text:
Does academia have a specific perspective on religion?
The response to many questions which connected/related issues of religious beliefs and adequate/correct behaviour of academia? For instance the recent (Will ISIS attacks hurt my PhD application as a Muslim?) featured many responses that suggest the proper perspective of academia upon religion would be undiscriminatory/unconcerned one.
This being only what I read out of that I wanted to know if there is a by tradition or convention agreed-upon way that academic decisions and actions should approach when interaction with religious beliefs cause either cooperation or conflict.
cooperation: if religious generates a field of relevant interest (like the theologies)
conflict: if the methods like peer review, seem to be in some sort of contradiction. Meritocratic review by peers (equality) versus potential ranking of persons according to some religious prejudice (i.e. non-believers being religiously seen as inferiors and not peers).
An answer to this question would either give insight why or why not it is by tradition, convention, methodology, etc. proper to think of a specific perspective upon religions from academia. As a third acceptable response a well substantiated suggestion on the reasons academia would be too complex to device such a repsonse would be appreciated too.
As too recently in many domains of science, mostly the "hard sciences" like natural sciences, seemed to have the notion of objectivity.
In else, e.g. some social sciences, and with a post-normal science understanding the issue of normativity has become increasingly challenging. Also in this respect especially the perspective on religious was to my understanding defined as a alternating/competing setting in which both (religion) and academic knowledged may stand complementary. Anyway this is only a initial suggestion what arguments might be developed in an response, as to foster and facilitate the answerability of this question further

Instead of wholesale downvoting of some, maybe a comment would be helping to improve the question further/better? At least a comment would make disagreement less seem simply motivated by believes, but by reason.  Right now my suspision is that disagreement is rather connected with the answer type "no academia does not / should not have a specific perspective?". If so it would help better to form that into an answer, right?

@downvoters, can you specify what excatly does disqualify this question. Both religion and science (related academia) exists and it is not political incorrect to ask about the understand.

I did not downvote, but voted to close as "unclear what you are asking". Please try to clarify what exactly your question is.

I don't understand this question either. From what I can tell, it also seems incredibly broad and unanswerable to me. See the [help/dont-ask], which advises asking specific, answerable questions based on an actual problem that you face.

@StephanKolassa, given the two answers provided, I feel modifying the question can be somewhat unfair, as I change/ modify the question, potentially impacting the validity of the answers. I will try to do so anyway, but take some more time with it. Besides especially the jakebeal answer did provide much of the inside,  I even if not expressed well enough looked for.

I don't understand the question. It is word salad. Academia is – or, perhaps more accurately should be – secular.
Even disciplines such as religious studies are secular (for if the study of religion is not approached in a secular manner, then frankly it's not valid scientific research).
Of course, there are still tricky situations, that should be mitigated as much as is reasonable. But personal beliefs aren't relevant inside the classroom or laboratory. As long as they don't irreparably interfere with someone's capacity to take a course or do their job, they just don't matter.

Your answer addresses indead my question, even though you say you did not understand it. It must be you understood some part of it. Since you mention that invalidation of the research by unsecular approach can occur, another aspect of my question was met.

Can those "tricky siutations" also occur for atheist/secular students?

@humanityANDpeace The wording was confusing, but I guess I managed to understand the gist of it. And yes, they certainly can occur. What if a biology teacher insists that creationism is a valid alternative to evolution – or even that evolution is wrong? This certainly has happened at schools, though I don't know first hand about universities.

your contribution @Moriarty is the more appreciated, as it contrasts the way that many dealt with this question. Since even the term secular exists, its coining must mean people tried to specify a relationship between religion and other setups of human organisation (e.g. state). Fact is the answer gave me a correct term. maybe it was too easy an question as to create lots of discontent (downvotes), sorry

Historically, academia and religion were quite tightly intertwined.  Consider, for example, celebrated ancient Greek philosophers such as Pythagoras and Aristotle, whose philosophy treated mystical subjects just as readily as practical ones, and indeed did not distinguish between them.  Religion continued to be a prime motivator in scientific investigation for many centuries, with no particular line being drawn between theological and other investigations: see, for example, the mixtures of theology, mathematics, and physics investigated by giants such as Newton and Leibniz, whose work remains foundational to much of our knowledge today. My knowledge of the history of scientific investigation in the Islamic world, South Asia, and China is much weaker, but I would be surprised if religion did not likewise play a significant role there as well.
Along the way, however, something interesting and completely unexpected emerged.  Despite the best intentions of those scientific theologians, the theological aspects of their investigations tended to be much less productive than the secular aspects of their investigations.  The Pythagorean theorem and Newtonian physics work in a way that requires no belief on the part of the person using them---indeed, they work even in the presence of great skepticism about their truth.  Faith turns out to be a very unreliable way of obtaining knowledge---at least any knowledge that people can agree upon, as demonstrated, for example, by the proliferation of Christian denominations with conflicting theologies.
As a consequence of these emergent facts, the scientific investigations of academia have become firmly committed to methodological naturalism simply because nothing else has turned out to work.
So, where does that leave religion in today's academia?  There are three main ways in which religion interacts with academia:

Religion is a thing that many people do, and thus it is an entirely valid subject of study, whether from a sociological perspective or from a pragmatic perspective.
Because people have a wide variety of beliefs (both religious and secular), academia, like anything other human institution, needs to make reasonable accommodations for those beliefs that do not compromise the academic mission.  For example, many people do not eat meat, so it makes sense to ensure there are vegetarian options available at a scientific conference banquet.
Some groups of religious believers perceive scientific work as threatening, and thus attempt to attack both science and academia in general, and to undermine them in various ways.  Academia, of course, needs to try to resist such attacks.

I don't see why "academia" should resist attacks.  You can agree with these method of acquiring knowledge or not, but are the theories behind the system and people who should be denfended

@Llopis Religion is a method of acquiring belief, not knowledge. You are confusing faith with fact.

No, I don't belief more for going to the Ka'aba. But from the believed with faith premises I can learn knowledge about how to act in a certain situation, that is theology: studying what I believe to learn more about what I believe.
Otherwise the more I go to the mosque, the more I belief?


text:
Is it appropriate to re-use data from previous publication for a new study?
Data from a published study was deposited on the Harvard Dataverse abiding by the replication policy of a scientific journal. I have no connections with the scholars who collected the data and published the study, but I am conducting related work so I downloaded the "replication" data and used it to also conduct some new analyses. I have now found some interesting results, and since my new tests are not part of the original publication, I would like to publish them in new articles (I will also use some original data that I have collected).
Question: is it appropriate to use data collected by other researchers and made public for replication purposes in other to provide new scientific insights? Should I ask permission to use the replication data for a new publication? In particular, shall I contact these authors and, eventually, agree with data restrictions or co-authorship requests?
Existing questions cover related cases where the same author(s) re-use old data, a case of scanning data from an existing publication, and a case where replication (apparently without extensions) is used to connect with the author(s), and a similar case where a database becomes available upon publication.

One requirement of Federally funded research is that the the researchers must have a plan to make the data available. That doesn't always mean publishing the data or providing a PUF, public use file, that can be easily downloaded. Dong so meets the requirement for a plan. The data you found is likely a consequence of that requirement. The purpose, of course, is to let anyone use the data.

Yes, that's not only appropriate, but -- next to replication -- a main purpose of publishing data. Not being able to build on published data would greatly limit the accumulation of knowledge and lead to wasteful duplication of data collection efforts.
Of course you must cite the data source. Perhaps you should even acknowledge its authors beyond this citation, especially if you have solicited any useful feedback on your work from them, which is something you should try. They know the limitations and "peculiarities" of their dataset better than anyone, and there might even be potential for cooperation.

Beware, of course, of the problem of forming a hypothesis only after you know the outcome of a particular sample and then using that sample to claim you have results valid for the population from which the sample was drawn.

@Buffy I'm not sure how that relates to using or not using existing datasets, to be honest. Surely you could but shouldn't hypothesize ex-post in both cases?

Just a warning to the OP here about the proper use of samples.

@henning to me the relation is obvious.  if i collect some data, I will need funding (in advance) to pay for it.  I am going to try to convince my sponsor that my hypotheses is worth funding.  Before I collect any data, I have committed to my hypotheses.  There may be some interesting non-hypothesized outcomes in my data.  Other than the hypotheses I pitched to my sponsors who is to say what is ex-post and what is not?  The temptation is strong to pretend one formed ones hypotheses before and not after analyzing the data.

@emory So then the temptation for ex post hypothesizing is greater if I don't reuse an existing dataset. Or do I misunderstand you? Perhaps you are saying, to the contrary, that pitching a hypothesis to the funder is similar to registering a hypothesis before the analysis? (And this almost-registration is lacking if I reuse existing data?)

