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Strategy for revealing pregnancy to new department/department chair
I am a new tenure-track assistant professor who is expecting a baby in January (just after spring semester starts). I will be arriving on campus in the next couple of weeks and need to tell my department chair I am pregnant quite soon, as the teaching assignments for spring classes will be made shortly.
I am assuming that I will not get any leave and I will need to teach my spring class, either in person or online. This is because I am in the US, and FMLA (Family and Medical Leave Act) protections don't apply until one has been employed for a year and the university doesn't offer anything beyond what is required by FMLA.
My current strategy is to shoot the chair an email mentioning that I am on campus now and that I hope we can meet before the semester starts. During the meeting I plan to be straightforward and tell her I am expecting. I will tell her I am hoping to stop my tenure clock for a year and ask her to strategize with me on how to meet my teaching obligation in the spring, given that I will be due around the second week of classes.
What are the most important considerations when having this type of conversation with my chair? My main concern is my reputation in the department. I don't want to make a bad first impression, and I worry that some people might perceive this  unexpected turn of events negatively.
Update: I took the advice here and met with the chair about a week after I got to campus. I emphasized my commitment to my various projects and my plan for not losing momentum. She took everything in stride. Although I didn’t get a teaching release, she arranged for me to teach an online class where most of the work happens in the second half of the quarter in order to meet my teaching obligations during the quarter when I gave birth. This put me back to work at about 4 weeks postpartum, but I could do it all from home. Ultimately, I still tried to forefront my work in work conversations. I don’t think that the pregnancy affected my reputation in the department.

Check your faculty handbook. It may specify how pregnancies are treated.

I did find this article "The strange duality of being a pregnant professor" but the author didn't specify much about how she handled revealing this information, just the order in which she did. https://tenureshewrote.wordpress.com/2014/11/24/the-strange-duality-of-being-a-pregnant-professor/

Faculty handbook says they follow FMLA (i.e. unpaid leave kicks in after 1 year). There is a committee to revise the handbook to be more accommodating, but I am not sure how much support that has and if the new policy will be in place for me.

I'll just add a point you may use to your advantage: if you end up starting to teach the spring class, do it for two weeks, then another person has to take over for some time, then you are back again, it makes the class more disorganised for the students and involves extra workload for both the other person and you. "Caring about the students" is never a bad look.

"I am assuming that I will not get any leave and I will need to teach my spring class" - the US never ceases to amaze me.  In the UK you must get between 26 and 52 weeks Statutory Maternity Leave starting up to 11 weeks before your due date.  In UK academia this would be on full pay.  Other European countries tend to be more generous with their statutory maternity pay rules.

@Jack: No.  The right to leave is immediate.  The right to SMP takes six months - but if you don't qualify for SMP you get Maternity Allowance (which is the same amount) instead - it's just paid by the DWP rather than the employer.

Re: what the faculty handbook says, my department is more flexible than the rules written there on family leave, and they would try to provide paid leave or full salary with reduced duties even if you just arrived.  So talk to your chair, and the sooner the better.

My college's policies were also more generous than what was in the faculty handbook (until we got the handbook updated).

Congratulations!

@MartinBonner People who think employers should pay people for not working for extended periods of time (through no fault of the employer) never cease to amaze me, so we're even. =p Being generous with someone else's money isn't being generous at all.

Any chance you could update with the path you took, and the results garnered ? And I'm hoping congratulations were in order.

I don't think that when and how you reveal your pregnancy (as long as its professional) will have much impact on your career, especially compared to the fact of being pregnant and having another child.
I would advise meeting with the department head as soon as possible and reiterating your long-term commitment to the department. You two have the same long-term goal: your being a successful assistant professor and earning tenure. It is in your department head's interest to be helpful to you.
Before going into the meeting, I would decide what I wanted. You mention wanting to stop your tenure clock for a year. Do you want an unpaid leave if possible? While it is good to be flexible, it is also good to know and communicate what your best outcome would be, in case they can accommodate you.
One outside-the-box solution might be if you could defer the start of your assistant professorship for a year and teach your fall course(s) as an adjunct.
If you have started thinking about grant applications or other things of interest to the department head, it would be fine to also talk about those at the meeting.
Good luck!

It sounds as if OP may have already talked to HR (human resource/insurance, etc) but I also urge to find the right person to talk to there (in person might be best). HR has likely worked through the permutations of the guidelines to make things work  for numerous faculty and staff already (and there may be some local common practices not spelled out precisely or examples of work-arounds that worked in another department that her chair is unaware of). If she has only been relying on reading and interpreting the HR related documents herself, an in-person chat can be helpful.

Thanks! This is helpful context. I can certainly start the meeting by talking about other positives and have some statements in my back pocket regarding commitment/excitement.


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I do not want my research presentation to be recorded: what's the proper etiquette?
I've been invited to present a talk at another university on a topic of my choice, and I have decided to share the literature review section of the paper I'm working on and haven't published yet. Wondering if it is okay to ask the organizers not to record my presentation? What's the right way to approach this situation? The lit review has strong hints about my research question, and I am worried about potential plagiarism since I have been burned before when I openly shared too many details about my research ideas. Should I hold back on sharing the niche I've identified in the literature since I haven't published the paper yet? So conflicted.

You tell the organizers you don't want your presentation to be recorded. That's about it. I've attended talks where the speaker said "these results are preliminary, please do not share" which is similar.
Although in your case I wonder why you are giving a presentation in the first place, if you don't want other people to know what your research question is. Like, what are you going to say in the presentation if you are not going to discuss your research question? Are you hoping to make your presentation so arcane that the audience cannot remember what you are doing? It doesn't make sense. You might just want to decline the invitation.

Yes, the not-recording request is easy, and surely granted. But people can take notes ... gasp... on paper, etc. Probably one cannot score the CV-padding "has given a talk" without imparting some information to other people.

Where there is an audience, there will be some recording. If not a full recording, there will be some who take photographs, voice notes, screenshots and the like. The organizers can never guarantee against these. You can only request them and hope the audience acts in good faith.
Crucially, you are allowed to choose the topic of choice, so why not choose something else? Also, a talk based on literature review alone does sound a little unappealing, although this might be field-specific.
It seems to make more sense to instead talk about something you've already published, give some insights into it that aren't already there in the paper, maybe show its connection with the evolving state of the field, etc.

Thank you, this was helpful. I'm a graduate student, and this will be a talk among fellow grads where we have the liberty to present our research at whatever stage it currently is.

Ah, thanks for sharing that. Your supervisor might possibly be able to help  refine what you share too.

source: Stack Exchange

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How to express about getting informed about a specific position
I am going to prepare a cover letter for postdoc position. I was informed about this position by my Phd advisor. I am looking for a proper statement about how I was informed about such that position, which must be express usually at the initial paragraph of a cover letter. May you please tell me how would be a good statement for this type of info.

Why do you have to express this in the letter?

I don't see any reason to express where you learned about a job advertisement, except if it was emailed personally to from whoever you learned about it, and not widely distributed. However, usually these are mass emails sent to a large number of people (recognizable by several factors). In that sense, I don't see any reason why you would need to state how you learned about the position - unless you want to make a point out of it, i.e. make it clear to Prof. X who advertised the job that their good friend Prof. Y (or maybe the very famous Prof. Z) suggested to you personally that you should apply, which hopefully reflects positively on you in the eyes of Prof. X.

Don't include 'who is a good friend of yours'. If Prof X is my friend, I don't need to be reminded. If Prof X isn't someone I regard as 'a good friend', this just sounds weird.

@avid That's why I said "indicating" - my point is that the OP maybe wants to indicate what I say in the quote. Not write this literally. And indeed, the square bracket part was meant not to be written in the letter by any means. I assumed this to be clear to anyone reasonable. (I mean ... seriously?)

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About sending email for postdocs after finding a potential mentor
Two weeks ago one of my emails was replied by a professor who expressed his interests in my work and consider me as a potential postdoc. He told me that he is going to apply for funding then will inform me.
At this moment, I do not know whether I keep sending emails to other professors for postdoc position or wait for email from potential mentor?

I recommend that you keep all your options open up until you have something firm. There are too many things that could go wrong for you to make assumptions that you "have" a position. Interest was expressed. Action was promised. A contract was not offered.
Don't mislead people, of course, but don't drop your other efforts.


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How will be determined the format of manuscript before submission to journal?
I would like to submit my paper to a math journal. In the section of instructions for authors there is the following statement which I am confused of its meaning, may you please help me to sort out of that.

The manuscript should be in final form; once "communicated'', little change will be allowed.

Does it mean that I must write my paper in the final format of journal  before submission?

I'd understand the quoted sentence as referring to the paper's content, not the format. (But check the rest of the instructions for anything about format.)

Usually, the journal's typesetters will get your manuscript into that "final form", so you don't have to do it yourself.
The sentence is saying that you should have all your content finalized before submission. Once the paper is communicated, you can't make any more changes.


