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How to deal with poorly written and formatted papers (as a reviewer)?
From time to time I receive papers to peer review that, in my view, fail to attain an acceptable level of writing and text formatting. Examples of usual issues are: common erratum, poor use of English, bad formatted equations, inconsistent use of punctuation marks, spacings, citations, references and so on. Bonus track is when the submission has not been processed in LaTeX and it contains poorly written equations (for the record my field is Mathematics). I do not consider myself an expert in any of these points, but I think everybody know how to reach a decent level, of course if you are willing to invest some time on it.
While in certain situations there are interesting scientific contributions to present, it is certainly hard to focus on them with so many styling distractions around. What is worse, sometimes they are hard to decipher because of an inconsistent use of notation or because a misspelling introduces a key change in the meaning of a statement. In my opinion, these are issues that could have been solved by the authors with a careful revision of the manuscript prior to submission.
For the sake of argument, let's assume a paper as described before, with a legitimate scientific contribution and let's keep apart from the question the scientific part of the report. When I face the review of such a paper, I often have the next dilemma: should I point the authors to all the writing/styling/formatting issues? Or should I briefly mention that there are serious non-scientific issues and encourage the authors to fix them? The two opposite arguments supporting each approach are:

On one hand, I feel that is my responsibility as a reviewer to ensure that the paper is going to have the best scientific/presentation quality possible after the reviewing process. And that includes helping as much as I can in both points.
On the other hand, if the authors should have taken care of all the non-scientific issues, I wonder why should I invest so much time pointing towards their improvement. In some sense, I feel they are being a little disrespectful with the reviewers and readers to submit a non-polished manuscript. In addition, maybe this kind of work could be done by the people in charge of the article proofs (assuming that the journal has them and that they do a good job...)

My current approach is to ask for a major revision and reply with a very detailed list of all the non-scientific issues I found, but I wonder whether I am overdoing my referee's duties. In addition, this turns to be also quite time-consuming.
EDIT: I am looking for an answer that involves a discussion on what are the reviewer's duties and limits regarding writing/styling. This is only partially addressed in this question.

Can you please elaborate why you think this question differs from the one you linked?

Sure @Wrzlprmft. I was looking an answer to the bold faced questions, which is related to what are the reviewer's duties regarding writing/styling. The question I linked is about how to provide suggestions on that issue, although incidentally discusses in the answers what are the referee's duties. But I believed that this last point deserved to be expanded in its own question.

If you cannot understand the discussion, you may just point out that the manuscript is poorly readable and suggest "reject, invite to resubmit". Some journals allow that option. "Major revisions" will work essentially in the same way.
I would not do proof-reading for the authors, it is not the reviewer's job.

I usually think that some amount of proofreading from the reviewer is nice, but if the paper is full of issues then a "revise and resubmit" recommendation may indeed be better.

One approach I have taken in the past is to prepare a referee report listing the non-scientific issues for the first couple of pages. I will say that such errors are found throughout the paper (if indeed they are) and urge them to proofread more carefully throughout before resubmitting.
Sometimes I will also try to find the author's website, and find out whether h/she is employed at an English-speaking university, and/or has teaching duties in English. If no, then I try to be lenient and generous with offering corrections; if yes, then I don't feel bad writing a curt request to bring the paper up to an acceptable level of presentation.
Nobody expects you to find and fix all these issues. (That said, it seems that some editors only want you to check whether the content is correct and interesting, and apparently would rather leave non-scientific issues to the copyeditor.)


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How do I link to a scientific article?
I want to link to a scientific article (actually so I can ask a question on another SE site) and I was wondering what is the proper way of doing so? I know going around a paywall is illegal and I don't want to do anything like that?
So what is the proper way to link to an article so that I may ask a question about it?
How do I maximize access to it? For example, I'm seeing the article behind Paywall A, but another user has access to Paywall B (where the article may also be available, but would obviously have different link.)

The most straightforward way is to provide a regular scientific citation. The users can then use their individual library or online service to access the article.
Alternatively, you could just provide a link to the most canonical location. Even if the reader can't access the article, he or she will find the bibliographical details there as well. (Thanks for this suggestion in the comments.)

It sounds like this isn't a paper but a hyperlink.  So while it can't hurt to give the other details that would allow someone to search for it, I'd imagine that providing a link to the most canonical location .... where most people would find it, even if behind a paywall, would be best.  I assume that the paywall would provide details (authors, maybe abstract) and simply ask for money to get the PDF.  One can then see if it is available other ways.

@Fred Douglis good point. I'll update my answer if you don't mind.

You're most welcome.

Perhaps a doi is worth mentioning as a way of linking to articles. www.dx.doi.org.

Trying to second-guess what a reader has access to in the mess of overlapping paywalls and authentication systems that cover academic literature is a lost cause. Better to provide a single clear link to the version of record on the publisher's website, and let the reader work from there to get access.
Usually the best way of linking to an article is with its DOI, or Digital Object Identifier. Journals and other organisations assign DOIs and commit to keeping them working for the long term: a website may change, resulting in different direct URLs, but the DOI will still work. To follow a DOI to its current target location, simply enter "dx.doi.org/" followed by the DOI as a URL.
As a globally unique identifier for an article it is also useful when searching for that article on other systems

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Joining a group for PhD, how do I judge the atmosphere before I sign?
I am looking to start a PhD project soon and I have almost decided on the group in which I will apply. But I know that I am a very sensitive person when it comes to any work atmosphere. I have to feel comfortable where I don't work alone in the corner of a room for 4 years.
What are telltale signs of the academic work atmosphere? When I visit the group with the professor, will he let me ask questions to students already there? What should I ask and to whom?

I would probably be a bad sign if the professor does not let you talk to your possibly future co-workers.
As to what to ask them, identify the conditions that allow you to feel right while working and try to see if these conditions are met.
Finally, do not forget that a PhD is also a human experience and try to figure out if some of the people there share your hobbies or interests.

Don't work for this guy: http://www.lettersofnote.com/2011/03/i-expect-you-to-correct-your-work-ethic.html

@Anonymous Unless you are a workaholic yourself. Also, my wife is a medical person and the attitude that you shouldn't leave your workplace until all today's tasks are completed even if it results in your coming home around 2 AM is not unusual there. You can say that the difference is that the treatment of patients is something that cannot wait, but not everyone lives in this world only and considers humans as the only things worth making sacrifices for.

Considering the increased mistake rate when you're tired combined with the high risk to humans those ridiculous working times in medicine are even more irresponsible than those in most other professions.

@CodeslnChaos Agreed, of course. If you can convince the hospital administration about that and make them overstaff the floors (the problem is that the load is very uneven from day to day, so to take good care of workload surges, you'll have to keep extra workers who may have nothing to do most of the time), I'll proclaim you a hero.

First off, if the professor is reluctant to have you talk to members of the group, this is a huge red flag.
When you visit, ask if you can sit in on lab meetings or seminars (some group setting) and observe the dynamic. Does everyone seem engaged and happy to be there? Is the mood collaborative and friendly, or authoritarian? Basically, put yourself there and ask yourself if you'd be comfortable.
Ask the professor about their advising style and philosophy. Some like to be very involved, some want their students to be independent. Make sure their answer works for you.
Most important one, in my opinion: contact a few of the other students independently, tell them you are coming to visit, and offer to take them out for a coffee or beer. This is an opportunity to ask them, in a relaxed non-work setting, about what they like and don't like about working in the lab. Do not tell the professor what the students are thinking, in any case.

Ask the supervisor to speak to the student without the supervisor present; any response other than an immediate "Oh, of course!" is a red flag.  Also be sure to talk with the supervisor's secretary/assistant (if they have one).

@JeffE what would you ask the supervisor's assistant? I have no idea

"Thanks for arranging my travel!  How do you like working here?  Are people generally happy?  What do you think of your boss?"

Contact the people who left the group, either by graduating with a PhD, finishing their post-docs, or through getting tired of it, and find out about their experiences. You can find their names on the group/professor website either explicitly under "students" / "post-docs", or by looking through the list of co-authors/publications. In all likelihood, they will be more independent in their judgments than the current members of the group who are financially dependent on the leader -- at least those doing their PhDs and post-docs. There is no point whatsoever in asking grad students about how they feel in the group in the presence of their adviser -- you will get them in an awkward position, and the leader will definitely raise a brow about you. Besides, the grad students usually don't have any other experience, anyway, so they have no reference point to say whether their atmosphere is better or worse than the average across the field. The "graduates" of the group will have at least one more work group to relate to.

