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Has the nature of the biological sciences shifted to cell/molecular biology instead of physical science/biochemistry/enzymology?
I study biochemistry at my university. It seems like most of the younger faculty come from a cell biology / molecular biology background, while older professors seem to come from more of a physical science / biochemistry / enzymology background (i.e., chemistry and math meets biology). From other universities in my state, this also seems to be the case. Why is this so?

Your sample is too small to make generalizations. But every major advance changes a field. And the time to change is normally 'one academic generation'. Einstein forced this change in physics, as did Galileo.

The 1980s saw the rise of biochemistry and molecular biology, often with new departments being founded for various (often departmental politics related) reasons. Bioengineering also got its start. Frankly, what can be done now routinely in the laboratory would have been science fiction 40 years ago. Compare the response to Covid-19 and AIDS - we just didn't have the tools back then.

Well in software engineering, for example, many students continue to learn embedded systems design and more bare-metal programming despite many never actually using it in employment. It's just concerning to me that the basis upon which many techniques that we use nowadays is not as strongly researched as the fruits of that research.

Yes, this has changed over time, as the number of easily answered open questions in classical biochemistry, enzymology and metabolism is reduced over time. This is much like chemistry itself, where many people (rightly or wrongly), believe that the fundamental principles of chemistry are effectively solved and all that is left is to apply them to real world problems (which many more academic types find less appealing).
This can be seen in the evolution of our own departments, where the department of metabolism (the department where Krebs worked out the TCA cycle) became the department of biochemistry, which was merged into the department of Molecular Biology and Biotechnology, which has just been merged into the School of Biosciences.
There are still groups that practice such things as figuring out reaction mechanisms for biological enzymes, or look at the various physical properties of biological elements, but they are rarely numerous enough these days to sustain a whole department. Instead, these days many people use the principles discovered through classical biochemistry, and the techniques founded by biochemists to student biological problems at a higher level of abstraction - how do the components that biochemists have revealed come together to form organisms and when they go wrong, how does that result in the organismal level phenotype.
Its worth pointing out that a similar process has happened in classical genetics. It happened earlier in biochemistry though. Note that while there is a nature genetics, nature immunology, nature neuroscience etc, there has never been a nature biochemistry.
This is not to say that their arn't still many people and openings working at the interface of physics, math, chemistry and biology. In many ways there are more than ever, but they study different problems - things like genomics, proteomics, gene regulatory system simulation and modelling and structural biology are all highly quantitative. Indeed, many feel the importance quantitative skills in biology in on the increase after a period where it has been left to slide because of the "unreasonable success of molecular biology".

I'm less familiar with those specific fields but I can answer a bit from my own field in biology, neuroscience.
The word neuroscience is quite new, credited to the early 1960s. Neuroscience degrees and departments are even newer; I earned my PhD from one of the earliest graduate programs in neuroscience and it was started in 1971. Even so, there was no "department of neuroscience" until a very recent (I forget the year, approximately last decade) merger of the physiology and anatomy departments.
Of course neuroscience as in the study of the nervous system is not nearly as new, and it's quite straightforward to talk about a history of neuroscience that exists before the word did.
I think you can say much the same for the fields of molecular/cell biology, though I can't give the relevant years. But it's a simple fact that no one doing neuroscience in the 1960s (and there are a ton of key findings in the field in that time period) had a degree in "neuroscience". Most of their students didn't, either, because most often students get a degree named for the department that their advisor is a member of. It takes some time to reorganize academic departments and rename degrees.
Of course as technology advances and key research questions in a field shifts, the number of people doing different types of research also shifts over time. I would not overemphasize the names of certain degrees in peoples' backgrounds, though, and I would caution against extrapolating trends you see in one university to a research field as a whole. These are certainly reflective of some reorganization in the field but it isn't a one-to-one relationship.

One of my favorite people, the late Bob Doty (I believe the 1rst president of SFN, and the founder of our Center for Brain Research) always struck me as the person as close to being a natural philosopher than anybody else I knew).  Scientists used to be much broader people than they are today.


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What does "Check the proof of theorem x" mean as a comment from a referee on a mathematical paper?
In the reviewers comment. A comment from one of the referees was as follows
"Check the proof of theorem x"
Does this mean the theorem is wrong, it should be just rechecked for typos or is it just to make sure it is correct?
Additional info: The theorem is one that I have proved myself.

Is "theorem x" a theorem you wrote yourself or one proven elsewhere ?  They may feel the theorem is incorrect or not applicable in the way you want to use it.

The theorem is one that I have proved myself.

Were there any other related comments?  Did you include a complete proof?

This comment could mean anything from "I don't believe this proof" to "this proof contains a typo."

@Kimball, there were other minor comments but unrelated to the one asking to check the proof and Yes the complete detailed proof was included.

@AndreasBlass, If  the proof was wrong, why not say the proof is wrong and if there was a typo, why not say exactly what the typo is?  I'm inclined to believe that the proof isn't wrong because if that were the case, it would've been mentioned to the editor. The referee can give little importance to fixable typos but he can't afford to forget to mention that a proof is wrong.

In that case it's not a very helpful comment.  I wouldn't write something like that in a referee report.  I also think if you add these details to the question it may get reopened---it's just currently formulated without enough info to understand the context.

@HichamKhalil I agree that this comment, or any comment with such a wide range of possible meanings, is inappropriate.

Since the theorem is one you have proved yourself, it should be included in the paper (either in the body or an appendix, depending on its importance to the main stream of argument) or it should be referenced if you already published it in another paper.  If it is already in the paper, I would recommend you take the instruction of the referee at face value --- check the proof to satisfy yourself that it is correct and clear, and make any revisions you need to make to correct/clarify.  Here is an example of what your response to the referee might look like:

Referee: Check the proof of Theorem 4
Agree - Minor edit: We have re-checked the proof of Theorem 4 as requested.  We are satisfied that this proof is correct (though if the referee has any specific concerns we are happy to consider them further).  In the course of reviewing the proof we decided to add some further clarification to aid understanding of our use of the Lehmann–Scheffé theorem (pp. 27-28).

and here is another example of what it might look like if you make no revision:

Referee: Check the proof of Theorem 4
Agree - No revision: We have re-checked the proof of Theorem 4 as requested.  We are satisfied that this proof is correct (though if the referee has any specific concerns we are happy to consider them further).  At present we do not propose to make any revision to this theorem, but we welcome any specific deficiencies in the proof being drawn to our attention.

Almost as if you have done this before... :)

Haven't encountered this type of referee comment before, but I've done a few revisions in my time.

It seems to me the referee ought to say what it is about the proof in question that the referee had concerns about. (Of course, that doesn't answer the question of what to do when you receive the report.)

Indeed, that would be preferable.  Which makes it all the more reasonable to just take the comment at face value, check the proof, and report the result of your check.

As a referee, I would never purposefully put such an incredibly vague comment.  However, I almost sent a referee report recently with {\color{red}\Huge Start reading at section 2.2.} because I had at some point stopped reading at that position in the article and wanted to remember where to start my refereeing work again.  (Thankfully I saw it when looking at the pdf of the report.)
It's possible the referee just jotted that down to remind themselves to look at it again, then forgot to go through and check that theorem's proof.

Hah, I put so many such comments in my drafts that, as I approach the final draft, I begin to get paranoid that I won't remember to remove them all.

@LeeMosher Couldn't you just use an environment for comments which you can turn off or which creates warnings when creating the pdf?

What Bruno did ("\color{red}\Huge") should work reasonably well. You most likely have some tool that can search for it. Just make sure when you start that the original doesn't contain this.

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Should I tell the editor I'm declining a review invitation because the authors are hostile about feedback?
I have been invited to review a paper for a good journal. The paper is certainly on my expertise areas. However, I have reviewed papers for the same authors in the past (and accepted some/most of them), and they tend to be quite hostile and rude in their replies. I try to be polite with my comments, even with the major ones, but these authors seem to take simple things such as pointing out typos as a big offense and reply with a very harsh tone. Editors seem to not care at all about this, perhaps because one of the authors is an authority in this area.
I will decline the invitation. My question is: Should I indicate this reason for declining in my reply to the invitation?
This is, in this case, I am a good fit for reviewing the paper but my reason for declining is that I do not want to go through this sort of unpleasant moments again.

Will the authors be given the names of the reviewers?

@JoelReyesNoche No, it is an anonymous review.

What exactly is the question: Whether you should decline to review, or whether you should indicate your reason to do so while you already made up your mind to decline?

@Snijderfrey Whether or not I should indicate the reason. I will definitely decline the invitation.

Why not state the reasons?

What is the worry? that the editor will blacklist you?  there is no need to provide any reasons.  In many cases, I'm sure that some invited reviewers don't even bother to reply to an invite, let alone provide a reason for the rejection.   I reject invites from journals I don't publish it.  Yet, I continue to get invite from them.

How come you know the authors of the papers you will review? Aren't these reviews double-blind?

@Stef This is not a double-blind peer-review journal. This is a single-blind one. Not all journals are double-blind.

Write exactly that to the editor.