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How many papers will be expected to be published as a postdoc?
I have recently applied for a postdoc call with financial support from goverenment not from a mentor for a specific project. In the application from there was a table to write about number of publications. I want to know about the normal range of number of expected papers to be published? In the field of Pure Mathematics and Mathematical physics. The period of postdoc is 3 years.

In my opinion the expected number depends on factors like how many collaborations you have, i.e. the expected number of single authored papers is lower than the one for papers with coauthors. Moreover, I also have the impression that the publication culture differs between different areas of pure mathematics.

Just to check, you’re sure this is asking about papers you propose to write during the postdoc and not hour current papers?  I’ve never seen the former, though I suppose it’s possible with the direction administrators are going.

I agree with @NoahSnyder ... the application form would ask about papers already written.

Even within pure math, a "paper" is a very variable unit of work. I've got one publication which took maybe 5h of my time and was published within 5 months of me starting to work on it; and I've got one where my estimate is that I spend around 1000h over a 10 year period on it. Length-wise, I've got something with 3 pages and something with over 100.
With the disclaimer out of the way, the number that came to my mind when reading your question is approximately 5 papers. That seems to me as the ballpark for how many papers you can actively/reliablishly plan for in a 3 years period without committing to any salami slicing. But a concrete project may have different predictions going along with it.


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Should I attach CV to my first email for a postdoc position?
I am going to send an email to a professor asking about her support for a postdoc position. I just want to know whether I attach my CV to my first email or it is better to wait for her feedback on my email and then send CV?

If you know they have a position, then yes. Otherwise it might be better to send a short note that is easy to reply to asking if they might have a position and offering to send any required information including a CV, etc.
This is a personal position, of course. I'd be more likely to respond to a short request and less likely to open or consider one that "floods the zone", unless I've advertised for candidates.
Your short note can just indicate your specialty in math and doctoral institution and date of degree. But even that is superfluous until you know they have a position.


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Rejection of papers
I have already submitted a math paper to an outstanding journal. How much percent is probably my paper rejected after 7 months being under review?
During this time the date of status has been changed without changing the status "under review"?

Have you talked to your coauthors or supervisors about this?

Once my supervisor told me the average time is 6 month, but now is more than average

7 > 6, quite right.

This is really impossible to say. It could be anything, as you don't know the reason for what you perceive as a long delay. Depending on the subject, it may have taken a while to find suitable reviewers. The reviewers, once found, might be busy with other obligations. They may be very carefully reviewing your paper and constructing advice for its improvement. The editor may have been displeased with one of the reviews and sent it to someone else. Lots of possibilities.
Hearing back especially quickly, usually means rejection, not this sort of thing. You will know when you know and not sooner. You can ask the editor, of course, how things are going and may or may not get a reply.
Even knowing the average time that a paper is under review is little help as the variation is quite large. Patience is advised.


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PhD research results in postdoc talk presentation
I am a PhD candidate and have been invited to visit two labs where I had applied for postdoc positions after initial online interviews. My question is regarding the content of my talk, which I think should include my PhD research questions as well as a big picture of my research interest. I was wondering about the following:

I am still working on getting results with respect to an important question before my final defense. Should I include that as ongoing work in the slides and mention that this question is being currently worked on?

Because this would be a significant contribution, however I don't have the results yet. Does that leave an awful impression since my results are still incomplete and it can leave the audience to wonder if and when I will get those results? I do have results on the other questions I have addressed.

Is it recommended that I have some idea about how my skills/ interests would tie with the research interest at the lab and include that in the talk?

Probably nobody's research is ever complete: it is always work in progress to some extent.Your audience are not there to hear your final conclusions. What they want to know is whether you, your skills, your research experience, your research attitudes are in line with their own organisation.
So, talk about 2 with examples from your own research.

Yes, it is good if you can tie your research interests with those of the lab. If you are hired you will be working, at least in part, on their goals, not just your own. This can depend on the nature of the position, of course.
And yes, it is great that you have uncompleted work in progress. The opposite can sometimes give the impression that you've done all you are capable of and don't have additional ideas. A new PhD is in a really good position if she or he can carry away ideas, partially developed, that will lead to future publications. This is especially true, for someone who wants an academic career, if those ideas can be passed on to future students who will also help advance the work.


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Is it self-plagiarism to reuse sources?
I've taken two classes in a row that require research papers to be written as an assignment, and since the second one has had a similar criteria for which topics are allowed, I decided to continue researching the same topic. However, after checking with the school's plagiarism checker, it flagged me for roughly half of my 2nd paper's sources being reused. Is this something I should be concerned about? The rest of the paper is completely original and not copy-pasted from my first one at all, plus all of my sources are cited correctly.

I don't see why self-plagiarism should be an issue dealing with exercises. You are not a researcher submitting to a peer reviewed journal instead of being a student whose work should be evaluated by teachers not peers, and possibly not only by automated process. And perfectly with a real interaction. I always smile when students are concerned with self-plagiarism. Go discuss with the instructors. Ok now I see sevensevens Answer. Plus 1.

In general, no (and how did you get access to your school's plagiarism checker)
If the papers are related they should share sources.  From a published peer-reviewed standpoint, I'd bet several papers reuse half their sources.
This sounds like a paper for a grade though.  In which case you actually have a 3rd option.  Talk to the professor or TA.  Bring the first paper and this paper with you and let them make a decision.  Assuming you didn't plagiarize, they'll see the content is different.
Remember, part of taking a university course is to learn how to write papers with novel ideas.  The professor and TAs are there to help you learn how to present your ideas without plagiarizing sources.  Especially coming before the paper is due shows a good-faith effort.

This is a paper submitted via blackboard, and before we are allowed to fully submit the paper, it has to go through a plagiarism checker called SafeAssign where it marks every possible instance of plagiarism for you to review before submitting the final version.
Also thanks for the advice, I'll go talk to him tomorrow then. The works cited page(s) were the only spots that actually really got flagged hard, the rest was relatively okay

@Nimbus125 - don't forget to tell us how it turned out.

the professor said it would be fine, thanks for the advice!

Self plagiarism is reusing your old work and representing it as new. You avoid it by citing the old work within the new, just as you would the work of any other author.
If I read your question correctly, you copied something like the bibliography of the old work, and maybe a section on "prior work" into the new paper from the old. The checker looked for identical sections of text and found these.
I don't actually see much of an issue with that, actually. There is a principle that applies and it shows up a lot in math and sometimes in CS. Often there is only one way to correctly say something. In math, the definition of the derivative is pretty standardized, for example, so every book and paper that repeats it has essentially the same text. A bibliography is like that. It uses a standard format and ordering and the items in it have a standard form. So two papers on the same topic will have large overlapping areas of the bibliography. That doesn't mean they are plagiarized.
A section on prior work might be a bit more problematic. You can avoid a charge of self plagiarism if you just state in the new paper that the prior work is the same as for the previous one and is repeated here only for the reader's convenience. Since there is a citation to the old work, there is no self plagiarism. But an automated plagiarism checker will probably still flag it.
The reason to avoid self plagiarism is that a reader of the new work wants a complete context of the ideas presented. The old paper establishes a certain relevant context with its citations and bibliography and if the new work doesn't point to the old one then the reader might miss that important context. So, we cite, letting the reader go back for more context as needed. But nothing you describe here seems to indicate an issue with this, as long as your new paper cites the old one.
Keep all of this in mind and be prepared to use it if you go see your professor as sevensevens suggests. At the most, you might have to make some minor changes to the text and add a citation or two for clarity. But make it the professor, not the TA, you speak to. Oddly, the professor will probably be less pedantic about such things and is the final authority over what you are permitted.

A final note: Often rephrasing something you wrote earlier to avoid automated checking is worse than just copying it and giving a citation. This is because it can seem to imply an intent to disguise. Copying large sections is probably not a good practice, but if it makes things clearer to a reader it may be better for shorter passages. But give the citation and state that the section is "repeated for convenience of the reader". Then it is clear.


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My name was added to manuscript as co-author without my consent; how to get it removed?
My name has been included in a paper submitted to a peer-reviewed journal without my consent, however I did not contributed anything to it. The corresponding author, a former colleague of mine, ignores my request to be removed off of the author list. According to the trace of the communications I have received, the paper is under review now. Thus, how can I professionally deal with this case to get my name removed?

I do agree with Bryan Krause answer. Butt insist on your colleague, it should work else the situation is indeed bizarre. Be polite, It might be that the other side did not think much and is convinced to make you a favour. Be firm but polite, say you are open for future collaboration, for instance.

Yes, it is definitely unprofessional and unethical to include someone as an author when they do not agree to be one.
If you have contacted the corresponding author and asked to have your name removed, and they refuse or ignore the request, all you have left to do is contact the editor.
Simply say that you have come to understand that your name was included as an author on a paper submitted by (corresponding author), that you did not participate in the work, and that you would not like your name associated with the publication.
That's it. No need to make further accusations or statements, that should be enough information for the editor to act. If it's a reputable journal, they'll realize how wrong this all is.

And if it isn't a reputable journal, you can wait for it to be published and then send them a DMCA takedown request.

