that rule, contrary to what @BillBarth suggested, all three LaTeX packages from the linked ACM site happily display page numbers in the in-text reference style, when citing in the \cite[page]{source} style.

@O.R.Mapper Awesome.  Then I would totally trust ACM's machine-interpretable de facto standard over their human-readable and ambiguous documentation.

Specifying which part of a long book or article you are referring to in your citation is a sound practice, but in general section, theorem or equation numbers are more common than page numbers for this task: [52, Section 3.5] or [52, Equation 3.23] rather than [52, Page 132-134].
Personally I use page numbers only as a last resource where nothing else is available: that is, when the section or equation I want to refer to does not have a number of its own.
I do not have a compelling reason for this, if not that section numbers are more robust to minor pagination changes, but this is the behaviour that I have seen more commonly.

Thanks, I aggree that section numbers or equations are more stable than page numbers. I think I will combine your solution with jakebeal's, e.g. "...as described in Sect. 3.1 of [52]."

Why are section numbers more stable than page numbers? For a formally published work (i.e., not on ArXiv), neither should ever change, except by the publication of a new edition of a book. But, in new editions, it's very common for section and theorem numbers to change, too.

@DavidRicherby: Based on the current practice, I agree. However, I also firmly believe in the principle of separation of content and presentation, and with that in mind, I do perceive the current notion of a "formally published work" as being a document nailed down to one particular layout as a relic from pre-digital times. Ideally, a "formally published work" is the published text in its published, logical structure, along with its internal references and attachments (images, tables, ...). Such data can be represented in any layout, and page numbers are indeed unreliable there.

@O.R.Mapper The logical structure isn't as fixed as you seem to be assuming. Some formats for mathematics number the theorems, lemmas etc. in the same sequence (e.g., Lemma 1, Lemma 2, Theorem 3); some in their own sequences (e.g., Lemma 1, Lemma 2, Theorem 1); some include the section number (e.g., Lemma 1.1). So, just as reformatting can break page numbers, it can also break more "structural" references.

@DavidRicherby: True, that numbering needs to follow a deterministic algorithm, of course. If it does, though, it is more meaningful than page numbers, that have next to no inherent relationship to the content.

@DavidRicherby: in a preprint, the pages are numbered 1, 2, 3, ... but in the published paper they are numbered in sequence with all the other papers, so the pages might be 140, 141, 142, ...  The section numbers will be the same, however. So in fields where preprints are common, citing sections or theorem numbers has practical advantages.

@OswaldVeblen Sure but in a preprint on ArXiv, the theorem numbers might be different from the version published in the journal.

@DavidRicherby I am not claiming that this works universally and with formal guarantees, but there are many real-world cases where section numbers are indeed more stable than page numbers. For instance, different reprints of a book differing only by misprint corrections, or faithful translations in another language. Also, many journal allow for the publication on arXiv of a postprint, that is, a paper in its final post-refereeing state. A postprint has the exact same content of the final paper, but different style and pagination.

@DavidRicherby: They could be in principle, but the page numbers are essentially guaranteed to be different, while the section numbers are relatively likely to be the same, in my experience. Things would be different in fields where they don't release preprints.

Just to be clear, I am not saying "you should cite section numbers from an arxiv version without checking that the ones on the published version are the same"; I am saying "you should cite section numbers from the published version, not page numbers, so that in 99% of the cases a reader without access to the published version can use the arxiv one".


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What is "call for nomination" for senior positions in university?
Job ads for senior executive positions in university always state Call for Nomination and Application.
Contrary to nomination for awards, the nominator cannot actually nominate the nominee, but just a useless introduction. The nominee should personally apply for the position. By the nomination, just the committee secretary asks the nominee to submit an application. Even without nomination, they normally send the call to many potential candidates to apply if they are interested.
My question is who should nominate who?

Nominator is a friend of nominee. Then, why he does not encourage his friend to apply by direct contacting him instead of the search committee to ask my friend to apply.
Nominator knows nominee from distance. First, why no contacting him directly. Second, why nominating someone qualified when we do not sure if he plans to leave his current job.

In general, I am curious if this nomination system has any effect on the recruitment process? If I think someone that I know is suitable for a position, I will inform him about the vacancy and encourage him to apply. Why should I ask the search committee to ask him to apply.
One may say that people are more interested to apply when they are invited, but we know that this is not a real invitation, as they invite anyone to apply, since the applications are reviewed together. Note that these jobs are not based on "nomination only".
EXAMPLES
In most cases, the job advertisement has a title of call for nominations and application, but in any case, there is an instruction for nomination along with application. Normally, nominations are accepted via email, while applications should be submitted online.
Dean, University of Virginia
Chancellor, University of Missouri System
President, Oakland University
President, University of Illinois
President, Southern Illinois University

I don't think this situation is as universal as you say. Can you link to an example?

@BillBarth it was the common procedure for almost all job ads for senior positions in the US university I have ever seen. I simply searched and added a few examples to the question.

Although I have no direct experience, I would imagine it comes from two factors, 1) a holdover from past practices in which executive selections were more democratic, 2) although all nominees might be invited to apply, the names and reputations of the nominators could still carry weight with the search committee.