As you feel apprehension over the refereeing process here, and the expected responses of the authors you definitely should decline the referee request. This is both for your own sake, but also because this is likely to bias your report in one way or another.
My suggestion for what to tell the editor would be that you have a conflict of interest, and are thus unable to referee papers by these authors. Do not elaborate further. This conveys the information that it is the author, not the topic or your general willingness. It is factually correct, without maligning (whether justified or not) anyone.

You don’t even need to decline because you believe you would be biased.  What you’ve described might later give the appearance of bias.  Avoiding the appearance of bias would be sufficient reason to decline this, although I agree with Arno that you should say the more neutral “conflict of interest.”

...except OP doesn't have a conflict of interest.

@henning They do! The conflict is between their interest in not receiving an angry response to their review and their interest in providing a rigorous critique of the submitted paper. If they have a bit of a vindictive streak, they also might feel a bit of an interest in really showing it to that jerk next time.

although this is meant to be anonymous, there is every chance that OP's identity will somehow become known or guessed by the hostile authors, who may exert their revenge on OP when it comes time for OP to submit the paper. This is how that works, boys and girls

@Deipatrous, if the authors are that hostile, one should definitely refuse to review their papers.

Strictly speaking. "No." is a complete sentence.

@Arno That's not what "conflict of interest" means; it is unwise to Humpty-Dumpty a word when you're intending to be clear in your communications.

@Xerxes except that is what conflict of interest means: "An 'interest' is a commitment, obligation, duty or goal associated with a particular social role or practice.". they have their primary interest: a duty of giving an unbiased review of a paper; and a secondary interest: not receiving an angry response, and therefore not potentially having a bad day

@Arno Should I declare a conflict of interest to my employer because I'm lazy? The conflict is between my interest in receiving a paycheck for performing the tasks I'm contracted for, and my interest in slacking off.

@somebody In American Business English (east coast flavor), "conflict of interest" doesn't fit here. The only way you could use "conflict of interest" here is if you were being funny/sarcastic or being disingenuous. (Fortunately for the OP, "Sorry, I can't review this one." is perfectly fine, no reason needed.)

oh hmm... is this a situation in which business english is normally used? (if not, i guess maybe it's normal to assume that such terms are used in the business sense anyway... in which case fair enough)

If I read "conflict of interest" I would immediately assume that the reviewer is working in the same field and the results of the paper conflict with the reviewer's work. It wouldn't occur to me that the reviewer might have a problem with the author's behavior. I really feel conflict of interest will be misleading and should not be used.

Reviewing is a purely voluntary activity that you are providing for free. In particular by reviewing a work, your are doing both the journal and the authors a favour (regardless whether you recommend to accept or reject). As a reviewer you should not have to put up with any abuse from the authors, or for that matter the authors wasting your time by not seriously considering your comments.
If you have had a bad experience reviewing the works of certain author(s), you are perfectly in your right to decline to review any of their future work (I certainly have a growing blacklist of authors reviewing whose work I consider a waste of my time and energy). Also, by all means, let the editor know why you are declining the review. This will help them understand why they are having trouble finding reviewers for certain authors, and maybe encourage them to take more proactive action on abusive behaviour by authors (or reviewers for that matter).
I strongly disagree you should phrase this as having a conflict of interest. This disguises the problem and suggests that the problem resides in your personal relation with the authors, when it is the authors' (unilateral) behaviour that is the issue.

Conflict of interest = the problem resides in your personal relation with the authors - Right, and I don't see how this would appear as an issue. That's exactly what CoI is for. The conflict can be of many type, and most of these would be perfectly reasonable to anyone. On the other hand, declaring the other party as rude would be unprofessional and likely backfire, regardless whether it's true.

@Neinstein I wouldn't necessarily use the word rude. But: "Sorry, I have no interest in reviewing the works of these authors, since past experiences have shown this to be an unproductive use of my time." is a perfectly fine response to somebody asking you to donate your time.

"Conflict of Interest" is where you are in a position where you might be tempted to act in your own interests rather than the job you are meant to be doing. For example when the paper duplicates work you already have in progress, and you might want to get it rejected so you can publish first. "I think the authors are rude" is not a conflict of interest - it's just a personal relation problem.

@DJClayworth Hypothetically, let's say your relative published a paper. Wouldn't it be a clear conflict of interest if you reviewed it? If possible favoritism counts as conflict of interest, why shouldn't it count in the other way? Supposedly, OP harbors bad enough feelings towards the authors that it's a concern.

@PasserBy If reviewers recused themselves on CoI grounds whenever they have an opinion on the authors, no papers would ever get reviewed (or at least not by peer specialists). Also it is unclear whether the OP has any strong feelings regarding the authors, other than not liking how they conduct themselves during peer review.

@mmeent It sounds like the crux is what OP thinks about the authors then. More to the point, it is not a question of whether it's just a personal relation problem, but the degree of animosity.

@DJClayworth If one might be tempted to give muted criticism rather than useful criticism, in order to not receive a rude reply, then that seems to be a conflict of interest by your definition.

@kaya3 Still not really a conflict of interest

@PasserBy Yes that would be  conflict of interest. But that's nothing like the case here.

@kaya3 I think that's just a bias, not a conflict of interest.

@chepner I merely point out that the definition offered ("Conflict of Interest" is where you are in a position where you might be tempted to act in your own interests rather than the job you are meant to be doing) is met in this case. Perhaps the reason it doesn't feel like a conflict of interest is because everybody has an interest in not receiving rude replies, whereas a conflict of interest needs to be something specific to oneself such that the same conflict wouldn't apply to somebody else who might do the job instead.

Decline and explicitly give your honest reason. However, don't do so in writing, as written communication is prone to misunderstanding of tone or intent. Write a brief mail requesting a phone conversation with the editor.
This gives you the chance either to open the editor's eyes, or to learn why their view differs from yours.

I agree about avoiding stating the specific reason via email as the internet is written in ink.

There are benefits of not declining the review. Especially for the case when the manuscript is from your field, to have participation and a word to say is important. You should remember that you are the one who shapes the field (together with your hostile colleagues).
Pragmatically, imagine a situation that some of your important papers were not cited by the aforementioned people. By reviewing their manuscript you have a chance to point this out. Your expertise can also be beneficial for improving the manuscript.
By declining the review, you will miss these opportunities, and, potentially, the manuscript will be reviewed by less qualified people.
As for the "pointing out typos as a big offense". Simply do not point out typos, it is not the job of referee to do that. Many do that bona fide, but you are not obliged. Focus on the essential things and escalate it quickly to the editor (divisional editor) if responses are not proper (not follow common rules of scientific discus). As it is expected from the authors that a manuscript must be rigorous, so is the review. Sloppy reviews should not be tolerated. If you have nothing to say and point out typos just to write something, it is a bad style.

Nooooooooo.
Make up some excuse that is not likely to backfire.
I believe you when you say they are unpleasant and feel entitled to do so because they consider themselves top dog in the field.
The editor is neutral at best. But the editor may also have a beer with dr top dog at a conference and spill the beans.

The best answer is probably still to neutrally declare a conflict of interest and leave it at that. But this response is much more realistic and frank about the potential danger of running afoul the Old Boys' Club. In principle, the OP should be able to be honest, but it could be personally very problematic for them, especially if they're ECR.

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How can I finish my PhD in the next year when I don't have any interesting results yet?
I'm doing my PhD in mathematics (Germany) for four years, and I have agreed with my supervisor that I should finish within the next half a year.
I am not very confident that this is a realistic perspective. I have worked on various things in the past four years but have hardly been successful in any of these endeavours. Apart from actually developing results, it was already hard to find good questions to work on. My supervisor has made it clear that it's not his role to help me find good problems to work on.
Anyway, I have been working on a particular project for three years. I have some results, but I would them deem quite disappointing for the time I invested. The project involved some algorithmic developments, which ate most of the time; but certainly, no one will award me any degree for having developed and implemented some algorithm that's neither particular efficient, nor particularly interesting, nor about which any theoretical properties I can prove. To summarize, my results are very, very weak (I'd say much less in mathematics than what I did in my Master's).
Thus, I'm constantly asking myself: "what could I write my thesis about then?"
When I approach my supervisor and tell him that I don't estimate my results by any means sufficient for graduation, he tells me to stay confident and to continue working on my project. I have started suspecting that telling me to stay confident is just the way of least resistance for him, which allows him to avoid an uncomfortable discussion.
I already noticed that my sleep quality, ability to concentrate, to enjoy pleasant moments or to optimistically look into the future have drastically deteriorated, and I am asking myself almost every day: "what could life look like when I actually have failed?"
How could I deal with the situation?

Is this pure or applied math?

@Buffy Pure, but motivated by applications. Somewhere at the border, I'd say.

Unfortunately, we outsiders cannot really assess whether you are dealing with imposter syndrome or are actually not accomplishing things. The person best equipped to make that assessment is your supervisor. An honest conversation with them about your doubts as to whether you have gotten ~85% of the way through a PhD-worthy project is in order. In general PhD students have a tendency to overestimate how profound a thesis really needs to be, but that's not an absolute truth.

(Cont.) Context from who's saying this: I dropped out of a (US) math PhD program after a total of 9.5 years (counting leaves of absence) this year. I heard a lot of this "you're just dealing with imposter syndrome" along the way to this outcome, and I deeply resent that.

"My supervisor has made clear that it's not his role to help my find good problems to work on." Welcome to German academia.