If you didn't contribute to the paper in any way, presumably you don't hold any ownership of the copyright, and therefore have no basis to submit a DMCA takedown request, which would require you to state under penalty of perjury that you are the copyright owner or an authorized representative of the copyright owner. The DMCA is intended to handle copyright issues, not "my name is on this and it shouldn't be."

@ZachLipton If your name's on the paper, though, it's listing you as one of the copyright holders.

How does the journal verify the identity of the OP? If it's as simple as sending an e-mail, what's to prevent someone from sabotaging researchers by pretending to be them and asking journals to remove them from the author list?

@vsv The editor could just send a confirmatory email to the non-author's institutional email address.

@nick012000 That's not how copyright works.

@Sneftel Isn't it? I'm pretty sure that copyright holders are allowed to give their copyright to others, which is what falsely listing someone as an author amounts to, IMO, though I'm not a lawyer. Feel free to ask a Question about it on the Law SE if you want, though.

At least in Germany, the right to disassociate your name from one of your works is part of the moral rights that are automatically granted as part of creatorship. One would hope that the same right applies even more so to works you didn't even create.

@nick012000 Assignment of copyright is done explicitly, not through putting a name on an author list. As Jorg alluded to, you may be thinking of "moral rights", but those cannot be assigned. Moral rights are held by the actual creator of the work, though. If someone's reputation was injured by someone else falsely claiming that the first person authored the work, that would be libel, not copyright violation.

@JörgWMittag : It's not just about moral rights. In Germany, for being associated with certain political beliefs, you can literally end up in prison. Therefore a method has to exist to prevent someone from being tricked (or faked) into publishing something illegal.


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Received comments from reviewers with major revision. Is it worth pursuing?
I recently received the reviewer comments for the work submitted to a decent journal. In the comments, the reviewers advised me to revise the manuscript. The editor noted that "If you are prepared to undertake the work required, I would be pleased to reconsider my decision."
One of the three reviewers commented that a stronger experimental validation is required before the paper could be considered for publication. My thesis is only related to modeling of an experimental process and the requested experiments cannot be carried out at this stage. I have validated my simulation results with published experiments, so I am not sure why the reviewer has asked me to do experiments.
Other two reviewers have given major revisions pertaining to my modeling which I can confidently respond through some additional simulations.
My question is that if I don't carry out the work asked by the first reviewer and address the comments of the other two, will my paper be rejected for not addressing all the reviewers? In that case, is it even worth pursuing?

The editor will decide based on their personal values and the traditions of the journal.  Internet strangers cannot help you, especially if we do not know which journal it is.

@AnonymousPhysicist But is it possible for a journal editor to accept a paper if one out of the three reviewers has rejected the manuscript?

@arbiterary: In general, editors can do whatever they want - they can accept a paper even if every reviewer recommended rejection.  (For a reputable journal, this will happen very rarely and only with good reason.)  In your case, you should ask the editor for clarification.

If doing that experiment is something you would like to do next, then indicate so. If you can't do the experiment or don't want to, that is fine too, indicate the reasons and rationale why, the pros and cons. Repeating the experiments only strengthens your paper. Whether that increased bar is required is up to the editor.

I've had a similar comment on my papers.  A reviewer wanted to see actual experimental results although my work was theoretical, and the experiments would only cover a case that I have already covered theoretically.  I argued but the paper got rejected.  Unfortunately, there are reviewers who only appreciate their way of doing things, and nowadays many editors are just 'robots' who click a button when all reviewers said yes.   Fortunately, the rejection was a blessing in disguise as the paper landed in a much better journal.

As the comments point out, this is up to the editor. Nothing gets published without the editor's consent, and nothing gets rejected without the editor's approval either. Reviewers can say X, but it's ultimately just a recommendation that the editor can ignore.
In your case the editor said "If you are prepared to undertake the work required, I would be pleased to reconsider my decision." I recognize this phrase because it's the default one given by Editorial Manager every time the editor makes a decision (editors can edit the default email of course, but often don't). In other words, the editor for whatever reason has not expressed an opinion. This means there's still every chance your paper is accepted, and you might as well make the case for acceptance by revising it.
That said, you should address why the first reviewer's comments are not applicable. Give your reasons why the experiments can't be performed ("cannot be carried out at this stage" is not convincing). Based on your description I'd certainly stress that you are modelling an experimental process and you've already compared to published experiments; you could also say that doing the experiments yourself would require resources & time & expertise that you don't have (assuming it's true, of course). If you can't convince the reviewer, you might still convince the editor, who can after all see the other two reviewers' comments.


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How should a job market candidate leverage his or her network?
I am a job market candidate who has really “worked” conferences for the past 4 years. Now when I go to conferences, I find it easy to have coffee with a variety of junior (and some senior) professors in my field from other universities. I get invited to their dinners. I chat with them easily at the cocktail hours. Now that I am on the job market, I am not sure how to use those contacts to their fullest potential.
I mentioned this to my chair (whose work is in a different subfield than mine is), and he said I should not contact my network about potential jobs at any particular university because I would sound too “desperate”. This strikes me as incorrect, or at least incomplete, advice.
Should I let proactively let people in my network know that I am on the market? If so, what is a good strategy for emailing people in my network and letting them know I am on the job market? (Do I send around my job market paper and CV? A link to my website?) Is there anyone I should not email?

I should not contact my network about potential jobs at any particular university because I would sound too “desperate”.

Oh, please. Your chair probably remembers the Good Old Days when you could submit three applications with your one publication "in progress" and get two interviews and four offers.
Yes, of course you should contact people in your professional network.  The academic job search is no time for shyness or modesty. You need to sell yourself. You need other people to sell you.

Ask them if their departments are planning to hire, and if so, what their hiring priorities are. (And no, you cannot get this information from the text of their ad.)
Ask some of them to write recommendation letters on your behalf.  At least in computer science, you must have at least one reference letter, preferrably more, from someone who is not from your home institution and not a coauthor, but who can still write in detail about the quality, depth, originality, and impact of your work. Congratulations, you've cultivated the perfect environment to find such people.
Write them to let them know you've applied, and ask them (directly, shamelessly) to put in a good word with their hiring committee.  You will not get an offer from any department, and you may not even get an interview, without a local champion inside that department; the champion doesn't have to know you personally, but it certainly helps.  (Of course, a better way to cultivate a champion is to knock your interview out of the park.)
Always thank people for any information or help, even if they just say "Sorry, we're not hiring in your field this year." or "Good luck!"

You have correctly guessed the generation of this advisor. Given the generational gap, do I need to be careful about which senior professors I email?

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What might be a "compelling" reason for applying to defend my ph.d. degree remotely?
I'm going to defend my dissertation soon and the school has a strict requirement for allowing remote defense. Under highly unusual circumstances they'll approve a remote defense, and they said convenience is not enough for justification, but "travel restrictions" are.
Right now I am out of the country and to be honest, the true reason why I want to apply for a remote defense are:
a) The flight ticket is extremely expensive and with great uncertainty, last time it took me some 5k USD to fly back to my home country (it's the lowest price I can get in 6 months), not to mention that required quarantine took me another 2k. Now it might be even more expensive considering that it's going to be a round trip, I probably need to budget of 20k or higher this time for just a round trip since there's aggregated quarantine requirement to get back to my country.
b) The flight might be canceled for no reason and it's not a random thing. As far as I know, they have canceled more than half the number of the planned flight this year. No one can guarantee that I can fly to the school nor back.
c) There's no guarantee that I can get back once I finished my defense. Say, if I get infected by COVID, I will have to wait for another 6 months before I can get back to my country, according to its policy. No exceptions are allowed. This will be another huge money issue, plus, if I get a job in my country I would not be able to return to my country and meet the job requirement on time, given a quarantine requirement of at least 28 days.
I don't know if the money issue sounds compelling but I guess that's not the one that will make the graduate school easily say yes? I don't know.
Things are changing as of COVID policies and my country has a really strict one. I really don't want to take the risk and do something that is foreseeable of low probability. I'm not sure if the school cares about whether I can get back to my country or how expensive and difficult the whole procedure is going to be.
Any suggestions?
Many thanks in advance.

What countries are involved here? These restrictions seem very onerous at this point in time.

@AzorAhai-him- 28 days of quarantine and these flight costs makes it likely that China is one of the countries.

You can request a remote defense, but the decision as to whether your reasons are sufficiently compelling is up to your institution.  We're in no position to predict what decision they might make.

@AzorAhai A small number of jurisdictions (mainland China, Hong Kong, Taiwan and Tonga) still have zero-COVID policies or did so in the last few months. In any case, I would think that a one-in-100-year pandemic qualifies as “highly unusual circumstances”.

I think it can depend how you choose your wording. If you say 'I have these reasons how compelling do you think they are?', you're less likely to succeed than if you say 'I am not able to attend my PhD defence in person because of COVID-19 travel restrictions from my home country of X'. Then if they ask what the restrictions are (they might not), pick two or three of the most compelling ones, and word them in a strong way (my country requires Y, which means I am not able to attend my defence in person)

I think you need to be making this case to your examination board and not to random strangers on the internet.  There's nothing we can do to change the policies at your institution - all you can do is make your case and ask them.  Either they will agree or they won't.