Did you decide on which project you will be working on? Did you propose it (freedom, at the cost of being on your own), did you get assigned to it (as a worker), or did you plan it with the professor (teamwork)? Chances are that whatever happened during this phase will carry on during the PhD.
How central to the supervisor's own work is the question you are going to work on? This will massively influence how much support you get from him, especially when competing with other team members for resources.
It is very important to find out how the team handles results that go against their main hypotheses/theories/assumptions. Do they pour in resources to discover whether they should abandon their preconceptions, do they assign you to another less threatening line of research, or do they put pressure on you until you give them the "right" result?
Do people help each other to conduct their work, or do every person concentrate on their own work?
Check the order of authors on their papers. Do the people who actually worked get first authorship, or do the most senior post-doc get first authorship, the head of the lab gets last, and everybody else gets authorship in order of seniority (BAD!)?
On conferences and social occasions, does the team hang together (whether alone or mixing with other teams), or does the lab head leave the students aside and goes looking for "important people" to talk to?
Do the team enjoy their own time together? Do past team members still nurture personal friendships with the lab head/team members? Do you know of closet skeletons, team mates turned enemies?
The most important: Do people, including the professor, look happy? If they don't, run for your life!

In our group, potential new starters are more than encouraged to talk to current postgrads - for example we normally take them out to lunch when they come to interview/present, without the academics in the group present.  This works both ways - a group that works as a team will want members that fit into the team.  If you are asked to present to the group at interview, that's inherently a good see (IMO), but the tone of a question session after that is a good gauge - not the supervisor's questions, but how the rest of the group ask questions in front of him/her.
You can get a feel for the dynamic of the group without asking directly - find out about whether they do stuff together out of work, for example.
Checking the order of authors as suggested by dmvianna is a good idea, but you need to do that in the context of the field - e.g. in my area of applied physics, postgrads generally do experiment+analysis+writing and are first author.  My perception of particle physics is rather different.
Your worry about being isolated is certainly valid, I feel very lucky in the group and department I'm in, when talking to people elsewhere in the university they are often quite lonely in their work.

Note: the group doing stuff together out of work isn't necessarily a good sign... It can, for example, mean that they don't get enough time out of work to have any other friends.

Definitely agree with Chris H about being perceptive of the context of the field when checking order of authors. But again, if you choose a field where you won't get first authorship during your PhD, be aware that you will have a hard time justifying that to future employers/funding agencies who are not savvy in that field.

@Aesin a good if pessimistic point!  However in that case they may be too sick of each others' company to spend any more time together.  But you also don't want too much pressure to join in - sometimes you just want to get on with your own stuff (work or otherwise).

You also need to realize that your behavior during the tour of the group is also a way for your potential advisor to see how you interact with other scientists. It will also be (if you take the position) your first contact with your future team mates! So be sure to show interest, take your time, ask questions… don't rush it!

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Should I talk about a unpublished paper in my SOP?
I have a draft of a unpublished paper that I hosted in Arxiv that I will be attaching with my application. Should I talk about the inspiration behind it in my SOP. Like how is the method behind the paper different from the existing methods for the same problem?
There seems to be this general consensus that anything flimsy or story-like needs to be avoided. Does talking about inspiration for a paper qualify as flimsy or story-like?
The paper is a single author paper that I never talked about with my recommendors so I am afraid that if I don't talk about it, people reading my SOP will not read it at all.

I have asked a related question, but this is the case when the unpublished paper's field has no overlap with your major

What is "SOP""?

Talking about an unpublished article that has inspired you is certainly fair game for a SOP essay in a graduate application.
Certainly the inspiration, and the differences between your approach and different, existing methods would be highly interesting to me.
I love to see undergrads who take initiative in research - they tend to make good Ph.D. students. Taking ownership and initiative in your project is a key step of maturity in grad school. So if you have already done so, that's a great sign.
And yes, if it's only in Arxiv and you haven't mentioned it to your letter-writers, I'm not likely to read the paper if it's not otherwise mentioned in your SOP.


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Plagiarism of Research Proposal Idea by Potential Supervisors
I really would like to know how to prevent a plagiarism of your idea or Research Proposal, when it is sent to several Universities and potential supervisors?  What can I do if one of the potential supervisors did not respond to me, nor did consider my research important, but later I notice that they are using my idea with other possible investigators?
What can I do in that case?
I am really frustrated and disappointed with that lack of ethics. I feel that this person stole my idea and my possible place in the University, and the possible fruits of my work and idea as well.
I really would appreciate your advice.
Thanks a lot for your wonderful website.

Probably you are ideas are not that groundbreaking that no one else can come up with them. It is likely that he came up with this idea independently.

Either your idea is not as groundbreaking, as Rüdiger says. Or else, if it is, don't send it around. Even if, say, 95% of the researchers are ethical, the probability of encountering one who isn't goes up as you send to more people. "Fruits of your work" - did you send them results?

Note that when submitting research proposals, many supervisors usually do not care about the specific idea itself, but rather whether you provide a good approach to execute the idea. As the others mentioned, it is rarely the case that a particular idea is new and groundbreaking by itself.

I understand and completely share your frustration here. It feels awful when your application is rejected but later the same idea is used by a person you put some of your trust in.
I don't have a universal answer which helps to avoid such things. Sometimes people suggest to be vague in your proposal, but I don't think this is really a good idea. After all, when you have an idea, and you think it is good, you don't want to sound like you don't know what you're talking about. So, I don't think you should somehow tweak your proposal to make it less easy to plagiarise.
Instead, I would suggest to maybe do better research of potential supervisors before you send them your detailed proposal. Perhaps, do a small polite exchange of emails and check if they are even interested to have another PhD/postdoc at this moment? Look at their history of publications, read a few papers - are they really working in the area you want to work in? Look at author's lists - is there evidence that a potential supervisor  was a guest/gift author in many papers? Are there cases when they re-claim someone else's idea as their own (by doing minor modifications and changing the name, etc.) If possible, get in touch with their current postdocs/PhDs and check what they think about the transparency and ethics of the research/publication process in their group. Or simply try to arrange a small chat with the potential supervisor - sometimes five minutes face-to-face tell you more about a person than a year of email exchanges.
Good luck.

"Look at author's lists - is there evidence that a potential supervisor was a guest/gift author in many papers?", How do you do that?

To be successful, your proposal needs to be related to the expertise of the supervisors.  So it is perfectly normal for the supervisor to do similar work if you do not end up working for them.  If it is for a PhD position, then it would not be unusual for the supervisor to direct the student to propose a particular topic or methodology.  It is common to find many people working on the same thing, but only those who make a good implementation get credit.
A research proposal, on its own, is not valuable research.  It is the implementation of the proposal which creates the value.  If you feel you have already completed the hard part of the project, what you have is not a research proposal, it is mostly finished research.
The answer to the question is:  you do not need to do anything.

Insert a copyright statement in proposal document and in your email footnote. Also, to be on safe side always keep record of email exchange, especially the email you sent with proposal document.

The first part seems completely pointless.

I agree with @TobiasKildetoft - there seems to be a widespread belief that copyright is an anti-plagiarism measure whereas it is really about rights of distribution. Something can be intellectually plagiarized and still not breach copyright. Conversely, if I typed up someone else's book and tried to sell it while still clearly stating the original author, that is not plagiarism but it would probably breach copyright

I don't think that will really prevent any issues. Plus, it may send a wrong message to the receiver.

I saw this practice done by professor from MIT. I was engaged in discussion about possible visit to his lab and he shared with me their on going work detail with a copyright statement "All rights reserved".

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Applying and interviewing for a faculty position without intent of accepting position
Is it ever a good idea to apply (and interview) to a faculty position at an institute if you know for certain (or with very high probability) that you are not going to accept a position there.
Possible advantages are:

Networking and letting people hear about your work.
Practice for later interviews.
Leverage: If a top institute offers you a position, that could be used to improve negotiating position with other institutes that you are interested in.

Is this something which is frowned upon? On one hand, I am guessing that departments wouldn't want to waste their time and money on a candidate that will not accept a position. But on the other hand it might be acceptable if the faculty are interested in hearing/talking with the candidate anyway.
If this is acceptable (or if it is not but someone still recommends it from the candidate's perspective), should the candidate give the impression that they are enthusiastic about the institution? (of course I realize the interests of the candidate might be different than those of the institution)

One significant risk with #3 is that the institution you prefer might just call your bluff.

Is it ever a good idea? Probably. Is it ever a nice thing to do? Probably not.

My rule of thumb is: if I wouldn't accept the position, I don't apply for it.

"[I]t might be acceptable if the faculty are interested in hearing/talking with the candidate anyway." In that case they can simply invite the candidate to give a talk.

Related at workplace.SE.com: http://workplace.stackexchange.com/questions/21463/attending-interviews-to-stay-sharp-if-you-reject-an-offer-and-then-apply-aga/

follow the golden rule - (treat others in the way that you would wish to be treated).  If you apply for a job you do not intend to accept and it is offered to you, it is highly likely that you will at the very least have inconvenienced the members of faculty whose time you wasted by having them interview you.  It may be good for networking, but the impression you may give may not be the one you wanted (I've seen this happen many times).