@henning Exactly.  Since there is no hypothesis registration before the analysis, it is entirely on your honor to not hypothesize ex-post.

@emory okay, but you could of course preregister also before analysing existing data, and I'm not sure most grant application really commit you to particular hypotheses. So while what buffy says is true, it really applies regardless of reusing existing data.

@emory That’s a purely theoretical argument. In practice, just as henning hypothesises, the opposite seems to be the case: people are reluctant to just throw away data they generated at great expense if it doesn’t support their stated hypothesis, so they start trawling it for insight. — Besides, hypothesis-driven research isn’t the only valid approach. Exploratory analysis is a common, and valid, alternative.

@KonradRudolph Exploratory Data Analysis is good.  Exploratory analysis to form hypotheses which are then tested against the same data set (while pretending to have not done the exploratory analysis) is bad.

A partial solution to the issue @Buffy and emory raise (and a necessary step) is that it should be very clear that the data used in the subsequent papers are the same dataset used for the original one. That's true whether the paper is written by the original author(s) or new ones, as this answer already states.

The data supporting scientific research is by default public. Hiding or withholding it must not be considered the default. So, you're really asking us:

is it appropriate to use data collected by other researchers and not withheld from the public (which would be strange and inappropriate) in order to provide new scientific insights?

Yes, of course it is, why wouldn't it be?
Just like when I cite a paper, I don't care whether the author published it to help humanity or to brag about their achievements - I also don't care what the official excuse is for doing the default, obvious and necessary thing, which is publishing the data.

source: Stack Exchange

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sort: votes


text:
Accused of not citing a source in an english final paper
So I turned in my final paper for English and was soon met with this
Dear -----,
On April 28, 2018, you were involved in a possible violation of the Code of Student Conduct.
Specifically, it is alleged that you failed to cite an online source used when completing your ENG ---- final paper.
I am a first-time freshman at this university and have absolutely no idea what to do or expect. I've combed through my paper multiple times but there is nothing present that indicates a misses citation. I have citied everything I have used and have included works cited page at the end. Is there any way for me to fight this and prove myself not guilty?

Is it possible for you to respond to that email and ask for more information? Or contact the person who marked the essay?

Here, see if technology can pick up what you missed: https://www.quetext.com Otherwise, I can't say we'll be able to help you much besides offer the suggestion of seeking more information from your instructor.

It sounds like you're confident you didn't do anything wrong, at least not on purpose. So I wouldn't panic.
The instructor may have used an automatic plagiarism detector. Depending how it was configured, it may have been too strict in identifying similar text, and the instructor didn't apply human judgement. You may have accidentally and innocently written a sentence that is similar to something online. In that case, I would just explain what happened.
Alternatively, someone else may have copied from you.

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text:
Is it right to be put as the last author although I have done the bulk of the work?
I am doing my PhD at a research institute, where we have just finished the draft of a 8-hands long paper to be published as a short book with a major editor. I have done the bulk of the work, i.e. at least 80% of the total. However, my coordinator sent me the draft back with the authors reordered by seniority, and I now figure as the last author although my contribution was the largest. I should mention this would be my first publication. Shall I react?

What are the conventions in your field regarding order of authors? These differ widely, and in some fields the last author is the most prestigious, as it implies that you led the work.

Is your coordinator one of the authors?

Some read the author list as those with the most qualifications did the least work...

I do not know the conventions of the field, which is Energy Modelling and Policy. Yes, the coordinator is formally one of the authors, although he did not contribute to the writing of the paper, he just provided some inputs.

That does sound weird to me... Normally it is either ordered by work or alphabetically. Sometimes this is disrupted if people are grouped by institution. But I haven't heard of an ordering based on seniority.

One question that is not completely clear to me: Did you wrote the (major part of) the draft or was it more like you did the work but someone else wrote the draft?

"I do not know the conventions of the field" - I suggest starting looking there, and then inquiring your co-authors.

The order of authors is often problematic and thus I guess this question will be closed as duplicate soon.
Anyway, you should discuss this with your coordinator and ask him why he prefers this order. My colleague is working in a similar area than yours and he is usually the first author, but there might be other reasons in your situation.
Even if you are not able (or not willing to) insist on your preferred order, there are other options to emphasize your contribution. For example you could add an "Authors Contribution" section where you can explain in detail who did which part of the work. Footnotes at the author names are a common alternative (e.g. "* These authors contributed equally as main authors" or "¹ AB developed the model ² CD wrote the manuscript").
This is not only a question of fairness, but there might also be a formal requirement for your PhD or later research positions like "You have to publish two papers as main author." If that is the case, you should ask your supervisor how to address this issue.

As a junior partner who is yet to earn a PhD, the ethics of it are of less concern to you than that you successfully complete your degree and find suitable employment. Yes, you are probably being abused here, but getting powerful people mad at you will have negative consequences - all on you.
I hate to see these situations develop and would (as a more senior person) have harsh words to say to your supervisor, but I can only do that as they have no power over me.
Hopefully this is only your first, not your only, publication. Hopefully you won't have people like this in your future. But you have to take a somewhat cautious route to that future.
It may even be, depending on the reputations of the others, that you will benefit from a visible association with them.

In other answers on this site I've suggested that ethical violations be reported to authorities, but anonymously. That doesn't seem to be one of your options here, I think.

Comments on the reasons for down voting are much appreciated. By others as well.

I'm not sure why I lost 1 rep for downvoting this comment but to be fair to @Buffy I will state reason.
Generally I agree with everything from Buffy.  Here, I agree with literally everything said except that Buffy doesn't provide a recommendation to at least attempt to raise this issue.  For that reason alone I voted it down.
In hindsight, I would like to undo the vote down as a comment is truly more appropriate.  However, the site won't let me. Sorry Buffy.

@SecretAgentMan, actually I don't mind some down voting. It is just good in general to know why. My opinion about my own posts is that if I never get any down votes I'm being too conservative. Some posts are uncomfortable for people, but that uncomfort can be a good thing. This one surprised me, however, as I was trying to keep the OP safe. Some other answers leave the OP at risk and not the one giving the answer. That wasn't the situation for the other answer here, however. Anyway, thanks for the note.

@SecretAgentMan, the rules here, by the way, is that downvotes cost you 1 rep. That is just to avoid rampant abuse. There are other abuse filters built in of course. I seldom down vote, though not because of lost rep. If a post seems dangerous or evil to me I'll downvote (and vote to close such questions), but I'm pretty accepting of things until they cross an ethical line or one that puts another in danger potentially.

thanks for the clarification. I'm pretty new here and didn't know. I should have left comments anyway.  Thanks!


text:
Publishing working paper before submission to peer-reviewed journal
Could the fact that I publish a working paper in a WP-series at the institution where I am doing my PhD jeopardise my chance to have it accepted in a peer-review journal? Since I know it might depend on editor/journal, I specify I was leaning towards Energy Policy (Elsevier).

The 'Guide for Authors' states the following:

[...] Submission of an article implies that the work described has not been published previously (except in the form of an abstract, a published lecture or academic thesis, see 'Multiple, redundant or concurrent publication' for more information) [...]
[...] Please note that preprints can be shared anywhere at any time, in line with Elsevier's sharing policy. Sharing your preprints e.g. on a preprint server will not count as prior publication (see 'Multiple, redundant or concurrent publication' for more information). [...]

Source
Additionally, the page 'Multiple, redundant or concurrent publication' states:

[...] Multiple, redundant or concurrent publication: An author should not in general publish manuscripts describing essentially the same research in more than one journal or primary publication. Elsevier does not view the following uses of a work as prior publication: publication in the form of an abstract; publication as an academic thesis; publication as an electronic preprint. [...]

