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Dealing with a passive-aggressive and seemingly biased advisor
I am an EE Ph.D. student at an R1 university in the US.
Over the last six months or so, I have been seeing some passive-aggressive behavior directed toward me. I am usually very patient, and I have learned to often ignore his unpleasantness either by saying to myself that he is under a lot of pressure or by thinking that this is all in my mind.
But lately, it is becoming more apparent that it is certainly directed only at me in the group. Here are some incidents that have reinforced that:

Three students (including me) get papers accepted to a conference. We all put in identical cost estimates for the conference (because we are all presenting over the same days in the same location). He says that the estimates sent by the other two are fine, but to me, he sends an email saying that my estimates are steep.

During a group meeting, one student presents a single plot, the other presents nothing, and I present a detailed presentation of my progress over the last week where I discovered something potentially groundbreaking. My collaborators at another university are visibly excited by these results. I did not include an equation in the slides (because it is a fundamental equation that we refer to all the time and is well known in our group at this point). He points this out, says something snarky about my slides to a professor sitting next to him, and then asks that professor if he was even able to follow my presentation. That person chuckles uncomfortably and says he'd rather not comment. I am not a terrible presenter. Not to brag: but I have won a national debate competition in my undergrad program. I can speak well.

Two students (including me) in my lab have finished enough research for an MS and moved on to new projects. The other one is taking one course this semester. On the other hand, I am taking a class, TAing a graduate course for my advisor, and mentoring two new Ph.D. students in our lab. Yet, he keeps asking me about my progress on my MS thesis but never asks the other student the same.

At this point, even the other students and a postdoc have asked me if I have noticed that my advisor is being unusually harsh with me. My collaborators and mentors mentioned that I am doing a good job. I am also on track to publish multiple papers in high-impact journals and have published two papers over the last six months.
I simply don't understand why this is happening. I am perplexed. Has anyone seen this kind of behavior before? Do you know why this was happening? And what can I do to address this? I have many more years of my Ph.D. left.
Edit: To answer a question posted in the comment section, I must note that as far as I know, nothing official has changed in the last 6 months. More than 6 months ago, I was not producing high-quality research (I had been in the program for barely a year at the time) and I was attributing his passive-aggressiveness to my lack of publishable results. After I started producing good results and high impact work, it started bothering me that I was still being treated needlessly harshly. I will also note that I have mentioned to him about some personal issues due to which I had developed some mental health issues and a bit of a drinking problem. I thanked him for his patience while I dealt with the problem. But now I have begun to think that my mental health issues may have been significantly exacerbated because of how he made me feel like I am worthless. However, thankfully, I have almost completely dealt with my personal issues and I am working efficiently and cheerfully :) (except for one teeny little problem that this question is about haha).

I am sorry that you are in this situation, but it is hard to explain why it has been happening to you as you did not mention what happened before that 6-month period.

Thanks for the question! I have amended my question at the end to include some possibly relevant information.

I don't know any explanation but I think this is a sign that you should try to get a new advisor, if possible.

There are two possibilities:
(1) Your view of the world is warped and you are overreacting / misinterpreting.
(2) Your advisor hates you or thinks that you are too difficult to handle.
The truth might be a linear combination of both.
If you can go to another faculty member that knows you well and is frank enough to tell the truth, you might find out in which direction the truth lays. I can think of innocent explanations for the behavior of your advisor and I can also see them as very troublesome. But I know neither you nor your advisor. A therapist might also be helpful, not because you are sick, but because this situation has the potential to get worse. Your university might have some help there. According to your explanation, you are dealing with a very difficult individual or at least a very difficult relationship. Asking a forum is not going to get you the right answer.
I would recommend looking for another advisor. Certainly you now longer trust your advisor and will not be able to take criticism from your advisor. Even if your advisor would suddenly become a saint and behave like one, your advisor will not be able to challenge you constructively.


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How to know if I have done and am doing good research?
My research field is a "hot" one. It is in modeling of additive manufacturing process. Majority of the research being carried out is experimental and some research is theoretical/computational. My research is entirely computational. Publications in my research topic don't go to top journals like nature or science but to applied journals like journal of thermal spray and technology, surface and coatings technology, additive manufacturing or computational materials science.
I read computational papers published by other groups from good universities (in the US and other places) and I often find them quite straightforward (that is, not much novelty in their work). In my research work, I always try to implement something extra (be it a different modeling technique, a different analysis method) to develop a distinctive new knowledge rather than a small incremental knowledge. Nevertheless, my work ultimately gets published in these journals only.
In such scenario, how do I know if I am doing a good work? My experimental collaborators are happy with my work and so is my postdoc advisor. But, how do I know that I am not generating noise? My past entirely computational papers have got just 3 unique citations each in 1-1.5 years. But my collaborative work (with experimentalists) has over 15 citations in same amount of time.