Please don't do this- you'll only be wasting the time of the search committee members.  Furthermore, you'll be doing something that is dishonest, and you do should not get into the habit of lying to people.
If it becomes apparent early in the search process that you aren't truly interested in the position then the committee will probably not invite you for an on-campus interview.  If you actually are invited for an on-campus interview, then there's a good chance that it will become apparent during the interview that you really aren't interested in the position.  If you feign interest and do get an on-campus interview and then get an offer but reject that offer, then you'll have left a bad impression with the faculty in that department which will effect your relations with them in the future.
The ways in which this can hurt the candidate are fairly limited, so the reality is that people can get away with this if they want to.  However, that doesn't make it right.

If you have a 'good faith' assumption that if offered the position and if the conditions were right you might accept it,  then it is not dishonest.  (Even if you have some other reservations or concerns from the beginning). And a candidate rejecting an offer doesn't leave a bad impression in that people do reject offers if they have received others that they prefer or conditions can't be negotiated to their satisfaction. But everything the OP say soundss as if there is not a good faith attitude going into the interview. And that means everything @BrianBorchers stated is very relevant.

It seems a little inconsiderate to me; the department will waste their time considering your application, and the further along in the interview process you get, the more of their time (and yours) you will waste.  But I don't think it's necessarily unacceptable.  You could argue that an interview might convince you that you would be interested in working there after all.
I'm not sure it's actually very helpful to you, though.
Your point 1 doesn't make sense to me.  If you want to tell someone about your work, just send them an email and tell them.  Sending an application seems ineffective; yours will probably be one of hundreds of applications read on that day, which won't help your chances of having them remember you.
For point 2, "practice application" seems a little silly to me.  But if you really think it would help, you'll get just as much practice by writing the application and then not submitting it.
Point 3 has some justification.  But for it to be effective, you have to go all the way through the interview process and get an offer.  Consider the amount of time you'll spend writing a compelling application and traveling to an on-campus interview.  And you'll have to spend that day-long on-campus interview insincerely convincing them how much you want to work there; not a very pleasant task for most people.  (If you don't do that, you almost certainly won't get an offer and it will truly be a waste of your time as well as theirs.)  Even if you do get an offer, it may still be lower than the offer you actually want, and thus useless as leverage.  Is it worth it?

In other words, if you're going to do all the work needed to get an offer, why not do it at a place where you might actually consider going ? This is the next level of "spent 1 hours googling to find the answer when just solving it would have taken 30 minutes"

@Suresh: I'd say it's three or four levels beyond that, but it's certainly the same phenomenon.

Thanks for your answer. In points 1 and 2 I was referring to the interview/seminar, not the application itself. Regarding point 3, imagine a situation where you are restricted for personal reasons, to accepting a position only in a small geographical region or at a specific institute, so it is important to maximize the chances of success. I could imagine it may help to have offers from top institutes elsewhere.

@Suresh of course this would be in addition to the place you actually want. As I mention above, in some cases the places you actually want could be, due to constraints, only one or a couple of institutes.

Meanwhile, someone who really wants the job loses out because time wasters snagged the interviews...Definitely a time to employ the Golden Rule on doing unto others as you would be done by.

A late response to Bitwise's comment above.  Having an offer from some other more prestigious institution isn't going to have a positive impact on your chances of getting an offer from my institution.  In fact, it's likely to hurt, since we may expect that you'll take the offer from the more presitigious institution.

I'm going to give a contrarian position and say yes, for two reasons:

There's something to be said for practicing for interviews you do care about. The job search visit is something of a unique and intimidating beast, and being able to approach it once or two without the pressure of feeling heartbroken if you don't get the position is a good thing.
You have the capacity to be surprised.

Now if you're genuinely certain you're not going to take the position, then I don't think you should bother. But if it just seems merely unlikely? I can tell you the position that I'm at right now was one where, both at the application and interview phase, I considered unlikely to be the right fit. I was wrong, and ended up taking the position and being quite happy.
What you do need to do is approach is with seriousness. It's still a job interview, and these people are spending their time and money to invite you out. Even if it's unlikely that it'll end up being the right fit, that deserves your respect. Similarly, if it's clear it's not going to work out, turn them down quickly so they can move on.

I want to argue for going to interviews where you are not 100% certain you would accept the job. However, I think that the reasons 1-3 proposed by the OP are probably not the right perspective, so I'll propose #4. (My assumption here is that the reason you are not likely to take the position is about fit, or research activity level at the university - not location.)

If you would not work with these people at these university, how seriously are you going to take networking with them? Even if you want to do this, no guarantee the effect will be positive if they think you aren't considering them honestly.
Practice is valuable. But once again, if there is a giant mismatch in fit between this place and your intentions, you can take the wrong lesson from your experience!
I don't think having an offer from a university on a different "tier" gives you much leverage. In fact, I'd be worried about snobbery from some universities - "If a candidate would consider working for University X, they can't possibly be good enough for the Ivy League," etc.

Instead, here's the 4th reason, which I think is much more reasonable:

You probably don't know what you want as well as you think. Are you sure you couldn't work at a place without a PhD program? I know brilliant, well-funded researchers at places like that. Wrong department name? Maybe the culture is aligned with your field more than you think - after all, they're trying to hire you! Don't want to live in [Region X]? Maybe there's a huge population of immigrants from your country there, which make it a much happier place than you'd expect.

I went on four interviews at places where I had serious skepticism about fit. Two of them I realized would be great, one plausible, and one was a worse fit than I had thought. Sometimes that happens - you just have to go in with an open mind, and an honest understanding of what your dealbreakers are. If you can truly 100% rule it out, don't go there - heck, don't apply in the first place! But unless you were choosing applications by throwing darts, you had a reason to apply to that department.

You already answered your question. You listed the advantages of going on an interview. You might think that you already have a decision not to accept an offer should they make one, however, you can never be certain unless you go on interview. If you dont have other commitments that are more important than this interview, I think it will be only beneficial to do an interview especially if this is a phone interview.

I am surprised that this is not the accepted answer. I think if there is some small probability that you would accept the position, you should move forward. You should not judge a book by its cover, and should not judge a department by its website. If you are a candidate that is competitive in many places, the school likely knows this. They are interviewing you/flying you out because they want the opportunity to convince you to choose them.


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I graduated last year and my advisor passed away unexpectedly soon after. What should I do now for subsequent academic job searches?
I received a PhD in mathematics last May. Last December, my advisor passed away quite unexpectedly.
My advisor was an extraordinary person; in addition to being a fantastic advisor mathematically, he was a wonderful mentor who I always thought of as a friend – this is very much a personal loss for me. My initial emotional response was that I should clearly leave mathematics forever. Rationally, that seems uncalled for. Before all of this, I had been aiming for academic jobs in mathematics. However, I expect that a recommendation (as well as other help) from one's advisor is a significant part of an academic job application (for example, this recent answer states that the letter from one's advisor is read first even when applying for a tenure-track job after a postdoc).
How does one go about an academic job search when one's advisor has passed away?
For example, my advisor wrote a letter for me for my job search out of grad school. Does one try to use that letter (via perhaps my graduate department) for subsequent job applications? Do I mention in every cover letter from now on end that my advisor has died (that seems horrifying, since I like my vague sense of denial)?
I am in the first year of a (3-year) postdoc, so I won't be on the job market for a while (in fact, it seems simultaneously very soon and too far away). Of course I can tell that my productivity and motivation have slumped in the last few months, and I know that I should try to get back into gear as soon as possible.
PS: It’s entirely possibly that there’s no ‘practical’ difference between this situation and other situations where one doesn't have a letter from an advisor (as commentor Sumyrda has said), in which case that would be a perfectly reasonable answer that I would happily accept.

Related questions:
While in more of a 'denial' stage, I asked this question to try to get at this.
The analogous question for current graduate students was asked here and here.
There are several questions about dealing with not having a letter from one's PhD advisor on this site, such as this one, or this one, or this one.

as someone whose (potential) adviser is also an amazing person, i can't even begin to imagine how you feel. i am so sorry for your loss.

I get why the first couple of related questions are different to yours, but the last one yo linked seems quite on topic. Based on that question's answers: explain the situation yourself or ask one of your letter writers to explain it. I'd also include the old letter, if you can get your hands on it.

Please don't leave academia!!!  Your advisor had a huge community of people who admired him, and I you will have no problem finding other people to write letters.  Those letters will mention your advisor's tragic passing, so there is probably no need to bring it up yourself.  Your current postdoc advisor is a wise person and I'm sure will be able to give you advise on who to contact when the time for letters arrives.  Of course, the rest of are always happy to talk too (nb for non-Aru's: I am a faculty member at Aru's former graduate school, so I know the situation well.  All of us are sad).

ps: it would probably be a little weird to try to include your advisor's old letter.  And anyway, you'll have proven more theorems during your postdoc, so you want letters that reflect your recent accomplishments in addition to what you did in grad school!