Source
To answer your question, you should clearly define what the WP-series really is. Is it just a collection of pre-prints or is it a primary publication? That's how you will get the answer you need.
In case of doubt, contact the Editor in advance.


text:
Should I let potential employers know I have a job offer?
I've interviewed for a few positions, one of which has made me an offer.  I'm very pleased with the offer, but I prefer some of the other positions.  I have the luxury of being able to take a lot of time to decide whether or not I accept this offer, so I'm certain I will hear back (either positively or negatively) from the other positions before a decision is required for the offer I've received.
I'm trying to decide between two courses of action, and I want to choose the one that will best help my candidacy with the positions I've yet to hear from.  Plan 1 is to do nothing and simply wait to hear back from the other positions for which I've already interviewed.  Plan 2 is to be in touch with the other positions to let them know I have an offer, and ask where I stand with them.
Would Plan 2 make me a more desirable candidate with the other positions, as they might see my offer as further validation of my credentials?  Or, might initiating with the interviewers in this way be detrimental to my candidacy, perhaps making me seem pushy or self-centered?  If so, I would rather just wait for them to run their course of action (Plan 1).  As I've said, I have plenty of time, so I don't want impatience to hurt me.
If there is a good chance that my meddling will be detrimental, then I'd rather be hands-off here.  However, if it's more likely that informing the other interviewers of my offer will give me a boost, then I'd want to do so.
Thanks for any clarity you can provide!
Edit: For a bit more information and context, the position I've been offered is a non-academic research position that my advisor has described as "prestigious."  The other positions for which I've interviewed (and which I prefer) are mostly academic teaching-centered positions (visiting assistant professors, tenure-track at smaller four year institutions).

What kind of position? The etiquette is different at different levels of the academic food chain, so it would be good if you could [edit] your post to add some context to this job search.

@ff524: I've added some more information.  I hope it is helpful and that it addresses your question.  Thanks!

The argument for plan 2 is that if you have an offer from employer A with a particular deadline but you would prefer to take a position with employer B, then if you don't say something, employer B could take too long to decide what to do and you'd be forced to take offer A before employer B gets around to making you an offer.
I've been on the employer side of this (as both employer A and employer B.)  Keep in mind that once a search committee has completed interviews it has to meet to decide on who should be offered the position and then this has to be reviewed by higher level administrators (deans or vice presidents) and that the process can take time (days or weeks.)  It may be possible to expedite this process if there's a particular deadline, or it may not.
I think that if you've decided that you'll take offer A by a particular deadline if you have no other offers (and that you wouldn't break your contract with employer A after accepting the offer), then you should tell the other potential employers about the offer and the deadline (I wouldn't mention employer A's name or the specific amount of the offer.) It's not likely to hurt your chances with these other employers, but it could help motivate them to get an offer out to you in a timely fashion.
I have received this kind of information from job candidates in the past.  Unfortunately, I've always had to say that (because we had other candidates scheduled for on campus interviews) that we couldn't make an offer before the deadline.

Since I'm not really facing a deadline, my situation is a bit different from the one you describe.  The offer I've received is for a non-academic research position, and they've communicated to me that if I need to I can wait a few months before giving them a final answer.  So if I were to communicate with other employers, it wouldn't be for the sake of trying to get information before a deadline, but for the sake of possibly making me appear like a more valuable candidate to them.

In that case, I wouldn't bother saying anything about the other offer until your deadline is approaching.

First of all, congratulations!
I think you should take Plan 1 at least for now, that is to do nothing and simply wait to hear back from the other positions for which you've already interviewed.
The reasons are,

You prefer some of the other positions
You really don't know  Plan 2 (to be in touch with the other positions to let them know you have an offer) will be helpful or harmful for you to get the other positions
You still have plenty of time to think about it.

During this waiting period, you may want to find more information about the organization who offered you the research position. Is the offer truly good? Would you be happy when you work there? (It seems to me you like teaching better).  In the mean time, if any of the teaching position offers arrives, you can make a smart decision then.

Would Plan 2 make me a more desirable candidate with the other positions, as they might see my offer as further validation of my credentials?

This is a bit of a crap shot, I am afraid. How this may be perceived also depends on whether the other institutions perceive your offer as less, about equal, or more attractive than their own position.
Case 1 - less attractive:
They will probably not care too much about your other offer. They assume that you will likely take theirs if you get an offer, and the fact that you have an offer for a position that they assume is easier to get won't fundamentally change their assessment of you. If the other offer is perceived as much worse they may question why you have even applied for this, and wonder whether you think yourself that you are very unlikely to get their position.
Case 2 - about the same:
In this case, I think this may make you seem like a better candidate. At least it will show that other people also think that you are good enough for the job you are applying to. It may be a minor factor, though.
Case 3 - more attractive:
They will probably assume that you will either take the more attractive alternative option anyway (and hence will be much less likely to offer you a job), or that you will negotiate very hard. Both are not exactly plusses for your application.

Thanks for your response!  A few follow-up questions: I wasn't planning on specifying anything about the offer to the other employers, but perhaps you recommend otherwise?  Would it be strange for me to just say I have an offer with no details about what/where/deadlines?  Also, concerning Case 3, if I communicate to the other interviewers that I would very much prefer their position to the offer I already have, will that convince them that I'm serious about taking their position, and not looking to negotiate if they offer me something?

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text:
Overcoming depression and getting back on rails with PhD work
I'm a first year PhD student (computer science), and I've felt that I lost this year up to now due to some life difficulties. I'm getting no financial support and I was forced to teach to get some money and pay my expenses. I have another personal problems that took me to a state of depression, where I've spent some months completely stuck in my work.
I want to "be back on the rails" and continue to work on this, but I'm feeling lost. I need to go back to the very beginning and find what a PhD is, and what I must do to advance the state of art with my current (weak) capabilities. At the same time I must to show some results to my advisor with what I already have in my hands.
I know that my "question" is pretty obscure, but I need some advices on how to proceed, from people with some experience in this situation. How can I overcome depression and 'get back on the rails' with my PhD?
IMPORTANT EDIT:
Some years later I finally got my PhD. I cannot believe I made it. At the time that I wrote this post it seemed utterly impossible to achieve this. If you are in the middle of a PhD you may try to endure and fight until the end. But if you are wondering about starting a PhD, please make sure YOU ABSOLUTELY LOVE your topic, otherwise you'll end like me when I wrote this. I didn't like my research area and the topic I choose. Everything else seemed to be way more interesting. I wanted to do everything instead of reading papers and conducting my own research. I felt unproductive and useless, and at some point my advisor started to complain about my lack of results. It was my fault since the beginning since I didn't followed a research area that I could have joy with it. I should have choose something that matched my abilities and preferences, for instance, I'm pretty good with programming, but my math skills aren't great, and yet I tried to enter a field that is dominated by math and advanced statistics. I couldn't do what I do the best, neither I was able to catch up with the involved math.

Not quite the same question but very good answers here: http://academia.stackexchange.com/questions/2219/how-should-i-deal-with-discouragement-as-a-graduate-student

I don't know what your specific question is. What are you looking for guidance on?

@aeismail
I'm sorry. I spent several minutes trying to elaborate a "specific question", but I couldn't. :(

You should specify at least the country. In the US, the primary activity of many grad students for the first 2 years is passing courses and preparing for quals - the 1 year you've lost is almost meaningless. In Europe, losing 1 year out of a 3 year program can have significant impact.

I'm from Brazil. In the first year we take some courses, and in the following 3 years we focus on research.

When a person is discouraged about his academic research activities, he may not be depressed at all and he may be so energetic in his non-academic life. On the other hand, when the person is depressed, he is upset with his daily life and his academic activities. He is always sad and upset. He has negative perspective in his life. I think the question is not duplicate to that post at all.

Glad to hear you made it, Danilo. Thanks for reporting back. I don't know the norms in this community, but I think your edit to 'finish' the story is an important one. :)

Glad that you finished your PhD finally.

Glad that you finished your PhD finally. I never imagined that I will read this post again after answering the question, while I will be still doing my phd. I started PhD  about 5 years ago and suddenly stuck with many personal family challenges. Of course, research go impacted badly, consumed savings and fundings, did odd jobs and got bad progress reviews. Now most of them are over, I didn’t give up. I’m pretty hopeful that in next 6-8 months I’ll finish. Even though I’m just starting experimentation. Let’s see how it goes. Now I’ll surely come back here when I’ll finish my PhD.

Depression is very common amongst graduate students and faculty. So know that you are not alone.

About 60% of graduate students said that they felt overwhelmed, exhausted, hopeless, sad, or depressed nearly all the time. One in 10 said they had contemplated suicide in the previous year. --  AAS Science Careers

However, there is very little that the community on SE can do to help you. We are not therapists and cannot provide a therapeutic relationship.
Know that there is no shame in seeking help. Your university almost always has a mental health clinic with free or subsidized service. Whether you prefer talk therapy or psychopharmaceuticals (or both) is up to you and your insurance plan -- but please do go seek help from specialists.

Totally agreed here. Psychotherapy has been very helpful to me as a graduate student personally, and I know a few others who have sought similar help during grad school.  There is nothing to be ashamed about for treating mental illness including (and certainly not limited to) depression or anxiety, just as there is nothing shameful about getting a physical illness treated. Unfortunately, because so few people talk about actually going to see a therapist, it can seem like nobody does it.  In fact many graduate students seek such help, and departments often (and should) encourage them to do so.