The potential candidates for this kind of high-level positions typically are people that already have a very busy job, and they do not actively search for jobs. It may be that the hiring process is more of the head hunting type rather than the advertisers passively waiting to get many applications and then filtering them. Of course, direct applications are allowed for the sake of openness and for not limiting unnecessarily the pool of candidates, but it may be the case that the ideal candidates would not apply uninvited. The search committee may not be aware of all the qualified people that might be interested of or suitable for the advertised position, so nominations are useful for them in order to bring new potential candidates to their attention. Once they spot a candidate, they may make them an attractive offer that is customized to the candidate. In the case that the nominator knows nominee from a distance, a direct hint by the nominator may not even attract the interest of the nominee to apply, while if the search committee finds the nominee interesting they may actively try to convince the nominee to apply through more elaborate methods than, e.g., a simple email that may not attract the attention of a very busy person.


text:
Is the classical chair system (in which a senior professor supervises junior professors) obsolete?
Historically, only full professors could have a specific chair, and assistant and associate professors could only wonder under supervision of a chaired (full) professor.
Now, every assistant professor is an independent academic, only with a lower salary and possibilities. On the other hand, a chaired position gains secured research funding, but no other faculty member is under his supervision (yes or no, this is my question).
I think the classic chair system still exists in Japan (at least to some extent). Do universities in West Europe and North America still have such system to place junior faculty members (assistant/associate professors) under supervision of a senior (chaired professor) faculty member?

I think the title of this question is misleading but am not sure how to fix this. Should this perhaps be something like: How common are faculty "chairs" and do they imply a supervisory relationship over junior faculty?

@BenjaminMakoHill you're quite right that the title is not clear and I tried to modify it. The problem is that when referring to chair people think about common chaired positions rather than classical system.

In which country? I hear there's more than one of them and they aren't all the same.

I know of no American university in which any tenure track faculty member works under any other tenure track faculty member in any official capacity.
The main difference between assistant professors and full professors is that assistant professors do not have tenure.  (Going far enough back in the history of my department, one sees "tenured assistant professors".  I don't know what that's about.  I am not willing to claim that nowadays no American university has tenured assistant professors, but I do not know of any.)  "Associate professor" is ambiguous on this point: in most cases associate professors have tenure, but at my university the promotion and the tenure are distinct processes with slightly different rules, although they are similar enough and onerous enough that candidates get pressured -- perhaps a little unfairly, in my view -- to carry them out simultaneously.  There are a few really good places where "associate professor" is a title awarded to young faculty for which their future tenure is by no means assured -- I'm thinking of you, MIT.  But that's rare.
You write that an assistant professor is "with a lower salary and possibilities".  I wanted to let you know that this really need not be the case.  Academic salaries are most competitive now at the assistant professor level; since annual raises have been meager or nonexistent in many recent years, an associate or even full professor cannot be counted on to have a higher salary than a new-hire assistant professor.  In fact the amount of our first offer to new-hire assistant professors in my department is very close to my current salary (I am an associate professor not so far away from promotion to full).  This means that if the candidate negotiates at all, they will get offered a higher salary than mine.  This has certainly happened.  (All this is a matter of public record.)  I think that there are no full professors in my department making less than new hire assistant professors, but there are some who are not making substantially more.
Also, in my department and at many others, assistant professors do not have fewer "possibilities": with the exception of certain voting rights in faculty meetings, they have identical privileges with all other faculty.  They may begin with less "service responsibility" than older faculty; that is probably an advantage.

A few institutions have "decoupled" rank and tenure, so that it's possible to be promoted from assistant to associate professor without being tenured.  From talking to friends, I believe this is how U. Wisconsin system currently works. (Though, of course, how much longer tenure will exist at UW is uncertain....)

You are also able to be tenured assistant professor in the university of Maryland system, even now.

@RoboKaren: That's interesting.  Is it just something that the system still allows, or are there actually any such people?

The system allows it. It's used for people who time out of their tenure clock but aren't yet associate level.

@PeteL.Clark I have to admit, when you made your comment about salaries, I looked up the numbers, and found it hard to believe that your new hires were getting such large salaries.  According to the AMS Salary survey, that would put you well into the top quartile of large public research universities.  On the other hand, it does bear out your point that new hire assistant professors at large public institutions are actually paid better than assistant professors at those institutions overall.

It seems like this may have to do with the (sort of) end of the recession and improving job market.  Apparently more people should be seeking outside offers.

The answer to your question is yes in my experience at major US research universities, assistant and associate professors will, in general, work independently from full professors or individuals with named chairs.
Despite the name, assistant professors are not usually assisting in the research of more senior faculty. There are exceptions including in very large multi-PI labs, in special non-tenured faculty research positions, and in other special circumstances. Of course, nothing keeps junior faculty from collaborating with senior faculty — and many do. If anything though, junior faculty are encouraged to do at work on their own or with their own students to demonstrate their individual intellectual abilities for the purposes of the tenure and promotion processes.
Named chairs usually refers to special permanent funded positions at a university. Usually, these chairs are in a particular area and have been funded to support a particular line of research. As you suggest, named chairs often come with special pots of research funding and are generally more prestigious. Some particularly old or famous named chairs are extremely prestigious.
That said, by no means do all full professors or senior faculties have named chairs. Additionally, it's increasingly common to see junior faculty with named chairs as well including in temporary "Career Development Chairs." Although named chairs are generally more prestigious than non-named positions, they do not usually signal a higher rank (i.e., assistant, associate, full) and they certainly do not suggest a supervisory relationship.

In Germany this depends on the university, and possibly also on the subject. I know of universities that still have a chair system officially.
I also know of a university in which the chair indeed is the superior of assistant and associate professors in the sense that they are in charge of the chairs full budget and also of the budgets for associate and assistant professors. But I also know universities that do not have the chair system (both officially and practical). However, I can't tell which system is more frequent… I tend to think that chairs are more frequent in Bavaria but I may be wrong.

Maybe an answer (or the question?) needs to distinguish between administrative and academic superiority then. I know of German universities where single senior professors are indeed in charge of the budget for their entire group, including administrative superiority to other professors, some of them junior professors, in their group. Academically, on the other hand, none of the junior professors answers to the other professors, and each of them supervises their own team of 10 to 15 postdoc and doctoral candidate level researchers.

