text:
A paper I received to review has (independently) duplicated work that we are writing up. How to proceed in light of peer-review confidentiality?
I did some research with some collaborators, and we have been writing an article ("paper A") describing the work.
A few days ago I received a request to review an article ("paper B") that covers most of our work. The authors of paper B have clearly worked independently on the same topic and beaten us to submission. (And fair play to them.)
This leads me to a number of related dilemmas:
The first, and I think easiest to resolve, is whether I have a conflict of interest in reviewing paper B. I think I can write a fair review, but I intend to tell the editor and allow them to decide whether I should proceed.
The other dilemmas arise mainly because I am bound by peer-review confidentiality. I should note that paper B is not available as a preprint.
Can tell my co-authors about paper B? I am convinced that confidentiality forbids me from showing paper B to them, but can I tell them that it exists and what it covers? My feeling is that the answer is 'no'.
But then, if I cannot tell my co-authors about paper B, then it seems I have to allow our paper A to proceed to submission even although I know of the overlap with paper B.
I am extremely uncomfortable with this, although one can take the view that since our work was independent, our paper A could still be published.
Furthermore, my first impression is that paper B is not suitable for the general journal to which it was submitted, but that I would recommend acceptance to a high-quality specialist journal, such as the one to which we intended to submit our paper A. This raises an unpleasant prospect: if our paper A proceeds to submission and publication, the authors of paper B might believe that I had rejected their paper and plagarized their work (a situation discussed in this question). This situation could arise even if I turn down the review request. Naturally, I want to avoid this.
How should I proceed? Could I ask the editor for permission to inform my co-authors about paper B?

The unethical to do would be to accept to review the paper, write up your paper and submit it and then reject the paper on the grounds that it duplicates an existing paper (yours). Apart from being unethical you would certainly make enemies and this course of action (hopefully) would have a negative impact on your reputation/career. Unfortunately, this situation is not unheard of... Of course I wouldn't recommend this, so I'm not posting it as an answer ;)

I hope you can find a fair way to publish your paper along with this one. The history of HOMFLY poynomial in mathematics provides a model. Note the initials of the (somewhat independent) codiscoverers in this joint paper: Freyd, P.; Yetter, D.; Hoste, J.; Lickorish, W. B. R.; Millett, K.; and Oceanu, A. "A New Polynomial Invariant of Knots and Links." Bull. Amer. Math. Soc. 12, 239-246, 1985.

I'll start by calling this a rather sticky situation indeed!

Also, don't forget to tell us what happened in the end and how would you proceed if you had a second choice-timeline.

@dalearn even stickier than when Sticky the stick insect got stuck on a sticky bun.

Is collaboration with Team B completely out of the question?  Perhaps they will understand your situation, extend their paper with the stuff you guys did differently, and add you as authors?  Forge a new "standard behavior" for when this comes up?  I know this is incredibly optimistic, but I have to point out that reasonable people could theoretically work this out in a mutually beneficial way.

How do you not run into "conflicts of interest" if you're an active researcher in discipline D, and review papers ... in discipline D.

Your question raises several quite serious ethical questions - thank you for posting it!
From the last part of your question it looks to me that you actually do have a conflict of interest, since you are afraid that what you write in your review may impact your future relations with this research group. I think it is best for you to withdraw from reviewing this manuscript, and fully explain your decision to the editors. I would even consider sending them a draft of your manuscript, if this does not violate your arrangements with other authors.
I am not sure your own paper can not be published. In my area it is not uncommon for two groups to produce similar results almost simultaneously (the second paper is submitted before the first is printed). This does bring some hard discussions sometimes, especially if the ideas are published on arXiv or presented at conferences. However, this does not stop papers from being published. Of course, you should not use anything from paper B to improve your paper A.
To summarise: In my opinion, it's best for you not to study paper B in too much details, withdraw from reviewing it, explain this decision to Editors, and continue working on your paper A.

I have seen circular reference chains before in academic research. (In fact I got there following a reference chain while researching my thesis.) Perhaps not taking this advice is the source.

I don't feel you addressed the issue of revealing the existence of B to group A. I feel it would be hard to continue "playing along" and potentially hold back ideas you might have had anyway as you've already seen them expressed in paper B.

@Basic The advice to avoid actually reading the paper in much detail is meant to prevent most of the "you've already seem them expressed in paper B" scenario.  But this just happens to be one of the realities of the review process.  Occasionally you are beaten to the punch, or you are inspired by the work to churn something else out, etc., and now you must wrangle in your desires to advance research in order to maintain your ethical standing.  It may not be easy to hold back on the existence of B, but without expressed approval from B's editors (and possibly authors), he must.  Somehow.

+100 for sending a copy of your own paper to the editor. No reason not to, and has great potential to cover your rear in the future. Maybe upload a hash of it up somewhere too (or use the Bitcoin blockchain), if you don't want to reveal the contents now but want to prove you had it later.

I will address the part of your question concerning whether it is okay to tell your collaborators about paper B, which was not discussed in Dmitry Savostyanov's otherwise excellent answer (with whose content I agree 100%).
Let me start with a general remark: from an ethical point of view, when one agrees to keep some information confidential before seeing that information, it seems to me that such agreement is inherently limited in its scope rather than absolute. As a (rather extreme) example, say a friend is offering to tell you a secret but asks you to promise to keep it in confidence. You agree, and he then tells you that he murdered 10 people in cold blood. Obviously the usual assumption that it is your ethical duty to keep your promise is no longer valid at that point (except perhaps if you are his lawyer or priest, and even then maybe not).
The point of the above extreme example is that the context of the confidentiality promise, of the information you have promised (based on only partial knowledge of the nature of that information) to keep secret and of how that information interacts with your own work and other ethical duties to other parties, matters. In the current situation, I would argue that the situation is unusual enough that it is not covered by the usual default rules about the confidentiality promise being a very strong and essentially inviolable one. You are in possession of information that is highly significant to your coauthors, to whom you have some ethical responsibilities, but also a duty to respect the confidentiality of the author of paper B to the extent possible. How to resolve that tension?
My answer would be that it is okay to tell your coauthors about paper B. Don't go into any details, and in fact as Dmitry suggested, don't even study paper B in detail yourself to avoid implicating yourself in a very clear conflict of interest and possible conflict with your own conscience. But it is not unreasonable to caution your coauthors about the situation and discuss with them how your joint project should proceed in a way that does not needlessly cause a large waste of your combined efforts. At least, if you proceed in such a way then I think a reasonable person would not judge you harshly for what is in my view a small (and make sure to keep it as absolutely small as possible) violation of the confidentiality principle that is done in order to serve a greater good and satisfy your ethical obligations to other parties affected by the information.

It's not often you see people use serial killing as an analogy here...

@zibadawatimmy It's not an analogy (keeping the secret is like not telling on a serial killer), it's a way to prove that you should not keep secrets under all circumstances, even if you agreed to do so.

A very good question indeed: a lot of us can face a similar dilemma.
I believe peer review is almost always about conflict of interest. [EDIT] As discussed in comments below, this assertion seems exaggerated.  However, pure open research might be rare. There are many fields where universal principles cannot be found, and discussed only at the level of truth. Incremental improvements are common. Grant funded research is competitive, and its evaluation leads to biases. To summarize it in a saying that exists in different forms:

to steal ideas from one person is plagiarism; to steal from many is
  research

Who is the original author? Wilson Mizner? Steven Wright? Joseph Cummings Chase? Asa George Baker? Is this quote a cut-and-paste from many? Sources are discussed in Quote investigator: If You Steal From One Author, It’s Plagiarism; If You Steal From Many, It’s Research
Because to be asked for a review of a paper, you need to share a similar  interest (unless the system is flawed: how many have been asked for reviews outside their area of expertise?). And in the academic world, working on a similar topic cannot often be done without biases. And some apparently act unethically. I learned about Paper A submitted in a conference in Country C, rejected, and a year later same conference (ICIP 2003, Barcelona) at the, people for country C (in fact, one was in the technical committee of the conference) presented a quite similar  Paper B, just aside to the guy presenting the resubmitted and now accepted Paper A. No proof.
In 1991, two groups, independently, published a paper on a very similar topic (chirplets). Paper A was published first, but Paper B was submitted first. Endless discussions followed.
If you withdraw your expertise, a clean and honest move, Paper B will follow its path to the reviewing system, independently of you. And quite fairly. Then, you can invite your coauthors to hurry, because you have heard that "a similar paper" was submitted. Or say them you have been asked to review it, and refused. And submit it to another journal. Hoping yours will make its way faster that the other, because better written, because of a fast editor, of a lucky hand of gentle reviewers. Perhaps, you can bet on a different field of application.
And as suggested by @Ian in a comment, why not openarchive (arxiv) your preprint, to set a date?
Whatever your choice, it would be difficult to act now as if you never received this paper to review.

Maybe also put up a pre-print......

@Ian Excellent suggestion

I'm not sure that peer-review is almost always about conflict of interest. If I work on organism A and you work on organism B, doing similar things, there is no conflict (unless your findings show universal principles that my data also show). But still, I'm qualified to review your work. Apart from that, I agree with your suggestion. I've also heard stories of reviewers holding reviews until their team do the same experiments, and I find it unethical.