@AndyPutman I'm certain the impulse to leave it all behind and find a nice actuarial job (say) is just an emotional response, and frankly a childish one - and one that he would strongly reprimand me for! My advisor has been a large part of my mathematical life for so long, it's just hard (and somewhat churlish perhaps) to remind myself that well, I did want to do mathematics before I even knew he existed (I didn't start college as a 'real' math major, so pre-grad-school desire to math was ~2 years, compared to grad-school/beyond of ~5 years; that's a lot of Tim-fluence).

(contd.) Anyway, math is still fun and shiny - perhaps a bit less so these last couple  of months, but everything else has been less shiny too. Asking this question really does mean that I want to make a decent go of the academic job market; I'm not seeking excuses to not try although I see that it can be read that way.

It's not a childish response!  You should never feel embarrassed about how your process your grief, though I'm sure that Tim would have wanted you to continue with your research.  My father passed away when I was a graduate student, and I thought very hard about quitting.  Death has a way of making even wonderful things like mathematics seem less important.  Keep working, take care of yourself (both physically and emotionally), and have faith that the practical aspects of losing Tim (e.g. getting letters) can be overcome.

Is there another professor from your committee or elsewhere in the department who knows you and your work well enough to provide recommendations? That person could say that your adviser thought very highly of your work and that they, too, believe you would be a valuable employee.

@AndyPutman Can you please turn your comment into an answer so I can vote for it?

This is a very difficult situation. As per the comment by Andy Putman, let your other letter writers explain the situation. Considering you got the Postdoc job, your current supervisor must have been impressed with what your advisor said in his letter. Your current supervisor can include a personal story about something your advisor said about you or even include a few of his favorite verbatim quotes about you from the letter of recommendation for your current postdoc. Anyone on a hiring committee will understand, and will possibly even be personally touched. This will not count against you.
I wouldn't send a copy of your postdoc letter in your application materials If your postdoc supervisor highlighted the strongest quotes from the advisor's letter. If he chooses not to do this or if your advisor's letter in its entirety is much stronger than the best few quotes from it and your postdoc supervisor still has the letter he could send it along with his letter.(note that in other fields this letter may be a bit inappropriate because it could contain a lot of detailed information about how you are a great fit for the particular postdoc position but as Pete points out this usually is not true in pure math).
Unfortunately this does not heal any wounds caused by the unfortunate passing away of your advisor and life long friend, but you should not worry about the letter writing situation. I can't say that I even begin to imagine the emotional pain of losing an advisor so close to graduation, but as someone who lost a parent while in college I greatly sympathize with you and I can think of no greater honor to your advisor than to continue in academia and continue doing great work.

I don't think people would assume you saw/changed your advisor's letter if the department sends it out.  That said, I agree it's unnecessary to send it.

"I wouldn't send a copy of your postdoc letter in your application materials because, it likely contains information specific to the postdoc that would be inappropriate." I'm unsure of your meaning.  If you mean that it is a letter recommending someone for a postdoc rather than a tenure-track job: sure, that's the situation, and it might be better to include the letter if it is very strong.  (E.g. if it says "She was my best student ever" then it would be a shame not to include this information.)  If you mean that it is targeted to a particular institution: no, probably not, in the OP's field.

@WetLabStudent: Quoting someone who is deceased from a letter that only you have access to is not ideal.  If the letter is extremely strong and well written, it makes a better impression to include the letter rather than isolated quotes from it....Ah, but I see you've already taken this into account in your answer.

This is a difficult situation, especially for a scholar just starting out and on the job market. But it is not unprecedented. On job search committees, it is true that the absence of a letter from a major professor usually raises eyebrows. However, it is just that: "why isn't there a letter from the major professor?" Therefore, in your own letter, when you describe yourself, you can make it clear without berating the point. "I received my Ph.D. from X university, writing a dissertation under the direction of John Smith (now deceased)."  It's really as simple as that.
I am a senior tenured professor and I still have such a description in documents that describe me and who I worked under, because my PhD advisor died some years ago.
The truth is that the letter from your advisor (this depends on your field, I suppose) is important, but the other letters are often more so. Scholars outside your university who are willing to go to bat for you can often carry as much, perhaps more, weight than a letter from your advisor. And over time, a letter from your adviser may even become a liability, if the nature of the mentor/mentee relationship remains the same, or if the tone of the letter does not adequately reflect your maturity and growth as a scholar after the degree.  Because you are fortunate enough to have postdoc, use that time not only to strengthen your scholarship but also to develop productive relationships and try to build a network of colleagues of your own, unconnected to your home university.  They are your future letter writers.

The department chair where you got your PhD can pick up the pieces.  Give the chair a copy of the letter your advisor wrote.  S/he can take it from there.
If you have any trouble with that, seek out another senior member of the department instead.

This is bad advice because (1) It means the letter was in your hands, in academia the letter is not supposed to be seen by the subject (even if the letter wasn't in your hands the fact that it wasn't sent by the advisor means it could have been, and that's a problem) (2) the letter was for a postdoc, it won't be exactly the same for a faculty job, and most likely it even says something like "for postdoc X at University Y" in the letter, at best the letter would read a little strange and at worst it would be completely inappropriate. (3) it's a bit creepy (my opinion - possibly not others').

There are special, extenuating circumstances in this situation.  Let's hope those who read the letter written by the advisor before his death, along with a letter from his department chair, show empathy and humanity.

@WetLabStudent: The answer does not suggest to send the letter to its intended recipient, or to a recipient of a hypothetical recommendation letter that might have been written, were the advisor still alive. It suggests providing the department chair of the advisor with the letter, presumeably to allow them to familiarize themselves with the late advisor's point of view toward the advisee's research and skills, so they can decide to what extent to take over backing the advisee's claims toward future employers.

That the OP almost certainly does not have (and should not have) a copy of her advisor's letter is one problem with this answer.  But more fundamentally: how will the chair "pick up the pieces"?  Other than coordinating sending a copy of the advisor's letter to future job searches [which is sometimes done when the time between the death and the PhD are both short; yes, it is a little creepy but death is creepy and this may be the best solution for the candidate], I don't see a privileged role for the chair to play: likely she will not be in the candidate's field, so should not write for them.

Aha, I checked the original post, and you are right, she doesn't have a copy of the letter.  She mentioned the letter -- but she doesn't have a copy.

What should the chair do?  S/he should write a letter more or less like this: I am writing a letter of recommendation for (advisor), in lieu of her advisor (name), who died x months/years ago.  I am able to write this letter with confidence, because (advisor) spoke and wrote highly of (student).  Etc. etc.


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What is the role of a PhD advisor after a student has graduated?
It seems from answers to certain questions (such as Should a mid-career faculty application include a letter from the former PhD advisor?) that the role of an advisor may continue after a student has graduated.
In general, what is the professional role of a PhD advisor after a student has graduated? Are they simply possible collaborators and sources of recommendation letters, or is there more?

I've seen this question: What is exactly the role of a phd advisor? which is related, but focuses on the role of an advisor during graduate school.
When should you stop asking your PhD advisor to do advisor like things? is related, but my question is what are the advisor-like things a PhD advisor might/should do after a student has graduated.
Here are some other related (but not duplicates as far as I can tell) questions:
How to handle not having my PhD advisor as a reference?

@ff524 I edited the question, but for clarification, the questions you mention above ('limited to letter-writing', 'is a letter a must', etc.) were written as subquestions of the main 'What is the role of...', to indicate what kind of things I would like an answer to refer to.

To the downvoter (in case it is not ff524), is there a way to improve the question?

All of the sub-questions you removed were about letter-writing. The question that's left asks about the role of the PhD advisor besides for letter writing, which seems to me to be already addressed by When should you stop asking your PhD advisor to do advisor like things?.  I'm still pretty confused by this question :( I think it would be a better question if you replaced "role of" with something much more specific, as you seem to have a particular type of role in mind.

@ff524 I disagree that the remaining questions asks only about the role of a PhD advisor besides letter-writing, but of course, as the author I am not an objective observer. I've made a further edit, which hopefully clarifies this point.

The main difference between this question and http://academia.stackexchange.com/questions/17409/when-should-you-stop-asking-your-phd-advisor-to-do-advisor-like-things, to me, is that this questions asks what are the advisor-like things a PhD advisor might/should do after a student has graduated. This does not appear to be addressed in the other question, or its answers.

I'm still a little confused, but I think the edits help, thanks. I'm going to edit the content of your last comment into the question, too.

@ff524 thanks for the edit, I think that was a good decision.

Once a person have graduated, there is not generally any remaining formal role for the Ph.D. advisor.  In theory, a Ph.D. qualifies them as generally capable of independent scientific research, and they have no requirement to depend on their academic "parent" any more.
In practice, however, no person is an island.  Most researchers do much better as part of a network of like-minded colleagues who can serve as friends and allies.  The Ph.D. advisor is a natural starting point for building such a network, both as someone likely to be a like-minded ally and also by helping build connections based on their own existing network. As the more junior colleague in the relationship, the benefits of interaction are likely to flow more more from the advisor to the former student, but the relationship is likely to grow more peer-like over time.
Just as with a biological parent, even after formal independence, this connection is likely to last a lifetime (but may not if the relationship is not good).  Also like biological parents, however, Ph.D. advisors (and others) often have a hard time adjusting their perspective and seeing their former students as fully "grown up."  This is part of why it's important not only to maintain a connection with one's advisor, but also to clearly establish a separate research identity.