The whole point of a tenure track position is to show that someone can independently work and lead a laboratory.
An academic career is extremely slow compared to most other careers. I don't know why anyone would automatically assume that people with ten to fifteen years of research experience, typically in their late thirties or early forties, cannot work independently or cannot supervise five to ten other people. The old system you mention typically degrade most assistant and associate professors to a low level administrator / secretary position.

While I share this opinion, I don't see how this is an answer to the question.

The OP asks two different questions in the title and the text. I answered the former.


text:
How should administration punish sexual abuse/trade for grade?
It happens that some students offer sex for grade.
Just considering the fact that popularity of this strategy can strongly weaken the quality of education, administrators should take some actions to avoid this.
What should a department head do to control this problem in his department?

How to punish?
Who to be punished? Student or professor? Or both ?

I am not asking about legal actions or university policies or discipline matters. I just wish to know What should a head/dean do in this regard to preserve the education quality.

"Just considering the fact that popularity of this strategy" say what?

I don't think this is a duplicate. The other question asks how an individual prof should respond to an offer; this question appears to be asking how the  institution should respond to an abundance of offers.

In most US universities, student discipline is outside the scope of a department head's duties; it is handled by a dean, or a university-wide disciplinary body.  Faculty discipline might involve the department head, but for a serious issue like this, it would probably be handled at a higher level.

Although I think this is a perfectly good question, it seems very hard to answer: any kind of practical answer is going to have at least a large legalistic component which details the rules of some particular university of group of universities.  That is not very inspiring for an international audience.  Is the OP perhaps interested also in the theoretical/ethical aspects of the question: i.e., never mind what the rules currently are at University X: what should they be?  That's still tough but at least answerable, and it seems important.

Or, what can a department head to do ensure a departmental culture that does not in any way encourage or otherwise tacitly not-disapprove-of such activities.

[Citation Needed] for popularity. "Common plot for a particular genre of adult film" doesn't count.

@xLeitix It is a conditional, you trivial thing.

@Insulin69 I was not critizing the grammar mistake, but the casual assertion that this concept (that I have never seen outside of silly movies and newspaper articles) is "popular".

@xLeitix He is not asserting that. He is asserting that assuming there is popularity of this, then it can weaken the education. Moreover it can be popular in a single department and still have this effect.

Initially, like xLeitix, my response to this question was "Say what?"
Then I did some reading. For those who are interested, here are some articles on the subject:

Sex, grades and power in higher education in Ghana and Tanzania
Kenyan tutor on 'sex for grades'
Teachers Demanding Sex for Grades
Liberian women battle against 'sex for grades' at universities
Sex for grades in Africa's academy

Given this context: if sex-for-grades is sufficiently "popular" in your department that it can "strongly weaken the quality of education," then you have a bigger problem then how and whom to punish the next time it happens.

What should a head/dean do in this regard to preserve the education quality?

In a department where sex-for-grades is common, you can't stop it by punishing it in an ad-hoc manner. You have to create a comprehensive policy; educate students, faculty, and administration about this policy; and then enforce it.
If you don't have a university policy (or your university policy is not sufficient), you can create a school-wide or departmental policy, depending on the scope of your position.
Your sexual harassment policy should clearly describe:

Exactly what constitutes sexual harassment,
What the consequences will be for those involved,
and (the most important of all), How to safely report harassment.

In addition, you should then take steps to educate

Faculty, on how to protect themselves against sexual advances from students (steps such as: keep a strictly professional tone in emails and other communication with students, have meetings with students with office door open, etc.)
Administration, on how to respond to allegations against students/faculty with sensitivity and discretion
Students, on how they can report harassment without fear of retaliation

Who to be punished? Student or professor? Or both ?

As for who to punish: any faculty or administrative staff member who

solicits sex from a student in return for grades, or threatens to fail a student who won't have sex with them, or
responds to an offer of sex for grades with anything other than a firm "NO"

should be punished.  Of course, it must say so in your policy and you must make sure to educate faculty about this policy.
Students are usually the disadvantaged group in this scenario, and punishing students could deter them from reporting sexual harassment. Therefore, I would advise against punishing students in most cases. I can think of a few exceptions, where it is appropriate to punish students: e.g., students who make repeated sexual advances, despite being warned more than once in an official capacity not to do so.

How to punish?

depends entirely on what kind of punishment you can enforce, as a department head/dean. I have no idea what kind of power you have as a department head/dean in your educational system.
Typically in the U.S. it would be handled at a higher level, as   Nate Eldredge pointed out, because department heads in the U.S. don't usually handle disciplinary matters.

In my university there is a rule which means markers are not allowed to have a 'conflict of interest' so if a professor is sexually involved with a student that is not against the rules however the professor would not be allowed to mark the student's work because it would be seen as a conflict of interest.
I think it's fair for professors and students to get involved with one another as long as they are consenting adults but I do agree that if that happens it would be unfair on the other students for that professor to mark the student's work (as I am sure most people would) and this is why I think a rule against that would prevent unfair advantage (or disadvantage - relationships can go terribly wrong!) so a rule against marker conflict of interest is a good way to prevent that happening.
If your institution does not have a rule about it, then I would say you need to accept what is done is done and learn from it because it is the responsibility of the institution to have rules about these things. You cannot really make it up as you go along because when you think about it, that is not fair either.
One final point: A student making unwanted advances and a professor has made it clear to the student that he/she is uncomfortable with those advances this is a different issue altogether because that falls under the 'sexual harrassment' banner and is unlawful in many countries and most likely against the rules too. The best way to deal with that is sort of carry on is to support the lecturer if the lecturer was unable to resolve the situation after step one e.g of steps:
Step 1. professor speaks to student and tells them they feel uncomfortable about the advances
If the problem persists
Step 2. verbal warning from the students personal tutor
If the problem persists
Step 3. written warning from the school/institution
If the problem persists
Step 4. final written warning
If the problem persists
Step 5. Expel student
If the problem persists
Step 6. Inform Police.
If the problem persists then the police would probably sort out a restraining order so just liaise with them and see what they can do according to the laws in your country.
Obviously, if the lecturer is trying to get sex and offering better grades then the same logic would apply. That is sexual harrassment and if a student complained about that I would go through the steps but step one would be to not allow the professor to mark work of the student (and probably not any other student either) until the matter had been resolved completely.