@George I agree. What I meant is that research is competitive, and its evaluation leads to biases. There many fields where universal principles cannot be found. I always keep in mind the quote "to steal ideas from one person is plagiarism; to steal from many is research".

@LaurentDuval Yes, that is true. And in many cases we can be in survival mode. Hehe. That's true. Whose quote is this?

@BioGeo I have added some sources for the quote

From the standpoint of advancement of scientific knowledge, it seems to me that you are likely better qualified to give actual intellectual commentary on the content of this paper than anybody else, save your co-authors.
If peer review only includes reading a scientific paper, then checks for accuracy are far more limited than the possibilities for someone who has actually duplicated the reported results in their own independent research and testing.
By definition, scientific results should be susceptible to reproduction.  Who better to comment on the accuracy of conclusions made in a field than someone who has actually performed similar experiments?  And who better to call a "peer" than someone interested and involved in exactly the same line of research, but independently?

Undoubtedly I am betraying a "misunderstanding" of the peer review process.  I expect such interchange as I describe above is expected to take place after publication.
However, the peer review system as currently established has not, in my observation, had an excellent track record for scientific advancement.  And at least one intellectual giant (who has worked through the system to the status of fully tenured Professor) agrees with me.
Thus my answer is written with no interest in mind beyond what is optimal for the advancement of human knowledge.
Very likely the easier action for you to take would be to operate in accordance with the current peer review process framework, as ably conveyed in Dmitry's answer.  However, I feel it is important to bring up this side note, at least so you can consider it during the actions you take.
The purpose of peer review should be to aid and advance the state of scientific knowledge across the world.

Mark Burgess's blog post, Why I stopped caring about peer review, and learned to love the work, is so pertinent I have to restrain myself from quoting it in its entirety.  And I don't want to quote his potentially controversial comments out of context of the conceptual structure he built.  But here is one excerpt from near the end of the article:

Science rarely waits for publications to appear anymore. The process is so painfully slow that when a publication appears, either everyone has already read it, or no one is going to. So much nonsense gets into print that it is scarcely a real accolade to be in print.
It takes months or years for a paper to reach print, and who can afford academic journals anyway? So, why would we not think: what if I just self-published my idea in a blog or a website? I could simply ask a smaller circle of people to comment honestly. And it would be searchable by anyone who might stumble across it with the help of modern search engines. Use the archives and the new social sharing sites. Technology can take prejudice out of the equation.
It is up to each of us to exercise best-effort, to listen and improve -- to not waste others' time. So why not wait until we have real ideas, questions, conjectures that inspire others, then write them carefully and put them out there to stimulate a research community, instead of trying to shut down others as competitors (or less important institutions). That is what is now possible, without an old guard to get in the way.

Surely, it is easier to stop caring about peer review when one has a permanent tenure )

@DmitrySavostyanov, I hope you read the article in full?  "I feel as though my own small success is in spite of rather than because of peer review, and the real world relevance of my work was recognized by the world at large even before it was grudgingly recognized by academia."  Also, he left his university position roughly a decade before he wrote that article.

I personally think you should consider this: you are not the first to submit this work to a journal. Which is unfortunate, but verifiably true. So admit defeat, review the paper as best you can, and work on revising and extending your own results so that you can still publish something later.
By the way, this assumes that the work is in fact an exact duplicate.  Given that you have done some work along the same lines, at first glance it may seem to be more similar than it actually is (this has happened to me more than once). So a very careful reading is in order.
As a side note, from what I have seen, the confidentiality strictures are frequently treated more as guidelines than real, when it comes to sharing with one's co-authors. Along these lines, I don't think there is anything preventing you from contacting the other group - maybe one resolution could be joint publication, depending on your field of work.
Finally a story about something that actually happened to a colleague of mine: He submitted a paper which was given to a reviewer working on a similar project, but months behind. The reviewer kept the paper in the review process until he could get his own work completed, and written up. He did this by raising objections to the content, to which my colleague responded in detail, then raising more objections, etc., all of which took months to resolve.  My colleague's paper was only allowed to proceed after the reviewer's work was published.
This clearly unethical behavior probably happens more often than one would like, particularly when institutional pressure is brought to bear on the reviewer. But I think this is not too dissimilar to your situation, although maybe yours is a less extreme case. But frequently looking at the extremes can point the way to an answer.

This.  Oh dear god this.  My wife has had this happen to her several times now, though because the reviewers are confidential it's difficult to be certain the authors and the reviewers were the same people.  but when you get 3 reviews and 2 go "4 minor points" and 1 does "3 page list of items some of which seem relevant but aren't".

IMO you have a conflict of interest and should not review the paper.  Even if you are able to review the paper impartially, this is not good enough.  Conflict of interest is also about maintaining trust in the system and this depends greatly on perception.  If, from the purest of motives, you reject this paper and then. later, publish your own very similar work how do you think others will view it, especially the authors?

This is a crucial issue with peer review. These are some suggestions, which are much pertinent in an era of open peer review and ongoing accountability.
First, DO NOT REVIEW the manuscript. Whatever your final decision would be, you could be strongly criticized for your revision as you cannot provide an independent review. In addition, your ongoing research project would be tarnished irremediably.
Second, proceed with submitting your work as it stands or doing whatever you now deem appropriate to improve it, but remember that you will always be liable to criticism by the authors of the manuscript (in the ideal scenario you should have turned down the invitation without even reading the abstract).
Third, do not tell any of your colleagues. I know this is largely unrealistic, but this is what the authors of the other manuscript would feel appropriate and demand.
You were indeed unlucky, but eventually the scholarly literature will reward the best paper. My more personal suggestion is though to aim for a mid-tier journal, in order to make sure your paper is considered and published well before the other has reached the scholarly literature.

You need to recuse yourself, citing a conflict of interest and explaining the situation. It is in fact accepted practice to discuss papers you are reviewing with collaborators and to share the MS to obtain a second opinion, as it were; and when they make substantial comments that you incorporate in your review, it is normal to acknowledge such a contribution. However, if you have a collaborator whom you suspect or fear might do something naughty after you tell them that group X has beaten your group to the punch, you may want to exercise a bit more discretion.
Another not uncommon solution that often satisfies all parties involved: if the paper by your group is ready to be submitted, discuss the situation frankly with the editor and ask for a side-by-side (well, one after the other) publication in the same issue of the journal.


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Recommendation letter for Ph.D. in Mathematics
I am going to graduate with my Master's in math, and I want to pursue my Ph.D. abroad. I would like some suggestions involving "Letter of recommendation" to enhance my chance in getting to the university.
I asked professors from my department (3 of them including my advisor). One of them (not my advisor) told me that she is willing to write it for me, but she thought that it might be not strong since she only knew me as a committee of my thesis defense. Actually, I met her during a few conferences that I did oral presentations of my work, so I think her letter should be strong even though I haven't take classes she taught. In fact, I think she has never taught on graduate level during my Master's. She is an expert in the field I'm interested, albeit with slightly different subfield, and I think her opinion in the letter might be strong.
Is it okay to have a recommendation letter from whom we didn't study with, especially in my situation?
Is it better that I should request the letter from another professor I took class in? In this case, I attended a class of another professor and did quite a good job (as I think, since I disccused with him further from the class). I believe he might be okay to write it for me, but during the class he expressed no interests in the field I will be applying, so I send a request and talk with the first professor above beforehand.

If a professor tells you they can't write a strong letter believe them. Professors know what a strong letter is and what a weak letter is. A weak letter will look bad with graduate committees.

@CameronWilliams She concerned about the familiarity. So, the graduate committees concern seriously on the familiarity of the recommenders?

Echoing a comment, if she tells you it won't be strong, it won't be strong enough. It isn't personal familiarity, which is mostly worthless in letters, but familiarity with your work and how you go about it. How do you overcome difficulties, etc.
The letter needs to be an honest and confident prediction of your success in doctoral study and beyond. If she says she can't make that prediction, then you should look to someone who can.

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text:
Confusion regarding manuscript status in IOP's article tracking system, the status of awaiting IOP staff decision made me very confused
In the ScholarOne Manuscript System, the status changed from "Awaiting Decision" to "Awaiting IOP Staff Decision". Do you know why the state changes from awaiting decision to awaiting IOP staff decision? In my previous submission, I received the referee's report shortly after the awaiting decision status. The status of awaiting IOP staff decision made me very confused.

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What safety measure is recommended when sending in paper for peer review
How do I ensure that the person doing the peer review of my work does not steal the intellectual property? I am asking because this paper is worth $1 million prize.

Does this answer your question? https://academia.stackexchange.com/questions/65817/how-can-an-author-get-assurance-that-his-work-will-not-be-stolen-by-journal-staf

If this is what you are worried about, instead of correctness of the paper, it is most likely wrong. In math, physics and theoretical CS people typically post their papers on arXiv before sending them to journals.