It looks like you could do with a break from your PhD. Take some time off-travel somewhere nice, do something non academic for a shot while and then return to review. You may also need the perspective of another supervisor for reassurance.

@Ian - that is a very valuable perspective; please put it in the answer box!

@Ian I don't come to this Q&A that much, but I've still noted that the imposter syndrome lever is pulled very early and often. Also at Workplace stack, where it's the new season's 'XY problem' . Anyway, it's refreshing to hear someone call it out. Hopefully enduring for all those years has given you some helpful insight to the world beyond just your PHD topic

I would gather together a summary of all the work you could include in your thesis (a 2 page document or similar) and get a second opinion on whether this would be sufficient for a thesis as it stands. You don't necessarily need amazing results to justify the work you've done in your PhD and pass.

I think you are doubting yourself. i would listen to your advisor

I am a pure mathematician, and I have to say that I am perplexed about your supervisor's attitude to finding problems to work on -- I would have said that suggesting good projects is one of the primary functions of a PhD supervisor. As a PhD student in pure maths, it is challenging to judge what an interesting problem even is.
At the very least, your supervisor should constructively discuss your own project ideas in terms of how interesting/useful they are to the wider maths community. They need to critique and engage with your work -- just telling you "keep going, eventually you'll get something" without actual advice sounds like they're not doing their job at all.
In my view, that is not OK! (Doesn't mean it's not still quite common, unfortunately.)
If your supervisor is unwilling to have an honest discussion about the state of your work, and not willing to help you, I would suggest talking to some other faculty member you trust. Does the department have an ombuds person to approach? Usually there should be a specific person that you're meant to talk to in order to discuss problems with your PhD progress in general and your supervisor in particular. If there is not, is there anyone you would trust with this discussion?
Hopefully such a discussion would open a way forward; this could for example entail:

Writing up all the separate projects you've worked on so far, tying up some loose ends, leading to a satisfactory thesis,
(If you have a bit more time:) Becoming a visiting student with a different professor (at a different institution) and doing a better-supervised project there to round out your PhD work,
or, if it comes to the worst, cutting your losses and jumping ship (I think this should be the last resort, unless you're desperately unhappy and sick of everything).

Which of these are reasonable or feasible is difficult to judge without knowing the details.
(I found myself in a somewhat similar unmoored position after 2 years of PhD in the UK -- I had one smallish publishable project at that point -- and got my PhD to a satisfactory conclusion by going abroad for 7 months to visit someone who was working on what interested me most. He ended up being an amazing unofficial supervisor; so far the mentor I've learned most from in my career.)

Fully agree: my first advise to any student whose PhD advisor tells them that it's not their responsibility to find good problems to work on would be to change the advisor. It's not their responsibility to solve those problems, but it's exactly their primary responsibility to find problems that are both interesting and solvable for their students.

Many professors throughout the world have this style of advising (if it helps I am in pure math as well). I personally find it extremely demanding of the students, but not completely unreasonable - it does tend to produce people that are more self-sufficient at the end of the phd, and of course the advisor should always help the student to refine the questions they are asking, if not to produce them.

I don't think it's that rare -- the uni I went to had a whole official programme for visiting students, and I in fact know plenty of other people who went to a different university to work with a different supervisor for part of their PhD, and obtained funding to do so (It wasn't free in my case either; I had a grant to pay for the fees). Of course I am very thankful to my supervisor there for taking me on, but he is not the only one by a long shot. I was introduced to him by my original supervisor, though, and I had another professor as a reference.

Health issues, including burnout, should be handled by a health professional. Most larger universities (I hope) have an office where you can connect.
But, for pure math, there is a skill that you need to develop. I assume you are working on real and serious problems or you wouldn't be getting stalled. True research results can't be scheduled. You can schedule work time, but not a finish point. You are working with the unknown and it remains unknown until you have some breakthrough, often just serendipitous, when insight finally (possibly after decades) finally strikes.
Doctoral research exhibits a three bears aspect. Some problems are too hard to do in the limited time. Some problems are too easy and have no significance. Others are "just right" and you can come to some significant results and finish.
I worked on all three types. The first was too easy and I was able to develop proved theorems every day. I gave it up after a couple of weeks after talking to my advisor. It was fun, but had no real significance.
The next problem was too hard and I couldn't begin to crack the titanium-like shell around it. Very frustrating. No insight. Gave that one up also, luckily.
The third problem was "just right" and I developed some very nice results over about a year. Process was steady, but not easy. Insight came. The dissertation was quite impressive (so some other faculty members said).
The trick is to know when to give up a problem. Put the hardest ones in the "future work" folder and maybe return to them when you have a secure position and no limited time scale.
Math is just like that. Some other fields likewise. But the unknown is, by its nature, unknown, perhaps in surprising ways.
I think Einstein worked for about ten years to come up with the insights leading to special relativity.

+1. Minor clarification about a tangential point: probably you mean that Einstein worked for about 10 years on general relativity (there were 10 years between the 1905 paper on special relativity on the 1915 one on general relativity, and it did not take 10 years to write the special relativity paper).

@Andrew, no, I intended special relativity. He started thinking about the speed of light around 1895. Discussed it with a few others, seeking insight.

From my comments on the question, at @cag51's suggestion:
Unfortunately, we outsiders cannot really assess whether you are dealing with imposter syndrome or are actually not accomplishing things. The person best equipped to make that assessment is your supervisor. An honest conversation with them about your doubts as to whether you have gotten ~85% of the way through a PhD-worthy project is in order. In general PhD students have a tendency to overestimate how profound a thesis really needs to be, but that's not an absolute truth.
To give you some context about the person saying this, I dropped out of a (US) math PhD program after a total of 9.5 years (counting leaves of absence) this year. I heard comments to the effect of "you're just dealing with imposter syndrome" many times along the way to this outcome, and I deeply resent that.

Given what I know about German math PhD programs, your PhD advisor is probably supporting you financially as a PhD student (correct me if I am mistaken here). If so, most likely, you will have to finish within half a year from now if they say so. Given that it takes substantial time just to write results of a dissertation, you simply do not have time for new substantial results. Unless you already have done so, my suggestion is:
Ask your advisor for a meeting during which you explain what you have done in your projects and ask directly if they (your advisor) think that this is enough for a PhD thesis (in their opinion). If "yes," then start writing no matter how unhappy you are with the results. If "no," ask how far are these results from a PhD thesis and what else needs to be accomplished. If the gap is small and you feel that you can bridge it within the next half a year, then work on both: Writing your current results and working on bridging the gap. If what they describe is enormous, then ask how you can possibly finish the work in the next 6 months.
A bit more specifically, since the main outcome of your work appears to be an algorithm, then much of your thesis will be a detailed description of the algorithm and explanation why it works, plus some theoretical background. Additionally, if there are competing algorithms, then discuss these and explain the difference, including advantages and disadvantages of the one that you came up with. The rest will be a computer code and maybe some examples of applications. (I saw such PhD dissertations, about 100 pages long, in my area of math.)

I felt the same way although I was in physics, not maths. So I think it is relatively normal and part of the process. A PhD is training in research after all. Since you seem at odds with your supervisor's opinion I think seeking the advice of a trusted 3rd party might help. Here 'trusted' would look like: someone who understands the field, who you trust the opinion of and someone who knows you at least a little.
I would also perhaps look for some guidance from your institutions welfare section - all counselling / well being people would say it is better to chat early. It can be so helpful to chat things through with someone not academic

Someone much brighter once taught me (by example) that finding the right problem to solve is more important than finding the right solution.
30 years ago, I started a Phd that I dropped out of 4 years later because I was in a similar position to yourself. Strangely, I saw some people who I wouldn't trust to tie their own shoelaces get PhDs faster than those brighter than me, leading me to suspect there is a good amount of luck involved (or the department just wanted to be rid of them).
After I left, I got a job in my field, made new friends, and otherwise got on with my life. It turns out that I didn't need a few extra letters after my name to have a meaningful existence.
If you decide to quit the PhD program, its not the end of your story, its just the start of a new chapter taking place in a much bigger world.

Interestingly, exactly same experience and now I live much much happier in comparison to when I was a PhD student.

You don't need interesting results to receive a PhD, just novel.
I think you are creating an unrealistic picture of a PhD in your head. Your PhD work does not need to be impressive in relevance, importance, interesting-ness, cool-ness, or anything like that. It just has to be:

Novel, if only a tiny bit (you can't only reproduce an existing study and leave it at that)
Follow the scientific method (for applicable disciplines)
Described in the dissertation (says nothing about papers)
Presented in a defense (says nothing about conferences)

Now obviously doing your PhD work in one area may end up being more useful than another, after finishing the PhD. For graduating per se, it is irrelevant. Or rather, at early stages (like qualifying exams) schools block research areas that are not suitable for graduation. So if you've been approved to work on that topic, you can rest assured that your school considers it acceptable for graduation.
The big question here is, how do you know that your work is sufficient for graduating? This would be a tough question, had your advisor not already told you (by saying you should graduate) that it is sufficient.
There is a separate matter of how you will get a job after your PhD, or what else you will do. But that's outside the scope of this question. However, in some sense, your advisor is not obligated to sustain you indefinitely as a student until you find the perfect job.
You should go to your advisor and tell him you'd like to start a thesis. Ask him for help with the outline. What should the major chapters be? Should all of your results be described in one part, or should there be multiple parts (each with its own intro/method/result/discussion sections)? Which one should come first? What are some past dissertations he can suggest to you as an example?
That will probably give you a good idea. Then try to start writing something - anything. Even just a table of contents or final concluding page of the thesis. If all else fails, you can start writing up the methods sections for things you've already done. Show this to your advisor and ask what to add next. Rinse and repeat.