"Nevertheless, my work ultimately gets published in these journals only." Do you actually submit to other journals? Regularly? If you do, are the reasons for rejection consistent between reviewers?

I submitted to other journals (journal of solids and structures, journal of mechanical sciences) just one time. It got desk rejected for not being rigorous enough for these journals. Very few papers from my field make it to these journals.

There are many scales on which you can judge whether your work is "good". On many of them, it seems that the answer from an outsider would be yes.
You are getting published. You are getting citations. You have collaborators (so you are worth working with). Etc.
One that is important in many ways, but easy to dismiss is whether you are happy in your work. Whether you think you are learning anything through it. Even people that don't publish but learn something can have a satisfying professional life. Their work is "good" if only in a personal way. The statement that you like to "add something" suggests that you are happy with the work and enjoy it.
You don't mention whether students like to work with you, at any level from undergraduate to doctoral studies. That can be a measure, as it may indicate that students feel your ideas are worth pursuing.
Do you have new ideas? Even ones that don't work out? Science doesn't plod along. It is fresh and "interesting" ideas that drive it forward. Ideas about "what might be true" but isn't yet known.
But the difference in citation count between your personal and collaborative papers is probably not a good measure since they are different sorts of papers. Some sorts of things get more citations than others.
Another important measure is how your career is advancing. Are your colleagues happy with you? Are you on the road to promotion? To higher pay?

I agree with the other answer that "good research" is not in any way objectively well defined, and that ultimately you will have to develop your own standards. If you get published in the best journals where this kind of work is usually published, obviously its standard is good enough for their standards. If you wonder whether you could publish in higher impact more general journals, you can try out to submit there and see what the reviewers/editors make of it. Before I had some top journal publications in my field, I had a number of things rejected there, and the feedback gave me a feel for what is required.
Obviously you can also ask senior colleagues you trust about what they think of the quality of your work, how can it be improved etc., but of course these people don't always have time to read your stuff properly (better they already know some). Ultimately one can never know whether they say all they think, but it could give you an indication.
One final comment about a thing you wrote: "In my research work, I always try to implement something extra (be it a different modeling technique, a different analysis method) to develop a distinctive new knowledge rather than a small incremental knowledge." This of course is good for your learning and experience, however it doesn't necessarily make an applied paper better if the specific application could also be handled with less innovative methods. Doing something nonstandard and new in applied work isn't an aim in itself, it needs to make the application better. Things done only in order to look original in the first place will not benefit an applied paper. If you develop genuinely new models or methodology, or if you are the first to use them in your field, you should consider writing a more general methodological paper about it that colleagues may want to cite because they can take your idea for their own application.

I think your question has no answer since "good research" is too broad and ill-defined a term. What do you mean by "good research"? Research that gets cited a lot? Research that gets you your next job? Research to be proud of? Research that moves your field ahead?
The answer to your question will depend on YOUR definition of "good research". And since this is really hard to do, I would suggest to reframe the question to something like: Is my research helping me to accomplish my goals xyz?

You say that your work is strictly computational, and not theoretical/computational, and I submit that such work is too limited by the lack of a theoretical basis to get in the top journals. A career in academia requires frequent publication in high quality journals.
You must get into the theoretical aspects of your field, maybe in a collaboration with a theoretician. But don’t let that person do all the theory. You should learn from them to do it yourself.

Are there computational papers in your field that get published in what you consider top journals ? If yes, then read them and see what is it that they do differently/better than you. At least that's how I would approach it.

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what should you answer to your potential supervisor's question: Are you applying to other programs?
I had an interview with a potential Ph.D. supervisor, and along the way, he asked whether I am intending to apply to other similar Ph.D. programs? I said: Yes, but that's because I don't know how admissions work.
Was that a good answer? What is supposed to be done in such situations?
Also, when the professor says: Ok, I will work with you to write the best competitive statement of purpose. Does that mean he is going to accept you?