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Funding during graduate study (phd, masters) in math in the US
I have some questions and concerns in mind:

When somebody says a program is "funded", does that mean the money is conditional (whether he TAs or not) or unconditional? Or is it clarified in context?
Is there such a thing as entirely unconditional funding? If it's not tied to teaching, will it always be tied with progress (or something else)?
Are there programs that will ask you to take out loans? In other words, do (most) schools generally have some sort of funding available? How does this depend on rankings/tier? Is there a specific ranking, say 50, below which you'll mostly likely need money through loans? Does it depend on type (masters or phd)?
For the sake of avoiding confusion, what are different sources? Fellowships, scholarships, the department, "TAships" (what is an exhaustive list?)

My personal concern is whether or not I can depend on being funded, even if I'm not a very strong student (or if I'm a student coming from a different discipline).

In my experience funding for math PhD students is almost universally linked to teaching, in that teaching is a required part of your job. However at the schools I am familiar with, you are guaranteed funding for N years as long as you fulfill your responsibilities. In other words, you will have to teach, but you don't have to worry about not being ABLE to teach and therefore losing your funding.

You have some questions and concerns in mind; so this question post is too broad. Please ask one question per post and before posting a new question, check precisely not to post a duplicate one.

When somebody says a program is "funded", does that mean the money is conditional (whether he TAs or not) or unconditional? Or is it clarified in context?

The vast majority of funding is conditional on some amount of teaching, TAing and/or grading.  The exact amount varies from program to program and, often, within a given program, both from student to student and from year to year.  Various government-sponsored fellowships will cut out all teaching obligations for entire years, but there will be other years in which teaching is required.  Most students spend five or six years in a math PhD program in the US, and most prestigious fellowships don't fund all of that time: e.g. the NSF graduate fellowship provides three (very highly paid) full years of support.  You should also be aware that some teaching experience is desirable bordering on mandatory for future career success, so even a candidate who needs to do no teaching whatsoever (e.g. a foreigner supported by their own government) usually does at least one or two classes.

Is there such a thing as entirely unconditional funding? If it's not tied to teaching, will it always be tied with progress (or something else)?

NSF funding is not conditional on teaching (the above link makes this clear).  Yes, all funding is conditional on satisfactory progress.  It has to be, because continuation in a PhD program is conditional on satisfactory progress and funding is conditional on being in the program.

Are there programs that will ask you to take out loans? In other words, do (most) schools generally have some sort of funding available? How does this depend on rankings/tier? Is there a specific ranking, say 50, below which you'll mostly likely need money through loans? Does it depend on type (masters or phd)?

The majority of PhD programs in mathematics only want to admit students who have (in some technical sense, anyway) full funding, through a combination of stipends and teaching.  Students who want to pay their own way are generally admitted in "non-degree programs" or in ad hoc temporary situations.  I don't know of a PhD program that advises students to take out loans.  In fact, I would advise the contrary: you should not attend a math PhD program unless you have full funding.  What constitutes full funding may be higher at a top program (but also depending upon the location of the program, the wealth of the institution and other factors) but so far as I know, less prestigious programs are no less likely to fund their students.
Master's programs are different: in many cases, it is harder to get funding for a master's program, though it is certainly still possible.  In some cases there is an across the board raise from the master's program to the PhD program: e.g. the same TA duties done by a master's student may earn less than if done by a PhD student.  Still I would not advise any student to pay tuition to enroll in a math master's program in the US.

For the sake of avoiding confusion, what are different sources? Fellowships, scholarships, the department, "TAships" (what is an exhaustive list?)

There is external funding and then there is internal funding.  External funding comes from a variety of sources, especially the government, especially the NSF.  Internal funding comes from the department and/or the university.  It is usually divided into a stipend -- which is what you get paid just by being there -- and an instructorship, which is what you get paid for doing tutoring / grading / TAing / teaching.  For more precise information you should consult the individual department.

My personal concern is whether or not I can depend on being funded, even if I'm not a very strong student (or if I'm a student coming from a different discipline).

The entire funding package should be given to you in detail when you are admitted.  It will not be a year-to-year deal: it will be guaranteed (conditional on satisfactory progress, which essentially means not getting kicked out of the program) for N years, where N is a number that will be given to you in advance and usually lies in [4,6].  Asking how often students get funded in years N+1, N+2, N+3 are good questions, by the way.


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Can I selectively send scores of my general and subject GRE to the university that I am applying to?
I made an account for general GRE and subject GRE. I have a pretty bad score in subject GRE. Few universities are not asking for subject GRE score and it would be better if I don't send them subject GRE score. When I try to send my score to university ETS sends both the scores from my account. Is their any way, I can only one score from the account?

Cannot you send them an email and ask them to help you with your problem? I have heard that candidates who have sit the exam more than once may choose which score to be sent to the institute they are applying to; but I am not sure.

GRE offers a ScoreSelect function.

After test day, you can send additional score reports for a fee and select from these options for each report you'd like to send:

Most Recent option — Send your scores from your most recent test administration.
All option — Send your scores from all test administrations in the last five years.
Any option — Send your scores from one OR as many test administrations as you like from the last five years.

You can only send by test date, though, so if you took both tests on the same day, you'll have to send them together. If this is the case, then I don't believe you can get around it.

You will select by specific test dates, so your scores are all from the same testing session.

This applies to both general and subject GREs.

The ScoreSelect option is available for both the GRE® revised General Test and GRE® Subject Tests, and can be used by anyone with reportable scores from the last five years.


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How should I write research description essay in my PhD application?
I am currently trying to apply for a PhD position in a university. For the completion of application I have to write two essays:

Statement of motivation
Description of research area (with vacant PhD position)

I have written my statement of motivation but I am unable to write a description of research area. In the application there are different research themes which have a vacant PhD position; we have to chose one research area from these themes. I am interested in one research area: its title is catalytic study of X-material . I have never worked in this research topic or material. So I am in a dilemma on what to write in my description of research area.
Should I write about the property of X-material, current research or should I make a research proposal for that research area (catalytic study of X-material)?

Normally, to be registered successfully for PhD project you have to write an abstract (10-20 pages) (and make a presentation). This should cover roughly and shortly:

state of the art
state of knowledge
open questions
the very specialized niche of your work and what the motivation is(better understanding, prototype, measurement accuracy improvement...)
how you are going to achieve this (probably), i.e. a reasonable working and time plan

As you are still applying for a PhD position, it has to be much shorter, so show to the committee that you can identify above points analyzing literature and summarize them in 2-3 pages.
To make things more easy, google similar current published PhD thesis related to this topic and read the preface (above points will often be summarized there within 2-3 pages). Don't write an essay, if the committee asks you to write 3 pages of decription of research area, write exactly 3 pages ;)
PS: Oh forgot, why are you are motivated for this topic you don't know again? Maybe after writing the description of research you should polish up the statement of motivation also a bit based on that ;)


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Is being a 'corresponding author' helpful to get research grants and apply to positions in academia?
I am a PhD student in the USA in the field of Aerospace Engineering.
My supervisor had mentioned that he will be the sole 'corresponding author' in all journal publications. Consequently, I am not the corresponding author in any of my publications.
I have noticed that some postdoc fellowships ask for the 'number of papers as a corresponding author'. This was new to me and I was wondering if it is common to use 'the number of papers as a corresponding author' as a criterion to judge candidates?

The point of giving the contact info for the corresponding author is that it should be useful info for some time. Neither grad students nor postdocs tend to hang around for a long time...

I'd say that in lab sciences  it is very unusual for a PhD student to be a corresponding/senior author.

@JonCuster That's not the definition of the corresponding author though. The corresponding author is the person who wrote the submission cover letter, reviewer rebuttal, and bugged the editor about administrative issues. Technically, the person who did this work should be listed as the corresponding author. In some journals, specifically PNAS, the status of the corresponding author as a member in the NAS, affects the review process.

@user71659 not necessarily. The corresponding author is the one to whom correspondence should be addressed and, at least in biology, my field, this is always the PI and not the student. For one thing, the student may leave the lab and is less likely to have a long term stable email address that can be included in the paper.

While it's subject specific, https://academia.stackexchange.com/questions/138017/how-is-the-corresponding-author-on-a-math-paper-typically-chosen/ may be relevant.

@user71659 and others: Please note that the meaning and relevance of corresponding author differs strongly between fields, see in particular: Does "corresponding author" carry an implied meaning? and What is the explicit meaning of “corresponding author”? Any general claim on this is probably wrong for some field.

@user71659 - Since the corresponding author is listed on the final paper with contact info, the role is not solely within the submission process - that information is for the benefit of the readers into the future.