Depression is very common amongst graduate students and junior faculty — and senior faculty.

'Depression is very common amongst graduate students and junior faculty' Do we have data showing that it's more prevalent in that group than in any other? I agree with the rest of the answer though.

http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2014_02_04/caredit.a1400031

Amended answer to respond to comments.

Ok, here is my (partial) take on the matter.
I completed a PhD, also in Comp Sci, but in theory rather than software. In retrospect, I believe it may not even have been a good idea to do so. I'm not suggesting that you quit, though; nor am I going to write my long personal story since it is, well, personal and long. So let's just make some suggestions:

Ask yourself this: "Is my self-esteem, my sense of self-worth, based on me succeeding academically? As a student and now as a researcher?" If the answer is "Yes", then you need to rewire your brain. Because even if you don't end up in a deep emotional crisis right now, you will at some point in the not-too-distant future, and until then you'll probably suffer most of the time. I was very afraid of asking myself that question, because I sort of knew the answer; but if it reaches your consciousness than you know you have to do something about it.
Suppose your PhD tanks. You don't reach publishable results, you wander around in circles, you need money and there's nothing you can do on campus to make enough - it goes up in flames. You advisor frowns and is disappointed. Your parents wonder "Gee, what's he going to do with his life now?" Sounds terrible, right? Can you live with that? The answer is: Of course you can. What you can't live with is spending your time trying to avoid this possibility, or imagining it out of existence. It may happen. Don't start spending all your time on planning for PhD failure, but try to entertain it as a real possibility. Try to "pre-accept" this failure and thinking of your PhD prospects as a sort of a calculated bet.
Some people bypass their emotional issues by making research breakthroughs relatively quickly; they supposedly never have to deal with the kind of anguish we go through. For us, however, it's all the more exasperating to see them progress while we're stuck. If you spend any time trying to compare yourself to them: "Why am I less successful/quick/able than that guy" - again, you're in trouble. You're thinking of the PhD as a sort of rat race. Unfortunately, it's half-become that in some fields. Your PhD is supposed to be something unique, that you are pursuing for its own sake (or because you need to apply the research personally). Don't adopt the goal of "getting ahead" abstractly in your PhD.
It is my (non-universal) experience that many people around you, especially senior tenured staff, can be total assholes about this kind of problem. It is so commonplace, so fundamental, so frustrating... and yet, they're just shuffling along untroubled. Even when all the signs tell them how you feel. And nobody prepares you for this. They make you think you're just, well, continuing your studies. Don't be afraid to develop a nice grudge :-)  and, on that note
A PhD candidate is not a student. That is, you are also a student, and research is a kind of study, but in that sense a Professor is also a student. You now have something between a strange kind of job and an also-strange kind of contract work (perhaps half-unpaid). I know usual capitalist class divisions (hired labor / capitalist employer) don't apply very well to academia, but I think it's emotionally (and sometimes financially) useful to think of it that way. Of course, you should be very committed to your job and take it seriously, not slack around...
Is your advisor actually advising you? Academically, at least? That is, does he provide guidance, suggestions on how to proceed research-wise and academic-life-wise? Clearly, you're not close with him, and he doesn't realize what you're going through. Do you think you could tell him? Or will he not 'get it' emotionally, and just end up thinking you're a weak person? I would say it's probably a good idea to share your situation with him even if he's expected to respond relatively poorly. Don't make excuses to him and try to hide what's going on. Better for him to think of you as a wuss who can't handle it than a dodgy person who can't be trusted to tell the truth.
You wouldn't believe how many people use psychotherapy, or take anti-depression medicine - in society in general and in grad school in particular. If you're, say, at the point of having trouble sleeping, or having other physical symptoms of depression or anxiety - talk to your GP (your doctor) and ask him/her to explain such possibilities to you.
Teaching is part of the calling of being an academic. Researchers should teach, regardless of money. It's good for keeping in touch with the foundations of your discipline, and what's more - it can help your mood. At least, it did for me. Still, if you need to do a lot of it to make ends meet, that sucks. There are academic staff labor unions for these kinds of problems (and for wider concerns hopefully), but I'm not going to suggest to you as a single person that all the graduate teachers should go on strike for better pay etc. Although they generally should :-)

Wow! I read every word carefully. Thank you for your answer!

This is THE MOST practical answer given here :)

@shivams: From wounded heart to wounded heart, my friend.

Your question is:

Overcoming depression and getting back on rails on PhD's work?

My advice would be to treat these as two separate problems.
First you must tackle overcoming (or at least learning to cope) with depression ... which you say is due to personal problems. You should prioritise this. Only then can you aim to get back on the rails with your PhD work. In terms of coping with depression, this may involve lifestyle changes, seeking counselling, and so forth.
Once you are healthier, you can then prioritise pushing forward your PhD work. It's important to keep communicating with your supervisor what is going on with you. Their job is to advise you. Let them know what is going on. Likewise set yourself small achievable goals. Thinking about a PhD in its entirety is very daunting. Break up your work into little milestones (no longer than a week, say) and try to focus on one thing at a time.

On a side note, there can be a pathogenic aspect to academia where working ridiculous hours and being depressed all the time is sort of implicitly tolerated, for students and staff alike. This is wrong. If you find yourself in such an environment, try to improve it. If this doesn't work, just get out. Learning does not require suffering. Research does not require suffering. Depression should not be a side-effect of a PhD.
If it is your PhD that is an underlying cause or aggravator of depression, I think you need to ask yourself: Is getting a PhD really worth it? Can you take steps to improve your situation? Could you find another PhD position elsewhere? Maybe you could try find a job or just do something different?

Thanks for your answer. I'm not interested in quitting the PhD, because it is my main objective in life. My PhD course itself is not the source of my mental illness, but my  poor performance on this course affects me a bit.

@DaniloM.Oliveira If you pin all the hopes of your life on this one thing, it will stress you out more. A good main objective of life is to be happy and be nice to others.

Depression is the root cause of why I didn't finish my Ph.D., so please take it seriously.
First divide things into stuff that you can fix and stuff that you can't.  Things that you can't fix include lack of sufficient money to study without work and the difficulty of your subject.  Things that you can fix include exercise, diet, and sleep patterns (@badroit).  Also, there are extra things that you can do such as using the campus psych help and medications.
It is surprising how much a change to logical exercise, diet, and sleep can help.  The only problem is that those changes take a significant amount of effort which is the original problem.  Nevertheless, try a "21 day challenge":  more than 7 hours of sleep a night (at night), no junk food nor soda, and at least light exercise (e.g. yoga, hiking).  Also, try to socialize, more than just drinking buddies.
As to the medications, I have found most of the prescription stuff of little use.  Zoloft, etc. had only a marginal effect.  The single most effective thing has been wheatgrass juice.  I used up to 4 oz of freshly ground wheatgrass juice daily, and after about 10 days, I noticed an improvement.  Within about 2 weeks of starting, my depression was GONE.  I haven't been without depression since puberty (~20 years), and it took me awhile to get used to it.  At first, I felt fragile, like anything might break it.  Then, all of a sudden, I could finally do all of the things that I wanted.
One thing to bear in mind.  No matter what type of medication you take, your mental habits still remain from the depression.  Be aware that one of your first priorities should be to change your mental habits (e.g. always seeing the bad side, assuming everyone hates you / makes fun of you / holds you in contempt, assuming that you can't finish anything, assuming that you are a horrible person or stupid, etc.).  These are just artifacts.  You will finally be able to change them like changing your clothes.  I know that that statement sounds stupid, but once the depression stopped forcing my mental outlook, I actually could gain control of it.  Big change.
Finally, you mentioned that you have weak capabilities.  That might be true or not, but that is FIXABLE.  That is the purpose of school.  You are in the process of improving those capabilities.  Where else would you expect someone to improve their academic capabilities.  So, don't worry about that.

The legendary physicist Richard Feynman struggled with a terrible bout of depression shortly after Hiroshima and was unable to work. He talks about it in  his book Surely You're Joking Mr Feynman. In the end, he decided to go back to his roots and just work on things that interested him - rather than what he should be working on. As it happens, while modelling the motion of a flying and oscillating plate (for fun), he inadvertently solved a quantum mechanical problem.
As a PhD student who has also wrestled with depression for many years, I have adopted this same indulgent approach: find a problem or task that interests you and work on it for fun. You'll be amazed with how often this leads to something publishable.