Given that you've said this paper is worth a million dollars, it sounds like you think you've proven one of the Millennium problems.  There are a lot of people who claim to have done this sort of thing, and they are almost inevitably wrong.  That you are worried about this suggests you have very little background in math. Trying to jump to a Millennium problem with no prior mathematical research is like a person in 1800 trying to build a rocket to take people to the moon. This is not going to be productive or at all likely to succeed.

@JoshuaZ: indeed, https://academia.stackexchange.com/questions/215730/what-is-the-best-way-to-submit-a-mathematical-solution-to-a-university (Collatz conjecture)

@BenBolker Ah, so not a Millennium problem, but another famous problem with prize money.

I have proof the collatz conjecture, and in doing so my method has revealed that if I publish it, your encryption and security are in jeopardy. How do I proceed from here. If I am not taken, seriously, I proceed with publishing starting Monday.

@Kevinswag  Your claims in your last comment make it even less likely that you have discovered anything at all. It is unlikely there's any deep connection between Collatz and encryption. However, this sort of extremely grandiose claim is made by people all the time with no mathematical background who claim to have solved major problems. Do you think all the others who claim to have solved the Riemann Hypothesis, or resolved P != NP, or proven there are are no odd perfect numbers were at all likely to be correct? Why do you think you are different than any of them?

The main safety measure is to send the paper to only reputable journals. It would take a conspiracy to steal the ideas and a miracle to get them published by someone else before you do.
Relax. Almost everyone is honest and reviewers are chosen for their ethical behavior as well as their knowledge of field.
If it isn't for publication, then make sure that you send it to people you can trust. These should be people with a reputation to protect.
In some cases, such as a prize competition, you might be able to submit it to the prize organization first.
But, there are no absolutes in this world. Overthinking it can lead to ulcers, though.
In extreme cases, one could file a sealed copy of a paper with a lawyer who dates and retains the copy. This would offer some, but probably not absolute protection, though at a cost. Older schemes had people mail themself a copy of the work and leaving it sealed on arrival, presumably dated by the postal authorities, though that dating might require an extra cost mail option.

To have a more rounded answer, you might mention Müller and Bednorz who discovered high-temperature supraconductivity in 1987. Since this was a major breakthrough and easy to reproduce, they were worried enough about being scooped that they announced it to the New York Times and submitted to a lesser known German physics journal with a trusted editor. People chastised them for not sending it to something like Science or Nature first, but obviously they had limited faith in their integrity in view of the temptations.

When 1.a discovery is an obvious breakthrough, 2. the author is not well known with a network of trusted people, 3. the idea is easy to understand and to appropriate, trust alone is not sufficient. Where arXiv is an option, it should be used. That being said, it is extremely rare that an outsider lands a major scoop and OP would be well advised to get opinions from trusted sources about their work.

I agree that arXiV would be the best way to establish precedence. arxiV submission will probably require an endorsement, which means OP would have to go through the process of getting opinions from trusted sources anyway ... https://vixra.org/ is dodgy https://academia.stackexchange.com/questions/105518/what-are-the-differences-between-vixra-org-and-arxiv-org but would presumably be an easier way to establish precedence ... (searching "collatz proof" on vixra gets 334 hits ...)

Thank you, Ben Bolker. Yes, I am very aware of all of the ridiculous attempts that I have seen. The approach that they have taken is juvenile from the beginning. My approach is what sets me apart. Many people will cry that they wasted so much time. I do appreciate everyone making their submissions public so that I can see why without seeing mine. They would think that any submission would be ridiculous. I agree everything I have seen other than mine is ridiculous.  I emphasize the word ridiculous again.


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LOR deadline confusion
Hi quick question about deadlines. I am applying to the MA in health sys management and data analytics program. on the website the due date is Jan 15th for the application. the website says that we should have "completed application and supporting documentation is uploaded into the portal two weeks before the application deadline." - does this include like everything but the referee form and references? (like i should have my transcript, letter of intent, cv, etc. uploaded but the referee list with emails and names and their letters can wait until the actual deadline right?)
i tried asking the deparment but i'm still confused. the email bounced back since everyone's off starting today, but it says "Admissions tips for those applying to Grad Studies:
Supporting documents (including reference letters) can be submitted up to 14 days after the application deadline (i.e., December 29th for a December 15th deadline). "
Does this mean that by Jan 1 (2 weeks before the app deadline), i should have my cv, transcript, letter of intent, and writing sample uploaded? do i still have time to hold off on the supplementary information forms' page until Jan 15 (the page below)?
[the main page of the application website][1]
if anyone knows or has advice for me, i'd really appreciate it. so far i only have 1 reference and i'm waiting on the second. i just don't want to overwhelm them
[1]: https://i.sstatic.net/Ap4rHO8J.png

What exactly does the text before "completed application and supporting documentation is uploaded into the portal two weeks before the application deadline." say? It seems pointless to have a deadline when everything has to be done before.

@MisterMiyagi it does seem weird that they want everything done 2 weeks before. on the website it says this: Start early!!! It is the applicant's responsibility to ensure a completed application and supporting documentation is uploaded into the portal two weeks before the application deadline. Late applications or incomplete applications cannot be reviewed by the admissions committee.

This makes no sense. Saying that the application is due two weeks before the deadline is a contradiction in terms. And then saying you can submit certain documents after the deadline makes things worse. So unfortunately, this is not some convoluted-but-standard language that we can help you parse; this is just unclear, and you'll have to ask them for clarification.

Ok thanks for the reply, I'll try and get in touch with them in the new year @cag51


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What is the best way to find an external examiner for an MSc (e-government)
I am an advisor trying to find an external examiner for my student for an MSc (area: e-government).
Currently the thesis is at the proposal stage (which also needs to be assessed by an external examiner). I'm a relatively young supervisor and therefore found it a bit difficult to find a suitable candidate. The person would have to have a Ph.D. and be proficient in English.  There is also some money involved (but the details can be only disclosed to those who are really interested).
My approach so far has been to check papers on e-government and try to contact the authors.  But maybe there is a dedicated forum where I could approach potential researchers in an easier way?

Although I haven't needed to recruit external examiners, I have served as one and have watched colleagues recruit them.  Typically, the advisor is working with students in an area related to the their own work, and thus can reach out into their normal professional network to others who work in a related area.  Thus, I doubt that a forum for making these types of connections exists---usually, you already have a bunch of colleagues who would be good candidates and who you already have some sort of relationship with.
It sounds like for your case, however, the student is doing something that pushes into a new area where you don't yet have a network.  Other people in your institution, however, probably do.  I would thus recommend starting by finding out who works in the area at your institution and approaching them: since you are both at the same institution, you are more likely to get a collegial response rather than a "who are you?" failure to respond.  Your same-institution colleague, then, can make introductions to good candidates for external reviewers.
If there's nobody working in the area at your institution, though, you'll need to fall back to what you are already doing.  I would recommend, however, that the best people to contact are not the luminaries in the field but others in a similar position to yourself: relatively young, and thus more likely to find it valuable for their CV to be an external reviewer.

It seems you got it right jakebeal. But in some cases you have to supervise someone that is not directly within your area of research (especially younger staff may experience this) and quite often during your early time you are in the process of building your professional network. I've consulted colleagues at my institution, but not much help (this can be true in big institutions). Anyway my own approach proved to be quite useful - i.e. review of the papers in the field and contacting authors as I finally got some response. Thank you for help

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text:
What does it mean when a journal is asking for declarations?
I want to submit my first paper as a Ph.D. student to this journal and in the guidelines section, the journal ask for a declarations section to be included in the paper.
I don't know how this section should look like since I've never seen one in a paper before, at least I don't recall I did.
anyone have an idea how to go about it maybe some examples should be nice.

Why not look at other articles in the journal? The declarations asked for seem pretty standard and straightforward to me; the types are in bold below "Declarations" in the link you gave.

There are a set of legal, ethical, and contractual obligations that every scientist is required to abide by. Many journals specifically ask about key aspects of these as a "checklist" to help ensure that the papers that they publish are consistent with these obligations.
In the guidelines that you link to, the declarations align with these categories as follows:
Legal:

Ethics approval, Consent to participate, Consent for publication: if you're doing a biomedical study, these are absolutely ethically required and often legally required as well.

Contractual:

Funding: Somebody probably paid for this research, and the funder likely included a contractual requirement to acknowledge that funding, often with very specific language.

Ethical:

Conflicts of interest/Competing interests: If your paper might have the effect of promoting or defending a company's product, your readers need to know that fact. Think about smoking research funded by tobacco companies.
Availability of data and material: Necessary for open science and reproducibility.
Code availability: Same as for data.
Authors' contributions: This is part of the move from guessing significance by author order into a more organized "movie credits" explanation of why people are on the author lists.