The flight ticket is extremely expensive

A reasonable person would consider that a compelling reason.

Plus the whole Covid thing and a general major shift in the perception of virtual meetings. Sounds like the university needs to change its policy.

@JonCuster I got back to my home country when the school was doing online courses and now everybody's back to on-campus mode so…… personally I agree the university should be more lenient but I guess they really don't care about the COVID thing (at least not as much as my country policy cares).

Not to mention the quarantine.

@Katie I would not assume "don't care about COVID" when "haven't updated the official policy" is a possible explanation. Occams razor and university bureaucracy and all. Who wants to make a big push in a committee to change a written policy when all they have to do is apply the existing subjectivity in the policy?

@BryanKrause Hanlon's razor also comes to mind:  "Never attribute to malice that which can be attributed to stupidity" (or institutional inertia, or incompetence).  Academic institutions are large ships which turn only very slowly.

It took my company two years of Covid to go from ‘here is the policy’ which changed to a new policy about twice, to ‘here is a graded approach’ we can apply without issuing a brand new policy if things change. Slow indeed…

@BryanKrause with changing government requirements and institutional inertia it's more surprising when things are updated promptly than when they aren't.  We're in a state of flux here too

While the answer is true, a university bureaucracy isn't a person, and can't be guaranteed to be reasonable.  You ave to work (with) the system to ensure that your request is considered by a reasonable person.  Also the multiple risks (covid itself, but also the risk of cancellation and disruption to the examiners and everyone else) may be a more compelling factor

You can only ask and learn, but I'd think that the combination of cost and COVID (including the lack of social distancing in air travel) goes beyond questions of "convenience".
If the defense is a few months away, then there is a certain amount of uncertainty that the best plans can actually be executed. There is a new variant sweeping the Earth at the moment.
You give good reasons in your post, but it is the department/university that makes the rules. It is worth asking. And it is worth getting your advisor to support you.

That's a good point. In fact, the school asks us to apply for a remote defense at least 14 days before the defense, so I still got some time. But here's the ambivalent situation that I don't want to apply too early to make them say "you got time and you should come", but then if they says no to my request 14 days before the defense,  I will have to pay for some 50k for the flight then.

@Katie I'd recommend figuring things out with them as soon as possible, rather than trying to play a game of  "chicken" where you raise the potential costs to yourself in hopes that they don't want to commit you to those costs. The aphorism "poor planning on your part doesn't constitute an emergency on mine" comes to mind.

@BryanKrause I think you are right. I should talk to them asap and figure out if they allow it or not.

@Katie Talk to your advisor first, if you haven't already.

can only second the advice to talk to your advisor - depending on who they are, they can have a huge amount of institutional clout, and can convince people that your request is reasonable (and it seems to be)

Minor note: the variant (Omicron) is new to OPs country (China) but its already infected most of the rest of the world. So its only sweeping through China.

@JonathanReez I assumed when I read this that Buffy was alluding to the Pi variant.

All your reasons are compelling. There are clearly major travel restrictions in place, and your reasons are not just a matter of simple convenience.
The pandemic counts as "highly unusual" circumstances. And in addition, your country has much stronger restrictions than most other countries, which make your circumstances "highly unusual" even within the pandemic.

Completely agree. Each of these reasons demonstrate a rather significant burden that's vastly disproportionate to the benefits of defending in person. Even more so when you combine them all. Most of these types of rules are intended to prevent people from defending remotely when they could reasonably do it in person with minimal additional effort. That's not at all the case here.

Your reasons seem perfectly valid to me (and most of the others here). However, the wording of your question and your reasons makes most of it sound like convenience ("oh, it's so expensive", "I might not be back in time for a new job").
Then, at the end of paragraph a and c, you mention quarantine. Short of not being allowed to travel at all, that's a really strong restriction. Put that first! Mention the details like duration and the fact that you cannot "home quarantine". Most of the things you put as your reasons (the cost for a ticket and quarantine, the number of cancelled flights, the personal impacts) are direct or indirect consequences of those restrictions and should be phrased as such.
Mention what happens if you get infected, but put that last, as it's only a possibility, while quarantine is apparently mandatory.
Don't expect the university to know those things already. You don't say where the university is located (US?), but here in Germany, COVID-related rules have become so complicated, I'm not even up to date with the local rules, let alone the rules related to travel to / from a random country.

It's worth pointing out that defending a dissertation is a [rite of passage] for completing a Ph.D. For many programs it's one of two rites of passage: (1) qualifying exam and (2) dissertation defense. The members of your committee went through these rites of passage themselves and suffered to make it through. They will naturally want to resist making it any easier for you to earn a Ph.D. than it was for them.
It's unclear from the original question what your long term plan is. Would you ever return to the country of your graduate school? Expensive airfare seems like an argument in your favor, but it may not be enough to sway your committee/graduate school. Maybe some other particulars of your situation would be enough to convince them:

You're working serving the poor and it pays little or nothing and it would be too expensive to fly back
You're doing some exciting research in your field, but it pays little or nothing and it would be too expensive to fly back.
You have some life threatening illness and the risk of being at the mercy of quarantine rules is too great.
You have a pre-existing condition and the risk of contracting Covid during travel is too great.


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Job applications and visible health condition
I would like to ask what the best way to proceed could be when submitting job applications given my health conditions: currently a postdoc in physics, I am affected by essential tremor (ET), the most common movement disorder, that in my case amounts to shaky hands and arms and probably affects voice also. The problem is greatly amplified by stress and nerves, while when I am calm basically I look completely normal. You can easily imagine how this caused me to battle with non-motor psychological consequences revolving around the anxiety and embarrassment that such a problem causes.
Given that I cannot avoid appearing scared during a job interview due to the aforementioned health problem even though I am as nervous as anyone else, and in view of the bias against lack of confidence and communication skills, that are inevitably damaged by ET, I feel like no one could take my application seriously without knowing in advance what I am battling with and trying to filter out the appearance to focus on the substance of what I say only.
Should I disclose the problem prior to applying to a position? Are there inclusive policies in universities or related scientific facilities that give me a fair chance of getting a job? I feel a bit dizzy thinking about my future, considering also that my tremors can only get worse with time (I am only 27).
Thanks in advance!

If you are already a postdoc, how did you deal with this problem the first time around? What makes you think it would be different next time? Anyway, in many countries there are laws which make it illegal to discriminate against people with disabilities when hiring. In the UK, for example, the vast majority of employers will ask you to voluntarily disclose information about your disability when applying. I suppose this is partly for statistical purposes and partly so they can make any necessary accommodations during interviews.

Is your condition and/or ET a recognized disability?

Thanks for the answers! At the moment the problem is quite manageable, especially after I started to take medication to control it, so it definitely isn't a significant source of disability now, far from it. My job interview took place online during covid, so that helped release some stress, but I have also done things in person.

Currently, my main concern is a more subtle one, namely that an unaware recruiter would misunderstand an occurence of shaky hands and/or voice during a stressful activity such as a job interview and as a result discard my application because he doesn't know I can't help but look way more anxious and terrified than I actually am. In summary, it is luckily far from being that bad to be called a disability, but at the same time it impairs my ability to behave perfectly normally under stressful circumstances (trust me, losing control of your hands under stress is anything but pleasant).

You might consider asking this question on Workplace.SE to get a broader perspective on the issue.

In general, I think you should directly address the issue at the interview stage (not at the application stage) in a casual way. I say this because I have a bit of a condition where my neck becomes very red and blotchy when I have too much adrenaline/am stressed. This has concerned interviewers in the past because they think I am having some sort of allergic reaction. I bring it up now because it is much more awkward when they bring it up first.
To address the issue casually, I would say (or perhaps pre-email) something like, "I want to give you a heads up that I have an essential tremor condition. It is usually not noticeable but it can act up when I get a burst of adrenaline - which sometimes happens in exciting situations like an interview. You'll notice my arms shaking, but its not anything to worry about." Here, you will notice that I talk about adrenaline and excitement, not stress or nervousness. I have found this phrasing has a more positive connotation.

At least in Europe, many universities start asking about health conditions already during the submission stage. I understand that this is more targeted towards more impactful disabilities which may require special care or fall under a legally protected class, but I would probably bring it up there already.
Additionally, what I would do is email the chair shortly before the interviews and inform them (in a very curt manner) about your condition. Your goal is not to make this seem like a big deal (it isn't), but to clarify upfront (before a narrative can form in the heads of people). The tone I would go for is similar to how I would inform them about allergies in preparation of joint lunches / dinner - it's an FYI first and foremost, not an apology.