About hose situations, I have came to be witness of two situations (taking away the part that there is a consensus between the two parts to get involved in some sort of romantic/sex situation; so I am supposing before hand that there is no harassment involved).

The lecturer or the student proposes intimate relations for a grade change
The teacher and student were involved in a romantic situation, also in this kind of scenario I believe is the same as case 1. Just because I believe there would be a bias for the lecturer or favoritism for her/his romantic partner

In any case, about your questions:

How to punish?
This is not an easy one. I have seen one case in a Faculty in which the Dean decided to keep  the lecturer involved in a romantic situation, just because he was very good in the topic he was teaching. The Dean only talked with him, and after some advices it was like nothing happened. For me it was a big mistake, they should have at least suspend him for at least one or two terms. I said that because after this guy was dumped by the girl, he still continue getting involved with other girls in the Faculty, but being more careful about his behavior for not getting caught.

In any case, I believe that people involved in these situations should be, at least, punished with a suspension. It cannot be left unattended.

Who to punish?
Here the situation needs to be taken with enough care, mostly for the part of the student. I mean if you make a public suspension to the student, and make public the reasons behind that decision; the student will mostly be facing harassment from their own classroom mates.

In this case, I believe to have a long talk with the student involved is enough, but the lecturer is the one who should be punished just because he is allowing that situation to happens and also if the is starting it, he is taking advantage of its position as a lecturer.
Hope this could help you in taking a decision.
Good luck!

Although both are problematic, a romantic relationship between teachers and students is quite different from sexual harassment. Age difference may be small, in case of a TA they live in the same residence and the relationship might even predate the student-teacher-relationship.  I believe romantic relationships can be dealt with professionally (delegate all grading to a 3rd party etc.), unlike sexual harassment, which is unconditionally wrong morally and a criminal offence.


text:
How do I cut ties with a bad supervisor?
I'm a biology PhD student (25, female). I've recently handed in my thesis after a long struggle but I've not defended yet. In short I've had a really bad experience with my supervisor and my PhD and want to get out of academia altogether but I don't know how. I don't want to quit before my thesis defense but I don't know how I can survive things continuing as they are.
To provide a bit more detail about my situation: I started my PhD straight from my undergrad. I was working on my final year project with my supervisor, she was constructive and helpful despite being strict. I enjoyed working with her. When she told me that my 3rd year project was a pilot for a PhD project and that I should apply, I was delighted. I could continue to work on my research for another three years!
My relationship with my supervisor went well for the first year of my PhD, I was producing results and we were getting ready to publish some of these results in a nature family journal. I think this is when I started having problems. There was a lot of external stuff going on, I was in a terrible flat and loosing sleep, and due to these factors I made a mistake taking down a sample size on one of the drafts (my supervisor insists on at least 5 drafts before anything can be considered finished). It was an easy fix, I just had to check and update some numbers; but my supervisor made it seem like the end of the world. She was so angry I was terrified for days. This was probably when I started to be afraid of her, but I made the fixes, the paper got published and everything seemed to go back to normal. But, I've had problems with self harm in the past and while I thought that part of my life was over, I found myself doing it again. I wasn't really thinking too hard about it, it was just stress and if I could do better I would stop I told myself.
Fast forward about 2 years. The self harm hadn't really stopped, and I was still exhausted but my supervisor was mostly friendly, so although I still panicked when she talked to me I thought things were okay. I briefly considered quitting halfway though my second year, but since I'd come halfway I thought I could make it the rest of the way. I was coming up on my PhD deadline (September), and spoke to my supervisor about whether she thought I'd be able to hand in on time. She told me that it might take an extra month but I'd probably be able to do it. Unfortunately, this was also the point that my supervisor got really busy writing a grant, and kept telling me she was too busy to look at my drafts. Fair enough, I know academics are busy people and that, in her world, my PhD is not the priority. My work slowed down, I felt like I was loosing all motivation. September slipped by, I wasn't going to make the deadline, but, my supervisor said, that's fine, I could hand in at Christmas. In the meantime, my supervisor arranged for me to teach her lectures and do marking so that I could be paid and so that she had more time to work on her grant. She also wanted me to do more data collection so that this time she could get a paper into nature. I asked her if I could prioritize my thesis writing, it was important to me that I handed in, and then I could work more on papers. She reluctantly agreed that this would be fine. Christmas passed, and she still wasn't happy with my thesis, asking for more and more rewrites, even if it meant going round in circles. At this point I was trying desperately to stop self harming, which I have more or less managed, but I was also becoming increasingly suicidal. I couldn't see an end to anything short of that. This was when I finally admitted I was having problems and started trying to speak to the well being services at the university. I have a councilor now, who is helping.
I finally managed to hand in in April, although I'm not confident that any of the work in my thesis is really mine (It feels more like the supervisor has written it). I thought things would get better, I've gotten myself a temporary job working with a conservation organization, lecturing for the students who come out on their expeditions. I also made the decision not to apply for a postdoc with the same supervisor, she'd tried to encourage me to take it, but I cant survive three more years of this. I tried to explain to her that although I thought the project was exciting, my mental health prevented me from committing to a long term post (I did NOT mention that I was terrified of her). Since then, she's been increasingly angry. She's told me in as many words that anyone else would have fired me on the spot and that I should be grateful that I can work on such a great project. She also keeps telling me that its very inconvenient for her that I've got this new job (as it will be taking me into the field and probably out of email contact for two months), and that she wants me to do loads more (unpaid) work for her before I leave.
I desperately want to get out of her sphere of influence, I'm still having suicidal thoughts on a near daily basis and I feel sick at the thought of having to meet with her, as she seems to always be angry right now. I need to defend though, otherwise all of this will not have been worth it. My thesis defense is set for September, although she tells me my examiners are angry because I am out of the country during June and July (although I asked her before I applied for the job whether this would be a problem and she told me no).
Is there any way I can cut contact with her without causing a confrontation or anything like that? I don't know whether I can work with her any longer but I don't want to ruin my chances of successfully passing my defense.
EDIT: I want to say thanks to everyone for their thoughtful replies on here. Its been a few months now and my situation is substantially better. I can happily report that I did in fact pass my viva, and was awarded my PhD in September. My relationship with my supervisor is not much better, but therapy has been helping enormously with my depression and anxiety. I have also ended up making the decision to leave academia, and have had a productive summer working as a teacher with a conservation organization overseas, and have been offered a job with a conservation organization here in the UK. I still interact with my supervisor as she is keen to publish work from my PhD, but I am much less emotionally affected by her threats and criticisms these days.
Given my situation, the advice I'd like to offer to anyone else reading this post is that things can get better, but it is rarely possible to cope with issues like stress, anxiety and depression alone. Seeking help is NOT weakness, it really can help, and you don't need to be afraid of judgement from a professional, they only want to help you. My problem with my supervisor left me feeling extremely isolated, I didn't think I could tell anyone without making the situation worse, but getting help is the most important thing.