I have watched several very successful (at the end) PhD graduate students both in my and other places over the last 24 years. Each of them worked on one project up to the last few months, produced very little (their afvisos knew it and complained to me) and then suddenly got great result. So this dynamics is not uncommon. Perhaps your advisor's suggestion is not that bad?

Somewhat lateral input maybe but hopefully useful (from someone who had a similar, but seemingly smaller-scale struggle with his own doctorate thirty years ago).

This is the advice I now give anyone doing research: "write the conclusions you think you want first".  You can then decide with everything you're doing whether it (a) supports one of your draft conclusions; (b) refutes one of your draft conclusions (which is also interesting, and you can just add the word "not" ); (c) neither supports nor refutes any of your draft conclusions (in which case, stop doing it- it's a waste of time, or, if interesting, something you can put in a section about suggestions for further research in the area).  The point is, this will help you focus, which is absolutely essential to finish in a finite time.
Use a large piece of paper, whiteboard, post-it notes, mind map or whatever, to assemble everything you think you have researched and found.  It's quite possible that you will, from a few feet back, spot a jewel you hadn't noticed.  (In any case the exercise will help with drawing up the conclusion list.)
Be encouraged by the fact that even if you're not finding anything earth-shattering, if you have done sufficient diligent research, you are making a contribution by researching and documenting something that doesn't work.  That is in itself valuable to other workers in the field!
In the end, it's down to you, both whether you decide to pursue it (in which case, do so whole-heartedly) or abandon it (in which case you must reconcile yourself to that decision, to avoid future regrets).  One of my friends and colleagues rightly described a doctorate as "a licence to drive" - which partly entails suggesting new areas of research yourself (rather than being dependent on a supervisor).
Assuming you do decide to finish (maybe in spite of your supervisor), and sort your draft conclusions out to achieve, then to get finished in a finite time, you could do what the same friend did: made a deal with himself that if he wrote a page of his thesis in a day, he could go boozing that evening.  There wasn't a single day he didn't get drunk :-)
Good luck

A PhD advisor has several functions, but the most important is setting standards for the candidate (and hence also for himself). It's his responsibility to decide whether the results are sufficient for a PhD. My advice is: don't barricade behind a mistake, i.e. wrap up what you've done and let your advisor take responsibility and decide whether your work is enough. After you've got your certificate, you can use it as toilet paper if you wish, but in any case it will be a closed chapter and you'll be free to move on with your life.

@Trunk Who's saying that's not enough? That's for the advisor to decide. Blame? Which blame? My advice above is to let the advisor take the responsibility for setting and enforcing standards.

@Trunk I see "a priori" no reason why the external examiner should cut anything to ribbons. Fear is always a lousy partner. Play all the cards you've got as skilfully as you can and look forward to success.

In my opinion, changing supervisor will work definitely.  You can prepare a report on what you have done up to now, and negotiate with other professors preferably outside of "Germany".

Changing supervisor and country four years into the doctoral studies probably means starting over and losing a lot of time. And there is absolutely no reason to suggest leaving Germany, or to put Germany in quotes.


text:
Applying for PHD in Europe: getting a recommendation
I'm considering applying into an (individual) PHD program, after graduating from a top Russian university (computer science) with moderately high grades in 2013 and 3 years of professional experience.
However, I didn't notice whether mentioning recommendation isan necessary case for applying within the official and semi-official sources, I suppose it would be useful. But I'm not entirely sure how it is technically done.
I have a supervisor at the university, whom I have not stayed in contact with since 2013. Is it appropriate to email him with "Hello, I've decided to apply into a PHD program, could you provide a recommendation letter"? Do I get it correctly: if his answer is "yes, sure", then I will include his email in my cover letter (or CV?) and my potential PHD supervisor will send him an email, if interested in my case? Is it true that I will not see the recommendation, at all?
I also have a job, which is (somehow) relevant to my potential field of study. Getting a recommendation from my employer would be possible, but is it worth it? In one hand, our company is small and not widely known. On the other hand, it is pretty innovative and lead by a professor of the same University, at which I got an undergraduate degree. He personally didn't teach me, but I think he can confirm my research skills, as research is what I mostly do as my job. The output were not academic papers, but improving stuff within our developing tasks.
If the target country does matter: I am interested in German-speaking European countries, primarily Germany.

By "(individual) PHD program", do you mean an "unstructured" doctorate as discussed in some other questions on this site?

@O.R.Mapper Yes, individual means the traditional approach when one is working mostly independently under the supervision of an advisor. Another approach is a structured doctorate, when researchers are rather working in groups and attending seminars.

@Roland Is it also true for Austria and Switzerland?

I have no experience applying to German institutions, but I have applied to programs in the US, Norway, Netherlands.  My answer is based of those experiences.
If the program you are applying to does not specify that you provide recommendations, don't put them in your application.  If the committee thinks you are a strong candidate, and they want a recommendation, they will ask for it.  It is entirely expected however, that you should be able to present at least two strong recommendations upon request, in which case you provide their email and phone number in the application.
Since you have both academic and industry experience, it would be valuable to represent both.  Email your supervisor from the University you attended and ask them if he/she can provide a strong recommendation for you.  Briefly summarize what your research included just to help refresh their memory.  It never hurts to mention why you enjoyed your research and why you are inspired to get a PhD.
Good luck!

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text:
I got a rejection email for postdoc position along with an invitation to apply as a visiting assistant professor. Is this a gentle letdown?
I applied for a postdoctoral position, and I got an email from hiring committee :
"Thank you for applying  ~ positions.  All positions have been filled.
But we have been authorized to fill a Visiting Assistant Professor (VAP) position starting ~. If you are interested in being considered for this new position, please let me know ASAP."
Is this a gentle letdown? Or is it means that there's a high chance for me to get an offer for VAP?

It means precisely what it says. It’s a mistake to read anything into it that isn’t stated explicitly. They are encouraging you to apply to the VAP position, and will consider you if you apply.

It means that there is some chance for you to get the visiting position. As opposed to "go away, no chance".
I'd wager that it's not clear what your chances are, but that there are some chances... Better a visiting position than no job, I think.

Isn't VAP just another word for postdoc?

@cgb5436 VAP (visiting assistant Professor) may be not as long as a postdoc 1 or 2 years vs 3 years. Otherwise it is the same.

@ cgb5436  In my experience, a VAP has a higher teaching load than a postdoc, most of the time.  There are many exceptions.

@cgb5436, a Vis. Asst. Prof position may only be for a single year, and will probably tend to have a higher teaching load than a "postdoc". A postdoc is for two or three years, and supposedly designed to help the person's research program, with a reduced teaching load.

Thank you so much for your answer. And Yes the postdoc position was for 3 years with a reduced teaching load.

There are too many assumptions in these comments. Read the announcement. A VAP could be (US) up to about six years, at which time the rules may require a tenure decision or an end.

@Buffy, currently, in math, in the U.S., it seems that "visiting" asst prof is not tenure-track, and will not last several years. Not that I can't imagine otherwise, but I've not seen any examples recently.

@paulgarrett, no, it isn't TT, but there is (or was) a principle in some places and the policy of one org (IIRC) that says that if you get hired in year 7 you have tenure. My information is old, of course.

@paulgarrett, see this for current thinking: https://www.aaup.org/issues/tenure

@Buffy, ah, yes, there is often some bait-and-switch, especially at some fancy places, where junior faculty are strung along as supposedly tenure-track, but never really had a chance... Similarly, the number of "visiting" (meaning no hope of tenure, and possibly no job the next year...) has increased alarmingly. Years ago, it seemed that most "visiting" faculty positions were for people who had a long-term job elsewhere, and were taking a sabbatical, ... That's not currently typical (in math, in the U.S., ...)

@Jib To be clear, if this is a position you would be interested in you should definitely apply.