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Is it ethical to submit a paper with the name of a co-author who cannot be contacted?
The paper in question is based on research my collaborator X and I did together some months ago. Our respective contributions to the research were around 2/3 for X and 1/3 for me. In terms of the actual text of the paper, X wrote about 1/3 and I wrote about 2/3.
During the writing of the actual paper, X decided to leave academia. I can no longer contact X: emails to the old address go undelivered and there is no forwarding address for physical mail. Attempts to find X through web searches and contact X through mutual acquaintances have been unsuccessful. X has thus not seen a complete draft of the paper, only the sections that were actually written by X.
In these circumstances, is it ethical for me to submit a paper with X's name on it, without a complete version having been checked by X and without X's approval?
If I do submit it, should it contain a note of the fact that X was unable to check the completed paper? I am considering the hypothetical possibility that I could have inadvertently introduced an error while writing the complete paper (and such an error might survive through peer-review and into publication); responsibility for such an error should be mine alone.
There is no possibility of separating out my contribution into a separate paper. Either the work has to be published as a whole or not at all.
I am in a field where alphabetical listing of authors is standard, so there is no question of the order of authors.

This is a very good question. Note that many journals require all authors to personally sign a statement to the fact that they read and approved the final manuscript, so you couldn't submit here at all, unless you decided to publish without X and maybe attribute X's contribution in a prominent place - more prominent than the acknowledgements, certainly.

I don't know but I hope it is possible and ethical to publish that work, I'm thinking about posthumous publications.

@Trylks I did think of the parallel with posthumous publications. This situation is rather different: X may at some indefinite point decide to return to academia, or at least resume research, so this paper may have some effect on X's future. (See my point about a hypothetical error.) And from a legal standpoint, there is another difference: a dead co-author's heir could sign copyright release forms etc.; an uncontactable co-author cannot.

I am fairly baffled that in 2014 you can truly not succeed in tracking down someone that you were in contact with one year ago and who had an academic position.  I assume your tracking down process including talking to someone in X's previous department, e.g. his thesis supervisor (if he was a student) or his department head (if he was faculty).  Was the answer really "We're sorry, X has vanished without a trace"?? (X doesn't have a cell phone, a facebook account, a gmail account??)

My first reaction to this question was, "I'd bet I could find them."

@PeteL.Clark Those are the kinds of routes I tried. X's former supervisor and colleagues are likewise unable to make contact. X seemed to have had only a departmental email account, which was closed some weeks later because X was no longer checking it and the mailbox was overflowing. X did have a prepay cell phone, but the number is no longer in use. And X belongs (as do I) to that select group who do not use social networking sites, but I had a colleague check Facebook and LinkedIn for me anyway. Web searches only lead to X's publications, talks, etc., all with obsolete contact info.

@Senex: But none of X's former colleagues even have a clue whether/where X moved to?  Was X a foreigner in the US or something like that -- could he have left the country entirely?  Does no one know of any relatives of X?  This is almost getting scary: maybe someone should conduct an actual investigation into X's whereabouts.

@PeteL.Clark As far as I know, no one knows where X is, but X did announce to me and other colleagues an intention of leaving academia. Yes, X was a foreign resident and may have left the country. Some of X's colleagues think that X had become disillusioned with academia, and thus that it is possible that X deliberately cut off contact totally. Personally, I think absent-mindedness is the more likely reason for not leaving forwarding addresses etc.

@Senex: Hmm, what a weird situation.  I think you have to be a little more than absent-minded to go off the grid so totally.  I also think that it's strange to close someone's university email account after a period of weeks without successfully contacting them.  I also don't know anyone who doesn't by now have and exhibit at least one non-university email account.  Anyway, I left an answer.

I think Pete covered the ground pretty throughly, but if your colleague was a foreigner, have you tried talking to the people at your university who handle paperwork for foreigners? The US govt tends to require a lot of information about foreigners when granting visas. They might have a forwarding address or phone numbers or something, maybe in his home country.

@PeteL.Clark I think the reason they closed the email account was that it wasn't being checked (this info comes from X's former departmental colleague). I think when an account are still being checked or is actively forwarding mail, universities tend to maintain them -- I have four so far. And thanks for your answer.

@FaheemMitha Thank you -- that's a good idea. I'll ask colleagues at X's university to explore that avenue.

@Faheem's suggestion is a good one.  I was thinking along similar lines -- try to look into the immigration status -- but that's a smart way to do it.  (It may well be worth an answer.)

@PeteL.Clark: While I agree not having a private e-mail account is unusual (though not unheard of, even among IT people, when they totally rely on instant messenging ...), why would it be unusual for the former workplace not to have any links? Some people try to somewhat strictly separate their private and their professional lives, and consequently don't indicate their private e-mail address at their workplace at any time.

Quite often the admin staff will have contact details from the applications stage.  They may be able to pass a message on even if they can't or won't divulge that information.

@PeteL.Clark I had this happen to me, and in 2014 its still tricky to track down a collaborator you never actually met, because you came on the project late, after they retired. In Thailand. And in a department where no one speaks Thai.

I am a bit surprised that people expect (yea, almost demand) some measure of being electronically contactable. I know quite a few people that went off the grid (and given the overload of information nowadays, I can kind of understand them). One does not have to do a "Grothendieck" to disappear from the electronic grid.

@Senex: Erdos would find your situation to be exactly that of posthumous publications; he referred to those who had stopped doing mathematics as "dead" (and those who had died as "had left").

This is actually the subject of a blog post over at Adventures in Ethics and Science. In general, it seems that several possible actions are defensible. However, whatever action you take, you should make sure to

Document your efforts to reach your co-author
Let the journal editor know at submission time what's going on

RetractionWatch is full of stories papers that were retracted for having been submitted without a co-author's knowledge. These steps can help you avoid that fate.
Given you've done 1 and 2, your choices are then:

Include the co-author, despite the radio silence, or
Acknowledge the co-author

The problem with the first choice is that authorship signals endorsement of the paper's contents. If the missing co-author has not read and endorsed the final contents, having his name as an author is misleading. However, you can resolve this to some degree by including an explicit statement (e.g., in a footnote) that Author X could not be reached to review the final version of the paper.
The applicability of this choice also depends very much on the journal’s official policy and what responsibilities each of the persons listed as authors have met. I'm sure we can all agree that it would be out of bounds to forge the missing co-author's signature on a form that needs to be submitted with the manuscript! However, even if you have to sign a form stating that all the authors have reviewed the manuscript, you shouldn't do that either - tell the editor you can't, and explain why.
The problem with the second choice (acknowledgement instead of authorship) is that the missing co-author has presumably done enough to warrant authorship of the paper. However, you could argue that an essential part of authorship is to see the paper through to publication - and that if the missing co-author has not done that, he does not deserve authorship. Again, if you do this, you must clearly document the author's contribution in the acknowledgements and alert the editor.
Which action you choose will probably depend on authorship standards in your field and the outcome of your conversation with the editor. Whatever the result, make sure you clearly and honestly communicate the contributions (and lack thereof) of the missing co-author to both your readers and the editor.

This is a typically clear and thorough answer.  "However, you could argue that an essential part of authorship is to see the paper through to publication - and that if the missing co-author has not done that, he does not deserve authorship."  Yes, I argue that.  I don't think this part is field specific or even particular to academia: if you're engaged in something jointly with someone else, and then you somehow disappear completely and are unable to be contacted for the indefinite future (an impressive feat, nowadays), then you have to expect that the other person will proceed without you.

I strongly disagree with "However, you could argue that an essential part of authorship is to see the paper through to publication - and that if the missing co-author has not done that, he does not deserve authorship.". First, it is matter of field (think about experimental fields where there are many authors; but for n>3 rarely everyone is writing the paper). Second, I can't imagine saying to anyone "So, you don't want to write a paper on our results? Fine, I will do it myself, being the sole author". Writing is vital part of research, but not the only one. (Otherwise, a great answer!)

@Piotr  Perhaps this was not clear, but "seeing a paper through to publication" doesn't mean writing it - it just means being available to clarify things to the other authors about your parts, reviewing drafts, signing any paperwork that authors must sign, etc.

@ff524 I meant the writing process. And in this case doing some writing, but not being available in the last stage is even more "writing contribution" than it happens in many fields. So a comment than after this contribution someone could be stripped of authorship makes me uneasy. I agree that it needs to be clarified that the other author could not review it (related to technical correctness, endorsement, etc). But then a note that authorship that is "in absentia" (i.e. your first option) makes the situation clear and I see no drawbacks. (Unless the journal has another policy.)

@Piotr personally, if I was lying unidentified in a coma somewhere for a few months and my collaborators thought I had disappeared, I would prefer they do Option 2 (acknowledgment). I wouldn't want my name on a paper I hadn't been able to verify, even with a note (that many readers won't read). (But maybe it's just me :))

@ff524 I see. For me it is the opposite (i.e. unless I find later a paper of quality below my expectations); actually, while undergrad two times I was informed of authorship after acceptance (back then: experimental physics; and I was happy). Moreover, for career stuff it is easier to say "Well, it uses my results but I was in coma, see this footnote." than "Hey, but I am the author of this great finding! See, I am in the acknowledgements!". Especially since most papers carry non-negative weight. However, for the OP's particular case it is also possible that author prefers to appear nowhere...

@PiotrMigdal I see it the other way. A paper to which I contributed but was only acknowledged won't help my career, but won't have a negative effect either. If someone publishes something with my name on it, it may help me (if it's good) but if it's low-quality, false, or misleading, it will negatively affect my reputation (even with the disclaimer). I don't want to take that risk.