What the potential supervisor really wants to know is whether he/she is your first choice. By "first choice", I mean "if we made you a fully funded offer but you also received other fully funded offers, would you accept our offer?". If the answer is yes, then he/she may be significantly more willing to help you write a strong application (not just for the position itself, but also for funding). Having said that, a reasonable supervisor would understand that people may change their mind as more information becomes available or if another place makes a significantly better offer in terms of funding.
Your answer ("Yes, but that's because I don't how admissions work.") is not ideal, but a reasonable supervisor should be understanding of the fact that many applicants do not really know the system very well.
Re:

"I will work with you to write the best competitive statement of purpose"

That is not an offer of a place, but it is a good sign. It means what it says. The prospective supervisor is offering to review your application to his/her institution and give detailed advice on your statement of purpose. This may be very useful, and implies strongly that the prospective supervisor thinks you are a serious candidate. But he/she may be keeping his/her options open in case a stronger candidate applies. Or it may be that decisions on admission are not his/her sole prerogative (the exact process depends on the country and institution).

Perfect! What would you advise the answer could've been? Also, would you advise I contact the professor again to illustrate my preference for him?

The obvious answer to the first is that you will apply until you are accepted into a suitable and interesting position. For the second, it has no implication other than that he is interested. He is willing to give you advice, but your admission can depend on several things. The SoP is only one of those.
In some cases, depending of place and field, the professor may not be directly involved in decisions to accept you. But nothing is assured until you get an acceptance letter.

I agree that no one should limit themselves to one option. I might implied my answer in a manner as the only format rhetorically speaking. But allow me to give an alternative method. Before any interview practice a psychological path in first impression by the what if factors yes I do understand nerves and how they play a role. But if we educate ourselves before we fear less. Just a suggestion not saying I always do this myself but my goal is to help. We all need to believe in ourselves and give our brothers and sisters a boost of CONFIDENCE. Thank for any feedback

Honestly I would try to keep the supervisor talking retrieving as much information as possible before ever making any assumptions that could harm my first impression. That being said. There is a missing verb in the phrase “I don’t how “in the original statement.

Sometimes it s not possible, when he takes you by surprise. Saying "No" is really not going to seem normal. Who commits to one program when applying to graduate school?!

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Letter of recommendations from computer science professor for humanities?
I am trying to apply for humanities (PhD is pure humanities) graduate school in USA next year. I am going to graduate with a bachelor in computer science. The application requires three letters of recommendation, how am I supposed to get those letters of recommendations? We studied zero humanities subjects. I study in Europe.

Why humanities? Which field? Are you intending to use the CS knowledge in some way? It would be good to address this in your question.

Updated the question!

Not really enough information here.

Ok, no inch of computer science is related to Ph.D. in humanities.

Well...Have you considered that the reason you’re having trouble finding recommendation letters relevant to study in the humanities is that you have no evidence of qualification for study in the humanities? This is not necessarily true since you’ve shared so little detail, but the generic CS graduate is no more in a position to start a doctorate on Occitan literature than the other way around.

I think your primary concern should be providing evidence that you have the background and potential to be successful in a certain humanities Ph.D. degree program, and it's hard for me to imagine a situation in which you can provide such evidence without knowing anyone who could write such a letter. It would help if you could provide some details about your background preparation for beginning such a program. For example, I've posted several comments here about people I've known who went into completely different fields, but they were all able to strongly document having sufficient background.

@KevinArlin What if you have a background in NLP and programming languages? :D

I suppose that you’re just going to have to work with the letters you have. You should let your letter writers know what the target program is so they can potentially tailor it to the best of their ability.
In any case, the point of the letters is mostly to indicate your research potential. This can definitely be indicated regardless of discipline.

Thanks, that s a good point.

How could a CS professor indicate potential for humanities research?

Lots of research skills are universal: creativity, diligence, ability to follow through, independence and more. If I were asked to write a letter for a non CS application  that’s what I’d focus on


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How do I approach a postdoc interview when my background is not same as the professor's?
My PhD research was applied mechanics. I used commercial finite element analysis software to simulate thermal spray process. My research did not involve developing any weak-form formulations or any new theoretical model. I just implemented existing models and the analysis was the novelty of my research. My publications are in applied journals like journal of thermal spray and technology.
Now the professor who's going to take my interview works in theoretical model and formulations development. His papers are in core mechanics journals. However, the advertised postdoc position description aligns with my research experience and I believe I can be successful there. But I cannot produce papers similar to the professor's profile.
How do I approach the interview in this case? Should I tell them that my research experience is applied and development of formulations is not my cup of tea?