I think that there is limited harm in being upfront. Ultimately this is something that you have to deal with daily and you can choose how open to be about it. If letting people know why your hands shake makes you feel more secure or confident, then go for it. Depending on where you are, you probably have some legal protections either way. As long as you have documentation supporting your diagnosis, it should not negatively impact your job search. More importantly, you presumably want to work in an environment that is supportive and accommodates you willingly. Being upfront prevents any misinterpretation or bias (which you are worried about) and has the added benefit of weeding out any departments/companies that would not accommodate you (or do so begrudgingly). Although it's worth mentioning that since you don't seem to need any special accommodations, I don't see most employers caring.
In the real world, you may not have the luxury of being picky about where you work. At least in the US, you don't really need a reason not to hire a candidate. Certainly there are companies that will try to avoid hiring someone who will require accommodations (despite the fact that it is unethical/illegal). Only you know your specific situation. This should not impact your job prospects but it might. Whether or not it would affect you more than appearing overly nervous is impossible to guess.
With that in mind, before doing anything or worrying too much, maybe you should consider having a trusted 3rd party (maybe your physician?) assess how severe your tremor is to the untrained eye. It's possible that a non-medical person might not even be aware of it during an interview. You could avoid the issue altogether if this is the case.


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How to release the copyright of a published book?
Nearly five years ago, I have published my book, and now I requested the publishing company to release the copyright and return it to me. They agreed as an exception, however, they want me to pay them $500 to purchase the remaining stock (9 copies) at a special 50% discount. Is this offer legal? I had a quarrel with them, and I want to take my copyright back without paying any fees. What am I supposed to do?

"I had a quarrel with them, and I want to take my copyright back without paying any fees." Well, you can't: It's theirs. You almost certainly signed a contract that says that the copyright is theirs. You can't unilaterally decide that you want it back.

You would be normally signing a contract when publishing, likely a separate copyright transfer agreement in this case. Now, I am not a lawyer but as far as the contracts go, you can either enter a new agreement with the company (you buy the copies, they waive the copyright, does not seem like a deal that terrible to me), or challenge the initial contract or their adherence to it. Offering you to buy out the remaining stock seems legal from that point of view - they are free to offer you any terms at all because this will be a new contract between parties. As to "are not they breaching the existing contract or some other law", I can not tell - there is nothing about that in the post.
So, whatever caused the quarrel in the first place might not be legal, but offering you these terms probably is.

What if I continue publishing my book in a self-publishing company without taking back the copyright from the prior publisher?

In that case you will be the one infringing upon a written contract, it is possible your existing publisher would just give up on pursuing further action but it puts you in a vulnerable position, and defending it may be way more expensive than $500.

In some self-publishing companies, the copyright page is done by the author. Is it possible to mention the prior publisher as the copyright holder on the copyright page and republish my book on this new platform?

This is not how copyright normally works. A copyright agreement, which you almost certainly have signed, states that you transfer the exclusive rights to publish, sell or otherwise benefit from this work to the publishing company, and receive your share according to whatever the agreement says. If they have an exclusive right to that work and they haven't waived it, and your agreement doesn't have carveouts for self-publishing or e.g. sharing electronic copies of your book, you violate that exclusivity clause by self-publishing.

I got it, thanks.

I'm glad you got it. It is good advice. Your other suggested actions would put you in peril. Copyright has actual value.

Thank you, everybody. I could finally convince the publisher to release the copyright without charging me any fees associated with this regard.


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Does telling people that I (undergrad) want to stay in academia come across as naive and/or big-headed?
I am an undergrad planning to apply to MA-PhD cognitive neuroscience programs either this year or next. I've decided to try to approach grad school in a way that will maximize my chances of getting a post-doc position that will lead to a tenure-track position. (For example, I've heard that the prestige of a PhD program/advisor matters, so I might have to consider applying to top-10 schools; I would like to consider job availability when choosing my field of study, etc)
Getting a tenure-track position is like winning the lottery, and there are many people who are much smarter than myself but who still end up in industry. I don't want to appear deluded or grandiose, so when asked about my career plans I say, "I hope to stay in academia, but I'd also be happy in industry..."
The only people I have to ask for advice are my supervisors (PI, grad student). They have been generous with their advice so far, but it seems geared towards people who want to end up in industry/teaching/etc. I assume there is a lot more I don't know that is specific to people who would like to stay in/sacrifice for academia, and I would like to ask my supervisors for guidance. I think I would get the best-quality advice if I point-blank said: "I am actually very ambitious, what do you recommend?"
But I'm not sure how to say this without coming across as naive or deluded -- or, worse, stuck-up (which is quite possible, because the people around me are extremely generous with praise and I am extremely socially awkward). Also, note that my PI has expressed that they would like me to stay in their lab for grad school; I don't want to come across as saying, "you're not good enough for me."

You can/should say what you wish_for... with, of course, the disclaimer that you know full well that it will be a tough road to get there. Also, it's psychologically much better to admit to yourself what you want, even if/when you know it will be difficult or nearly impossible to obtain/achieve. Don't pretend "you don't want anything". :)

FYI… your PI is “in academia” if they are a professor…. Academia is teaching so when you say their advice is for people who want to end up teaching, I find that confusing…

The words you're looking for are: "I know it's a long shot, but I'm shooting for an academic position." If you've thought seriously about a backup plan (which is a very good idea...something more specific than "industry"), you could mention this as well. When speaking to your advisor, you could ask something like "What sort of things should I be doing to close the gap between myself and the students who get into top grad programs?"
Do bear in mind that even if they understand the question, your advisor may not have much background working with "elite" grad students, in which case their ability to offer specific advice may be limited.

It's not really a long shot. Look at your university, check how many students they take in, how many people are employed in good academic positions, and you calculate your chances. Then consider that many students, including excellent students, don't want an academic career, that you actually have set down a goal for yourself, that you are willing to work hard for that career, that you know you have talent, it's not that unlikely.

It depends on many factors, including how you define "academic position," but for an alternate viewpoint, see Is it still possible to get a decent job in academia (specifically physics) nowadays?


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Writing a paper on occasion of birthday
My colleague and I intend to prepare a paper on occasion of our advisor's birthday (he turns 65 in two years). As the preparation and publishing of a math paper takes some time, I commenced planning now. We both have defended our theses.
I would appreciate any tip on this issue. For instance, the quality of journal and the number of authors. In addition, should we share our idea about such paper with advisor?

What sort of paper. Is this an advancement in Mathematics or a retrospective of your advisor's work?

as an advancement in Mathematics

Whatever type of paper, I have to say this is a really nice idea. upvoted.

I'd think it would be better to do some kind of a non-trivial contribution in the actual working field of your advisor. But "just" a paper would suffice, probably. You might want to organise a special issue, though, as recommended below.

As you are aware, timing the publication of a Mathematics paper is basically impossible as you don't have control over editors, reviewers, publication schedule, etc. But assuming that you want to proceed anyway, I'd suggest that you not make it more complex than it already is. If the two of you have the sufficient ideas and can write the paper, then stick to that. Bringing in others is likely to make the process slower, not quicker.
This is just opinion, but I'd suggest making it a surprise, and just noting the advisor in the acknowledgements. But make it a paper everyone will be proud of. If you tell him you might get an objection.

Thank you for your reply. To my understanding, if we prepare separate papers would be better than a joint paper, am I right?

If you want to write separate papers (I have no opinion on that), then you might contact several other of his students and just suggest to them that they might also want to dedicate their next paper to this prof. That might make it easier to assure that at least one of them is published before the big event. Some of them will already have a paper in progress and adding a dedication should be acceptable.  However, for political reasons, it would be good if you could reach every living student.

If your advisor has had a large enough impact on his field or sub-field, it may be possible to organize a special issue in honor of his birthday. For example,
Donald DeAngelis had a special issue of Ecological Modelling dedicated to him. The first article was titled "Next-generation ecological modelling: A special issue dedicated to Donald DeAngelis on the occasion of his 70th birthday".
The entire issue may be found here and a non-paywall press released here.

+1. A lot of work to organize in a short time, but yes. Great suggestion.

Useful vocabulary item: festschrift.

@PeterTaylor Thanks for teaching me a new word!


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post doc research and problem with its progress
In order to get postdoc in math I need to write a research statement. But I am thinking about some questions and appreciate your answers.
Is it possible to express several topics in research statement which some of them might be not related to each other?
What should I do when a research subject in my research statement for postdoc will not have any progress during doing postdoc?

Your question is very general and hard to answer. The answer also depends crucially on the kind of post you are applying for. Basically, some postdoc posts are created to support the research proposed by an applicant (i.e. you are a PI on their own project), but many posts are created to support an existing project (you professor is PI and you are Research Assistant/Fellow).

When you are a PI, you can propose any research project that interests you. However, remember to use SMART objectives. If you propose several disconnected research directions, think how realistic is to achieve them in a timeline of your post. Consult more experienced colleagues if needed.
When you are a RF on an existing project, make sure your application relates and reflects the topic and aims of this project. Check PI's bibliography and the information available about this project.

If you do not think you can make any progress for the chosen topic during the post, it is unlikely you will get any funding for it.


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exchanging emails between professors
I am going to send an email (including my CV) to a professor who has offered a postdoc position. Regarding recommendation letters or (any other contacts such as exchanging emails about me) between potential mentor of postdoc and my Ph.D. advisor, I would like to know that : Will the professor of postdoc send email to my adviser directly to ask a recommendation letter or any other questions about me without informing me?