@chessofnerd I just applied. Thank you for your advice!


text:
How do we resolve author ordering dispute for rewritten paper with new contributor and less contribution from original first author?
(note I work in a field were author ordering is important and is meant to reflect relative contributions). The situation is the following:
Me and a colleague (who I will call C from now on) independently conceived of a research idea. I joined C and two other colleagues who had just started working on the idea. In the months that followed, I ran the majority of the experiments and wrote most of the code; C wrote some code in the first 2 days and was active in discussions / planning afterwards, and also ran two experiments (i.e. ran the code written by me and colleagues).
When we decided to write up a paper, C proposed that we be co-first authors, with him being listed first. I agreed. He wrote most of the related work and discussion section, and I wrote most of the rest of the paper (in both cases 'most' meaning roughly 'everything apart from ~2-3 paragraphs').
The paper was rejected from a conference. A new person joined the project; we ran a number of new experiments and re-wrote most of the text of the paper, including most of what C originally wrote. C contributed in small ways to the second iteration (e.g. making a figure from data that I collected).
ETA: To clarify, C agreed to the addition of the new person as author, and he was actively supportive of the idea of re-submitting the paper, doing new experiments, and re-drafting sections. Unfortunately we did not discuss a new author ordering before submitting the revised paper (this was obviously a mistake).
The updated paper has now been accepted to a conference. I and all authors apart from C think we should probably change the author ordering (currently me and C are co-first, with C listed first; personally, I believe that I and another author both contributed more than C).
ETA: The other author who I think contributed more was involved from the very beginning (and proposed the flagship experiment), not the new person.
There are a few complications:

We already publicly posted the first (rejected) version of the paper on arxiv, with C listed first.
C vehemently disagrees with changing the author order
C also does not want to discuss this or talk to an external mediator
C may be having mental health issues

What is the best way to proceed here?
The ideal would have been to find consensus, but that seems unlikely.
We are considering getting an external mediator involved even though C may not be willing to talk to them, as they may be able to provide a somewhat objective opinion and I want to avoid taking a decision unilaterally. Is there anything else we can do?
A key point here is that I am worried that C cannot currently represent his case as fully as he could otherwise due to mental health issues.
Some possible outcomes:

We leave the author order as-is.
We leave C as co-first author, but make my other colleague co-first author as well and change the listing order.
We make the strongest change, making me sole first author and C third
Something else?

Do you hope to continue collaboration in the future on other projects?

No, we won't be collaborating in the future.

Does the conference really matter? In some fields, conferences are not important enough to pick fights over author ordering (although it could mean a difference in funding).

reading this type of questions, I'm so glad that in math the ordering is alphabetical

There is a new person X in the process - is C fine with X being added to the author list (as long as C remains co-first) or does he want the original author list without X? If he doesn't want X at all this is a huge issue.

I'd leave it as is.  I must say, my own advisor many years ago let me be the first author on our joint publication.

@ZizyArcher C is fine with X being added to the list; the issue under contention is just the ordering

@Mihail I find that the strongest supporters of alphabetic ordering are people whose surname starts with A, B, C or D.

Many journals request the contribution from each author to be listed. this can also be added to the acknowledgement. Even if this may not resolve the issue it may highlight any ambiguities in views and make them clear, such as who cam up with the original idea etc.

A note for the recent change in the title question made by user @blahdiblah. In many cases, perhaps most, the fact that the original first author didn't "contribute" as much to revisions is probably irrelevant and even false. "Contribution" isn't time spent or keys pressed. It is related to the intellectual content, which may not and often does not change much in revision. The key ideas are there from the first version in many (most?) cases. In math, for example, the key idea might originate in a five minute conversation over coffee.

@Buffy Yup, I agree. My goal was to add context to the title since there's a whole category of authorship. The asker raised a lot of different issues and I picked what seemed to be the most important to them.

@DmitrySavostyanov Not gonna lie, my surname starts with A

@Mihail, even in math, the alphabetical order is not a rule. Plenty of papers are published using the order by contributions.

@HichamKhalil I haven't seen that in pure math yet. Can you give an example?

There's a bit of a gap in your narrative around:

A new person joined the project; we ran a number of new experiments and re-wrote most of the text of the paper, including most of what C originally wrote.

From my perspective outside your group of authors, it sure sounds like C got pushed out of the way and you expected them to be okay with not having the same role in the paper anymore. It seems like you did this without C's blessing or agreement. Even if they were moving slowly or someone else was itching to get things done, your original agreement with C holds until you renegotiate.
The better time to negotiate this change would have been before the new person came in and did a bunch of work.
You have to reach an author order that everyone agrees with, so you don't get to choose from the possible options you've listed, you only get to come to agreement with your coauthors about one of them.
I'd be careful about referring to C's mental health in any of this. I don't know if you mean to imply that their mental health is somehow making them stubborn or unwilling to cooperate, or that the reason you pushed them aside is because of their mental health, but neither argument looks good for you.

There is a third possibility regarding mental health, which is strongly hinted at: C is having  a hard time, and the OP wants  to treat them fairly during negotiations that C would struggle with

To clarify: C agreed to the addition of the new person as author, and he was actively supportive of the idea of re-submitting the paper, doing new experiments, and re-drafting sections.

@atlas And was okay with the new person doing all that work and taking over authorship?

@BryanKrause With the work, yes; unfortunately we didn't discuss changing author ordering at the time. Another clarification: the person who might take over authorship (in addition to me) is one of the people who was involved from the beginning, not the new person.

re mental health: I hesitated to mention it in the post, but it seems like a crucial part of the problem; I think C would be able to better present his case under different circumstances. I also think he usually would not refuse to discuss the issue with the rest of us, even given an outside mediator.

@atlas If the new person isn't involved in the dispute, why even mention them at all? Seems irrelevant. But in general, the key is that you had an authorship agreement, and didn't revise it. Instead of communicating with C and letting them know that either they had to do these steps themselves or otherwise it was necessary to rethink authorship, it seems like other people did more work and tried to use that work to grab authorship. That doesn't seem fair to C.

Generally you have to resolve author order co-operatively since any author can refuse to let the paper be published. In reality, however, power relationships come in to play and subordinates often yield to superiors, whether fairly or not. And, since any one can stop publication, one jerk can foul up the process if they like.
Trying to drop an author can leave you with plagiarism issues.
You had an agreement originally. I'd guess that the best, certainly easiest, solution is to just maintain that. It gets you over the hump and you get a publication as does everyone else. Copacetic. A publication is a good thing even if you aren't as high in the author order as you think proper.
Very few careers depend on author order of a single publication.
And, in future, discuss these things early on and probably avoid working with C, at least.

Why do you think the OP should avoid working with C? From other answers, it is also not fair for C to get pushed out by new people doing more work without the renegotiation of authorship.


text:
Are you limited to the interests of the professors or your advisor during graduate research?
I am applying to school for a degree in food science and am looking at potential schools and advisers. I've stumbled upon a particular subset of food science that I really want to get into, but only seems to be currently pursued by a couple professors at a certain University.
If, for some reason I am not admitted to this University, or the professors conducting research in this field do not accept me in their labs is there still the possibility of gearing my studies towards this type of work? If my graduate studies advisor had similar research focus, just not exactly the same, would this increase my chances of getting to work in this area? Is it worth it to mention your interest in this field while contacting potential advisors, even if it does not relate to the reason you consider the professor a good match?

It will vary from professor to professor. Some will be comfortable branching out, some will not. This is something you will want to discuss with potential advisors after being accepted, e.g., during a university visit. Something to keep in mind is how this will affect funding. They may be willing to branch out, but can't fund you with their existing funding sources.

@mikeazo: your comment is spot on. Would you consider expanding it a bit (maybe on how to "sell" the OP's intention to a professor working in a different specialization) and posting it as an answer?

Somewhat related: Should postdocs work only on the projects they are hired for, or can they work with other people in the same research group on other projects?

One possible problem is that your advisor may not know much about your topic of choice and can only provide limited help.

If you can establish communication with one or more of the professors working in your target area, you could ask them to suggest people and departments who might be open to research in their area: "I'm really hoping to be admitted to your department and work with you, but can you suggest some alternatives in case that is not possible?". They know who shows up to their conference presentations and asks them interesting questions.

One anecdotal data point: my work is only 'subfield' related to my adviser's, but not 'sub-sub field' related. However my work is of interest to the lab, there just isn't anyone doing it at the moment. So my lab has resources for my experiments already, and a history of doing them -- just the old prof left and a new one came. Provided you can work / learn independently, it's a good arrangement for future job security.

Say you're a professor reading the application of a prospective student who wants to work on topic X, which is not your specific interest (your interest is Y). You may be thinking along any of the following lines:

"I'm doing Y, and I have lots of interesting research ideas around Y. I want students to help me explore these ideas in Y, so I won't supervise a student in X."
"I'm doing Y, and I can supervise students in Y reasonably well. But supervising a student in X for the first time would require a substantial extra investment of time and effort on my part, and I'm not able to offer that right now."
"X is really interesting. It would be useful to develop expertise in X. But currently I only have funding for Y (and PhD offers in our field are always funded), so I can't take on this student unless they are fully funded by an external fellowship."
"X is really interesting. It would be useful to develop expertise in X in this research group. I'll take on this student even though I have no interest in or expertise in X." But then this advisor may turn out to be an ineffective advisor for this student.
"X is really interesting. I don't have any expertise in X specifically, but I do know about the closely related field Y, and I think this expertise would enable me to effectively supervise a student in X, so I'm willing to take on this student." (It may or may not turn out to be true that expertise in Y will translate to effective supervision in X.)
"X is a major up-and-coming topic, which is why I just hired that postdoc with expertise in X to start this fall. With her help, we could definitely get a PhD student started in X."
"I wouldn't take on a student whose main topic is X, because that's not my primary research interest. But if the student was working on my topic, Y, I would be open to also pursuing X with him as a side project."

Since you don't know which of these apply, if you contact this professor, it would be a good idea to indicate that you would be very happy working on Y (if that's true) in addition to your interest in X.