+1: Three down votes, no comments, and the question seems reasonable: Shocking. Appalling treatment of a new member. Be ashamed.

Summarising the first two paragraphs would make it easier for me (and perhaps others) to understand. I tried: My research focuses on applied mechanics (analysis using existing techniques) and I'm interviewing with a professor focusing on theoretical mechanics (developing new analysis techniques), who is advertising a position in applied mechanics. As it stands, I'm a  little confused by the details. I'm also a little unclear about the position you're applying for: Is it a position in applied mechanics? If not, what aspect of your research experience is it aligned with?

Perhaps the professor wants to branch out into a new, applied area, and needs someone with the skills to do so. You wouldn't have been offered an interview if they didn't think you were a good fit for the job.

Why did you apply for the job?

My background is in computational mechanics, so I have some background to answer your question. It seems to me that you and the professor would make a good research team because your research interests and experience are complementary. Do not assume that the professor wants you to work on weak forms and model formulation. S/he might want to go in a more applied direction as @astronot said. Instead of assuming that the professor wants to produce more papers like s/he has done in the past, ask in the interview what you'd be expected to do.
Second, it might also be useful for you to learn weak forms, just like it might be useful for someone with a mathematical background to learn applied stuff using commercial packages.

I don't know you field, but I would suggest talking about your research and what makes it exciting, talk about the professors research and why you think its interesting.
Think about how your work and their work can be combined.
Look over the job description and see if there are 'keywords' for skills/experience/knowledge for what they are looking for, and if so, make sure you can sell yourself for each of them.


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Leaving my tenure-track position for industry in January 2021,
Things have really gone downhill in our department because of Covid-19, and I and a few other colleagues (also on the tenure track) are planning to leave at the end of this semester, for industry.
To whom should I first resign with?  The Chair of the department?
My mind is made up, so I'm seeking the least painful path forward.  I have a job offer lined up already.
Thanks in advance.

I'd say the chair, yes.  But if you have any shred of consideration for them, tell the chair or the dean or whoever, but tell them now, immediately, rather than spending more time asking the Internet for advice on how to do it just so.  Losing faculty midyear is going to severely disrupt their plans for getting courses taught, and they'll need all the time they can get to have any hope of resolving things.

Chair. But soon after that talk to your PhD students (if any). It's really hard if they hear it from someone else.

Presumably this depends on the local legislation and organization of the university. Could you specify a country or at least a continent of the institution?

It seems it is too late given the organization of many activities (teaching, research, planning, etc.) that are related to you, except that your contract with the university will end in this December.

Check your faculty handbook and contract.

@NateEldredge - of course, given Covid and things 'going downhill', the chair and dean are likely preparing themselves mentally for something like this. It doesn't make it easier on them, but if the writing is on the wall everyone can see it.

@JonCuster: Yeah, it's quite possible they're expecting people will leave, but they need to be told which ones.

@NateEldredge - oh, absolutely. This is a pretty lousy time for everyone and clear timely communication will help make it be slightly less lousy.

When I left I first informally talked to my direct line manager to whom I usually reported (which was in my case the head of the department). Then my official (and signed) letter went to human resources to formalize the termination of my contract. Then talk to your PhD students / postdocs etc .. It was a slightly different situation as I left after I already had tenure but I guess the same procedure might work best for you as well.


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Shouldn’t algorithmic problem statements and respective editorials be considered as worthy of publications in academia?
Shouldn’t  the algorithmic problem statements and their editorials designed for online international programming contests, which are published on well known coding platforms like Codeforces, Codechef, Topcoder etc. be considered as worthy of publications in academia?
Before publishing the problem statement online, the moderators, testers and editorialists of the platform review the problems and rigorous testing is carried out. Also testers and editorialists are invited from all over the world based on respective expertise and their review, tested code and editorial is made available online for further discussions and improvements.
Each problem statement is open for feedback, ratings and corrections/bug reports from the users.
Also, before publishing, the statement undergoes intensive plagiarism, quality and novelty checks.
Authors of the problem statements also submit their solutions in form of tested code, logical explanation, proofs and test cases to the hosting/publishing platform.
In short, these problem statements also undergo a rigorous review process.
Any perspectives are appreciated.

Unless you already have the knowledge and reputation to do something at the level of Hilbert's problems, probably not.

Probably you mean something more specific than "academia," because I have no idea what those are.

Are you talking about the solutions of those problems? Or just the problem statements?