As a past PhD student in the domain of software engineering, and having some personal problems during my PhD; I can totally relate to you.
First of all, doing little/nothing (in your opinion) during the first year is pretty common. In fact there is a lesson in itself. That is, a year, is not a long time in a lifestyle of a researcher. So you can plan your years ahead more wisely.
Second, you need to understand that, doing a research in computer science is sometimes is very hard; as many big successful companies are doing great things, and for marketing purposes, bragging about it publicly; and you need to sit and think about a contribution that is not tackled before, with limited resources (e.g., time, budget, etc.). Hopefully in near future you will find the purpose in your research, and will be happy about your role in the computer science domain.
Third, you need to start exercising on a daily basis. Sitting long hours, and trying  doing a research in an office environment, sooner or later will effect your mental health. So plan a light workout at least 3 times a week.
Fourth, eat well. If you use any self medication (cigarets, alcohol), stop them. They will contribute to your moods.
Fifth, work during reasonable hours. Do not work more than 8/9 hours a day. Do not work strange hours (late nights, midnights).
Hopefully by balancing your life, you will start feeling good and then great again and will continue your research.
If you still have the problem, contact the student union at your university, they can help you get some time off, so you can tackle this issue professionally.

Talk to people
Talk to your advisor, your professors, your TAs, your fellow students, your friends, your family, the people at your school's graduate office (often just waiting to help), or a counselor if you have access to one. People on the internet don't count. It might be tempting to get stuck in your own head and believe that you can figure everything out on your own if you just work hard enough, but clearly that isn't working.

Don't be depressed! Always, Be hopeful! Posting this question means that you still have a lot of hope within yourself. You just need to get it recognized by yourself and acknowledged. Try to think, imagine and act in such a way, read, write and watch such stuff which provides you hope.
Since you have mentioned about the first year that is some what about the course work. Let me tell you the fact that you have lost nothing, if you have passed the courses you took and, maybe, only something very little and not everything (of course, not a complete year) otherwise.
The fact that you have no financial support is something that happens to many and you are not alone to be in such a situation. You are rather lucky that you have made it up by teaching. I personally know those who have had similar situations in grad schools and were forced to take odd jobs.
Try not to think about that personal problem much. Your too much mental involvement in that is not only harming you in your present, rather it would leave its marks on your mind and would also be destructive for your future. Remember not to think about the things too much which are not under your control.
Forget about showing results to your adviser so far. He won't kick you out of the PhD program. Try to bring your problems in his knowledge, otherwise, it won't work this way for rest of the years during your PhD. Do not try to be a superman, just be realistic with your life, work and supervisor. Try to keep him in 'CC' about the challenges (not problems) of your life and work.
Keep your emotions under control and remember that: "PhD is also a patience test". During the course emotions won't let you complete it at several occasions and they might even force you to quit. But, please! don't let your emotions hinder you work, your life will be okay.
Best Luck!

This might be helpful advice for those who're just down about their progress, work assignments, etc. But clinical depression isn't situational/temporary sadness; clinically depressed folks can't decide to just "not be depressed." I say this as a long-time skeptic whose experience was that exercise and talking to colleagues, etc. could go a long way, but have recently realized that some depression is a medical condition that often needs management through medication (which can be a seemingly-miraculous intervention). When talk and community can't get you there, medication can be a lifesaver.

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


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When is it appropriate to publish independently without an advisor?
With pre-preprint servers readily accessible, I'm wondering if it is possible for graduate students to directly publish their work without their advisor. Is this taboo?
If a student conducts independent research whose intellectual property has been acknowledged (in writing) by the advisor to belong wholly to the student, is this sufficient permission for the student to publish independently?
For context, I've shared my findings with my faculty committee who all gave my work positive feedback, and I work in a competitive field with a risk of being "scooped". My PI manages a big lab and my paper has essentially sat on their desk for several months. Is it within my rights to publish directly ie. on bioRxiv?

I don't think that pre-preprint servers substantially change the playing field of this question. Typically, the ultimate goal still is to get the work published in a peer-reviewed venue, and at that point, it would be rather strange to change the author list compared to an earlier pre-print submission.

Ethical standards for authorship treat anyone equally; there are not special rules about advisors and students.

See also https://academia.stackexchange.com/questions/21320/aftermath-of-rightfully-submitting-a-solo-paper-without-my-advisors-name?rq=1, https://academia.stackexchange.com/questions/92906/publishing-a-paper-without-supervisor/92911#92911, https://academia.stackexchange.com/questions/31266/publishing-my-work-without-advisor?rq=1

Ethically, if the intellectual content of the paper is yours you can publish it as a sole author. You need to acknowledge the help you get that doesn't rise to the level of authorship.
However, in some fields, it is difficult to separate the "contributions" of people like advisors who provide an environment in which the work can be done and which couldn't be done otherwise. In some of those fields, the advisor is traditionally also an author of all work. Some will disagree with this convention (I'm one), but it exists.
It is also, for a student or often a postdoc, a mistake to anger a supervisor as they have power over individuals that can be, and too often is, misused. So, you need to analyze your situation and act in your best interests. You may need to accept a less-than-optimal solution if it advances your career and gets you to the point of independence.
If you don't know how your advisor would react to your publishing without them, then it would be useful (essential) to find out, perhaps with a conversation with them in which you can judge their reaction.
What is ethical and what is optimal, or even advisable, may not align.

I think the question in the title has been answered by others on this and past threads.
I think it's worth noting that if the paper has sat on your advisors desk, then it is already somewhat implicit that they will be a coauthor on the paper. Thus, acting unilaterally to post the paper to a preprint server and/or trying to publish it yourself might be viewed differently by your advisor than if you had written and submitted the paper completely without their input or knowledge.
In any case, the best thing to do is talk with your advisor. Even if you can ethically publish the paper yourself, dealing with the fallout of an upset advisor may not be in your interest. If your advisor is reasonable they won't hold such a conversation against you, and if they are unreasonable, then the consequences of having such a conversation are likely to be much smaller than the consequences of publishing the paper without them.

In general it is very good for students to publish single-authored papers. If you later apply for a position, people studying your application will not have to wonder which part of the work you did.
Your advisor's career might benefit marginally from being a coauthor, but it also benefits from your academic success. So even a selfish, unethical advisor should not object to you publishing independently. Only a very abusive advisor would. (Think of a certain chloroquine guru.)

"Your advisor's career might benefit marginally from being a coauthor..." This really depends a lot on the career status of the advisor and the expectations is the field. Quite a few PIs feel a large pressure to publish as much as possible. And in some fields, it is unusual to publish alone as a PhD student.

In my general field of biology, there is zero benefit to publish single author papers. First author, yes; single author, no. For someone up for a faculty position, they may benefit from authoring papers without their PhD advisor but it doesn't matter that they have other coauthors, just that they show some independence from their training.


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Asking a potential PI to visit his lab after succesful skype interview
I couldn't find any threads here related to my particular situation, so I decided to ask here. Please guide me to a thread if you think it's already been answered!
So, last month I emailed a potential PI that I'm very excited to work with about openings in his group for a PhD position, and he emailed me back about setting up a skype call. I think the interview went well, and he asked me to let him know when I submit my application. He also talked about me with another professor in the same department, who also reached out to me for an interview, and I think that interview went well as well.
I submitted my application a little while later, and emailed both the professors that my app is in, and they said they will look at it soon, and also asked me to let them know if I got into any other programs, and they may be able to respond faster.
All of this sounds like positive news for me, but here's my question - I want to visit the group and see how the lab, and meet the PI in person once, but I don't know if they have the time to talk with me again, especially in person, since they have already interviewed me once before...
Any ideas on how to ask for a lab visit without sounding too imposing? (This school is in the U.S. for computer science PhD BTW...)

The way to ask is just to ask. If you have any time parameters for when you'll be available then mention them. If they have the time and interest then they will likely respond. Otherwise they just might indicate it isn't possible at the moment. Note that people are likely busy at the moment with end of term approaching. And during the break may be more or less possible and more or less useful.
But just ask. Not a problem.
And, in CS, note that not everyone will have a "lab" as you might think of it. But you might be able to sit in on a meeting with other students.

Thanks for the quick reply @Buffy. I was thinking along the same lines. I'll shoot him another email and hope for the best!


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How to deal with author's extensive self-citation?
As a scientific journal reviewer, how can I deal with a manuscript where the authors cited their own works extensively (14 times) in the manuscript?

I don't think you can determine excessive self-citation just by counting.

Are the citations relevant? Perhaps the field is small and a lot of the work is done by a few people? I.e. a large portion by the author themself.

There are a lot of works done previously in the field. However, the authors only cited their own work and include some irrelevant text in the introduction in order to cite their own work.