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text:
Etiquette when a student attends a conference with his/her supervisor
I am attending a conference with my PhD supervisor! So, I was a little bit nervous how to treat for example in welcome cocktail, during the conference time and at the gala dinner! Do I need to accompany him most of times? Or only need to be around? It is such a long time doing research with him, but never able to communicate easily! This is hopefully a chance for me to improve my relationship.

i suspect you mean etiquette, rather than ethics.

This is not a good question to ask random internet strangers with expertise in academia.  Etiquette questions are very culturally specific, and we have zero knowledge of your cultural situation.  It also depends a lot on (i) you, (ii) your supervisor and (iii) the current state of your relationship, about which we again know nothing.   I suggest you seek advice from those closer at hand.  In fact, having a brief conversation with your advisor about her expectations might be a good idea.

Supervisor pub time is always a lot of fun, and is a nice way to get to know your adviser on a human level. Not to mention that it creates opportunities for networking.

Some of the discussion in http://academia.stackexchange.com/questions/46334/ask-a-professor-to-attend-a-conference might be relevant.

There's no ethical dilemma here. You might tag along with him at first to let him introduce you to some people in the field he knows, but after awhile of that, you should feel free to introduce yourself to people who look to be more your age or status (younger looking people are more likely to be students like yourself). Also, at the dinner, you should feel free to introduce yourself to people whose talks you attended and the people at your table.
The above assumes you are comfortable in such social situations. Not everything at a conference is business. Network and enjoy the social aspects of the events if you can.

Let your advisor advise you, i.e. ask.
At which occasions does he/she expect you close by? It is far better to discuss this once before the conference than you having to bother him/her five times a day.

you are both there to network -- that means he want to talk people other than you, and he expects you to talk to people other than him.

You will most likely also hang out with other phd students and post-docs. Here you can do a lot of networking and have some fun after the lectures during the day. Sightseeing together or enjoying local activities, such as karaoke, is huge fun.

"karaoke is huge fun" Oh you


text:
How can you identify which are the strongest PhD programs in particular subfields?
I'm an undergraduate student (United States) majoring in X, applying to PhD programs with a research focus in subfields Y and Z.
I conjecture that the best universities for Y and the best universities for Z are not necessarily the same, and I want to narrow down my PhD applications to universities that are known for one or both of these subfields.
None of the professors at my university's X department do much research in either Y or Z, and they seem to not have the greatest idea where I should apply - I usually get generic answers like Prestigious University U, which may or may not be what I'm looking for.
The other concern is that I've taken a few graduate classes regarding Y and Z, but in no way am I fluent in the fields, nor have I done direct research in these fields. As such, it would be difficult for me to attempt to read research papers about Y and Z to try to back out which universities produce the best work.
How might I go about finding the strongest programs in Y and Z?

This may not be a direct answer to your question. But I would assume that the reputation of the advisor is what matters the most! Rankings, not so much (unless top 5-10, which already have great professors).

Two suggestions:

Look at the research publications of faculty in your area of interest and then look for the most widely cited research in this area.  You can easily find such information using tools like Google Scholar.  Then find out where the authors of these widely cited papers are teaching.
Look at what happens to graduates from the different programs.  Many faculty have web pages that list their recent PhD students, some universities publish graduation programs that include lists of graduates, and there are sometimes other ways of identifying recent graduates of a particular Phd program.  If you can't find those people on the internet, that's a strong indication that they working in academic careers.  If you find them but they're teaching at community colleges and regional comprehensive universities, then that tells you a lot about how well the graduates have done in academic careers.

For my program, Computer Science, one of my advisors pointed me to this as being the "industry standard" for determining PhD program rankings; at least in CS.  Several important criteria are taken into account, and rankings are provided for each.
However, as another poster pointed out, looking at the faculty and their publication track record with respect to a certain discipline is a good way to assess the quality of a university (i.e., famous people in the area you're interested in tends to equivocate to that university having a prestigious program for that discipline).
It's also helpful to have university rankings, along several research-oriented dimensions, by discipline all in one place... My 2 cents though.
Best of luck!


text:
Dissertation tribute/acknowledgement
I've recently completed my dissertation and would like to know the correct way to add a few words of tribute to a late family member.
I'm aware of adding an acknowledgements section, but I am not too sure that it would be right. From a little research I have found that the acknowledgment section thanks everyone who has helped you whilst you have been researching and writing your dissertation.
I would like to know if anybody has any information or examples on this.

Search for "dedication" + thesis. Here's one example that combines a dedication with further acknowledgements.

There are absolutely ways to do this.
First, if you feel like they genuinely helped in some way, the acknowledgements section is perfectly appropriate - this need not necessarily be serious. For example, I ended up thanking my mother-in-law for spending some time talking to me about how certain aspects of what she does work, along with Stack Overflow and the folks who make Dr. Pepper.
Many thesis documents also include a dedication, which is much more personal. For example, mine read:

To my parents, for teaching me to ask questions, and to $WIFE for seeing this through with patience, love and understanding.

Lol at $WIFE ... Should have thought of that for mine


text:
My advisor wants to co-author a paper on my thesis work, but drags out the submission, claiming it isn't ready. Should I submit without him?
I have just finished my PhD thesis defense in applied mathematics. My supervisor suggested me the initial problem. He was not an expert in the small area that I was working, and thus the assistance from he was minimal. As we had so many disagreements in the research direction, our relationship was rather uncomfortable. The good thing was that I finally got the problem solved, with assistance from some external experts.
After I finishing my PhD, I extracted a paper from my thesis. My supervisor insisted that he should be authored as we had discussion on most of the result, and if I submitted without his name, he would appeal to the journal editor. But on the other hand, he deliberately holds on to my paper. He keeps on saying the paper is not clear and is thus not ready for submission, but there is no revision comments from him for several months.
Should I submit the paper alone with only name? It seems each side is highly risky for me.

Why is it risky for you to wait for your advisor to feel comfortable with the state of the manuscript? Why do you need to publish quickly?

The first things that jump out at me from this question are these:

Why do you think that your advisor is dragging his feet?
Why do you think your advisor is incorrect about your paper not being clear?
What is the time schedule on which you expect to publish?

Now, this may in fact be the case, but in my experience, in most cases even graduating Ph.D. students are not very good at writing effective scientific papers.  Your writing here does not argue you are particularly different: I am not speaking of grammar (which is relatively minor), but the fact that you have made strong assertions without presenting supporting information or giving key pieces of contextual information.
I would thus guess, a priori, that your paper is indeed unclear and not yet ready for submission.  Moreover, I would guess that your frustration is coming not from your advisor "dragging feet," but from you feeling unclear on what steps you need to take in order to edit your paper into a state that he finds satisfactory.
That is what I think you need to address in your plan to move forward.  Focus on one piece of the paper at a time, e.g., start with the abstract and ask for specific and concrete feedback on how it is problematic and how to improve it.  If you can meet regularly with your advisor and start learning the pattern of what is missing and what you need to do to improve it, then you can likely get the paper into a submittable state in a reasonable time.

He keeps on saying the paper is not clear and is thus not ready for submission, but there is no revision comments from him for several months.

The main problem is that we cannot decide whether the opinion of your advisor is reasonable. May be the paper is poorly written, and he expects you to clear up the structure of the paper before really reading it. Or he is just lazy and uses this accusation as a pretext. We cannot tell, and you are biased, since you have no problem understanding things you found out yourself.
I think you should try to explain your results e.g. in a seminar or in a more private surrounding to see whether your style of explanation is actually understandable.

Disclaimer: When I first read the unedited version of the question, I assumed that, since OP recently finished his/her PhD, they more or less figured out how to write papers during their studies, and that the question was more about an authorship conflict.

Should I submit without him?

You seem to present two options: wait for your advisor to review, possibly modify, and approve your manuscript, or submit the paper as the sole-author. It is not entirely clear that you should be rushing things on your manuscript at this point, whether or not you truly believe that your advisor deserves co-authorship, what the advisor co-authorship norms are where you are at, etc. Anyway, moving on ...
Unfortunately, I cannot say which course of action is the best one for your particular situation. As with anything, it helps to understand the consequences of any potential actions you take.
If you submit your paper without resolving this conflict with your advisor, then that could irreparably damage your professional relationship with him. This, in turn, could lead to no support from him for your future career endeavors, such as in the form of letters of recommendation, networking and collaboration opportunities, etc.
If you are OK with the above outcomes, then, if you do decide to submit, you may face some additional challenges. As highlighted in an answer by user Peter Jansson to this question, if your advisor decides to contact the journal, then this could result in a long, drawn-out dispute. You may emerge from the dispute with a paper, with either you as the sole author, or with you and your former advisor as co-authors. You may also emerge from the dispute without a paper published in that particular journal at all.
From your post, I get the sense that you are worried that your advisor is dragging the review process out needlessly. However, if you are willing to entertain the idea that your advisor deserves to be a co-author, my "advice" would be to attempt to rein in your advisor's manuscript review time, by sending them frequent reminders, that you are going to submit by such-and-such date, etc. And, who knows, you might end up with a stronger paper as a result of his feedback.

If you really believe he/she is deliberately delaying submission, here are two suggestions:
1) relay your frustration at a seemingly unending process and ask to make a list of objective goals that, once accomplished, ends with publication. That way, it will be clear what needs to be done
2) ask to add a 3rd party reader.  You'll benefit from another set of eyes and it will be more difficult to delay 'just because'.  Perhaps the 3rd party will agree it's not ready.