Generally, while submitting problem statements, you are implicitly expected to provide the editorial/solution to your own problem statements @scaaahu. So, the author submits problem statement, test cases, editorial and same has to be submitted by testers and editorialists from their end.

Please answer the simple question: Do you submit solutions? Yes or No?

Sir, @scaaahu, Yes!

Sir Deepak Tatyaji Ahire, I want to friendly inform you that most people (especially women) in the world/in international forums do not prefer to be refered to as "Sir".

No.  Those contributions are not peer-reviewed (in the traditional sense) and they do not describe computer science research (in the traditional sense).
Regular authorship of accepted IOI problems (for example) would be considered valuable service/outreach work, which should definitely be mentioned in an academic CV.  But that value derives at least partly from the rigorous screening process that IOI problems go through before they are actually used, which comparable to peer-review.  I wouldn't expect contributions to platforms like Codeforces or Topcoder (or StackExchange!) to carry as much weight.

Update: Until the question was edited, I was not aware of that Codeforces, Codechef, and Topcoder also required a rigorous review process.  But I would still argue that those contributions are still not research of the type that is normally valued in academia, so I would still classify them as service (or outreach, or educational) contributions rather than publications.
But really, I think "Should these be considered publications?" is the wrong question. The right question is "Are these valued as scholarly contributions to the author's target academic community?"  That value comes from two sources: content (Are the contributions of the form that the community values?) and reputation (Do trusted people in the community advocate for their value?)
For example, my theoretical computer science research papers have little or no value to biologists, historians, or competitive programmers, because those communities are looking for things that my papers don't provide.  Yes, they're publications, but not in any sense that would matter if I were to try to switch careers.  The only way that could change is by someone who is already trusted in the biology, history, or competitive programming community publicly declaring that my papers actually are important for that community's work.
I'm not aware of an academic community that would value Topcoder problems as the same kind of thing as research publications.  Those problems are not intended to expand the boundaries of human knowledge; they serve a different purpose.  And so my answer is still "No."

sir, I respect your point, but before publishing the problem statement, the moderators, testers and editorialists of the platform review the problems and rigorous testing is carried out before the problem goes online. Also, the testers and editorialists are invited based on respective expertise and their review, tested code and editorial is made available online for further discussions and improvements.

Sir, @JeffE, kindly have a look at the modified question.

To complement @JeffE’s excellent answer, I think it’s worth making explicit what the flawed premise behind your question is. You seem to think that what gives value to academic papers as markers of professional achievement is that they undergo a process of review by experts, as well as the fact that they are “submitted”, “published”, and that some “feedback” is given on them.
The problem is that you are fixating on cosmetic aspects of the process of academic publishing that are by no means specific to that type of activity, and that have only a tangential connection to why the activity is valued the way it is. In fact there are many types of creative works that undergo all of these processes that you listed. If I wrote a novel or a cookbook, I would have to submit it to a publisher who would find someone to review and critique it. Eventually it might be published if it was considered good enough. Similarly if I wrote a script for a film or TV show I wanted to get produced, or wrote an essay I wanted to get published in a newspaper, or made a work of art I wanted to exhibit in a gallery or museum. None of those things are in my job description as a researcher in a particular academic discipline (math in my case), and none of those things are things my department will give me any professional credit for doing - although I’m sure my colleagues would be quite impressed if I did them.
The same goes for writing problems for a programming competition. It’s a fine activity that I’m sure is intellectually quite challenging and rewarding, and as JeffE said may even have some academic value as an educational activity. But research it isn’t, and it won’t be valued in the same way as actual research.


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How to edit the pre uploaded full text article on ResearchGate
I found my article pre uploaded on ResearchGate.
But the fact is, I updated it and republished it in the same journal and it has same DOI.
I want to delete the older version of the article from ResearchGate and upload a new one.
Is there any way to do this or ResearchGate updates it automatically?

Contact researchgate. If they know about the problem they may fix it.

There is no solution to this as of now.

If you wish to replace the old full text, do this:
Select the research item >
Click on the downward-facing arrow underneath/beside the item's title ("More V") >
Select "Remove" >
Select "Remove my public full-text" >
Upload the new full text by scrolling down and clicking "Add full-text publicly"
OR
(I haven't tried this yet) Upload the new version to the last version ("More" > "Add file" > "Add a new full text"), then delete the previous version of the text if it still exists.


text:
Should we add reference of achievement awarded to a project in the final project report?
My project received the third prize as part of the open project fair hosted by the entrepreneurship cell of my institution.
Is it good to add any kind of acknowledgement or reference to this achievement in the final project report which will be published via some recognised publisher?
Any suggestions are appreciated.