I'm so sorry that you're in this awful situation. I sincerely hope that you are getting professional help for your mental health issues.  Your mental and emotional health are worth far more than your PhD. Do you have other faculty mentors besides your advisor that you can discuss your situation with?

Is it normal in your field/country that you don't have direct contact with your examiners?

Thank you @JeffE  To answer your questions, I do technically have a second supervisor, but I have never met with her about my project (my primary supervisor tells me its more of a formality to have a second one in this case) and she is currently on long term sick leave. I dont feel I can talk to anyone else in the department in case it gets back to my supervisor. I am in the UK, and have been told all contact with my examiner should go through my supervisor (told by her), so I dont know what the norm is.

She says "the examiners are angry"? No, she is angry. She clearly tries to manipulate you and make it look as if all is your mistake. We do not know enough about her for more judgement, but clearly she is a highly unempathetic person; furthermore, she is trying to squeeze you like a lemon before you leave. She does not care about you and you do not have to feel obliged to her. I take it she is not one of your examiners, correct? In which case, she may try to influence them, but she does not really make the decision - which is good. As for "others would have fired you", how would she know?

Above is a comment as it does not directly answer your question. So, an addendum: is it an option to keep low profile until your examination? If so, try to do so. Stay under the radar and get over the exam, and then, do not continue working for her. Do not be tempted by coaxing or threats. Until now, the situation is not your fault - I repeat: not your fault. You couldn't know that it would devolve as it did. But, if you continue to work for her after the PhD, it is your decision. It is ok for now to indicate that you might continue with her, to soothe her. But do not actually do it.

I suggest that you enquire about who makes the local arrangements for your defense and who needs to be present. It might be possible that someone other than your supervisor can act as your point of contact and that your supervisor need not attend.

I dont feel I can talk to anyone else in the department in case it gets back to my supervisor. — Does your university have an ombudsman? What about faculty outside your department?  — I dont know what the norm is — Ask your graduate director, or other students in your department, or even Academia StackExchange!

There is not a way of cutting off contact with her without some some confrontation or general unpleasantness. That's not a reason to avoid doing it. 2) Don't continue working with her after your defense. It's not going to get any better, and you have other options. 3) Finish your degree, then run like hell. Get a postdoc, continue up the academic path, and eventually your supervisor won't have any ability to mess with your life and career.

Many people are under pressure. That is the reality of academia, and I would say, probably a fair share of society - although it's reasonable to say that it takes a while to realize for many of us. It could be that your boss is bad at managing their own pressure and the leakage hits and burns you, but nevertheless one must need to learn to regulate pressure - ones own and the consequences of others in one way or another. It's a shame there aren't more courses about this in undergrad university. I don't think I ever saw one when I enrolled anyway.

@K.Grayson I'm very sorry you're going through this, just a thought, unless this is not your name, might be worth using a nickname or something similar to protect your anonymity.

Moving forward, what's the ideal scenario?

This is not really a question about your PhD or your supervisor; this is a question about your resumption of self harm. You need to seek help for that immediately. You mention you have a councillor, but it's not clear if this is really helping you, or if they're providing an echo chamber. Please seek medical help as soon as you can! The rest will fall into place. Put "procrastination" on your agenda, on the assumption you'll never get around to it :-) Good luck!

Yeah, some of that ("self harm") is not wise to comment on publicly, except anonymously.  If you didn't choose an anonymous name, you might want to see about changing your name, preferably in a way that minimizes public records.  (Maybe a moderator can help, if needed, for safety/privacy reasons.)  Best to do soon before (more) web crawlers permanently store (more) copies of this page.

@Nobilis Thank you for the concern, this is something I thought about before making an account. K Grayson is not my real name.