Usually, one should not do this because it might have implication on your current position, especially if you are not selected afterwards.
Especially in academia, people might know each other very well and in such cases one might be tempted to make a short phone call or talk at a conference.
If you want to avoid this, you should explicitely mention, that you don't want that your current advisor will be contacted because [insert good reason here].

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


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some questions before applying for postdoc
I appreciate your guidance on the following questions:

Should I inform my adviser before applying for each an every postdoc position?
Should I send my research statement to my Ph.D adviser before sending it for postdoc applications?

Your PhD advisor? (Why should they be informed before you apply for your next position?) What research statement? (Why should your PhD advisor be sent such a statement?)

@user2768 A PhD advisor could offer useful feedback on the research statement. Many postdoc positions want one. The adviser could also tell if the institute and the people there have good reputations in the field.

@TommiBrander That might be a reason, but is it the OP's reason? It's difficult to offer advise with so little information. (In my first question, I meant to ask: in question 1, does "advisor" mean "PhD advisor" or some other advisor? That's unclear as stated.)

I mean by advisor, PhD advisor

In general, you should be communicative with your PhD advisor about your applications. This is so that they can do their job and advise you about the process. Their input will be invaluable to you. In particular, you will probably want your PhD advisor to write recommendation letters for you.
You should tell your advisor in advance that you are planning to apply. (Although it is usually not necessary to specify exactly where.) And, once you have applied, you should tell them where so that they are on the look out for a letter request.
However, if you have a problematic relationship with your advisor, then that's a big problem that you will need to navigate. If this is the case, then your question should make this clear.


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How to apply for Post-doc
I am a last year Ph.D student and intend to apply for a postdoc call starting in September. As I have not submitted my thesis yet, is it possible to apply  earlier? And how can I ask my adviser to send recommendation letter while still I have not defended my thesis? ( I mean how can I explain my adviser this demand?)

If you were a mathematics student applying for postdoc positions in the U.S., it would not be too early to apply now; it would be too late. My department, for example,has already hired most (perhaps all) of the postdocs for positions starting in September.

Applying for a postdoc before defending your PhD is a very common situation which your adviser should be familiar with. Just say to your adviser that you are applying for a postdoc and that you would like him to write a letter of recommendation; there shouldn't be any more to it than that.


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How much independency does a postdoctoral researcher have?
I am a postdoctoral with governmental grant, means that it is not a grant from a research supervisor for a specific research project. Of course, when I was applying for this grant I was asked to connect with one of the professor in university X and I provided a research proposal. During working on the research related to my proposal, I am working on some other aspects which are not far from my proposed research in cooperation with some other scholars and professors outside of my university. I would like to ask your opinion on whether it is normal for postdoctoral researchers to have collaborations with other people as well?

As a pure mathematician, I consider your situation entirely normal. But I can easily understand that an experimentalist, who needs postdocs to keep the lab functioning, could have a very different opinion.

Can you explain why you think this would be an issue?

@AzorAhai-him-Because it is my first experince after obtaning my PhD

I would like to ask your opinion on whether it is normal for postdoctoral researchers to have collaborations with other people as well?

Our opinions don’t matter. The professor in charge of your grant is considered your supervisor, and whether it’s okay for you to spend significant time on outside collaborations depends on, and only on, the professor’s opinion. It’s likely okay, and yes it is somewhat normal at least in some disciplines (e.g. math), but you should simply ask them.

How independent a post-doc can be depends on a lot of things, but funding is one of the more important ones. Since the institution you will be working at isn't funding you, they have little (but not zero) control over you.
However, and very important, is that collaboration is a good thing. A very good thing. It can boost your future prospects tremendously, both for getting a permanent position and for continuing to do good research.
But, you don't need to feel that you must submit to the views of others if you differ in some way. But those sorts of relationships are destructive potentially in any case.
Think of your colleagues as collaborators, not superiors or inferiors. Share ideas. Build a backlog of ideas for future research. Build a large cohort of collaborators. But, you have the freedom to set your own path.


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Can an editor review manuscript without sending to reviewers?
I submitted my manuscript to a journal one month ago and the status is "with editor" up to now. As the editor of my paper is one of the leading scientists in the field of my research paper (mathematics), I would like to know that can an editor do the review of paper by him/herself without sending to other reviewers?

Journals have their own rules, of course.

You cannot infer anything from this. It is perfectly normal that it takes more than 6 months until you here anything from the journal again.

Yes, an editor can review a manuscript themselves, but you cannot infer an editor is reviewing themselves when a manuscript has been with "a journal [for] one  month...and the status is 'with editor' up to now."

Even if the editor can have a conflict of interest?

@user21820 an editor can review, that doesn't mean they will nor should. Conflict of interest is one instance when they shouldn't.

The editor may simply not have had the time to look at your manuscript and find a suitable reviewer. Or he may have contacted one or more potential reviewers, but they may not have accepted yet, in which case the editorial system may still show the manuscript as "with editor".
Also, of course, editors do look at manuscripts themselves. They typically don't write full reviews themselves, but they may desk reject, i.e., reject it without even sending it out for review, if the manuscript is obviously not within the journal's scope or of too low quality. ("Obviously" is obviously subjective.)
If you fear a conflict of interest, it would be good to account for this before submission, by either asking the manuscript to be handled by a different editor (assuming the journal has more than one), or by submitting to a different journal.

I am an editor at a mathematics journal which uses a (IMHO) pretty crappy online editorial system. When a paper is assigned to me, I find it much easier to work with referees "off the grid" rather than using the infernal editorial system. (For example, the system insists that I input in an entire page of details before sending a referee request to someone who most likely will ignore the request anyway.) So I don't think you can infer anything at all from the fact that the online status says "with editor."


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Should I use an author's code made available on request to help retract their highly cited paper?
I am working on an ML-based problem for my undergrad thesis, based on an experimental dataset and prediction results published in a paper two years ago by an associate prof. in a very high ranking journal - the paper has 200+ citations. For months, I'd been trying to replicate the paper's results using the methods provided as well as those of my own but all in vain. The paper states that the code used would be made available on request, so out of curiosity I mailed the corresponding author for it.
I received a quick response, and for another month I was trying to decode how the author obtained their prediction results. One day when I was discussing implementation issues in my code with my supervisor, I spotted a grave error (or manipulation trick, as it seems to me) that completely invalidated all results in both their main paper and supplementary information. I was dumbstruck.
I found a very similar question on Academia SE - but here's a slight difference. I asked my supervisor to permit me to write an independent comment on the article as I tried to reach out to the authors regarding the mistake (or intended manipulation, as the case might have been), which they did not respond to. The authors deliberately avoided producing graphs that could demonstrate the error (as most papers in the field do contain those graphs) and did not define the exact performance evaluation metrics.
The problem is that I'm unable to convince my supervisor as he thinks that (1) the paper might be retracted or significantly altered as it provides both the code and the experimental dataset and (2) it would be an malpractice on ethical/humane grounds to request the authors' code and then use it to bring their published, widely-cited article down that also helped them gain grants.
I believe I should at least publish a comment or request the authors to collaborate to work on this together as answered in the linked question above, but I think the latter is unlikely given that a likely retraction would affect their grants.
What would be the best course of action in this case? How do I convince my supervisor to help preserve academic integrity and not let my months of efforts go to waste (as unfortunately, academia and thesis committees still undervalue reporting poor/negative results in a thesis)?
EDIT: I found it all out too late as I have less than a week for my thesis defence.
EDIT 2: I think I must clear a few more things. The paper was the first to present the dataset and results of its kind. The authors provide the data preprocessing code publicly but the model development code on request. Also, I think I can analogize the exact error in the paper with a simple example. Imagine you want to compute estimates of a quantity and require scaling it down in proportion to a reference. Instead of scaling the quantity down, you scale down the root mean square of the estimation errors between the true unscaled quantity and your unscaled estimate and exclaim you get spectacular estimation results!

Two things are unclear in your question. What did you say when you contacted the authors about the mistake? And what does (1) mean - why does the possibility of the paper being retracted or significantly altered make your supervisor unwilling to act?

@Ian, probably, but I first-authored a journal paper published in the same field last year so at least I thoroughly understand the results.

@toby544 I asked them if there was a reason behind the thing I believe to be a mistake (which was a simple numeric scaling on reported errors). My supervisor thinks so as it might hurt the authors' career/repo and he found it unethical to use their own code provided on request, although he himself has disproven several published papers' results through comments based on independent experiments.

@Ian I do not have an answer to your question; it's also a reason my supervisor advised against writing a comment.

This sounds similar to the academic paper that persuaded many countries around the world to adopt austerity.  Once the flaw was found, it made very little difference despite many people pointing it out. https://www.bbc.co.uk/news/magazine-22223190

Is the author someone at your institution? How close are they to your supervisor?

The idea that it would be unethical or malpractice to use the content of a publication to refute said publication is so incredibly backwards. That's almost as concerning to me as the idea the the author intentionally fudged their results.