Is the report to a professor for a class or something that will be published?

@Buffy, yes, the project report will be published online

Just by the university, or yourself, or via some recognized publisher. I'm trying to determine how formal the process is here.

recognized publisher

This is really just an opinion based on the comments here. I'd suggest that you leave it out of the publication, but inform the publisher's editor of the award. Ask them for advice about including it or whether the publication can add a note instead.
For a less formal "local" publication or a report to a professor, I'd suggest putting it in.
On the other hand, if I saw it in the publication, I doubt that I would object. But it doesn't really add anything to what you say in the report.


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Is it a good idea to add cross references in conclusion
Is it a good idea to add cross references in Conclusion section of a research article?
For example, can we refer to results described in previous section of paper in the conclusion section?
Any suggestions are greatly appreciated.

Can you give an example of what you mean?

@NateEldredge, Sir, added in the question

Seems to be pretty standard.

Yes....... ....

Are you asking about writing something like "We showed X (Section Y)"?

@ GoodDeeds, Sir, yes

@DeepakTatyajiAhire It might be better to add such an example in the question then. I don't know the answer to your question, but such a style does not seem to be common (in my field), with the conclusion section referring to high level outcomes rather than specific parts of the paper.

Yes, if your paper is quite long, that could be helpful.


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Difference between a research paper and technical note
What is the difference between "Research Article" and "Technical Note"?
What purpose do they serve?

I don't recall having seen the terminology "technical note" before, and I suspect it may mean different things in different fields or even different journals in the same field. I have seen (and even written) technical reports. These were usually early versions of papers, or parts of papers, or minor pieces of research that would not be publishable on their own.


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Paper rejected due to short reference list
Recently I submitted a paper to a journal and I got the following feedback from the Editorial Office:

The reference lists of manuscripts submitted to our journal should include a variety of English-language journals that reflect the diversity of resources in the scholarly field of the manuscript.
I regret to inform you that it was found to be unsuitable for publication because the reference list did not contain sufficiently diverse, English-language sources.

Now, my question is, if some research is novel and does not have much information about it on the internet (for eg, a newly developed algorithm), then how will such papers get published, if the editors reject it on the basis of the size of the reference list rather than focussing on the quality of the manuscript?

"if some research is novel and does not have much information about it on the internet" I think that would actually apply to the majority of published papers.

The editor should have given more specific feedback.

The comment is more about the quality of the references, rather than the number.  The editor is saying that if you cite 100 similar papers, this is not as useful as citing 10 different papers.

Improve the literature review/introduction section in the paper so that you are referring to a diverse range of references which give evidence that you are aware of the wider context which you are working in.

Are most of your cited works in English, or in other languages?

The all cited works were in English

In case the list of references is not considerable suitable, for whatever reasons, the referees may simply say so and request for an improvement. There is absolutely no reason why a paper should be rejected simply by counting (I have been there: a journal that I won't mention has a rule of having at least as many references as a fixed factor of the number of pages, so I simply had to add a few since it was the only request, of the journal, not of the referee).

My guess is that this was not the only reason that the paper was rejected. It doesn't seem like an adequate reason by itself. There could have been multiple reasons for the rejection, with the editor focusing on one of the more salient ones. If so, they should have been more clear.

the editors reject it on the basis of size of the reference list rather than focussing on the quality of the manuscript.

I think that's a false distinction. From the view of the journal (and most publication outlets I know), one aspect of a manuscript's quality is that it needs to defend its novelty by appropriately considering related work.
The feedback does not mention the size of your reference list, but a lack of diversity, which indicates that your article is limited in the perspective of considered related work. For example, if your algorithm uses a new idea from X to solve a new problem Y and presents applications in Z, you should discuss papers about X, Y (or similar problems), and Z.

Often, most of the citations in a paper are not work that you directly rely on.
Of course you cite a paper if you use their model, their method, or if your model or method or algorithm is a direct extension of theirs.
But you also cite papers of people you solved (or attacked) similar problems or used related methods. You discuss what they have done and how it differs from what you do. Ideally, you can argue that some problems in the field are solved, but the one that you are working on, is not.