Anecdotally, it never crossed my (or any of my academic mentors') minds that this might eventually matter for something, but I once applied for a job in Denmark that explicitly asked to point out papers as corresponding author.

@JonCuster even that is field-dependent. In math, published papers usually list contact info for all authors, and the corresponding author is often not even indicated.

@EspeciallyLime - in the old days, all authors had an address listed for them. Then someone would have a little asterisk next to their name in the author list to add a footnote with an email address once email became common. Then the journals started specifying that email address as the 'corresponding author' to indicate that, yes, sending email to that address to ask questions was OK. And, of course, various journals have expanded things further. But the original intent of the corresponding author was they were the first point of contact to the authors about the paper for readers.

In biology, a corresponding author is generally a person with overall responsibility for the research. It is often, but not always the last author listed. While the first author is usually the person that did the most work, the corresponding author is expected to be au fait with the details of the work of all people listed as authors on the paper (which the first author may or may not be). They are expected to continue to have access to all records and data related to the paper in perpetuity.
Research in biology is often conducted as part of a research program. The corresponding author will generally be the person who is in charge of the complete program, not just the single piece of research being conducted here. The goals and aims of the larger program will be determined by them, even if the idea for the individual paper is not theirs. Thus, they will understand how the research fits into the larger goals and aims of the program, how it relates to work that came afterwards, etc.
Thus it is normal that the person nominated as corresponding author is a senior person. Often the last author (senior author as some people say). A junior person being the corresponding author would suggest a degree of autonomy and independence (it would suggest that the last author was last author purely out of senority, rather than because they were actually responsible for the research). This may be exactly what funders of postdoctoral fellowships are looking for.
So yes, being corresponding author is advantageous, but it is unusual for a postdoc, at least in biology.
To pass probation (similar to tenure in the US), I had to have 3 papers as first, last OR corresponding author. To get promoted I had to have 3 corresponding author papers. So for us at least, it's not expected that we will be publishing corresponding author papers until our first promotion after tenure.

This answer is a bit surprising to me. It sounds like we're in similar situations (UK, Russell group university, biology faculty) but this is completely different to my experience. I would have said there is effectively zero prestige in being a corresponding author, and it's often just the first author by default, or their PI. Our probation and promotion paperwork also don't put any weight on corresponding author at all. The heterogeneity of academia never ceases to amaze me.

This is a personal view and it may not be valid in all fields, I realize. But my view is that "corresponding author" is a job, not an honor. It is who should be contacted by the editors and later by readers for questions about the paper. With this view, it is best that it be someone with stable contact information, now usually an email address. That suggests that students may not be the best choice if they lose their university email after graduation.
"Principal author" or "first author" in some fields is a completely different concept. In some fields the concepts are foreign and not used.
Principal author, in some fields refers to the PI of a lab. The one that supplies the infrastructure in which research can be done. In some fields they are listed last. In some fields it is interpreted that they had little part in the actual research beyond infrastructure and maybe general guidance. Sadly, in some fields, some interpret this as "this person really did this work and the others are just being carried along".
First author, in some fields, is usually listed first in the ordering of authors on the document and the implication is that they did the majority of the work, perhaps (or not) coming up with the research question and driving the whole project intellectually. Those fields in which first authorship is considered important often have bitter fights over who should be listed first. I find this sad.
In you current situation, however, for purposes of applying for jobs and writing CVs, I suggest that you just add a note at the end that the supervisor insists on being corresponding author (as I think is appropriate). This could short-circuit any feelings that you aren't adequate in some way.
As for grant applications, I think it would be foolish (though I can't rule it out) for those evaluating an application to look at such things and give them weight over what is being proposed in the grant and the information there that backs up the application. Maybe first authorship would give a bit of confidence in those fields in which it is a vital concern.

While it can be viewed as a job, I've never understood why some (people and journals) insist it can only be done by one person. Instead of trying to predict whose email will be most stable, why not let the authors slap multiple addresses on the paper and benefit from redundancy?

Much of this is field dependent. I'm a public policy phd student, full disclosure. But, corresponding author is just who you reach out to for matters of code (in my case) data and other matters. It also is conferred, naturally, based on contribution (ideally). So, so long as you played a central role in the developing of the topic, the code, the design and all quintessential elements of the research process, you can then (theoretically) become the corresponding author.
But note, in my case, I'm far enough along in my development that I can ask my mentor if he wants to work with me on something, where I'm lead author. Because I have my own research questions and I'm generally always finding new stuff to work on or study, and I don't need anyone to hold my hand to do research (not saying that you do, by the way). So yeah, it's field and context dependent.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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Why don't professors give talks at their own departments?
Why don't professors give talks at seminars in their own departments?  They travel to other schools to give talks, while seminars at their home departments consists of talks given by visitors.  Is there a reason for this?

They do in many places. Often, this happens when the seminar is out of budget for inviting people from foreign places; but not only then.

They also do in all the universities I have been to.. (biology/ecology/geography departments)

Cross-pollination is more important than self-pollination, mostly because self-pollination typically happens anyhow.

If people want to know what the researcher in the next door is doing, they have quite a lot of occasions to ask - even knocking at the door and asking. Visitors are there for a short time and organized seminars are more efficient.

Even if they don't do talk in their home department, all their graduate students do it several time + defenses etc, so about everyone who is interested is familiar even with the fine details of local professors ' work. Also one main goal of those seminars is to spread knowledge between institutes, give exposure what happens in other places. If you are interested in local lab's work, you have many other ways to talk with them.

In most of the departments that I have known, the professors do indeed give seminars within their own departments. The few exceptions I have known are either fairly small or else have some sort of problem with their seminar culture.
Now, it is certainly true that most talks in any department will generally be given by outsiders---there's a lot of incentives to have visitors give talks (e.g., building collaborations, faculty candidates), and there's just plain lots more researchers outside the department than in it (see Joy's Law).
Still, there will be many possible occasions where an internal talk would be of interest, and I believe that healthy departments see it as a valuable way to keep people in the department connected to one another.

We do an interdisciplinary series in my department. We choose an annual theme (one year was "pain", for example), and then have several rounds of talks where generally two people present: one from the humanities, and one from outside the humanities. Almost everyone is from our university, but part of the idea of the series was to get people to know folk elsewhere on campus they might not otherwise meet.

My department (math) had a special series of seminars by our professors so that grad students could see what everyone was up to and who they wanted to work with.


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Is is unethical to review a major revision manuscript just by reading the point-by-point response?
I'm new to peer-review and my experience in this domain was receiving a reviewer report rather than providing one.
A while ago, I have requested a major revision to a manuscript that I have been asked to review by a journal. The major revisions I requested included some modifications in the figures as well as rewriting the whole introduction among other modifications. Since the comments were a lot, I have requested a major revision rather than a minor one.
I have received the revised manuscript and have been asked to review it again.
Would it be unethical to just go through the point-by-point response and check that the modifications I have asked for were included in the paper, without going through the paper in detail, as if it was the first time I'm reviewing it?

Is there an author summary of the changes?

check that the modifications I have asked for were included in the paper – Not your question, but I just want to emphasise how important this is: I have done several reviews were the authors simply didn’t do what they claimed they did, sometimes including straightforward but important things such as fixing an axis label in a figure.

@Wrzlprmft I wonder why - non-existent figure changes could be failure to use the re-upload process properly after all, and that's an easy fix, but maybe they really hope you wouldn't notice

@ChrisH: In the specific case in question, it was definitely not a technical problem such as failing to upload the new figures. They did change the figures, just in a completely different manner. I never learnt why this happened; at some point I just gave up and the editor followed. But anyway, we digress.

I think it's perfectly reasonable to primarily review changes in a new version of a manuscript that you have already reviewed. I would assume that most reviewers do this rather than pretending to start from scratch, though it is likely necessary to go a bit beyond "just by reading the point-by-point response" to accomplish this.
Consider all changes
I would say a reviewer should consider all changes, not only changes made in response to their own comments. It's possible you will find fault with the way the authors have responded to some other reviewer's comments, or the authors may have made other unrequested changes as part of their own iteration, as indirect response to a reviewer comment, or in response to other new information in the field.
Use a complete "diff"/tracked changes, not just author responses
If the authors/journal have not provided a "tracked changes" or "diff" version of the manuscript, I'd recommend making your own using software to verify that the authors didn't make any sneaky other changes.
Cross-reference changes throughout the manuscript
For a thorough review it may be necessary to cross-reference changes listed with other sections of the paper. For example, if you suggested a change in methodology and the authors made changes to their results section, you should be checking that this methodology is properly described in their methods section as well as elsewhere in the paper.
One example I've often found in published papers are cases where I suspect a reviewer had the authors correct some statistical mistake like concluding two groups are "the same" or "not different" because a p-value was larger than 0.05. The paper may show the correction in interpretation in the results section, but their abstract, discussion, etc still use the faulty interpretation - a careful review should be able to identify inconsistencies like this.
Not every "major revision" has the same scope
It's not clear simply by the designation "major revision" just how much of a paper is impacted: it's both possible for a major revision to involve practically the entire manuscript as it is to involve a narrow but crucial aspect. A reviewer will have to judge on a case-by-case basis how much of the manuscript they need to check; it's not possible to answer the title question here in a yes/no way that applies equally to every possible circumstance.