@DanielR.Collins No, the author is from a different country and hasn't worked before with any of us.

Your advisor is wary of the harm that could come from making any comment, and my inclinations would run the same way, but there is also harm in leaving things as they are. You say you spent months trying to replicate the paper's results: since the paper is highly cited, it is likely that others will also waste months of their time on this method if it goes uncorrected. Wasted months, especially early in a career, can have serious negative consequences: a PhD student might run out of time or funding and never complete their PhD, a postdoc who wastes months might fail to become competitive for a faculty position, and an early career academic who wastes months might not make tenure.
You did the right thing by reaching out to the authors first. Since they have not responded, I think writing a comment of your own is the right thing to do. If possible, frame it as a "clarification" of the method and its results rather than as a "correction". E.g., state that the results can be "misinterpreted", leading to over-confidence in the approach. Perhaps you could ask the original authors if they would like to be co-authors on this clarification, to give them maximum opportunity to save face. If it can't be framed as a clarification, then it is appropriate to frame it as a "correction", but you will minimise damage to the authors and your relationship with your advisor if you avoid implying that the original paper was deliberately misleading. Perhaps instead, you could present it as a case study for why there needs to be consistency in the types of figures and metrics presented in this type of work?
Alternatively, you could reach out to the editor privately to discuss your concerns. If this was really deliberate, the authors have probably taken a similar approach in their other work -- or might do so in future if they are never called to account for it. Unfortunately, editors vary in how receptive they are to this kind of discussion. Some would rather not know and would rather not get involved.

This is the way to go. I once requested the R code underlying a published paper. In this code I found a statement of the form x = a/b+c, which looked weird to me. Sure enough, when I disinterred the original FORTRAN code (of which the R code was a re-implementation), I found the correct x = a/(b+c). Now this was a pretty central equation. I wrote the first author pointing out the mistake only noting, 'I hope that your results do not change when you have fixed this typo', well knowing that sure they would. I never received an answer...

"Some would rather not know and would rather not get involved." I am saddened by this. :(

Thanks for the answer. I'll try reaching out another coauthor regarding this first and then discuss with my supervisor to proceed as you say. I received the code from the first author when I mailed the corresponding author for the request, and I had been communicating with the first author until he stopped (or missed) responding.

You are right, but being the whisteblower can also nix your career.

I think both you and your supervisor are confused.
On one hand, you do not retract papers as a third party. The journal does, or the authors do. You can criticize existing papers. This does not retract them. You may want to be strategic about how you criticize as a junior researcher because not everyone takes criticism well and because unfortunately not everyone will take the necessary time to understand and come to agreement with you.
On the other hand, one of the main reasons for providing code, and the reason many journals now require authors to provide code, is to allow results to be verified by third parties. You've used it exactly as is appropriate.
Steps to take would involve contacting the authors about the mistake you've discovered and/or getting some input from others to make sure you correctly understand the mistake and aren't making one yourself. I think you're better off assuming a mistake rather than intentional fraud at this point; it's possible, but accusations of fraud cause people to behave defensively. I think if the goal is to correct the record that's the most effective path. It sounds like you've already done much of this; if nothing comes of it you might be stuck there.
As for your own work, you do not need to rely on a paper you've found to be flawed. If you need to benchmark your own work against something, don't use this example, or use your corrected version.
It might be worth publishing a Comment on the paper if it's sufficiently influential, but I think you need guidance and advice of a senior academic to help you through that process. I wouldn't advise continuing on your own.
As far as your undergraduate thesis, the expectations for an undergraduate thesis are generally low among academic work and typically you would not necessarily be expected to produce publishable work, though it may help your future career (i.e., graduate school applications). You will need to work with your advisor directly to understand how best to present what you have done. My personal opinion would be that taking some result in the literature, attempting to replicate it, failing to replicate, obtaining the original code, and demonstrating that there is a mistake in the original code sounds like a fantastic undergraduate thesis. I would not necessarily put this in the realm of "negative results"; usually a "negative result" means that you haven't changed the state of the art at all, whereas here you've found an accepted result is wrong. All the most important results are the ones that find accepted results are wrong, those that just confirm what's already known are boring. I'm not the one who grades your thesis, though, so check with the person who does.

I found it all out too late as I have less than a week for my thesis defence.

This by itself seems like a poor excuse, though; you also say:

For months, I'd been trying to replicate the paper's results using the methods provided as well as those of my own but all in vain

So overall, this isn't something that's come up just in the last week, and you've had months to work with your advisor on contingencies, alternative approaches, etc. You have more information just coming up recently if you've only recently received and processed the original code, but that's not your entire undergraduate thesis.

Thank you for the answer. Yes, I didn't mean we can retract somebody else's paper - I meant publishing a comment or mailing the journal's editors could lead to this - although we won't do the latter before discussing the mistake with the authors. Edited the question title to reflect that.

I had a similar experience very early on in my PhD studies, and I received some very sound advice. First: "the guys who wrote that paper are far busier than you; you have spent more time reading it than they spent writing it". Second: "if they didn't know how to value critical input, they probably would never have reached such dizzy heights". So go for it. Also there's a big middle ground between making a simple error and committing fraud: namely taking a short-cut when you're busy and deadlines are looming.

@MichaelKay Many thanks for the insights! Indeed, I've seen this shortcutting happen in my field very often and going unnoticed as data/code is not provided.

It's normal to make mistakes. I make them, you make them, everybody does. Pointing out others possible mistakes must be polite, friendly, and kind, because thats the way you would like to be threated if the positions were reversed - and they can well be, sooner or later.
In my experience, I have found several flawed papers. I am happy about the outcome in one case in particular, which I am going to quickly share with you. To give some context, please note that my field is condensed matter experimental physics.
I had several issues with one publication. I wrote the corresponding author and received some answers. I didn't find them compelling and asked again. The corresponding author never replied to me again. I then wrote the journal editor, said that I had these unanswered questions, that the corresponding author was not responding, that I thought that paper seriously wrong, and that I wanted to remain anonymous in the process. The editor took this seriously, even though it took them about 2 years to complete their process. They contacted external referees, who checked my comments and agreed with them. Asked the paper author to reply. The authors reply was reviewed, and found lacking by the referees. In the end, the editor published an expression of concern that lists all this info, saying they can't verify the validity of that paper and to be cautious with it. This way, I think I did my part, yet remained safely anonymous. I have several other examples but they didn't work out quite as well. So, there's hope. Good luck to you

That's an excellent outcome and suggested process. Thanks for sharing it here!

It's an interesting story, and well done protecting your anonymity, but the outcome is still weak sauce. Also, the OP makes it rather clear that his case does not concern "honest" mistake.

Thanks for the insights. 2 years are enough for too many papers to cite erroneous papers and I'm not sure if authors care to remove references to a retracted paper unless it gains enough limelight. I concur that I should remain anonymous as long as direct communication with the authors doesn't work out.

You can comment on the paper at PubPeer.

(+1) I absolutely agree with this. PubPeer is exactly was made for exactly these kinds of scenarios, as you can comment anonymously.

Will the authors be informed of my comment on their article at PubPeer even if they don't have an associated account on PubPeer? Edit: I noticed the website manually requires entering current email addresses for some authors to be notified; for some it extracts their emails, shown masked by *.

I'm a senior professor in physics. I disagree with those who say to ignore your advisor's advice. Not because they are the boss or always right, but because you and they are collaborators and partners and should do things by consensus and do nothing to harm the other. But to the question - a PhD student of mine recently tried to replicate an experimental result published by a well established researcher elsewhere and got a negative result. We reached out to him and he and his student were supportive and shared all their experimental details, which we repeated again and still got a negative result. My student wrote a paper explaining our non-result and shared it with the well established researcher and he was fine with us submitting it to a refereed journal. But because we cannot explain how the others got the "erroneous" result, they are not sure if they will retract. The point is - research should be open and transparent. Anything less is unprofessional and hurts the field. I think your advisor should send the original authors a certified hard copy letter through the postal mail and explain the situation and politely challenge them to cooperate.

Thanks for indicating this as an option. I would definitely appreciate if the concerned authors would explore co-authoring a correction paper. I once found a minor error in a paper in an experimental field, mailed the author regarding it, and they were more than glad to correct it!

Let’s start by assuming the authors are well intentioned and have made an honest mistake, and that you are completely correct that it is a mistake in their analysis which invalidates the large majority of the conclusions in their publication.
As an honest, well-meaning scientist would you feel comfortable continuing to mislead many other scientists with incorrect results, potentially wasting months of their life’s reproducing results that are not reproducible? I don’t think so. Even if no one wants to be in that situation, if not reporting means that potentially many other people will be wasting their time, then obviously the morally responsible thing to do is to report it. As an honest scientist I would also come to this conclusion myself. Now the other part of the question, should you report it? I would try to get the authors to admit it first (also to ensure you didn’t get anything wrong), and to give them the opportunity to correct it themselves and “do the right thing” on their own. From the point of view of the journal it is much easier to judge if the authors themselves admit something was incorrect rather than involving a set of independent experts to judge and decide. Now if the authors don’t want to admit it, it becomes more complicated (not morally, because morally it is clear), but in terms of social and political aspect. Here, you will be more limited by the support you get from a supervisor, you can always act on your own but just be aware that this kind of "politics" exist at all levels of science, from funding, to journal editors and reviewers.