You have handed in your thesis, which is very good and a very reasonable point to stop working with your supervisor, especially if she's not paying you anymore.
At this point, it is only the thesis defense, and usually it is hard to get this wrong. You should realize that you defending your PhD successfully is almost as relevant for your supervisor as it is for you.
In my opinion the best time to stop working on this project is right now. Look for something else (which you already seem to have), concentrate on new projects, and tell your supervisor that you want to continue with your career / life after having handed in your thesis. You have already communicated that you don't want to work with her on the long-term, so is clear that you are going to look for other long-term opportunities.

I have worked in a group for two years where I also had problems with my supervisor, these were partly due to me, partly due to him, but in anycase our co-operation did not work very well, so I left and found myself another supervisor for my PhD studies. My relationship to my previous professor even got better, because I believe, I was relieved of my stress in my relationship with him. This kind of personality conflicts are very common in any kind of environment, where you need to deliver consistently...
But after reading your post I got the impression that your problem is a lot more of a personal problem. I think it is not only due to the character of your supervisor or how she treats you. Many people have problems with their bosses but your reaction is a bit outside of the usual range of reactions. It seems you have a hard time with stressed situations and these are unfortunately situations which you cannot avoid in life from time to time. It also seems that you show these rather certain behavioral or psychological patterns in these situations. You also mention these patterns are not showing themselves only with regard to your current situation but are recurrent. These give me the impression that your perception/interpretation of the outer world is somehow pushing you into this hole of destructive state of mind.
My advice would be: please seek professional psychological help. Psychology is not the most exact science but there is a lot of accumulated information in that discipline, which can be of help to you. It can help you to transform your perception of the facts and see light where you have seen only dark before, see hope in the future, whereas you feel deep in a dark well with no light reaching you and no ladder to go up. It can help you break those destructive thinking patterns. Communicate more with friends, family whoever you have around you. other people have gone through similar situations, I can guarantee that. I also took therapy for multiple years in my life and also during the time I was working with my previous supervisor. From my experience it definitely helps. Also I don't know how much the university councilor can help you, I would rather ask the councilor to give you the contact of a proper therapist since your problems seem to be transcending the usual student-supervisor conflicts. You do not continue playing basketball with a broken leg, so first keep your mind healthy to be able to use it for science.
I believe if you seek professional help and come to a more peaceful state of mind most of these problems you have mentioned above will be solved automatically, or will not seem to be problems at all.
In regard to the comment by JeffE:
I see your point, but I know also from my own experience, when you are so deep in a dark skate of mind, your interpretation of other peoples attitude gets also also compromised. I think the "problematic, abusive boss" is something more or less common in the todays world (of course, I am not trying to normalize it or saying it should be like that), but I found some of the phrases by the OP much more alarming, such as: "self harm", "increasingly suicidal", "I desperately want to...", "I was terrified for days". I believe these and the recurrent self-destructive state of mind is the more alarming pattern than the pattern of abusive supervisor. From my experience, first thing to do is to come back to a healthy state of mind, where you can judge the situation unbiased and take the right actions based on these healthy judgements.

While I strongly agree with your advice to seek professional help, this answer seems unreasonably dismissive of OP's advisor's abuse.  The situation OP describes is not just "cooperation not working very well".

@user73885 It is clear that one's own perception colours the interaction, but there are some of the supervisor's sentences that raise red flags; and they sound plausible. Of course, if two highly sensitive people get into a negative feedback cycle, bad things can happen which are not - strictly - one side's fault. Nonetheless, the current case sounds more like the supervisor needs to be kept as much at a distance as possible.

I sincerely hope that you feel better. I understand your situation, as I was under similar pressure to finish my PhD. I didn't go as far as becoming suicidal, but I cried at home fearing that this situation would never end, or I'd never get my PhD after all these years. Sorry!
There are multiple points to make here, and I hope this helps:

Failing you is most likely not an option to your supervisor. Why? They won't fail you after having you work for them for years. It's like saying "hey look, we had that student who worked with us for a few years and his work published a few papers, but eventually we found out he's a horrible student". Do you hear how ridiculous this sounds? It'll harm them a lot, and I suspect they would even have to answer to a higher authority on that if they fail you. It's good that you submitted a thesis, because that's your way out.
Shit happens. I feel that you're incapable of handling mistakes and/or pressure. Although this may sometimes look as a motivation to make things perfect, you have to understand that shit happens, and people are not robots. They get angry, and they are not necessarily nice enough to apologize. So, learn to own your mistakes and even more importantly, learn to move on. Seriously this is very important for any serious job in the future. The stress curve never goes down with age!
I'm glad you're consulting a professional regarding your suicidal thoughts because that's not something I think you can handle on your own, and it's important to know that.
Since you handed your thesis, now is the time to stop working for your supervisor, especially if you're not paid. However, I would like to recommend that you start to think about doing more friendly confrontation without panicking with her. If you're thinking that all the people in your career are going to be nice and friendly, you got that all wrong. Almost in every workplace, there's the professional awkward person who does what he does very well, but is socially unpleasant, and you have to learn how to handle such relationships.

Good luck!

I doubt it would "harm them a lot", but I also agree that the supervisor has little reason (assuming basic sanity) to fail her student, and it's certainly not in her interest to do so. And I think "would even have to answer to a higher authority on that if they fail you" is unreasonably optimistic wrt how academia works. Insofar as there is a "higher authority" goes, they won't care.

@Faheem too optimistic is a good description to what I said. But a professor failing such a student will definitely get bad reputation for it, unless it's the only time he does it. The guy published nature papers! That's kind of a big deal!! What kind of professor fails a nature publishing PhD? That would be very peculiar and will not help the supervisor in any way.

The poster said "nature family journal". Is that  the same as Nature?

@Faheem That's close enough. The whole nature family is quite demanding and not easy to get into.