I'd recommend making your own using software to verify that the authors didn't make any sneaky other changes - This sounds like a lot of work, no?  Is there a simple way do to this for pdfs with lots of symbols and equations?

@Kimball In my area it's pretty standard that reviewers are provided with a version with changes already identified. There are certainly a variety of tools for PDF, LaTeX, and .doc format files; whether they'll all handle math symbols and equations I'm less certain about, in my area it would be unusual to have more than a handful of equations. Possibly others would have a better suggestion for very math-y papers.

If it's not simple to identify the diffs with automated tools, then I would say it's fine just to skim or spot-check for changes.  If you start finding a lot, then consider either rereading the entire paper, or asking the editor to ask the authors for a detailed list of changes.

diffchecker.com is great for that. No need to reinvent new software

@doublefelix I've proposed using software, not inventing it.

@BryanKrause Sorry about that, I misread "making your own using software" as "making your own software". Sounds like we are on the same page. I will leave my comment up because the link can be useful.

If you would consider doing an inadequate review, after agreeing to do a review, unethical, then consider this unethical as well. You can't assume that the authors did the absolute minimum necessary to cover your points as this would seem to imply.
If the authors have done their job well, they have, indeed, done a major revision, implying that, while your points may be addressed, other things may be affected as well.
I suggest that you either decline the review, which is perfectly ok, or plunge in and do a complete reanalysis of the paper. I suspect it will be easier than the first read, but new things may require comment.

No, but do check the author's responses to other reviews, if any.
Starting from scratch is a lot of work. I doubt the authors do a full rewrite of their manuscript every time they receive a reviewer report, so neither do you need to do a full check.


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Research schedule for postdoc application in mathematics
I am currently applying for a postdoctoral research grant and one of the requirements is a schedule of research work.  In experimental fields such as biology I can imagine how such schedule may be structured, say from this to that date conduct this or that experiment. In mathematics where no hypotheses are tested in the same sense as in experimental fields, no data are collected (in general) and detours or changes in approach are not uncommon, how can such a schedule be outlined?

This seems like an excellent question I'd ask my former (or current if that's the case) PI about. Surely they've written a fair share of research grants.

This sounds very strange for mathematics for exactly the reasons you mention. Are you sure they want an actual timeline?

If this is about the grant applications from Academy of Finland, which is possible given the timing of the question, then the format is the same for all academic subjects. It includes mandatory discussion of ethics and data management, also. I suppose other funding opportunities might be similar.

I have never served on a grant committee, but I have experience as an applicant. Even though you obviously do not have any experiments or data collection planned, you surely have some idea of what you want to do, and how you want to approach that. And you know how many years you have available. By estimating the relative difficulties in each step, you should be able to come up with a rough idea of a timeline. What I believe they want to see is that you are able to give a realistic estimate of how difficult your proposed research is and how much time it will cost. You also might have different somewhat indepdendent projects in mind. Are you going to do the sequentially, or in parallel? Maybe you plan a research visit to another university. Answering such questions gives you a rough schedule that you can include in your proposal. I don't think it has to be very long or detailed.
Clearly during the course of the research it might be necessary to change the plan, because things did not work out as anticipated. But that is no different in other disciplines I am sure, and the reviewers are surely aware of that.
In short, the main goal in my opinion is that you should be able to show that you have a realistic assesment of how your proposed research can be completed in the alloted timeframe.


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Is increasing the DPI of a low resolution image a good idea?
Today after a paper of mine got accepted I received this from the publisher (Elsevier):

We have received the above article for publication, unfortunately
  figures x1, x2 and x3 are of low resolution and of insufficient quality
  to reproduce well.
The minimum resolution requirements are 1200 dpi for black and white
  figures and 300 dpi for colour figures. If you are converting your
  figures to TIFF files, please ensure that the resolution is correct
  before scanning them.

The figures are digital 512×512 gray-scale images in the PNG format. The source of the images is not me. I had converted them to EPS files using Inkscape. The source of some of the images is: https://github.com/cszn/DnCNN/tree/master/testsets/Set12.
How do I resolve the issue? Should I just save the same images using 1200 DPI in EPS format and send it to the publisher?

Do you think the figure is of publishable quality regardless? If so, there's a good chance if you write back to Elsevier they'll simply go ahead with the figure you've given them.

From a technical standpoint it makes no sense. The publisher could do a better job in resampling the image because they know in detail the technical capabilities of their printing machines (if it is a printed journal) and the processing pipeline.
But by enforing a higher resolution, the risk of misprints is given back to the author so you can not complain if something is not visible.
Therefore: Just resample it...

What do you mean by resample?

@Wrzlprmft when you are changing the resolution of a picture, you have to write all the new pixels - and there are different ways to interpolate missing information. A nice article can be found here: https://www.photoshopessentials.com/essentials/resizing-vs-resampling/

The comment you received is aimed at obtaining images of higher quality for publication.
Processing the files you sent them will not solve this issue.
If it did, the typesetters would already have done this themselves – this is what “insufficient quality to reproduce well” hints at.
In your specific case, the images seem to be digitalisations of historic photographs.
Thus, the only way to improve the quality is to obtain higher-resolution digitalisations of these photographs.
If you cannot do this, write exactly this to the publisher; they are most likely going to accept this.
Also note that if those images are test cases for some image-processing algorithm or similar, they should be printed exactly as they are, and this is what you should write the publisher.
The entire remark about the resolution probably doesn’t apply to you but was made for illustrations, plots, and similar.
These are almost always best provided in a vector format (which has infinite resolution, if you so wish) and even if using a pixel format, they can be produced at arbitrary resolution.
The resolution requirements are aimed at those researchers who insist on working with pixels in this case.

You can certainly export at 1200 dpi, but the image will become smaller. I notice that these are photographs, where some important details may be small in size. You will need to take a call if the size corresponding to 1200 dpi is large enough for your purpose.
If not, pick an intermediate dpi that is a suitable trade-off, and send that with a note to publisher.
A deeper issue is converting between a rasterised format and a vector format; both are different types and should be used appropriately. I suggest you ask the technical aspects of this question at Graphical Design SE, it may help avoid such problems in the future.


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Pursuing Masters to get a better job
I am going to apply for the masters program in computer science to various US based universities. I am  eager to apply to their professional courses which do not have thesis/projects in their curriculum, commonly known as MEng and MCS programs. These courses are more inline with the industry needs and that is where I eventually want to go after graduation.
As an international applicant if I apply to a program stating that I want to get a job in US because of better opportunities and doing masters there would help me in achieving my goal would it be frowned upon by the admission committee? How else can some convince that this is the right program for him?

Can you please share your views on why is the question downvoted?

As an international applicant if I apply to a program stating that I want to get a job in US because of better opportunities and doing masters there would help me in achieving my goal would it be frowned upon by the admission committee?

No.  That's what professional master's degrees are for.

IMHO, that means it's needless and pointless to say that. So you can spare people reading the application from wasting those valuable seconds.

I can't argue with what JeffE answered, but I would like to add that the reason you mentioned "I want to get a job in US" will be frowned upon by the US embassy if they knew about it, which means that they might not grant you a visa even if you were accepted by a university.

You should maybe steer clear from saying things like "I want to get a job in the US". Rather say you're passionate about computerscience and would like the experience of studying abroad to look at things from a different perspective, or to enrich your culture, etc..
There are plenty of good reasons to study aboard - but already talking about work I'd avoid ;)


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Paper got rejected, should thank original referees when sending it to another journal?
I got a paper rejected even if the associated editor and the referees liked the paper - it was more of a question of fit. Now I am sending the paper to a similar ranked journal that might be a better fit for the paper. The anonymous referee gave lots of good constructive feedback. Should I thank him in the new version? I am reluctant to it for two reasons. First, the referees or editor at the new journal might correctly infer that the paper was rejected elsewhere and that might bias them against the paper. Secondly, even if the referee was anonymous, given his tastes and comments, I am almost sure he is someone I already thanked in the paper but of course I can not be 100% certain of it.

Related: Acknowledging a reviewer from a journal from which the paper was rejected

The referees/editors of the new journal won't be biased against your paper because of your acknowledgements, because you shouldn't include any acknowledgements until the paper is accepted anyway.

@Sverre in my field, usually submitted papers display acknowledgements, the lack of acknowledgements might raise questions

I find it very strange if you're expected to include acknowledgements in the paper that goes out for review, as what you say there will pretty much reveal your identity to the reviewers.

@Sverre: in my field (economics), double-blind reviews are very rare. The referees in most journals always know the identity of the authors. Also it is impossible to implement double-blind review in practice since by just searching the title of the paper (on Gooogle) sufficies to reveal the authors' identities...