Both referees raised this point that unnecessary self citation is not accepted. However, the authors did not address this concern appropriately.

then you could state in the review, that you don't see how the introduction is relevant to this work (explain or cut it) and point out the missing citations to other work done previously in this field.

Given that the purpose of the introduction is to set the context of a paper, I think that "irrelevant text" is a judgement call and nothing more.

14 is not too much, I had to review a paper with 30 self-citations and 5 other citations. However, I rejected the paper on different more pressing issues.

My main concern was the authors hindex that increased from 0 to 9 just in two years from 2022 to 2023.

@David Your role as reviewer is to assess the paper in front of you not police metrics.

@David Most websites give a h-index with and without self-citations, you can very easily see if someone is trying to inflate their h-index by excessively citing their own work.

@JackAidley as a reviewer I am familiar with my role, otherwise I must have not been invited to do a review. What i am thinking is to understand whether the paper in front of me is of enough quality or it has been written for other than scientific purpose?

I forgot to mention that the first author published her first paper in 2022, and now in 2023 they cited their works 14 times in tbeir paper which I am doing a review for. There are quite a lot of previously published works on this topic but they only cited their own works that they have published since 2022.

Present clear arguments in your review that describe which self-citations are irrelevant and why you argue that this is the case.
Assuming that this is a reputable journal, this forces the author to either remove these citations or provide evidence of their importance in their rebuttal.
However, note that, as mentioned in the comments, the number of self-citations is not an indicator of whether they are appropriate or not. If the author has worked on related topics a lot, then it may well be appropriate to provide all these references. If this is the case, but you nevertheless want to argue that there is an unfair balance between self-citations and citations of other relevant publications, mention this in your review and provide examples of important papers that are missing.

You can also point out other works that should have been cited by the authors, though that isn't necessarily damning either. Context is required.

You could just mention as a side comment in the review that the number of self-citations might be interpreted by some as a reflection of the vanity of the author and/or an attempt to game citation metrics, and that in either case it may be in the author's self-interest to investigate which self-citations might be removed from the citation list without any substantive loss to the manuscript.

There are a lot of works done previously in the field. However, the authors only cited their own work and include some irrelevant text in the introduction in order to cite their own work.

If this is the case, you're accusing the authors of misconduct. Therefore write all your concerns into the confidential-to-editor box, and let the editor handle it.

Actually, one doesn't need to cite all works done previously in the field. It is a question of relevance to the current paper and only that. It may be misconduct, even if only sloppiness, or it may not. But mentioning such, rather than a accusation, is fine.

@Buffy yes, but the key part is "include some irrelevant text in the introduction in order to cite their own work".


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How long after the application deadline does it take a search committee to schedule telephone interviews?
I know this can vary from department to department but in general how long does it take for a search committee to decide on a short-list of candidates once the deadline for submission has passed?

This is so variable; throw-in Covid so lots of stuff is done by email rather than in person, and who knows?

In my experience, hiring timelines are much more variable than people tell me they are.

Thank you for your feedback.

@physicist It may be hard to give an objective answer, but I don't think the question is a duplicate and I am interested to see any additional possible responses.

Please remember that in the 90% of the cases deadlines are absolutely arbitrary.

I believe this is a matter of weeks normally: from within one week to a month or two tops.
There is a need to have a meeting to agree on the candidates, and the committee members need to look at the candidates beforehand, which can amount to hundreds of initial candidates.

one week would be lightning fast in my world.


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My teacher accidentally put one of the codes on my test and I used it
On my programming midterm, my teacher gave me one of the codes for the question on accident. I did not mention this to the teacher and used it as my answer and deleted where he gave it to me. The reason I did this was because, each student had to answer 10 out of 13 of the questions and I answered exactly 10. So if I were to go ahead and tell him during the test he would have told me I was not allowed to answer it. However, I was not as confident in the other two options so just hoped he wouldn't notice. Now I understand that I am at fault for using the code. However, my professor took off all the points for that question. This is the part that I do not see is fair. He is at fault for giving me the code but again it is my fault for using it. I do think a more fair approach was to do just grade the test as if that question was not there. Being that it is also his responsibility to check the test beforehand. Do you think this is fair or should he have just taken the question off my test.
Also forgot to mention everyone had a different test and was taking it at different so the other student who take the same test as me was not with me while I was taking it.
What appropriate options do I have?

It sounds like you cheated on a test and are not happy with the consequences. Is it moral to steal from someone's house if they left their door unlocked? I don't think anyone on this site can help you with that situation.

What's your question? Is it Do you think this is fair or should he have just taken the question off my test.?

I’m voting to close this question because it is a rant without an actionable question.

@RichardErickson, I added what seems to be the obvious question. I think it is within the OPs intent. But, yes, I didn't notice that when I answered.

How he "accidentally" gave you the code is unclear, how could you have deleted it?

Wht precisely is meant by "code"? On what does this code have to do with the solution to the question in the test?

@JochenGlueck, programming computer code. Probably in an electronically transmitted test that was editable.

@BryanKrause "Is it moral to steal from someone's house if they left their door unlocked?" yes without any doubts! It's their door, the goods inside are their goods. The part about the morality is "was the thief stealing out of need?" and whether he broke or not a lock is not moral, it is just a technicality...

OP, if it was finance, you took some risk, using the code, aiming at the big rewards of a perfect score 10/10.
Your bet did not pay out, but the risk turned out to be minimal, lucky you.

If the professor gave you the code as part of the exam then there was no fault in using it. However, removing it without comment, was deceit. Had you not done that then there would be no basis for any complaint against you.
I can't say your professor was wrong in denying points, nor do I know exactly why he did so. But it would be worthwhile, for a lot of reasons, to ask for a meeting with him to see if there can be a happier resolution than losing all the points. Don't complain that he is unfair, but explain what happened, even admitting that you removed the code he included.
But deceit in any form is an offense.

I do think a more fair approach was to do just grade the test as if
that question was not there

You are absolutely right, one should always judge with the maximum objectivity other people fairness avoiding to bring his/her own bias.
In fact I do think a more fair approach was you to notify the teacher, and you answer one of the other questions, instead of the one with the code.


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Errors in 'old' articles that keep getting referenced
I have come across a couple of math articles published between 2005-2010 that have clear errors in them (the articles have a common author). Most of the errors are typos but a couple of errors, let's say, reinterpret basic theory. No erratum has been issued for the articles. The journals are peer reviewed (which is another story) but they are not from what one would call top-tier journals. However, I note that these articles have been, and continue to be, cited despite the errors - sometimes by articles in journals that are considered top-tier. In one case this has kept perpetuating a typo error in an equation. (It seems those citing the articles just accept what was written - again another story).
I have written to the author but no reply. The journal response was basically that unless the author wants to correct it, nothing much can be done.  It was also said that as the articles were now 'old', correcting them was - in their words - not efficient.
My question is should I persist in having the errors corrected? Or do I just leave such errors to be repeated? I have considered writing a letter to the editor for publishing to highlight the errors - in the hope it will 'force' a correction the original articles (assuming the letter would be published). Ideas welcome.

I'm having difficulties to understand which kind of errors you are referring to. Do the typos change the mathematical meaning of the results? And what does it mean to "reinterpret basic theory" in mathematics? Correctness of mathematical results is not a matter of interpretation.

@JochenGlueck - I'm not getting into specifics as this question is about how to report errors found in an old article. Hopefully the answer can also apply to articles on other topics and not just limited to math.  If I want to explore the math errors specifically, I can raise that with the appropriate math community on StackExchange.  PS: oh, yes, the typos do effect the results (otherwise why would I raise them as errors).

The nature of the typo is important. The typo may be small enough to be considered trivial to experts in the field, such that they are unlikely to even notice it. If the citing papers don't make the same mistake, that's a hint that this may be like pointing out someone's typo within Stokes' Theorem. Politely let the journal know about it once, then there is unfortunately little else you can do. Personally, I think going a bit nuclear on the editor like you've suggested is a touch much for an "um, actually..." technicality/error.

Welcome to science in 2022. See also Ted Hill, How to publish counterexamples in 1 2 3 easy steps. But don't worry, you might succeed in just 15 years.

(An easy thing you can do right now is to point out the error in a paper or preprint you write. This way, at least if a reader follows citations backwards using Google Scholar, he will eventually find the correction. Many errors have been corrected this way. This isn't that much different from journals publishing errata in the next volume.)