I think its worth pointing out that this context-setting is one of the most important parts of a paper. Putting a result in its proper context tells the reader why they should care.

tl;dr: Your editor is right: a limited bibliography reflects poor quality of the literature review. Improve your manuscript by finding relevant work of others and comparing your results with them.
Even if your algorithm is completely new — and this is a big if, because most new algorithms are actually variations and combinations of previously known ideas — you probably want to show that it is useful. To demonstrate this, you need to apply this algorithm to solve an important problem, and compare the results of your new algorithm with other methods that were previously used for this class of problems. Hence, you need to discuss the origins of your problem, the context in which these problems appear, what other methods have been proposed, and why are they not good enough, so your algorithm is needed. All these statements must be supported by references.
An overview of the research landscape is an important part of any research paper, and the bibliography supports this part and reflects its quality. If your bibliography only includes the papers of your research group, it is very likely that your research misses some aspects of a bigger picture. In this case your paper can mislead readers in believing that you are the only group actively working in this area. Your editors are right in rejecting it.
So my advice is: add more context about the problem (with citations), and about the work of others (with citations). Compare your algorithm with other methods used for the same problem. Clearly demonstrate in your manuscript why your new algorithm is not just new, but more useful, than previously used methods. Then submit the manuscript again.

Breadth
Even if you specific algorithm has not been discussed, you should point the readers to related algorithms (maybe in other contexts), or to others algorithms that solve the same problem.
Language
The response has a weird focus on English-language references.
If you have a comprehensive set of references that are not in English, you might want to add some instances of

This problem has been discussed in [normal references]. The closest work published in English we could find are [as closely related papers in English as you can find].

This allows you to include the relevant references and satisfy the editor's request of references in English.

I don't think it's weird to expect that most references are in English for most fields nowadays.  E.g., in math, if all of the papers I reference are in Chinese, then (1) they won't be verifiable to a majority of international readers, and (2) it indicates that the problem is not of broad interest, as almost all quality original research papers are written in English now (or occasionally still in French in my field at least).

References are also most helpful when the reader can actually read them, so if you're publishing in English, I'd expect many of the references to be in English too, especially when you've got some flexibility in what to cite (e.g., "The role of X is controversial, with some studies finding A [ref, ref] and others finding B [ref, ref]").

There are areas in research where most of the work is done by a national group. I know of methods which were done primarily by Russians, others mainly by French. Both group publish a lot in their native language and have even conferences in their native language. So the body of papers might even be non-English. Still, they also visit international conferences and publish in English, too. But correct references might be in Russian oder French. You cannot change this. I heart similar cases for Japanese research.

@Kimball French and Chinese are both non-English, and thus do not count as parts of literature review according to this editor.


text:
Failed my 2nd Qualifying Exam in PhD. Absolutely devastated. How to proceed?
I just failed my 2nd Qualifying Exam in my PhD program. It was supposed to be a 60,000 word paper but it was an incomplete work.
I am in my 4th year at my PhD and my research is in field of humanities. My major is Geography. It is an integrated course, as in I joined as soon as I got my Bachelor's. I am doing my research on a multidisciplinary and very practically useful subject based on sacred forests and urban landscapes (I won't go into details). But, I was going through some intense emotional time for 6 months (June to December 2020-a critical period) due to personal tragedies in my family. Also low funding is also a problem. I am an international student. And pandemic is just making it worse.
Now, I feel absolutely devastated.I am not going to get a chance again at re-exam, and that is fine too. I can understand why they wouldn't want to invest in such a bad student. I do work very slowly, but sincerely and did learn and correct accordingly as my advisor said for this 60,000 word hell. Though I could not do field surveys and data collection due to strict travel sanctions, I tried backing up my research with more literature. The problem here is my research is focused on a more practical part of urban forestry, and it is so niche that there is a severe lack of academic work on my topic, if you don't count ancient scriptures (which is hardly academic).
I realise my mistakes and I am willing to do everything to correct them. I just need some more time. But being told I am not suitable to be a PhD student just based on the incomplete paper (it was just 40 pages long) hurt me more than being told how my research was absolutely useless. I am aware that my research IS useless at current stage, but I had all the future work set up in proper parts so it becomes relevant. I was not sure if I can give reasons about tragedies and poor health because last time I tried that they had said 'so what? even pregnant ladies do phd" and that was that. And that is fine too. But being told I am useless as PhD student was like taking a direct hit on what defined me. It was sort of an existential crisis. The shame and incredible sense of loss is palpable and making me clam up instead of working to get out of it.
I know it is not the end of the world and I am sorry for long sob story. I want to know how to proceed? Is it possible to get into a PhD after failing quals? Or do they dismiss you if you have failed quals? Should I immediately apply to a PhD or gain some work experience before?
Thank you.