Let us continue this discussion in chat.

If you can document that you have made a good faith effort to find X, and have been unsuccessful, I would think you would be covered on both the legal and ethical fronts. There's no reason for all your work to go to waste just because your associate has gone into hiding. If the publisher/journal won't accept them as an author without their signed release, publish it under your name and very prominently acknowledge their contribution (as a special note in the introduction). Make sure the journal is aware of this special case, so neither you nor the journal are blind-sided if X shows up. Note that you have been unable to contact them and would appreciate hearing from anyone who can reach them (and, needless to say, readers will likely have a hard time contacting them).
If you decide to publish "jointly", explain in an introductory note that X did not review the final work, any errors are solely yours, etc.
Do you know for sure that they simply left academia, and didn't in fact die? Have you checked "white pages" phone listings? Have you checked online death records?

The story makes me a bit concerned about the safety and well-being of X.  I might try to vocalize that concern to X's former department head and see whether she has anything to say to allay it.  If really not, then perhaps you might try:  "I am concerned that X might be a missing person.  Would you be willing to help me contact the authorities about this?"
Somehow though the vibe I am getting from you is that X really just definitely left his own career and does not care or want to be contacted by his former colleagues.  Academics are famous for being a little distant, but truly making oneself unable to be reached is quite unprofessional and even irresponsible behavior.  How much can you worry about the future academic career of someone who is willing to sever all contact with his former coworkers for the indefinite future?  It is very strange and by the way disrespectful to you: did he say anything to you about your project or did he just completely leave you in the lurch?
Let's hope that X is still alive and well, but he certainly sounds like he had a dramatic "death" in the sense that Paul Erdos used the word: i.e., he has brusquely left the academic community.  So I think that dealing with this as you would if he were actually deceased sounds strange at first but is a reasonable way to go.
In this circumstance I would do as @Dirk suggested: don't put X's name on the paper.  Dead men don't write papers.  Less preciously, there is an inherent dishonesty in listing someone as a coauthor in this situation.  Rather you should carefully explain the part of the work that was due to X and that you unfortunately lost all contact with X and are forced to write and submit the paper on your own.  Should you expect to have to explain yourself -- and in particular, explain that you did try the things that everyone (including me) thinks should have worked to reach X -- to a journal editor?  Yes, absolutely.  Is this going to create additional hardship for you in trying to publish the paper?  Yes, it certainly might.  It's kind of a crappy situation for you, honestly.  But I don't see what else to do.

The story makes me a bit concerned about the safety and well-being of X. — I know people who left academia with both their head and their middle fingers held high, and (sadly) other people who committed suicide rather than leave academia, so I'm not as concerned about his safety.  His decision to abruptly end his academic career does not necessarily indicate a desire to harm himself personally; it could mean exactly the opposite.

"His decision to abruptly end his academic career does not necessarily indicate a desire to harm himself personally; it could mean exactly the opposite."  Sure.  When I don't hear from someone for a while, I start to wonder whether they might have fallen into a ditch somewhere...but only a bit.  I agree that it is most likely that this person has simply slammed the door on his previous professional life.  But still you wonder...that's why I suggested talking about it to X's former colleagues.  If they're not alarmed in any way, it would allay my concerns.

I had a student who left the lab abruptly and couldn't be reached at all for some five months. I discovered that he had stolen some expensive equipment from the lab, and thus was evading my efforts to contact him.

Coincidental aside: Your mention of Erdos and dead men writing papers reminded me of this, which I first ran across some years ago. I do not know any details behind it, but I suppose if there were one person prolific enough to be publishing papers 7 years after their own passing, it would be him.

@cardinal: I believe that Erdos himself would have said that he has "left"; he specifically used "died" to mean "stopped doing mathematics".  But you are right that sometimes the deceased appear as coauthors of papers, Erdos more than most, so what I said used some poetic license.  However, putting a deceased person's name on a paper is evidently a delicate undertaking, and in some ways the OP's situation is even more delicate: at least the deceased are guaranteed (source: B. Franklin, 1789) not to show up later and complain, as the OP is (reasonably) a bit concerned about.

If people die, they still are being authors (its called "posthumous publication"). Gathering notes, and editing them, does not grant right to strip the late author of authorship (even with respect to legal rights, let alone moral rights). "How much can you worry about the future academic career of someone who is willing to sever all contact with his former coworkers for the indefinite future?" - while, emotionally, you might be right, I don't thing that it is a good way to go (~ "they are dead, they don't care").

"at least the deceased are guaranteed (source: B. Franklin, 1789) not to show up later and complain". Their estate can certainly be alive and well, and complain about something. As I said before, if you have documented all reasonable attempts to contact him, you ought to be considered "covered", but the law has done strange things before.

@Phil: I think you are taking things too far.  In practice, it seems to me that a coauthor of an academic work is a much better custodian of the intent of the deceased author than their "estate".  I can't imagine a realistic scenario in which a law suit would be brought (what are the "damages"?  what is the "reward"?), but I am not a lawyer and not really interested in the legal aspects.  I think the question of ethics is the more pertinent one.

@PeteL.Clark, you wouldn't believe the kinds of things an estate could potentially sue for, if they feel the reputation of the deceased has been sullied and there might be some money in it. At least in the US, the legal system is wild and capricious. Even if a lawsuit is likely to fail, they can still use it to shake you down in a settlement.

I agree that in the US anyone can sue anyone else for anything at any time; I actually included this phrasing in a draft of my previous comment.  One must always be aware of this.  And yet for the case of purely academic research, I do not see what financial interests are at stake: the authors of a journal paper do not legally own anything in any manner of which I am aware.  So I don't see much to worry about here.

[This was mentioned as a comment to the question, but since a couple of people thought it useful, I'm promoting it to an answer.]
If your colleague X was a foreigner, try contacting the people at his university (usually a separate office or division) who handle paperwork for foreigners. The US govt tends to require a lot of information about foreigners when granting visas. They might have a forwarding address or phone numbers or something, maybe in his home country. You might have to go through X's ex-department if the people performing these services refuse to give information, citing confidentiality issues.
As far as whether to include X's name as a co-author, add him to acknowledgements, or omit him entirely, I would lean towards not including him as a co-author, but including him in the acknowledgements, and adding a note that you would like to have him as a co-author, but don't feel you can reasonably do so; and including a brief description of the circumstances. It is unclear whether acknowledgements require permission, in fact I asked a question about exactly that some time ago. Generally, I play it safe and ask for permission, but under the circumstances, I don't think anyone will blame you if you don't.

Typically, yes, it would be unethical. You should always allow co-authors the chance to review a paper.
However, this case of missing co-author is a different situation.. I'm sure if you try harder, you could find X. If you have exhausted all resources and absolutely cannot find X, you might consider bending the "rules" a bit and publish the paper with X's name.
You might also consider contacting the journal editor for their feedback.

Thank you for the answer, but could you expand on "I'm sure if you try harder, you could find X" with any practical suggestions? I'm not sure what else I could try. (A colleague semi-seriously suggested a private detective...)

@Senex private detective was going to be my suggestion.

+1 for "ask the editor" (or editor in chief). If you can't find X, you're going to need the editor's sign-off to proceed without him.

Given that the co-author has likely left the country, a local private detective would be useless, and a foreign private detective would be difficult or impossible to hire (even if you know what country the co-author disappeared into).

Your university/department probably has a protocol for investigating research malpractice (ie the people who would be responsible for any disciplinary investigation if the "missing author" made a complaint about the route you eventually choose). I suggest you approach them for advice now. And definitely approach the journal editor for advice - they may have seen this before.
Ethically, there is no perfect solution. One thing to weigh up when considering whether the missing author should be an author: are your results controversial in any way? Do you have any reason to think that the missing author might disagree to any significant extent with what you've written? If so, this should weigh heavily in your ethical analysis of the various options.

I am surprised that a certain issue has not been raised here:
Copyright
Depending on the country the copyright of his work may either lay with him or the university. If the university owns the copyright for his work than indeed with proper permissions from the publisher and proper acknowledgments it would be quite ethical to publish such a work. If however the author still owns the copyright it would be absolutely illegal to publish his works without his consent. Now, as far as I know most universities handle this quite well and it tends to be a standard clause in any contract, but it is absolutely something you should check as I have heard about universities where this was quite explicitly not the case on an ideological basis (just check your own contract).
Associating X's name without his consent
Another issue that has not been raised is whether it would be ethical to publish X's name in the first place. Personally I am inclined to argue that in case that the copyright lies with the institution and author X has disappeared in such a way that you were not able to find him, it might not be in his best interest to publish his name, nor add any value for you. Now, don't misunderstand, I am not arguing for not mentioning him at all, rather I would refer to an anonymous author in the author list and in the acknowledgements describe the situation without mentioning his name.

If the university holds the copyright then publishing without him would perhaps be legal, but that does not make it ethical.

@Nate Eldredge: to clear that up, I meant this as an answer in addition to the other answers, not stand alone. I do however think it's unethical to publish X's name without his consent.