Patience is a very valuable virtue, especially in science, and especially in literature publication. A couple of months is not a long amount of time. I would suggest that you need to get more irons in the fire so you stop focusing on just this one. Perhaps 3 months is a long time in your field - it took me almost 3 years to push out my last paper from my PhD work.
As mentioned by Mad Jack, what you decide to do depends on whether you want to maintain your professional relationship with your PhD mentor.
Another solution is pre-print, like http://biorxiv.org/about-biorxiv . Perhaps there is an equivalent for your field. Present this option to your mentor - you could get additional feedback from peers before you submit to a journal.

Any supervisor has obligations towards the institution and society, must uphold certain standards and his performance is being evaluated.
If you truly deem that your supervisor is showing incompetent, inefficient, undercutting behaviour or any blend thereof, it can be useful to report these allegations to the supervisor's supervisors (head of department, head of human resources or the like). You could do this in a mild form by asking to have a confidential conversation to gauge where you are. Perhaps your supervisor is a re-offender, so to speak.
There, be prepared to bring arguments as to why, when, where, how, and to which extent you perceive your supervisor to be incompetent, inefficient, and so forth. A list of significant facts and circumstances that have steered the development of your studies so far, can help with this. Doing this will not be different from what other answers suggest. I am positive that making this properly will greatly help your professional standing, although it can take some emotional energy. The hope is that this process will help you revise your situation, by making it more objective, and find acceptable compromises.

Also, you need to hope that the person you speak to is of a better league than your supervisor in any regard that matter. Assuming this is the case, he/she will be motivated to encourage agreement and progress between a member of his/her staff and a young researcher.

In general, ghost and guest authorship should not be regarded as acceptable, although they occur. Your supervisor might be under the pressure of justifying a grant on a topic about which he is not competent, and it is not your responsibility to fix this magically. And your department may be ranked according to the research outcomes. So there are several factors at play. The thinking that your research is not just your own and that you are contributing to the overall progress of your institution may also help relativise the situation.
It might help to add as co-authors the other people who effectively helped you.


text:
Is there any rule in US that prohibits recruiting as faculty the students studied in the same university/institution?
There is a phenomenon in my country. I am not judging whether it is correct or not because of my ignorance on it. My honest opinion, as per my current knowledge, is that the phenomenon is bad as whole.
The phenomenon is as follows:

A student completes either doctorate or post graduation at university
or any academic institute named N. She gets appointment as assistant
professor  in the same institute N whenever vacancies are present.
Although the percentage of such people vaires, the percentage is
significant. It may be above 50% in most of the cases. It is not just
happening in normal institutes but also in premier institutes.

I am providing two examples just for reference: Anna University, IIT Kharagpur.
The medium of instruction in most of the institutes is English only. This question is not about discussing advantages or disadvantages or judging this phenomenon.
The question is only about the existence of laws or rules prohibiting the happening of this phenomenon in US. Is there any such rule?
If not exists country wide, then are there any universities with existence of such rule?
I am not asking about permanent prohibition, but at least with some restriction to avoid that phenomenon.

Does this answer your question? Do universities prefer not to hire their own PhD graduates in faculty positions?

@GoodDeeds This question is about US only.

Some countries allow it. Some countries, such as Germany, strongly disincentivize (but not strictly forbid) it. I think in the US, this is not explicitly banned, but they prefer to get faculty from elsewhere (which makes sense, as it reduces "inbreeding").

Very institution dependent. As one example, MIT seems to have many of their own. Others not so much.

There is certainly no such general rule in the US. However, many (not all) universities would prefer not to hire their own graduates immediately, but are probably happy to bring them back after they have established themselves elsewhere, perhaps with a post-doc or a faculty position elsewhere.
There are complementary reasons for it. The most fundamental one is that  many faculty feel that a student has learned about as much as can be learned already working with the faculty of the home institution and that it will do them good, professionally, to be exposed to the ideas of others at a different institution.
The lesser reason is that by spreading out their doctoral graduates they are also spreading out their own ideas. Another way to put it is that a new institution will benefit from the ideas that their recent graduates might bring to it.
These combine into a situation where a department is more likely to bring in people with new ideas, a definite plus.
The combination of these tends to make the world of scholarship more interconnected with more collaboration possibilities. This is, perhaps, less important in the internet age, but it was pretty strong previously. And those interconnections can be vital in driving knowledge (research, scholarship,...) forward.

I'll also note that most faculty hiring at research universities in US requires a broad search; at least national. It can be very difficult to pre-select a candidate and then write a description of a job that will only really apply to that one person. I know of one case where this was attempted and the description provided was very detailed and exact. After it was broadcast, at least three other candidates appeared who met the criteria at least as well as the one originally desired.

Also for the benefit of the university, hiring outside the university prevents academic or intellectual inbreeding.  When I was considering graduate programs, a professor suggested this.

Usually US universities have anti-discriminatory laws regarding hiring of candidates, which would forbid them from not hiring their own PhD students as tenure track or tenured faculties. Whether the practice is widespread probably depends on the University.
I know of examples where PhD students were later hired as an Assistant Professor (Tenure Track) in US universities. However, in my (limited) experience, such phenomenon is quite rare.

Not a lawyer, but my understanding is that the US only forbids discrimination on certain grounds (that is, regarding protected groups). Graduates of a particular university are not a protected group (you'd probably have a good case if it were a ban against, say, HBCU, but that's not the same as this situation). I think it would be perfectly legal to have "breadth of experiences" as a hiring qualification that counts negatively towards graduates of the same institution.

The typical anti-discrimination laws cover such things as age, sex, race, national origin, and such. It doesn't forbid all preferences. But, generally, the preferences need some logical basis or they might be questioned, even if not legally. A preference for people over 6 feet tall would be looked askance at, even if not strictly illegal. I doubt that having an inter-faculty basketball team would be enough of a "valid" reason. A preference for rated chess players might be more logical - even if weird.

@BryanKrause: You are probably right. However, I feel that no University would likely risk a lawsuit by declaring that they won't hire their own PhD students. I could be very wrong though.


text:
Is thanking email recommended after a response from author?
Suppose I read a research paper and contacted the author for a resource through email. The author responded to the email.
I have no further queries or requests to ask the author.
In such context, do I need to compose a reply mail thanking the response provided? Or is it a kind of disturbance for them if I compose mail without any substantial information and just to thank?

You should send it. It assures the original author that you received the email and have no other problems.
Would they be disturbed by it? Probably not, because 1) it's not spam since they're likely to be interested, and 2) it only takes a few seconds for them to process your email.
That said, don't compose a very wordy email - a couple of sentences should suffice.


text:
Why do formal research papers keep statements that should be interpreted informally?
In several domains, I came across many popular research papers that do contain statements that should be interpreted informally. If someone interprets them formally, it leads to a totally wrong perception.
The issue is that the authors use the formal terms in-order to make the statements that has to be interpreted informally. The statements I am referring are not the plain English statements, which can be equivocal in nature.
For example, consider the following answer from other stack site

You're right! The generative model f is not the same as the
probability density (p.d.f.) function pdata. The kind of phrases
you've referred to are to be interpreted informally. You learn f with
the hope that sampling a latent vector z from some known distribution
(from which it is easy to sample), results in f(z) that has the
probability density function pdata. However, merely learning f does
not give you the power to estimate what pdata(x) is for some image x.
Learning f only gives you the power to sample according to pdata(⋅)
(if you've learned an accurate such f).

I interpreted in wrong way and tried to understand for much time and I end up in asking that question (on other site). I came across many such formal phrases from research papers.
In general, there will be no explicit remainders or hints or guidelines or suggestions to know which statements to be interpreted formally and which statements has to be interpreted informally in a formal context.
What is the primary reason behind encouraging such phrases either by journals or authors?

I moved to chat the technical discussion.

In the two examples you give, I don't agree the statements need to be "interpreted informally". Rather I would say that the meaning is clear within the context of the problem. For example, suppose you have a function f(a,b,c,d) or an expectation E_{a~p, b~q}[ f(a, b)]. Often authors will just write f or E[f] respectively. There is no mistake, it's just the notation is being left out. It's basically the same thing in the examples you point out. "our generative model learned pdata" is just a shorthand for "we learn a model f(z) which maps a latent space z to an output S so that we can approximate drawing samples from pdata by drawing a sample z". And that's not unclear or "informal", because the latter is just a definition of what generative model means in that context.
Specific problems can have their own language or jargon, and it can be confusing to read papers without knowing it. Part of becoming an expert in a specific problem is learning how people think about that problem.


text:
Getting a funding position as a foreign MSc student in Finland
I got an admission for a master’s programme in data science at the University of Helsinki, Finland. However, because I am from Asia, I don’t get a tuition-fee remission. Is it possible for an international MSc student to find a funding position as a teaching assistant or research assistant in the beginning?