In my field there is a particular paper that set out the "canonical" calculation for the predicted signal spectrum. It's still highly cited because the method is clear, but there is a critical integration error that makes the actual result incorrect.  It's become something of a rite of passage for students to discover this

Neither the journal-level impact nor the age of the papers should matter. The articles still form part of the current stock of scientific discourse, especially if they remain to be cited.
You already reported it to the editors and the authors first. They did not bother to publicize the error.
A next step could be to publicize it either in a letter to the editor, as you thought about already, or to do it via 'post-publication review' platforms like PubPeer. You can do it anonymously or with your name attached to your comment.
(Note that PubPeer comments do sometimes lead to corrections or even retractions.)

Have you considered publishing an erratum / corrigendum yourself? An introduction to the topic with a correction (and possibly some other minor additions) would be welcome in a lower-tier journal, I believe; this especially if the error continues to get cited and propagated.
You can cite several examples of other papers that build on the incorrect result, so that their authors also have the occasion to get notified (I believe many authors have a 'vanity search' active so that they get notified for citations to their own papers).

(+1) And the title of the paper could be “A cautionary note on …”. One of my late colleagues told me about an academic who ran up their publication list with lots of these cautionary notes. ;-)

Note that not every error in a math paper necessarily invalidates the entire paper. You don't say that what gets referenced in those citations implies that what is false (or unproven) is actually true. The citations could, in principle, be of other, correct, parts of the paper.
Moreover, if the errors are widely known but not considered important or relevant to the purpose of the citation then those errors matter little, except to novices who might be misled.
Another issue in mathematics is that some papers have flawed proofs, but no one doubts the validity of the theorem. I once worked in an area with the reputation that all papers had such errors. Many of those "flawed" papers were by very eminent mathematicians.
And, if the errors are both serious and you have evidence questioning the results themselves, not just the correctness of the proof, then you have an opportunity to write a correcting paper. If you get that published, people will wake up to your concerns, especially if those results are important to what is cited from the flawed paper.

Note that in Real Analysis, epsilon-delta proofs that are three or so levels deep are devilishly difficult to get right - even for experienced experts in the field.
And note The Magical Number Seven ....

If a paper in a top journal cites and uses a flawed result in an important way, I'm sure the author of the paper would like to know about it. You could write to these authors and say you believe there is a mistake in the cited work, which led to a mistake in this author's paper. This would both serve the purpose of correcting that particular top-journal article, and raising awareness of the issue.


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Does making the second author an equal contributor affect its supervisory role in a 3-author paper?
I am a PhD graduate and I supervised a Master's student in a research work that lead to a publication. The Master student is the first author, then it is me, and then is the name of our advisor. Since I had an equal contribution to the paper, does stating me as an equal contributor affect my supervisory role of the work?
Because I am planning for a post-doc position and I think it may be important to have a paper in which I supervised another student.
p.s. I am publishing in the field of computer science (ML, Computer Vision)

Making two authors to equally contributing ones does not imply anything explicit about their roles for the research, just like the author order which does not follow any real rules. There are some field-dependent conventions, but also those are subject to interpretation.
A way out would be to include an author contribution statement to your paper where you explicitly state the roles of all authors. You could for example use the CRediT system (and I encourage you to do so) which also includes the contribution "supervision".

Honestly, I have an itchy feeling about this, especially in a field like CS. There are those that will assume that a PI/advisor/supervisor did all the work when they appear in the list of "authors", rather than in an acknowledgement of other contributors. In math, and it was my practice in CS as well, to not consider any sort of authorship on my student's research output. And yes, they got some help from me, just as I did from my own doctoral advisor.
Having you as joint "first" author clouds the picture even further. If you want to emphasize that you were the advisor then let the student be sole first author (I won't suggest sole author, though it would be my practice).
Write an acknowledgements section in the paper that lists yourself as a contributor.
The difference for one publication between first and second authorship is so small as to not be worth polluting the space. And if the student objects to not being sole first author, then all the more reason to let it go. If you want to be a great advisor then boost your students.
There is something special about a student's first publication. Twenty years from now your generosity will be remembered. Forty years. Etc.

Just that I get it right: Do you suggest to have have people in the contributions statement that are not authors? The CRediT formalizes the contribution statement and I cannot remember having seen non-authors included. I must admit, however, that it is an interesting idea. Anyway, in my field contributor=author holds true in 99 % of the cases.

My thesis thanks my advisor for his help, but he was not an author. My own doctoral students thank me for my help but are all sole authors. Not every contribution rises to the level of authorship. It can be subtle, of course, but for people who aren't actually 'peers' such as student and advisor, there is no harm in stepping aside in favor of the student's sole authorship. there are too many questions on this site in which advisors abuse the relationship.

@Snijderfrey, note the above comment. Note also that in (pure) math and in much of CS, author order is alphabetical with less worrying about the specific "weight" of contributions. It aids collaboration, actually, even if your name is Zzysmansky.

Apart from different concepts of authorship, I think we also have different concepts about what a contribution is. But there is no need to resolve this right here, I think. Honestly, I think whether the first two authors are equally contributing or not is virtually irrelevant anyway because it is regularly overlooked. I understand why early career researchers worry about this, though.

@Snijderfrey, yes, fields like chemistry (yours?) seem to think differently than much of math and cs. Part of it is that in some of the sciences the PI provides the basic infrastructure that permits research to happen. In pure math and theoretical CS that isn't so much the case.

@Snijderfrey Some fields like high energy physics have very long lists of authors. In such cases a CRediT listing is quite unwieldy: https://www.nature.com/articles/nature.2015.17567

@Buffy Thanks for your answer. I need to note that it is not the case that the master's student did all the work. We both worked somehow equally (in developing the idea, implementation, and writing) and he is totally Ok to mention me as an equal contributor. The only concern is that it might suppress my supervisory role.

@Buffy, I would love to see a CRediT statement for that article! The author order most certainly does not say much, does it?


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How to Self-Study in Ph.D math
I was recently admitted to the Top 10 Universities in Math Ph.D. The department is really strong at the Number Theory, I am primarily interested in the Number Theory so it is a good thing. I will be most likely find some faculties that research the Number Theory and wrote a Ph.D thesis on that(provided things go well).
Although, I am also interested in Mathematical Physics. Potentially in the future, I would like to study topics between to Mathematical Physics (for example Mirror symmetries) and Number Theory. Having said that at the University, no one studies Mirror Symmetry, KdV equation, Hitchin System, or Geometric Langlands(there are experts of usual Langlands though)... This means that almost no faculties researches on the topic that I am curious about it.
So my question is in this case should I abandon my curiosity about Physics, and simply focused on Number Theory? Or even there is no facilities are researching on Mathematical Physics, is it worth to keep study it? In this case how to self-study it as a graduate student?

Will you enter with a bachelors or a masters? is this the US or elsewhere?

I have a Bachelors got in U.S and again American Program.

Just FYI:  There can actually be a big difference between what mathematicians think is "mathematical physics" and what physicists think is "mathematical physics."

For US study you will be busy enough with one topic. Your first goal is to pass the likely comprehensive exams and find an advisor. This probably requires some advanced coursework. Then you need to dive very deep into your research topic. And, keep an open mind about the specialization until you need to choose a dissertation advisor.
However, focus on what is most important.
But, you don't need to "abandon" other mathematical areas, just delay deep dives. Put them on the back burner for a while until you are in a position to set your own agenda.
Along the way, however, you will need to take breaks for your own mental health. Exercise is good for that. But fairly casual reading (and note taking) of other math ideas can also give you a break as your mind switches "gears" in a new area.
A good practice when you read, either in your specialization or elsewhere, is to keep a notebook of ideas that you might want to explore in the future. Review it occasionally and add current thoughts. Finishing a doctorate with a notebook of possible research is a great place to be.
It is possible, in face to face situations, to have informal conversations with many faculty members (coffee lounge is good for this). If you know they have a specialty that interests you, ask for papers you might explore for this. It is good to have some guidance.
Once you get a tenured position you will be free to wander the highways and byways of math, physics, ...
Good luck. Have fun. But focus.

Potentially in the future, I would like to study topics between to Mathematical Physics

The future can wait a while.
So first priority : get your PhD in any mathematical topic.
Once you have a PhD you can try steer your career in whatever way you want.  However until you have a PhD (which for most people is going to be stressful and non-trivial) you need to focus on getting it the simplest way possible with as few other goals interfering as possible.
If you want to keep an eye on the mathematical physics side (whatever you personally mean by that - there are different interpretations) then that's fine.  But don't let that become a distraction from the primary focus : the PhD.  I would not think of it as self-studying mathematical physics - that's perhaps pushing the boundaries of letting it distract from the goal of a PhD.


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What it really means when my research guide says I was a serious student
I have completed my masters degree and moving out of my institute. I sent my research guide a thank you note. In return, he told me that I was a serious student and my final presentation was good. But no mention of my research work.
What does that really mean? Does it mean that I was serious, but not innovative enough to conduct a good research? And only my presentation was good, but not the actual research work?