If a co-author had died while a paper was being prepared, I would normally expect to see them continue to be listed, along with a footnote mentioning that fact.
The situation here is slightly more woolly because it requires more explanation and in the case of a death there's no risk that the co-author will reappear and repudiate the work. Nonetheless they seem close enough and a footnote along the lines of "X did A work but was unavailable to contribute to the final draft of this paper" would be appropriate.
As others have said, flagging the situation with the editors and any local ethics committee would certainly be prudent.

"in the case of a death there's no risk that the co-author will reappear and repudiate the work" -- I dunno, they could have placed an affidavit with their attorney brutally dismantling the work and your personal character, to be published on the anniversary of their death ;-)

I would also say, yes, it is not totally ethical to have X as a co-author if he did not approve the final version. If all attempts to contact X fail, and also you are sure that X left academia for good, it would suggest to mention X's contribution in the acknowledgement in a honest way.

Presenting a joint work as your own is more unethical that including the name of the author who was not accessible to review the paper.

@Alexandros I would suggest to extend your view as an answer so that there is space to elaborate a bit more and give reasons. Probably more users share your view than mine…

@Dirk, expanding his view as an answer wouldn't be answer to the question as the OP never asked about removing the missing co-author's name..

There is, of course, the possibility that the foreign-born author fears problems or retaliation at home if they published.  Not knowing the topic, I can't say, but the persecution of Salman Rushdie's "The Satanic Verses" with a fatwa and death threats springs to mind.

This is certainly an interesting idea, but it does not answer the question of whether/how the OP should submit the paper.

Also, if the missing author did not want the paper to be published with his name on it, he could have just told his collaborators as much - I don't see how disappearing without a trace would help.

This is not entirely facetious.  I do know of Iranian researchers who have to be very careful how they advertise their joint papers with Israeli coauthors.  (But they did tell their Israeli coauthors about their need for discretion.)

Does not answer the question, but points to an aspect a lot of people might overlook. No reason to downvote this.

Can't you just rewrite the article? That is, keep all the ideas, techniques, etc., but produce an entirely new text? That would at least deal completely with the issue of copyright. In that case, you would be the sole author (though you must include a very generous acknowledgment note, for sure).
Even if your article contains experimental data/lengthy calculations, you can reuse that data as long as you remake tables, graphs, etc. as your own work. Again, conspicuous attribution is required.
And speaking as someone who has herself gone away abruptly from a doctoral research position, you should consider that the troubles you are going through right now may very well have been fully foreseen and intended by your MIA colleague. So that if you manage to finally track him down, he may simply refuse to publish or even flat out refuse to talk to you. And he's fully entitled to do so. (Not trying to imply that you mistreated your colleague in any way; I certainly felt mistreated before I left, and if someone ever came looking for me, for whatever reason, I'd tell them to shove it. But in my case I rather doubt anyone will.)
So, the gist of it, as I see it, is that you are fully entitled to use the ideas, data, that is, the substance of the work itself (with very explicit attribution and acknowledgment); but you cannot in any way list him as a coauthor without his formally expressed consent (that would be misrepresentation on your part); and you certainly cannot publish anything he actually wrote while omitting him as an author (which would be plagiarising).
On a final note: Keep in mind that, though he may appear to be missing, it is very possible he is still keeping an eye on whatever your lab/department is doing. If someone from my previous workplace did anything like that to me, I would be sure to be back to give them as much grief as I possibly could.

Rewriting someone's words does not remove their claim to authorship for their other intellectual contributions. (NB: I'm not necessarily arguing that the missing author should be kept as an author, just that rewriting the text does not suffice to remove his claim if he has one.)

@ff524 It certainly is enough, since the new text will by definition not have been authored by the missing person (as long the new phrasing is sufficiently original). You appear to be assuming that the authors are named for their ownership of ideas, which is certainly not the case. If it were, any person whose work you built upon substantially would be entitled to block publication of your article. What I'm suggesting is that the OP treat the joint article he currently has (in whatever state it is) as an unpublished internal tech report and cite it accordingly in his newly written article.

In every academic field I'm familiar with, substantial intellectual contributions to the original work a paper describes are considered possible grounds for authorship.

There are a lot of extremely negative sentiments in this answer that I do not want to engage.  But just one easy thing: the answer seems to assume that the OP and X were in the same department.  A careful reading of the OP's comments reveals that this was not the case.

Yes, you are correct: Possible grounds for authorship, meaning, if that person has contributed significantly to the substance of the work, even if she had not written a single word of the final publication, merits her listing as an author if she so wishes. Which is clearly not the case here. So my proposal at least puts the OP in the clear from a strictly legal standpoint (ie, copyright) and is, at the same time, the most intellectually honest course of action, as it neither misrepresents (only the OP is the author) nor defrauds the other guy, since he is dutifully credited.

@PeteL.Clark Indeed I had assumed they worked in the same department, but, really, what difference does it make? If you're free to cite any random article from any complete stranger, why wouldn't you be free to cite a substantial piece of work with which you were demonstrably involved, even if it exists only as a draft?

Well, since you ask, for instance it makes your last paragraph look completely paranoid.  But I am not going to further engage with you on this --  I find the way your answer hypothetically evinces extremely hostile -- even menacing -- behavior to be disturbing.

@PeteL.Clark Well, the OP's in a potentially hostile situation, unless you really believe all the whimsical 'X is just distracted'/'X must have fallen down a well' scenarios posited by the majority of commenters above.

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


text:
Does taking a course pass/fail undergrad look bad for PhD admissions (already accepted into a MS)
I’m a undergrad civil engineering major in my last semester. I’ll be going for my master’s after graduation, and I've already been accepted to said master's program. After my masters there’s a good chance I’ll go on to a PhD at another institution, potentially in Europe.
I’m currently debating whether or not to take an intermediate CS class pass/fail. At the graduate level, my subfield is fairly computational, despite undergrad civil curricula not being so. While not required for my major to graduate, I thought it’d be nice to get a little more CS experience to prep myself.
I’d prefer to take the course pass/fail since it’s quite difficult and my life is a bit busy with research/work. Would any graduate schools down the line care about this as I apply to PhD programs? It’d be the only pass/fail course on my transcript and I otherwise have a ~4.0 GPA. While not a major requirement or a course most civil undergrads take, it’s still relevant to my field so I feel like it’s a grey area. Without taking it pass/fail I think I'd get a B or if I'm lucky an A-.
I'm not sure if I’m overthinking this, but I’ve gotten this far and just want to choose wisely. Another option I've been considering is just keeping up with the textbook readings and self-teaching myself the material.
**Note I consider this to be a somewhat unique case since I'm already into a MS program. Also, this course is technical but not a major requirement or anything anyone would expect a civil engineering undergrad to have, despite it being quite useful to my eventual study.

The masters and PhD are to be in what subject?

both in civil engineering,  in an area of water resources that uses computational fluid dynamics.

Yes, you are overthinking this. Many moons ago my university allowed a small number of P/F courses. I used them all up and nobody ever asked about them.


text:
How to survive a mean professor
I am an undergraduate student who has been conducting research with a professor for the past year. Unfortunately, I have been feeling defeated lately because the professor I am working with is extremely callous and patronizing. Every time I interact with them, I walk away feeling like the dumbest person alive. Although we initially got along for a couple of months, things changed after I made a minor mistake. Since then, this professor has been really hard on me. They even threatened to write me a negative recommendation letter for grad school as a result of my mistake. Whenever I ask them questions, they respond in a condescending manner, as if I should already know the answer.
To put it simply, it feels like the professor has thrown me into deep water and refuses to help me stay afloat. I am really tired of being treated this way. Even though I am trying my best to do well, things are starting to feel really heavy. I dread interacting with this professor and sometimes feel like quitting. I don't know why I am writing this, but I guess I am asking for suggestions on how to proceed. Should I confront the professor in a mature manner? Should I tell another professor or someone in a position of power at the school? I am at a loss.

Does this answer your question? How to deal with an abusively condescending professor?

To revive an old academia SE cliche: run, don't walk. "I dread talking to her and wish I could just quit." Yes! Quit! The meagre benefit you might gain from continuing is far outweighed by the negative effects of this professor's horrendous behaviour.

wish I could just quit
Can't you? Be very wary of the sunk cost fallacy here. I reckon that eg trying to get a good recommendation letter and some research experience out of this project is ultimately going to be fruitless and a harrowing experience. There are great mentors around, try to find one!
As far as formal complaints are concerned, in most cases you wouldn't be the beneficiary even if things go well (but rather, future generations). An exception is if this is an obligatory research project, and a complaint might lead to you being assigned a different mentor. To see whether this is worthwhile, look into your department's stance on bullying, hostile environments etc. Unless they are very proactive on this issues, a complaint is probably not going to get you anywhere (after all, she is "just" mean).

Thank you for the response. I really appreciate it

You have a right to file a formal complaint. To this end, you should document several cases which, in your opinion, reflect her arrogant or unfair attitude.

Before filing, certainly make sure to discuss this issue with your mentor or/and with an ombudsperson at your university.
However, always mind the old rule: pick your battles. Often, it is easier to simply disengage from dealing with an abusive person, and to cut all the ties. I understand that you have invested a lot of time and effort into this collaboration, and it may be difficult to interrupt it. But on the other hand, your health and your psychological condition are more important than your achievements. Your academic or professional success is only second to your health -- please keep that in mind. Always.