Well, let's go through this step by step.  I read in a comment that you are in the UK, but I will pretend you're in the U.S. since that's the country I know best.  You may have to adjust some of what I'm going to say, to account for the difference of country.
First, please see a doctor immediately.  If you can't get an appointment for the same day, go to a hospital.  (Take along plenty of interesting activities with you, and a meal, in case you find yourself having to wait several hours to be seen.)  You can print out the question as you wrote it here, and just hand it to the doctor, if you find it difficult to initiate a conversation verbally about the self-harming behavior and the suicidal thoughts you've experienced.  If you're up to it, you could optionally edit it down to a brief introduction, or do some highlighting of the parts that the doctor needs to know to get started working with you.
Let me explain.  It can be helpful to be followed by an MD, even if you don't start medications, and even if you are in treatment with a psychologist or other sort of therapist.
If medication is prescribed, ask plenty of questions about what side effects to watch for, how long it takes to see improvement, and under what circumstances you should discontinue the medication, or seek immediate medical attention.  Keep a symptom log, to share with the provider when you go back for med checks.
Second, inform some department administrator (or even a secretary) that you are taking some time off due to health problems, and ask them to inform your supervisor.  Initially you can be vague and leave it at that.  You can ask the doctor's office, clinic or hospital, or a friend or relative, to do this for you, and it is even possible for a voicemail to be left while the office is closed.
Once your health is stabilized sufficiently, then you can go on to the next part.
In this part, you apply to the appropriate university office as a student with a disability.  In the U.S. this would be the "Office of Students with Disabilities" or a similar name.  Documentation needs to be submitted.  You may need to get some evaluations done.
The process of getting at least some sort of provisional diagnosis, and documentation to satisfy your university, may slow down your graduation date, but I would encourage you to think of Aesop's tortoise that won the race by not hurrying.
Once you're officially recognized as a student with a disability, the disabilities office can explain to your department and your supervisor what supports you will need, going forward.
I would like to explain what it means for a student with a disability to be able to utilize a university's educational services without discrimination.  It's taken me a few years to start to really understand this.  It means that you and the university need to figure out what supports will level the playing field for you, so that you can get the same meaningful benefit from your education as a non-disabled student can do without special supports.  This isn't rigorous legal language (which varies from country to country anyway) -- it's just an attempt to get the concept across.
In your case, since conversations with your advisor tend to aggravate the feelings that increase your chances of self-harm and/or suicide, it may be helpful for those conversations to be mediated, in other words, for a neutral third party to be present during those conversations.  I have found, through direct observation, that this support can be surprisingly helpful, both in reducing the student's fears and anxiety, and also in reining in the educator's behavior.
You have years ahead of you for figuring out whether there are some patterns in your perceptions and reactions that may have contributed to the situation you find yourself in currently with your supervisor.  And for figuring out what qualities, weaknesses of character, errors in judgment, stressors, etc., in your supervisor's life may have contributed to things developing the way they did.  But for now, I recommend just postponing all those questions.  There is no need to point any fingers or attribute any blame anywhere at this time.  At this time, you and the university simply need to find a set-up that will permit you to continue your studies without feeling unsafe.
It may turn out that the best way of supporting you for your final phase of your studies is for a different supervisor to be assigned.  I wouldn't recommend starting out with this as a hard and fast request.  If the appropriate people at your university see your current supervisor behaving badly, after the office of students with disabilities gets involved, I don't think you'll have to make a request.  There are certain requirements on professors, and if your supervisor can't honor them, you can expect the university to protect you one way or another.
Note that retaliation is not only morally wrong, it is also illegal in the U.S.; I would be very much surprised to find out otherwise in the U.K. context.  So I think you can set your mind at ease on that score.
If you can find a support group, that could be helpful for you.  Also, I would expect there will be a suicide and crisis prevention hotline that you'll be able to call for moral support, or just to say, "I'm having a difficult day," or "Today is a bit better."

Giving answer for people in your position is hard.
I would suggest firstly tak with some psychologist since I think you need to talk about it and ventilate it out.
Then you need to think about your priorities.
And you have full right to be astute. I would say to her that you will continue working with her but later would change my mind. The only negative can be future impact on your reputation since you are dealing with manipulative person.


text:
Will my creating and hosting a popular online educational website improve my odds of admission to grad school?
I created a website 2 years ago; it's a non profit educational website, it's mostly like udemy but a tiny version. It's all free because where I come from they're really a low income community so I want to benefit them with what knowledge I have. I have uploaded many courses (only relevant to my field and area of expertise) and it has an exam; if you pass it you get a certificate of completion and it has a signature of my area of expertise syndicate to accredit it. I also used to do seminars on weekly basis and I have many many students who reviewed my course and put 5 stars on it and attended my seminars.
For some reasons I stopped and now I will apply to a master's degree in 10 months.. The unfortunate thing: where I come from there are no undergraduate research opportunities and I'm really afraid I won't get accepted due to lack of experience. However, I decided to do review articles to boost my abilities but the question is:
Should I really make a little bit of time and invest it to make my website grow and keep on doing this, because it positively influences and helps me in my application to add a bonus or make my CV look decent, or is it useless and a waste of money and time and should I leave it? I'm not even sure if this counts as teaching experience.
My field is pharmacy and my country is Canada.

Hosting an educational web site may help you if you want to attend graduate school in education. But likely will not help for graduate admission in other subjects.

@GEdgar, you might develop that into an answer.

First, I am neither Canadian nor a pharmacist, so take my advice for what it's worth.
From what I can tell, you website / seminar series is already well developed, has been used by many students, and is quite popular. I will not speculate what weight this will carry toward graduate admissions. But whatever this weight is, I suspect it will not change much if you put additional time/effort into further development. You already get credit for "having built an impressive educational website", so there is not much room for improvement in this area.
On the other hand, I would hesitate to say that any further work would be "a waste of money and time." It sounds like you are providing a great service to the community, learning a lot, and perhaps even having fun. It is unusual for "outreach" initiatives to be this successful, so I would not discourage you from continuing if you were inclined to do so.