Country of institution or national background of the letter-writer might be in play here, see e.g. https://mobile.twitter.com/birchlse/status/1324715727631384580?lang=en

I think the only person that can tell you what that really meant is your research guide.

Don't read too much into it and, especially, don't read anything negative into a positive statement. People don't always remember to say all of the things that they might want to say. I don't read anything negative in what their response was. But it is more likely that they were just focused on a few things, like your presentation and so  mentioned only that. And a quick note from a busy person isn't likely to be complete.
If you really want their opinion and a projection about your future in research, you need to sit down with them and have a conversation. Focus on your next steps, more than the past, however.

For context, I was a very good undergraduate student, honors and all that. I once had an elevator conversation (literally) with my mentor and most important professor who said, frankly, that he thought I was losing focus and needed to reorient. A bit devastating, of course, but he simply said what was in the front of his mind at the moment. That is likely what your professor did, but with a positive twist, rather than a negative one.


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Could it be a problem years later if I forgot to include some things in my thesis?
I graduated 3 years ago with a MS degree and a thesis. I recently discovered that I forgot to include some data - tables and list of datasets. All my final analysis has been included. Can there be some problem about this in the future?
I have a couple of sentences such as : "For the list of datasets used in this experiment, see table xx". I do not have that table. I guess I was in a mad rush at the end and forgot to include those.

What percentage of MS theses are ever read, after the degree is conferred?   My guess is that the answer to this question means you can sleep easy ;)

Can there be some problem about this in the future?

What sort of problems do you mean?  It could certainly inconvenience someone in the future if they try to build on your work and have to reconstruct this data.  I'd recommend writing to your advisor to send the additional data tables in case anyone could benefit from them, assuming you don't have in mind doing anything else with them yourself.  You don't have to describe it as material you forgot to include (although, in light of the edited question, there's no way of saving face since you referred to it in the thesis as if it were included).  Instead, you could reasonably say something like "While going through old files, I discovered some potentially useful material that never made it into my master's thesis, which I've attached to this e-mail.  Feel free to make use of it if any future students work on related projects."
On the other hand, you don't need to worry about being punished or having your degree revoked, assuming there was no dishonesty or fraud involved.  There's always more material you could have included in your thesis but didn't, and this is not relevant once the thesis has been approved.  Omissions or even mistakes won't invalidate your degree.

I think this advice is spot on -- no dishonesty or fraud, then don't worry about it.  There are more important things in life than a master's thesis.  Time to move on ...

In addition, if your thesis is on line someplace that you control, you might include an "addendum" with the tables.

If you are asking, "Can somebody claim my degree is improper?" then no, you are in no danger.  You really did the work and advisor and your institution have accepted the work as worthy of an MS degree.  Your degree is real and solid.
If you are asking, "Can somebody have real problems trying to build on my work?" then yes, it could be a real problem.  If you want to be a good scientific citizen, then you should get in touch with your advisor or the department staff and find out how to add a correction; in these days of digital documents, it should be possible.

@phresnel There is no allegation of plagiarism or dishonour here, or any suggestion that the asker's university is "foul". As such, I find your comment rather out of line.

@phresnel I don't think there's any reason to assume misconduct from the OP's question.

Even if the university cannot allow a correction to an approved thesis, you could post on-line either or both of a corrected copy or a short note containing the missing items. If those works clearly and completely reference your thesis, anyone trying to build on the thesis is likely to find them.

@dirkk: Just not prominent ones was what I meant with "public cases". While I don't see how the linked article answers whether a title can be revoked (maybe I did not read hard enough) I realise my knowledge is too limited for a serious discussion. Sorry to anyone, going to delete my comment noise.


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How to reference original paper in expanded journal version
Many journals allow to submit an extended version of a conference paper as, for example, Springer:

Expanded versions of papers which have previously appeared in
  conference proceedings will be considered and this request must be
  made at the time of submission; the authors must clearly state the
  conference publication and provide a statement of revisions/updates
  that have been made to the journal paper.

When writing such an extended version how do you reference the conference paper? I can imaging several possibilities:

Treat it like every other paper in related work
Ignore the conference paper completely and present all results as if for the first time.
Clearly indicate that you wrote the conference paper as "... in [1] we showed that and shortly review the approach ..."

What is correct way to write an extended journal (in CS)?

I cannot say specifically about CS field, but, in general, I would just provide a note (either at the beginning, or at the end of the paper), saying something along these lines: "The present paper is an extended version of our paper, presented at ... conference [1]. This paper significantly expands ... and ...".

@AleksandrBlekh Can you please turn this comment into an answer so that I can vote it up?

Like other papers you mention in your text, refer to them and cite them.

@jakebeal: Done - thank you in advance! Should I delete the comment?

You write the journal version so that it is entirely self-contained, as if all results were new (regardless of whether they were already present in the conference version).
Then, in appropriate places, you refer to the conference version and explain how the current version is different. For example, you could have a footnote on the first page or an acknowledgement in the end of the paper, along these lines:

This is an extended and revised version of a preliminary conference report that was presented in FOO 2015 [1].

Here [1] is a reference to the conference version, and you include it in the list of references as usual. There is no need to cite it elsewhere.
If it makes sense, you can also discuss the difference between this version and the conference version in more detail e.g. in the "Related work" section. This might be a good idea especially if the journal version is not just an extension but some results are fundamentally different. However, in straightforward cases this is not usually necessary.

(Please note that this answer is specific to computer science, which has its own peculiar approach to conference publishing. All other fields are different.)

I cannot say about the CS field specifically, but, in general, I would just provide a note (either at the beginning, or at the end of the paper), saying something along these lines:

"The present paper is an extended version of our paper, presented at
  ... conference [1]. This paper significantly expands ... and ...".

In CS particularly, there is usually a step during the paper submission process in which you are required to disclose whether a part of your paper has been published elsewhere (or some similar phrasing). There you list the paper(s) your current paper expands.
Further, you state in the cover letter the circumstances in which your new paper was created (e.g. "in the conference proceedings, we show that [...], this approach is improved in this paper by [...], yielding [...] results. for better comparison, a new experimental setup was used, so the results of the conference paper are rerun in the new environment, which affected the conclusions [...]"  - you get the idea). In other words, you state in a few paragraphs (keep it short though, 1-2 paragraphs should be enough) what's new in you paper compared with the previously published one and how is that significant.
As for your paper, you use your conference paper as any other reference (including the related work review), but a clear emphasis on the relation between the papers should be made (e.g. in the related work section). The style depends, you can be personal or not, it doesn't really matter. I stick to the same style I use for other references, i.e. I don't explicitly state that the cited paper is written by me.

I think that it is disingenuous to use the prior paper just like any other citation without acknowledging the relationship between the two.  In my opinion, that can seem to be inflating the support for your conclusions by making it look as though an independent work has reached the same end-point.

This could be impractical, as you do not just draw a single statement or result from the prior paper, but (in some sections) make cobstant use of it.

I wasn't clear enough, I edited the answer accordingly. The last section deals mainly with referring to the paper by not emphasizing the author, as this is unnecessary (the citation clearly indicates the author(s)) and can be taken as self endorsement. The relationship should be acknowledged and emphasized.


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Getting scooped and is it appropriate to volunteer to write a highlight?
To solve a long-unknown crystal structure, we were scooped by another group using the same state-of-the-art technique. A peer-reviewed top journal article was published online in the past few days.
Question:
Besides finding another view, doing other experiments and reorganizing for publishing which we are actually doing, is it appropriate to volunteer to quickly write a highlight (or some other types of paper) to show a more comprehensive background and significance of their work which they somehow didn't cover much?
Supplementary Information:
We find it's the first work of that group on this material system. We think maybe it's a coincidence that they happened to acquire this crystal in experiments, and they make great efforts in structure analysis to finally come to a solution. We don't find any misconduct, - they made a giant leap for this problem.
We have been long devoted to this material system, and have tried many other methods for over 4 years, and finally came to the same state-of-the-art method 2 months ago, but it was too late to acquire good enough data to publish.
We know highlights are usually written by invited senior exports (some may further needing contacting editors in advance), while our group don't have much impacts on this field. But for this certain material which is little known to all before, we have already published articles and we are confident that we are one of the groups who know it most.

Who are you talking about volunteering to? This other group or a journal? If they work in the same field as you, I would definitely reach out to the corresponding author if you intend to write a highlight. If it's not so relevant in their field but it IS in yours, perhaps this is unnecessary.