My experience is from Jyväskylä, not Helsinki, and in pure mathematics. Things might work differently, but maybe this is still useful.
Teaching assistants
These were typically recruited among the better students. Much of teaching happened in Finnish, especially at the lower level courses, and as such, knowledge of Finnish was assumed.
Getting such a position right at the beginning might be difficult, but if you are skilled, and have good command of English (or even better, know or start learning Finnish), it might be possible. I doubt Swedish would help quite as much.
Research assistants
Research assistants were recruited among promising students and often involved writing their master's thesis, but might also involve research. Often these were summer jobs.
Connections
If you, or someone at your university, has connections to the faculty, you should try to ask via them. In particular, if someone can recommend you as an excellent student and a potential PhD student, the chances that someone will arrange a position for you will vastly increase.
Ask
It never hurts to ask. Contact information: https://www.helsinki.fi/en/programmes/master/data-science/contact
Scholarships
If you have not looked at it, the scholarship webpages of the university might be helpful: https://www.helsinki.fi/en/admissions/scholarship-programme


text:
Access to databases stopped in Slovakia – how to deal with it
Starting from January 1st this year, access to all scientific databases and publications have been stopped for Slovak universities and Slovak Academy of Sciences. The reason is simple, the authorities have not paid the bill even for the access in year 2016. Of course, we can ask friends or authors for sending us requested publications, but this is a step back, and we don’t want to bother other people.
What could you advise for researchers in Slovakia, what can they do in this situation?

You are probably looking for an answer that is more sustainable and elegant than "get whatever you can on LibGen and SciHub, ignore whatever you can't"? Hmm, interesting question...

Not that it is really relevant for the question, but could you be more precise on what databases and publications you mean. There are many publishers and companies and there is not just one bill to pay. Also a link for some reference would be nice.

@darijgrinberg: yes, we are looking for systematic an legal solution.

@Dirk: We lost connections to SCOPUS, and Elsevier, at this stage and there was an announcement that we may lose some other access, too.

So, your situation is similar to Germany's (probably a bit different, as the universities in Germany agreed in the joint action). I do rely on preprints and asking authors so far. I don't think that asking authors is bad. Usually they are happy to share and it only costs them a few clicks.

I feel like consulting with a lawyer or a chancellor/dean/president of the university system to address the original problem also needs to be done. Getting access is fine, but losing access to research databases is a serious research issue that will greatly affect a large amount of research and literature.

SCOPUS and Elsevier are not "all scientific databases and publications"

Individual access
This question details a few ways to access scientific publications, without resorting to now-unpaid subscriptions.
Collective access
Research into ways of influencing your government's decisions that are legal in your country.

Writing an open letter to a relevant person in your government (that'll likely be your Minister of Education / Minister školstva) and distributing it through Slovak Academy of Science / Slovenská akadémia vied for other scientists to sign could be a good start.
Depending on what is legal in your country, organizing a protest march / a picket could also be an option.
You are likely not the only person annoyed by these changes: find others who will be willing to join your cause.

If there are people high up in the hierarchy of Slovak Academy of Science that sympathize with your cause, they are likely to have some influence on your government.

Comments are not for extended discussion; this conversation has been moved to chat.

There is a possible legal solution, but I AM NOT A LAWYER AND CAN NOT PROVIDE ANY GUARANTEE. Be sure to talk to a lawyer, before you try to do anything.
So the obvious answer is using SciHub and LibGen, but they are not legal. What as far as I know is legal is using peer-to-peer networks, such as torrents, because here the Slovak (and European) legislation should be a few steps (maybe even kilometers) behind the reality. So the solution would be to set up a peer-to-peer network for distributing articles (yes, just like torrents). Every user would join in and offer the access to his articles (authored by him) and could on the other hand get article authored by anyone else in the network for free. This would be just like writing an email to the author, except very automatic.
Since Elsevier, Springer mostly gives the authors right to share their work with colleagues, friends, etc. this would maybe even comply with their policies.
Unfortunately I do not know of such network.
Update: for anyone interested, there are at least promises that the problem will be solved, see this article.

I'm not sure that wouldn't be illegal too. The point of a peer-to-peer network is that every seeder shares the data with every downloader, so either every paper gets a maximum of seeders equal to the number of authors, or papers will be uploaded by people who did not write them and have no right to distribute them. What's more, many authors are outside of Slovakia - You're suggesting that it wouldn't be a copyright infringement if there was a world-wide network of automatically distributing copyrighted papers.

IANAL, but I'd be very interested in what would happen if such a peer-to-peer network would be designated (and led like) an "invitation-only research collaboration work-group", since Elsevier gives you the right to share your article with such a work-group. I wouldn't bet against Elsevier though, if they were to take you to court for it.


text:
How to cite a reference which disappeared?
During my PhD, I wrote a couple papers referencing and using a set of notes available online, which constitute(d) the draft of a textbook (and laid down techniques and lemmata I used). [1]
Now, I am in the process of writing my thesis, and noticed that this online resource (originally title Asymptopia) had disappeared from the website of the author, which now states:

A few years ago I decided I might actually finish if I split the Asymptopia manuscript into two parts. Currently I am working on the empirical process bit, which has acquired the temporary working title MiniEmpirical. Some chapters have reached a reasonably complete form. Those chapters are in the Mini subdirectory.

In particular, the material I want to reference is gone.
Of course, this is entirely up to the author, and I have nothing to argue against this. But that does put me in a bit of a pickle, as I don’t know of any equivalent resource to cite (the exposition of the techniques was both very clear, and adapted to what I am using). I personally have a PDF copy of this resource which I saved before it disappeared, but—of course—it is not up to me to make it available.
What is the correct way to handle this? Cite the previous draft as if it were still there, possibly with a relevant link to a cached version? Something else?
[1] Bibtex entry:
@misc{Pollard:2003,
    author = {Pollard, David},
    title = {Asymptopia},
    howpublished = {\url{http://www.stat.yale.edu/~pollard/Books/Asymptopia}},
    note = {Manuscript},
    year = 2003
}

What percentage of links posted in published articles are dead?, Citing a link that was removed? ; How should you cite dead urls in a thesis?

I personally think this is not your responsibility to control the sources availability over time. If the official provider's URL is added, it's usually enough. There are numerous means to retrieve the metadata; the easiest one, as mentioned by @JeffE, is WbM, also there is Google cache.
BibLaTex supports a urldate = {YYYY-MM-DD} field, which adds "visited on MM/DD/YYYY" info to the reference in bibliography, assuring the reader which date can be used to restore access if the link is dead.
More technical aspects regarding handling external data sources with BibLaTeX are discussed on TeX.SE: URL of cited web site in bibliography

I am not convinced by the very first line" I personally think this is not your responsibility to control the sources availability.  Surely, if I cite something that is not available to the reader, this is unprofessional -- isn't it? (If the source disappears afterwards, this is a different matter; but here we are talking of a thesis currently being written referencing a resource no longer available at the time of the writing)

@ClementC. I edited the answer to underline that one must assure the source is within reach at the moment of publication. These days if something has even been put online, it is practically always reachable by various means, and it has nothing to do with the professionalism of the one who cites (again, urldate is your saver). The other thing is, if you don't trust the source anymore because it vanished in a short period of time, then you probably should get rid of it entirely.

I see -- thanks for the edit, esp. about the proper BibteX format!

@ClementC. You are very welcomed, good luck with your manuscripts!


text:
Emphasis on new terminology in technical paper: title, abstract and body
I have two new terms that I introduce in my paper: resource security and CerberOS (the second is the name of the system). I use these terms in the title, abstract and body. How and where is emphasis best placed?

For the title, I use title case:

CerberOS: Resource Security and Sharing for IoT Devices

For the abstract, at the moment, I’m italicizing but not capitalizing resource security at first usage, i.e.:

bla bla bla ... resource security.

I am italicizing CerberOS on first usage, i.e.:

We made CerberOS.

I was thinking of doing the same for the body.

Is this too aggressive with the emphasis for the abstract? I was also thinking of capitalizing, but that is even more emphasis. Perhaps only capitalize resource security in the body?

Sidenote: In LaTeX it is almost always better to use \emph instead of \textit for single words or short terms, as this is intelligently handled in a full italic surrounding (e.g., if the journal style makes the entire abstract italic).

I would do the following:

Always capitalise CerberOS, but never italicise it¹. Capitalisation (and some other things like OS) clearly indicate that this is a proper name. It does not need emphasis to indicate that it’s a new technical term referring to some concept (or similar), because that’s simply not what it is: It is neither referring to a concept nor to a technical term.
An exception is using italics to indicate that you are talking about the term itself, e.g.:

We chose the name CerberOS because we are based in the Albanian city of Cerber – there is no connection to the mythical beast.

Italicise resource security on the first usage in a sentence¹, even if that’s in the abstract. If you give a more detailed introduction in the body of the paper, it may be reasonable to italicise it on its first usage in a sentence there as well¹. Do not italicise it in paper or section titles¹. Never capitalise it¹.
The rationale for this is that one would expect the names of new concepts or similar to appear in titles and titles are not for explaining, but giving structure and a quick impression about the contents of a paper or section. The abstract and the body of the paper on the other hand are intended to be understood and here marking new terms is extremely helpful, as it lets the reader know that the term is new and nothing that they are not supposed to already know it.
I see no argument for capitalising it that would not apply to many other technical terms as well and lead to papers in which every second word is capitalised.

¹ Except for situation where you would italicise/capitalise almost every word, such as the beginning of sentences or entire paragraphs in italics.

Thanks, this perfectly answers my question as well as correctly identifying the inspiration for CerberOS! (A security Operating System )