I am aware of a situation where a student filed a complaint about a professor simply because the professor was exceptionally tough and demanding in regard to research. His standards and requirements were extraordinarily high. On that occasion, my sympathies were with the professor.

Your situation, however, looks different. If she becomes, as you describe, frustrated when you ask her questions, and if she responds to you as if you should have already known the answer -- then this is a bulletproof indication of her not being qualified to supervise undergrads, no matter how good a scientist she may be.

I cannot help from recalling a wonderful quote from Khalil Gibran:

"I have learned silence from the talkative, toleration from the intolerant, and kindness from the unkind; yet, strange, I am ungrateful to those teachers."
At the earliest stage of your scientific career, you got an opportunity to discover that in academia, as anywhere, there are people of all sorts. This lesson is bitter but valuable, because it has prepared you for meeting and dealing with (and, when possible, avoiding) such characters in your future life.
This said, try to disengage from that person, if your circumstances permit you to do so, or if you feel that this is damaging to your psychological wellbeing. Put your health first.

Thank you so much for this. It means the world to me.

@Elizabeth_555 May I reiterate this: put your health first, success second. I know what I am talking about. For my degree, I paid with my health. It was a bad deal.


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Choosing a conference and a paper publishing house - is it only a student responsibility when cooperating with supervisor?
I wrote an article that was a conference paper with my supervisor. It is to be published online in Conference Proceedings Magazine. Just some of the few of the chosen articles are about to be published in an quarterly magazine which is more "prestigious" in my field with more points.
When I was on my 1st year of PhD (now Im on my 2nd) I informed my advisor I wanted to join a conference even without an oral  presentation but only with a written article. (just to test myself in the international academic environment). It was me who found this event but I was a bit unsure of the field, did not know which conference is worth to apply. My supervisor never offered other conference or paper possibilities. Only when he realised that this event was international he immediately wanted to join in.
I agreed and was happy. We split parts for 50% and that is how it was signed by us.
The challange for me is that he was never interested in theme and time of the event, organisers themselves, he did not even check their website, any information. The organisation sent many emails regarding the conference, articles, presentations but he never checked them. He told me I needed to be responsible for everything. So I was.
I made sure he knew the organisation, the academic stuff, article deadline and everything even though he never checked anything by himself. Whenever we met I was telling him about the conference and the deadline, organisation.
But when the article deadline was approaching he started calling me and asking me questions that made me uncomfortable and I was in a bit shock. He did not know that the conference articles were firstly published in Conference Proceedings Magazine and later only chosen ones in some better, more prestigious magazine by the same publishing. He did not know that those magazines were published only online and started slowly accusing me on choosing bad conference and bad publishing house. He thought that articles would be printed in a paper version of a magazine.
I gave him those information way before.
I just only want to know if its obligatory that only a 1st year PhD student is responsible for everything? Is it normal that the advisor does not know the publishing house and the conference organisers ?
The deadline was in march this year and of course I sent our article.I am just not sure about his attitude towards this situation. Please clarify this.
What are your suggestions?
Thank you

What stage of his career is he? Early career...winding down?

In my opinion he is in the middle of his career (not sure though). But I am his first PhD student with my colleague.  Before us,  he only supervised master degree students.

There are both valid and invalid reasons for such behavior, but, for some advisors, putting the task on you could mean both trust and forcing you to get the experience that you will need in your career.
Normally, venue would be a joint decision for a joint paper, I hope. Some advisors would impose their will on you, though. Is that better or worse?
On the negative side, which you seem to be focusing on, (worst case) the person is just lazy and disengaged. Hopefully that isn't the situation here.
Midway between, you say that you are the one who found the venue and it might not have been known to him, even in the best of circumstances. So, he leaves it to you.
But it is, in fact, good experience and you will need that for a successful academic career.

Thank you so much for the answer. I am a person who needs to have some 'solid' background for any task I do. And when I don't know I usually ask for help. In that situation I did not feel I had this confidence and a 'solid background'. I thought he would help me choosing a 'good' conference or paper. Actually my other pHd colleague who has different supervisor told me he was given all the instruction about his first conference and paper by his supervisor. So it was different. I thought that the 'first' - conference, paper or anything needed to be carefully checked by an advisor.


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Starting a research with a professor as a business professional
When I graduated from college in 2012, I was quite excited about my job (although it is a small hi-tech company.) My goal has always been to either start my own business or get back to school for PhD. Ultimately, be able to live a life filled with research, and learning.
I have been working for almost two years now. And before going back to school, I really want to publish a paper and make myself a better PhD candidate. And ideally this would help me better discover my field, gain confidence, and maybe discover assistantship opportunities.
I think I've found a quite interesting topic for a paper that also leverages my work experience in transportation technologies. The paper is about accident prevention and I am targeting a public health professor.  I contacted the professor and I was not able get any response back yet. (It has been 2 days.) I am not sure about the right strategy to follow to communicate such idea and gain her interest. I wrote an email with 3 paragraphs and 350 words. And briefly tried to explain the  possible research context and my intention in starting a PhD. But maybe I was just supposed to ask for an appointment? It is a wise way to sent a follow-up email stating how valuable I think this paper would be? and ask for an appointment?

I feel like a question like this was asked before, but I can't figure out the right keywords to find it.

Many professors take a while to respond to emails. I would give it at least a week before you follow up with her.
When you do send a reminder, keep it brief and polite, and send it as a forward of your previous email, so she won't have to go searching for your other message. Reminding her of why you think the paper is valuable could be a good strategy--if you do it in a way that's not heavy-handed and that you think is true (i.e., it's actually of value to her career aside from another line on her CV).
It's always nice to give her multiple options for responding--you might include a line to the effect of, "If you'd prefer to chat about this over the phone, I'm happy to schedule a brief call at your convenience." Saves her time from having to compose a reply email.

Your question doesn't specify how well-adapted the proposed research is to the particular public-health professor you've contacted.  I think this is a key issue.  Let me explain:
Most academics have broad training, some expertise across a wide range of areas, and then are true masters (in some cases, the top ones in the world) in a much smaller range of topics.  I considered at this point giving examples from my own experience to indicate what sort of things which are "up my alley" that would get me to respond quickly rather than to be interested in principle but respond only much later or never, but this ran into the following issues: (i) the examples would be meaningful only to mathematicians with some experience in number theory, which I think the OP is not, (ii) unfortunately every time I came up with what I thought was a description of "my alley", I could then think of someone who sent me work or questions in that area to which my response was inadequate or even non-existent! But I think there is a lesson here: when you send a paper (or a question or an idea) to anyone, it is always a bit of a crapshoot: you may well get absolutely no response, and the reasons for this may have absolutely nothing to with you or your work.  In fact history is filled with examples of much more famous mathematicians rejecting -- or worse, ignoring -- much more important work.
The moral of the above paragraph is this: you should cast a wider net.  If there is one faculty member that you feel is the perfect person to get involved with, then you may as well contact them first, and the job of your message ought to be to convey to them why they are a perfect match for the project at hand (and that the project at hand may be worthy of their time).  Even so, your perfect match may not see it that way or may simply be too busy to give you the attention you deserve.  (Again, apologies to all the people who sent me good work or asked me good questions over the years to which I did not respond.  I definitely respond to some of the correspondence I receive; I do not always have time to respond to all of it; and I sometimes make what looks in retrospect to be bad choices about what to respond to.  In particular, something promising that I don't have the time to think about at the moment tends to get put on the "answer later" shelf, but my algorithm for addressing correspondence does not have a step which ensures that the answer will actually come later.)  It is okay to write twice to someone when you think it is important, and the repetition can be distressingly effective: as I wrote elsewhere on this site, unfortunately for some types of correspondence I implicitly assume that if I only hear about it once then it cannot be so important.  This gets me in trouble from time to time, but not as often as it should.
More likely though there will be several people who could help you with your idea.  The classiest move is to contact each of them individually and explain why their expertise is well-tailored to your idea.  The chance that you hear back from any one person increases dramatically this way.  And then you can get started with the person who you hear back from.  In some cases this may result in getting emails later on from people who were interested but didn't have time to reply.  Those, as they say, are the breaks.


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Medical school admissions vs. STEM PhD admissions in the United States
I read an article in the past - I forget the source now, but I believe it was credible - about how American STEM PhD programs (and master's programs) admit a lot of qualified international students, e.g. from China and India, in order to help fill the skills gaps in the U.S., but an interesting phenomenon was that American medical schools don't act in the same way, effectively not admitting international students and preserving the acceptance slots for American students.  If this is indeed true, why is that the case?  Doesn't the United States have a skills gap in medicine and a shortage of medical doctors?