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text:
May I reveal my identity as an author during peer review?
I have a very specific question regarding peer review. We recently submitted our work to a well-known journal and received a fast peer review decision. One reviewer said that our paper was missing an important component, and cited our work to support their claim. They requested us to use the approach presented in our previous paper. This paper, however, was written by me. This make me believe the reviewer does not know my identity. Their comment does not make sense (they are clearly not familiar with the topic). Is it inappropriate to say "We did this like that back then but now we found a more optimal method"?
Unlike here (In single-blind peer-review, can you reveal your identity without the editor's consent?), I am not a reviewer but the author.

You didn't already write in your paper about the previous work in the field, even yours, to discuss how your current methods are better?

You need to talk to the editor, not to us!!  I wonder if supporting your contention that the reviewer has it wrong could be supported by you through "a personal communication with the author of the previous paper" and then clear it up at the galley stage.  Don't do this without talking to the editor first.

If a person is reading your paper in the future and has the same question as the editor, how would they find out the answer? Seems like you could address the feedback with an extra paragraph.

No, you should not do that. The articles published by that journal become somewhat trustworthy because there is a quality control procedure in place that articles have to go through. Part of that is double blind review. It is the journal's decision when to deviate from that procedure, not yours.
Moreover that should not be necessary. You have substantive arguments for your choice, so present those. That is a more valid form of argument than "believe me because I am the author".
Regardless, the reviewers don't decide, the editor does, and the editor knows who everybody is.

@ Maarten Buis, Thank you very much. Would you explicitly point it out to the editor in this case or refrain from it after all? The context is a special issue in a Taylor and Francis journal.

We were once so successful at disguising our author identity that the reviewer thought he did "public us" a favour by claiming that we (blinded us) were ursurping our (earlier published) work. We cited it appropriately, but without overemphasizing (to hide our identity) and created substantial innovation, but still the reviewer felt he needed to defend the previous "public us" authors. So, our paper was rejected. This, and a couple of other experiences convinced me that double blind does not really work.

@CaptainEmacs Yea, it can be ridiculous. I also find it dishonest to hide that your work is a continuation. With more than two authors, the reader has to scrupulously compare the author lists to find out. Silly to enforce that.

@CaptainEmacs That is pretty ridiculous, but based on your description it sounds to me not like a failure of the double-blind peer review system, but a failure of the editor handling your paper to do their job - they're supposed to make a sensible decision about whether to accept your paper using the reviews as evidence, not just "rubber-stamp" the reviewers' recommendation.

@DavidZ It was a high-class conference. I do not think that the area chairs (or whatever they were called) have the time to sift through all the vagaries that may occur.

@Karl "Dishonest"? Seriously? I am a bit surprised that you managed to interpret our scrupulous treatment of the submission rules as dishonesty. There were clear instructions to not leave any trace of authors' identity and that's what we did. We did not hide the references, but we phrased it in such a way that we looked like a 3rd party. I would never have hidden past work, and there was very substantial novelty in our new paper, so we had no incentive to hide past publications. All we did is write it as if we are a 3rd party, as explicitly instructed.

@Dr.M that is a really hard question. I can imagine situations where that would make sense and situations where it wouldn't, and I find it really hard to pin down where the line between the two is. All I can say is use your best judgement, and if you are uncertain ask help from someone who knows your discipline and your paper. I don't think there is a general answer.

As tempting as it may be, I don't think this is the right place to discus the merits and demerits of double blind review. And lets stay away from personal attacks. Lets just assume that Karl did not mean to call anyone dishonest, and leave it at that.

@CaptainEmacs I'm slightly surprised how you read an offence into what was meant as an assent, but don't worry. ;) Be assured I otherwise totally agree with you.

@Karl I read the "dishonest" as directed to me, but with your hint, I now understand that you meant the consequences of the double-blind process. Apologies, unfortunately, it seems I misread your message, and from the reaction, it seems others did, too. I think this permits an amicable resolution of this conversation, thank you for the clarification.

Think about the reviewer's comment on its merits. It points to previous work in the area that they think should be cited. The fact that it's yours is irrelevant.
The reviewer is representative of your eventual readers. If the reviewer is confused there's a problem with the paper. Perhaps you need to revise it to refer to that earlier work and explain why it's not relevant in this one.
If you think that's really unnecessary, then respond to the editor explaining why you are rejecting the reviewer's suggestion.
Speculation about whether the reviewer knows you wrote the other paper is irrelevant.

Mostly agree with this, except the reviewer isn't saying "Cite this previous paper," they're saying, "Use this previous paper's method."  But for multiple reasons, there is a failure of communication (either in writing or reading the paper (or both!)) because the gap between what the author intends and the reviewer's interpretation seems very large.

+1 If it's unclear to the reviewer why a certain method was chosen instead of another, then the paper is badly written in that respect and needs to be revised to make that aspect clearer. It's unlikely that the reviewer is much more stupid than the average of the general readership.

Very much so. If the reviewer thinks the previous work is significant enough that you need an explanation for why you've diverged from it - take that as a complement over the previous work, and follow their advice.

This comes down to "does the journal you submitted to practice double-blind peer review?". You should know this, because if the answer is yes, you probably rewrote your paper to anonymize it.
If you didn't rewrite your paper (and since you seem surprised that the reviewer does not know who you are) I would assume the journal does not conduct double-blind peer review, in which case yeah, go ahead and tell them the method they suggest does not work as well.

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