Your first concern is pretty close to the point. I really see no benefit in thanking the reviewers in a subsequent submission of the paper. It just takes you pretty close to a grey area where theoretically no harm would be done, but in practice there is often some degree of bias involved. Again, no benefit, only potential harm.

I don't see a gray area here at all.  If someone has helped improve your paper, you must acknowledge their contributions, either by co-authorship, citation, or acknowledgment.  Yes, even in the submission.  Yes, even if there is some small chance that the new referees will notice that your paper was rejected elsewhere and will let that fact unprofessionally bias their review.
Even if your submission is double-blind, you can always thank ███ █████ and ██████ ██ for their helpful comments on an earlier version of the paper.
Less forcefully: It is never a mistake to sincerely express gratitude.

even if the referee was anonymous, given his tastes and comments, I am almost sure he is someone I already thanked in the paper but of course I can not be 100% certain of it.

You are not supposed to know who the referee is.  So don't guess; just thank the anonymous referee.  There is absolutely no harm in acknowledging the same person twice, once by name and once in their role as anonymous referee.

Do you feel grateful for the reviews? Then acknowledge them, perhaps together with the reviewers of the current round. If they are supposed to be anonymous (but you can guess/know who they are), just leave them their anonymity.


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What might the editor do if my supervisor contacts a journal to claim authorship of a paper?
When I was doing my PhD project, I got an idea to solve a different but related problem. However, my supervisor said neither the motivation nor the initial result were interesting, and so he refused to offer me help on this topic. Then, I did a paper on my own with a lot of work afterwards, and submitted it to a high standard journal, and it was accepted.
My supervisor knew this, and he commanded me to add his name to the paper, otherwise he would write to the editor. I asked him what his contribution was. He had nothing to say, but insisted he had spent time to discuss the result with me.
So, if he writes to the editor, what would happen? Or if the paper has been published, then he has nothing to do with it? I am pretty much sure he can almost show nothing about the evidence of the contribution.

Possible duplicate: Should I put my supervisor as coauthor of a paper?

In fact, I am more interested in what the editor will do with this situation

For reference, in the question aeismail mentioned, the next step was a formal allegation of misconduct

Your question about the relationship with your supervisor is a separate question from what the editor might do. Separate questions in the same problem domain should be asked in a new post.

Answers to these two questions may also help you. How/when to become independent in research as a graduate student? and Advisor's/University's rights in the PhD/MSc alumni's research projects and publications.

Somewhat unrelated to the main question: Do you have emails or other written material verifying your claims that the professor indeed initially was not interested in the problem, or otherwise would indicate that he might have given up on his claim to authorship? Similarly, are there any emails implying that you might have asked for guidance from the supervisor?

"Or if the paper has been published, then he has nothing to do with it?" Not sure what this sentence means.

In other words, if the paper is under review, it is very likely that the editor would withdraw the paper if he receives a letter claiming the authorship.

"He had nothing to say, but insisted he had spent time to discuss the result with me". A warning -- this appears confused. Did he have nothing to say, or did he say something you disagreed with (that he contributed by discussing the result with you)? You need to be absolutely clear what "contribution" means in your field before you can begin to assert that your supervisor didn't do it. If running the lab as PI is seen by the editor as a contribution to every paper that comes out of the lab, that's going to inform their actions.

He said as long as it was part of the PhD thesis, the supervisor had the right for the authorship. He threatened to report it to the ethics board of the department, but he did nothing.

The short answer is that the editor will likely ask for more information from you and the adviser in response to a letter such as your adviser apparently plan to write. I doubt any action will be taken immediately and without some research if the editor is taking the task seriously.
As an editor, I would find this sort of case very difficult since I would (most likely) receive two conflicting pictures of the story. Editors have the power to take whatever action they find appropriate. Their decisions may of course be disputed and the story could go on. In a case that is relatively similar in parts (case link), an editor has turned to the Committee on Publication ethics to get support in a decision. Their case portfolio can also be of help to editors.
Obviously, following the linked case, an editor will try to have you and your adviser fix the problem yourself, it is after all primarily your problem. Hopefully the editor will come up with a plan for further actions, perhaps, as in the case, bring in a mediator and finally, if all fails, make a decision based on the existing facts that will be final. Some similar line of action seems appropriate and was also deemed appropriate by COPE. What route an editor will take may of course differ depending on the case but the aim will be to try to resolve what is right or wrong will be the aim and if all fails a suggestion on how the journal will proceed will follow.

COPE has a series of flowcharts on how to handle the most common issues : http://publicationethics.org/resources/flowcharts .  See specifically the 'if you suspect ghost, guest or gift authorship' chart and the page on 'how to spot authorship problems', and maybe the 'ethical problem' chart

Further to Ben's comment: I'd say that your advisor has burned bridges with you, which is unfortunate.  There is a lesson in this for doctoral students.  Choosing an advisor is a life-altering decision.  Personal compatibility and reputation are as important as professional reputation.
The filial obligations run in both directions: whatever you do in your field will reflect in some degree on your advisor.  It's in your advisor's interest to help you along professionally.  It is unfortunate that your advisor has chosen to take this sort of action.  He (She?) apparently wants the hit in an "A" journal.
What can the editor do?  Anything she wants to do, actually.  You don't say if the paper is in print yet.  The best case for you is that it is not in print yet.  Adding your advisor as co-author is still possible, and this whole mess can remain relatively closely held to you, your advisor and the editor.  If the paper has appeared already, the editor could do anything from withdrawing the paper (very bad, as that action reeks of plagiarism or other academic dishonesty) to issuing a corrigendum note (not as bad as withdrawing the paper, but bad).  In the short run, the best case for you would be for the editor to do nothing.  I'm not sure that is in your long-run best interest, however.
What should you do?  Someone has to be the bigger, better person.  Your advisor has already (to the extent that your version of the story reflects the actual history) revealed him(her?)self to be a rather petty person.  I'd say to add your advisor as co-author.  The power dynamics are pretty asymmetric here and you are on the weak side.  Unless you care to go to your University's research ethics system with a complaint (and you'd better have irrefutable proof the situation is precisely as you say if you choose this route) and ruin your advisor's career, there isn't much you can do.  Whistleblowers often do not fare well.

To me this is awful advise. You should not put someone as a coauthor of your paper to "be the bigger person". Publishing a paper with non-contributing authors is also misconduct by those contributing authors who let it happen.

The case is far from as clear-cut as you suggest.  Picking one's battles is important, and I see enough gray in this that it is a battle worth avoiding.  If the case is exactly as presented, then maybe it's a battle worth fighting.  Maybe.  When I look at the upside and downside risks, I'm not certain.  To expand a bit, we do not know what form the "negative comments" took.  If they were detailed comments about why it was not interesting and what would be interesting, then perhaps the advisor feels a substantive contribution was made.

I fail to see any gray area here. The way this has been described, the advisor is as close to having made a negative contribution to this paper as is possible.


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Is the Cambridge Certificate of English accepted in US?
According to CEF, CAE and CPE are the highest level possible. If I apply to some top US university/college, will they accept a certificate from Cambridge instead of TOEFL?

You should read the minimum requirements of the program at the university to which you are applying. Some universities only accept TOEFL, some other only accept IELTS, some universities accept both of these, and some universities accept those certificates like FCE, CAE or CPE as well as TOEFL or IELTS. (Some other universities also accept the English tests which are designed by themselves.)
I have seen some tables in which the minimum scores of each test is mentioned. For instance a university may accept a 7.0 of IELTS, 100 iBT (internet based TOEFL) and an A of FCE.
So the only advice I can give you is to check the minimum English language requirements of the university and the program you are applying.

Seconded. And even if the university does not state it at the web page, it does not hurt to ask. If you have a very good result at your test, they may make an exception if it is clear that your request is about saving the money for another test rather than circumventing the requirement that you speak and write English well.


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Is there any difference between one-year MScs and two-years MScs?
I am currently intending to apply for a master degree in Health/Clinical Psychology. I would like to ask if there is any difference in terms of qualification between an one-year MSc and a two-year one, that is, if they are recognised as of same value in any possible field of application. If not then what are the differences between them?

I am not sure about your field, and it also probably varies by university, but generally one year MScs are just course based, professional degrees that offer little to no funding (Meaning you pay out of pocket). Two year degrees, on the other hand, generally are thesis based degrees, are often funded (not as often as PhDs). Sometimes 2 year MScs are also course based, but I would look at credit requirements. Some schools offer programs where you can do the equivalent of a 2 year program in 1 year (non thesis based).
In my field, Earth Sciences, a 1 year or 2 year non thesis based MSc is generally reserved for people who want to teach in High school (USA) or their company wants them to brush up on some new techniques in the field. Those who want to go on to a PhD program, or, get a high paying industry job (in oil/gas) tend to do thesis based degrees to be competitive.
So more credits = better degree. Thesis = better degree. In general, of course.