To substantiate the claim: "In 2014, 1,901 foreign applicants applied to M.D.-granting programs in the United States and 409 of those applicants were accepted. Of those accepted, 300 matriculated into medical school." https://students-residents.aamc.org/applying-medical-school/article/applying-international-applicant/ Stated reasons I've found is few slots (but not exactly why the slots are reserved), and scarce funding - most people going to med school must self-fund in some way. https://www2.clarku.edu/departments/prehealth/resources/international.cfm

This may have changed but we studied cartels in college and the American Medical Association (AMA) was called a cartel by my professor.
In the US the AMA not only sanctions the medical schools but puts a count on how many students can be accepted. Since there are a limited number of slots competition is more fierce.
There is no external body limiting STEM or other graduate school departments.
STEM and other PhD can get grants as they are producing a product (thesis) that can be (and often is) sponsored.
In medical school the only product is medical training for the student. There is little to no incentive to sponsor a medical degree.

Please check my edits and roll back if you're not comfortable with them.  The main thing was that I removed the editorial comment at the end, which isn't relevant to the question.  (By the way, what you mentioned is not the only factor.)

An important difference between graduate education in the arts and sciences (and engineering) and graduate education in professional schools (fields such as medicine, law, and business) in the US is that most graduate students in science and engineering are financially supported by teaching or research assistantships that cover tuition and pay a stipend for living expenses, while most students in the professional fields pay tuition (as much as $100,000 per year for medical school.)
Very few international students can afford to pay tuition for these professional programs.
Most of the US citizens in these programs take on substantial student loan debt with the expectation that they'll earn enough after graduation to pay off their debt.  For students in medicine and business, this has worked fairly well.

Yes, you're entirely right that funding matters here, and it probably creates an additional selection effect. As you say, the pool of international students who would actually attend U.S. medical schools is small because of cost, and they probably tend to be richer. But even among wealthy international students, those who are more academically talented would probably often apply to academic graduate education instead of med school, because of cost. (Talented international students who deeply want to be doctors might train in a different country or seek an MD-PhD program for cost purposes.)

Very few international students can afford to pay tuition for these professional programs I am not too sure about that. I do know that there are a lot of wealthy parents want to send their kids to US medical school, but can't because they could not get the admission. Many of those wealthy parents have money like tens of millions USD$ and they are willing to spend millions of USD$ just to send their kids to American medical school. Medical doctors have the highest social level in here (Taiwan).

By a lot in my comment above I do mean at least hundreds of thousands. Hundreds of thousands of dollars is nothing to them


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Is it worth it going to academic conferences as undergraduate without any research to present?
In particular, I would like to focus on CS Theory conferences like STOC or FOCS.
I am interested in the presented topics and, of course, it would be useful to learn more about it for potential graduate research. But on the other hand, one can always read the presented papers when they are published. It seems that the most important part of conferences is networking, however, I do not see myself being efficient in networking at this point yet.

Yes. I don't know about SIGACT, but my ACM SIG (SIGPLAN) offers workshops exactly for people like you at all sponsored conferences.

If the conference is "affordable" to you in terms of time and money, go for it! It will be a great way to see more about how academia works. As others mention, there are often some workshops for students, and poster sessions are great ways to learn about new ideas and ask (even basic) questions.
You may not get very much out of going to more than one conference without presenting, though. (If you love the first one and it inspires you to work hard on your research, maybe attending another without presenting anything would be a good thing, but much of the value for you at first will be in understanding how academics communicate with each other.)
Also, check if there are interesting conferences coming up in your region. Often local students can volunteer to help with registration desk or other key work during the conference in exchange for admission to some parts of the conference. This would be a way to get many of the benefits of attending the conference, without having to spend a lot of money to do so.


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Should I agree to submit a paper with my name as coauthor although I did not read and understand the whole paper?
I finished my PhD in natural sciences in 2015. At some point during my PhD studies I did some measurements for some other scientists.
Now they are about to submit a paper containing my data, and I am listed as a coauthor.
I barely remember the experiments. I did not read the paper (yet).
Do I have to read that paper? Do I have to read it often enough to fully understand it? Should I disagree being listed as a coauthor?

Are you still in academia? That might affect the risk and reward involved.

No, I directly went to the industry. Chances of going back to academia are around 0.

I read the manuscript. It sounds valid. My data fits the other measurements of the group. There are no claims, which I would mistrust. Should I be co-author?

The guidance from this question about declining coauthorship may be relevant. If there are other relevant details in your case that distinguish it, you may want to clarify. (I suggest accepting with gratitude, given current information.)

Although doing a "service" by providing measurement data does not usually warrant co-authorship, some groups still decide to do so to show appreciation.
Many people in academia would accept this as it boosts their CV, and if anything wrong was found in the research after publication, the corresponding author has the highest authority.
I would give it a read and accept it if you are happy with the paper. If you are really worried, you can ask the authors to remove your name and explain you feel you did not provide a significant contribution.

As previously stated, they are acknowledging your participation in the data gathering and making you co-author. I would accept it. When possible read the paper and if not certain all that it's about; ask someone that would know and it doesn't have to be the author.


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Is it common for college students to drop a year or 2 between UG and graduate studies?
I've heard of people taking a break for getting work experience or internships and jobs and so on ... is this the norm ?

Not especially common. But make sure you don't lose ground in skills and desirability for grad study if you do it. One year would be more common than longer, I think.  It may vary by country, of course. But your profile implies you shouldn't have to worry about it for a while. Wait until it matters.

@Buffy "Not especially common" is going to be very field-dependent, and I'd say at least in the US in my field this has changed a lot recently from being "not common" to "very very common" - though in my field most people get that work/research experience in academic labs rather than internships/work in industry.

It may not be common, but it's completely normal.

I can't say if it's the norm, but I don't expect that working for a year or two after undergrad would be frowned upon by graduate admissions committees. So long as your job is related to your field of study, you'll be augmenting your academic studies with real-world experience, which can indeed be valuable in preparation for a graduate curriculum.
Personally, I applied for grad school straight out of undergrad, but didn't find the funding I was hoping for, so I worked for a year and then tried again. I received more and better offers the second time around.

It was pretty striking watching this unfold in my graduate program (in the US). I came right out of undergrad as did many of my peers in the year I started; in subsequent years, almost everyone had some post-graduate experience, either as a lab tech, as part of a masters degrees, as a post-bacc program. The simple reason is that those people had much better research resumes than those who had only done undergraduate research.

I think the answer depends upon the field. Personally, I've known many people who work for a few years as technicians or other jobs before they decide they want to go to graduate school in the life sciences. I've also known people who could not get into the programs they wanted to they worked in research labs to build up their skill set.
This post on UC-Berkeley's also demonstrates that people often take some time between undergrad and grad school.
Also, some programs such as MBAs either require or strongly prefer applicants to have professional experience outside. This US News article talks about work experience expectations for MBA programs.


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Picking advisor that you will also ask letters from to transfer
I am wondering whether it is worth asking your advisor for a recommendation letter to transfer right away (*).
Background: I just finished the 1st year of my math PhD and will reapply to transfer to a different university. I'm already at the point of picking an advisor. I've done all courses and qualifying exams, so in my 3rd semester I'll do the oral exam and start writing my thesis.
I narrowed the advisor to 2 options. The pro of the 1st is I've done enough work that future research will be faster, the con is (*). What I've done with the 1st: reading course, research, paper ready to submit, 2 more papers in preparation. What I've done with the 2nd: 2 courses last year.
I plan to continue in academia, so staying at my current university is not an option. However, I won't let the next year go to waste. If there is any research left to be done when I leave fall 2024 for another university, I will finish it in the form of published papers since you can't do a thesis twice. Lastly, I have to ask for a letter because it will be the strongest letter and letters are the most important part of graduate applications, so hiding transfer plans is not an option.
There are 2 similar questions, but both do not cover the advisor choice aspect. Unlike those questions, I am already set on both transferring and asking for a letter, this question is about whether to choose a different advisor.

The question is a little confusing. You seem to say that you are about to choose an advisor and then immediately ask for a letter to help you transfer. Why do you need an advisor at all in that case? You want letters from the people who know your work best. Perhaps you should ask both of these people to write for you. In any case any reference will need some information about why you are transferring.

@EthanBolker Both of these will be letters regardless. I need an advisor because it's necessary to select one before oral exam and thesis writing. If I don't do those and instead spend more time self-studying + doing unofficial research, it will backfire if I fail to transfer. Also, the department will be suspicious that I'm zipping through everything so quickly and now I've decided to do "nothing" for the entire fall semester. Each semester has a minimum credit requirement, satisfied through research or courses, but I'm done with courses.

You should probably try to get advice from both these professors about the best way to move your education forward.

I'm confused, are you trying to transfer advisors or programs?

@AzorAhai-him- Transfer programs, more precisely to a math PhD at a different university. Question updated

Now I’m confused.  If you are to transfer, why are you continuing now and choosing an advisor?  Is it obvious that the work you did at your current university - in terms of courses and oral exams - will be recognized elsewhere?  Why would some at a future university take you on as a student?  I could go on…

@ZeroTheHero Because transferring is not a guarantee. If I don't transfer because I get rejected from all the schools I apply to, then I'll have to continue. Besides, even if I do, I might as well use all the time from now until fall 2024 wisely. I may have to redo courses and exams, but I don't care since they're easy. Any other questions?