First a bit banter.
Sadly, this is the sad truth about academic research. Peer review system is flawed and will never be able to sort adulterated results from the real ones. First of all it would take almost as much time as writing the paper to validate the results. No one will to review if that would be the case. It is simple to solve it in computer science: submission of source code to the journal in confidence can solve it. Simply by reviewing the code, many of the problems will be found. But, it is not that easy in other fields.
Now here is something that happened in my field:
A very influential paper has its results wrong. I am not sure about the reason, maybe they got the metric wrong or it is completely fabricated. Everyone comparing with that paper published another result which was consistent with each other. The original paper is never retracted or corrected. We always write that the measurement criteria was probably different. In reality, measurement method was given in the paper and same as everyone else. It is nigh impossible to prove any wrong doing even if there is one. Sadly, even in this digital age, publications are treated as static data. There is very little incentive to change it. Any disruption in this system might cause so much harm to innocent researchers who has made future plans.

What would be the best course of action in this case?

In terms of your thesis defense I am not sure any action is needed. It does make an interesting story, and you might relate it during your defense presentation in the "challenges" section.
In terms of the published paper and its conclusions and how they are affected by

the thing I believe to be a mistake (which was a simple numeric scaling on reported errors)

I agree you should proceed cautiously; either with your advisor or another individual established in the field.
But you could also, after considering the risks, just go for it and write something yourself and accept any possible s*** storm that may ensue, either from your advisor, the authors, or elsewhere. Some folks in the academe can be vindictive and paranoid when their own reputation is at stake. This is completely AYOR! (1, 2)

When someone says you can do something AYOR (at your own risk), it means you can do it, but you're responsible if you screw it up or hurt yourself. And there's a good chance you will.

In terms of the angst and frustration that something published seems to be wrong, the injustice of a high citation count from a seemingly wrong result, and the perception that this was achieved by possibly intentionally incorrect scaling of errors, all I can say is take a deep breath and get used to it.
We must coexist with (who we feel to be) unethical colleagues and peers. They can become our paper reviewers, our funding approvers, or our own Ellsworth Toohey (hidden antagonist) to our own (idealist) Howard Roark.

Obligatory XKCD (386) Duty Calls

This is Science. We publish results to share knowledge, and as a check.
Put aside speculation as to motive.
Ask a polite question. You got an unexpected result using the data and code kindly provided by the authors. Perhaps you or they made a mistake. Perhaps both. Explain as clearly as you can what you see. Do not speculate. Ask for input from others.
Do this publicly.
For the sake of everyone, put aside ego and emotion. We are all Human and fallible.

Be aware with how you think of the original authors. In your post you suggest a manipulation trick, which is a serious accusation. Given that they provided you with the materials readily suggests an honest mistake. If they would have consciously manipulated the outcomes they would probably have delayed or find excuses not to give you the code. Also keep in mind that your mail notifying them of the problem may have urged them to review their own work which may take a lot of time (especially since they probably no longer have time allocated to the work). So all in all I would suggest good faith in your future actions. But yes it will benefit science if this mistake (if shown to be as substantial as you claim) is corrected.

Sounds like a complicated and annoying situation. Thankfully, the answer to your question is really easy:
You contact the editor and make a case for why you think the conclusions of the paper are incorrect/ not supposed by the data provided. I would suggest full transparency with the editor, so include the full story (editors are fast readers, so don't be afraid to be verbose)
Whatever happens next, happen next.
And for what it's worth, your supervisors opinion on this is completely irrelevant. You can take their advice and they are more than welcome to provide input, but the decision to contact the editor or do whatever else is yours and yours alone.

As long as you don't act with the intention of getting their paper retracted, but rather having the result corrected by whatever legal means necessary you are morally in the clear.
A note on Edit 2, when scaling a quantity, the uncertainty is also scaled by the same factor.
For example, if you have a measurement of 2 cm give or take 0.5 cm, and you multiply this measurement by 0.1, the new values are 0.2 cm give or take 0.05 cm.
In this example it's not important if the uncertainty is from measurement, standard deviation, or standard error, they are all treated the same for this kind of scaling, unless there are multiple variables.

Thanks, I forgot to mention that they did not scale the exact error values but the RMS of those errors - updated EDIT 2 to reflect that.

@Kartik this is not necessarily an incorrect thing to do. It sounds like the scaled the standard error which is the error of the mean and this is likely fine and correct, it really depends on a few things. If this is the first time they swapped to standard error, that's shifty, if they took the RMS of standard errors that's potentially wrong, do some reading up on error propagation. Remember when doing error propagation there's 3 kinda of errors you can work with, exact error, standard deviation, and standard deviation of the mean (standard error), the last 2 use the same rules.

Write to the author(s) who's code you spotted an error with. Inform them of your finding. Importantly, CC the editor of the journal the paper was published in while also in the body letting the author(s) know your doing so.
If the authors fail to respond to your inquiry, write a follow-up email and request support from the editor.
If both the author(s) and editor fail to respond, write a third email informing them you plan to publish a paper reporting the issue.


text:
Applying to jobs in multiple disciplines. How much does name of degree matter?
I'm currently a second year masters student applying to PhD programs but are at a bit of a crossroads and wanted to crowd source some opinions.
My research interests are in a subject studied significantly by people in two different disciplines (I'll call them disciplines A & B). A is strictly in the physical sciences, while B is very diverse and encompasses research ranging from the physical to social sciences. There can be some differences in how each discipline approaches the subject, but frequently there isn't, and people from both generally publish in the same journals, present at the same conferences, etc.
My bachelors is in A and I am in a B department for my masters. I really enjoy my current department, which is small but generally well regarded, and advisor, who is prominent in his field and extremely supportive. Additionally while in a different school, my current University has a world class A department with great people working in my field of interest. There is a some cross department collaboration, and I've taken classes with/have good relationships with the relevant professors in A. As a result it's very tempting to stay with my advisor in geography for the PhD, while also collaborating with people in A on research, publications, etc.
However, when I think of future job prospects in academia I start to get worried. In my country (the US) the job market for A is alot better than B (there simply aren't as many B departments, and A departments are frequently better funded ). And ideally I would like to be able to apply to jobs in both types of departments.
My logical mind wants to say that if your research record is good, you publish in the same journals, present at the same conferences, have people in both disciplines on my committee, etc. that it shouldn't matter the actual name of the PhD.
But I know hiring is not always logical. And I worry I will always have an uphill battle with hiring committees, compared to people with PhDs in A. And going through faculty pages for many departments I see relatively few people with PhDs in B in A departments. And most of those are people from Europe where research on the subject is far more concentrated in B departments. Conversely I see more people with PhDs in A hired by B departments.
So I'm left wondering if I would be better served leaving for a PhD program in an A department (again since my undergraduate is in A, and I have grad coursework/research experience in A , I am qualified). But that of course would mean leaving a great situation with a wonderful mentor, excellent resources, and numerous collaborators.
I know there are potentially other routes to help when applying across disciplines (try to do a postdoc in A).
But wanted to see what other peoples experiences applying to jobs across disciplines were, and if people with more exposure to the hiring end of things had any insight.
Thank you!

A potentially helpful exercise is pull up the CVs of the younger assistant professors in A and B departments and see where they got their PhDs.

@StrongBad I've done that extensively, and again I see far more faculty with A PhDs end up in B Depts than vice versa. And certainly a big piece of it is just probability, as I mentioned there are more A departments in the US.

Before I say anything else, I want to say that the answer to this can't be easily generalised and very much has to do with the particulars of your discipline(s). Mine isn't going to be like yours and without telling what A and B are, any folks here with direct experience will not be able to offer it.
That said, I have a BA, and MPhil and a PhD in "apples" and for the past 7 years have been permanently employed by an "oranges" department". If I told you what the two subjects were you would look at me blankly as you tried to figure out how there could be any connection between the two. To say that there isn't crossover of people between the two disciplines is an understatement. That said, about 4 years ago I was offered (and turned down) a promoted position in an "apples" department ("oranges" matched the offer), I've had some "apples" departments attempt to poach me, and I'm considered an applesologist among other applesologists still, while mostly passing for an orangologist in those circles. I am now moving to another University's "oranges" department. I'm keen to stay in "oranges" as there is a lot more funding in that field and PhD students that I graduate have a much better chance of finding work than if they were in "apples".
This is the long way to say that if your A and B are close enough that there is any crossover whatsoever amongst the faculties and researchers you are looking at, you are likely fine where you are. I've always found that what research I do and how well I do it is far more important than what discipline is printed on my degree (because seriously, the two disciplines I am set between are like apples and oranges). If your current location gives you excellent support and the opportunities you need to do excellent research, and as long as you keep your network going across both A and B, you should be fine. Generally speaking...

Thank you, that is reassuring. For clarity A=Geology & B=Geography.