Normally, it is possible to put in hardship applications (concerning health and other force majeure circumstances)  before an examination. Unfortunately, this is much harder after the fact, otherwise every failed student would try that. I do not know if you can try for another PhD, but I assume you can, though I would probably pick a different place to do it, where they do not know you. It might be a good idea to work for a bit or do something else to distance yourself before trying again. Make sure you learn - I mean, really learn - from the experience what not to do again.

Should I immediately apply to a PhD or gain some work experience before? --- I recommend work experience from what you've said. What you've described does not sound like an ivory-tower area that you can pretty much only pursue in a university setting (e.g. medieval literary analysis, realism art aspects of cave paintings, gender issues in dystopian science fiction, etc.), and even if it were, if you find yourself pursuing it no matter what you do job-wise, then you'll have the answer as to whether you should try again. (continued)

You might find that you can happily pursue your interests and gain employment without a highly specialized and narrowly focused research degree. Indeed, obtaining such a degree is likely to limit your employability to a handful of highly specialized and narrowly focused areas, unless you can prove your competence in less specialized areas, which a few years of work experience will provide, and you will probably find it easier to get this experience before you get your degree and find yourself being classified as "over qualified" for such positions.

Just my personal opinion:  I agree with those who say to try the work-world or something else.  Of course, depending on your major, it may or may not be easy to establish a career in non-academic organizations.  If you have a master's, you may be qualified to teach at various community colleges, etc., and you certainly could tutor other students, among many other options.

I have evidence that it is possible to do a good PhD in a new university after failing to pass qualifiers in an earlier one. In fact, the person I'm thinking of finished at a higher rated university than the original.
However, in this case, it took the efforts of a faculty member (and mentor) of the person to strongly advocate for the candidate's admission and to express complete confidence in their ability. The candidate had a bad experience with many factors at the original place but turned out to be very well respected by faculty at the second.
You have a hard road and it may not be possible to travel it, but look around you for any advocates that will argue for you. If you are currently suffering from burn-out you will need to get that under control. But advocates can help with that, also, just from their attitudes. Having a new advisor in a new place might work wonders if you can convince people of your ability and likelihood of success.

@Dragon Zakura: Buffy's first paragraph also applies to me, including the upgrade in university rank. In fact, for me the two universities in question were my 3rd and 4th graduate attendance stints --- the first at the highest ranked university I attended graduate school, the second at a then only Masters level program in my field where I got a Masters degree. (More details in the comments to this question.)


text:
Use of "this reviewer" in a review
I sent a article for reviewing before publication.
In the review I received, I had the following comment:

From very similar studies this reviewer knows well that [...]

This is the first sentence of a bullet list, with each item being largely independent of each other.
There was no mention of a reviewer earlier in the review.
I have two questions:

It seems to me that "this reviewer" refers to... the reviewer her/himself.  Am I correct?  Of note, the reviewer may not be a native speaker.
Is it widely used?  Especially compared to using "I" (just like other reviewers do)?

Not really a question about Academia

For your second question, see: https://academia.stackexchange.com/q/154165/19607

This might be more suited for one of the English language sites.

It reminds me of military boot camp where the construct "This recruit" is preferred over "I".

It refers to the reviewer writing the review. It's not that widely used (and personally I don't like it), but I have seen it in reviews, and as a native speaker I don't find it that unusual. It allows the reviewer to respond in the academic third person (a bit like saying "the authors" in a paper) - a grammatical construct to allow them to write with an academic tone.
Personally I just say "I think"!

"We" is not third person -- it is first person plural.

It is possibly an overreaction to the often made assertion that a person should limit the amount of times they refer to themselves when discussing something to avoid seeming self important.  It's certainly possible a non-native English speaker could consider this to be more strict of a rule than it actually is but I think anyone can fall in to a habit like that.  In my case I was told not to start a sentence with "and" or "but" when I was in school and even though I've read it's acceptable I still jump through hoops to avoid it in my writing.

@nanomam well, if we can be singular as a pluralis majestatis, why can we not be third person in whatever is the opposite of pluralis majestatis?

@nanoman you're right, edited

When I see or have used something like “this reviewer”, it’s often been a deliberate attempt to take emotion out of a contentious (or potentially contentious) disagreement between the reviewer and the authors.


text:
How should be your relationship with your PhD advisor
What kind of relation should one have with their supervisor ?
Could one talk informally with them ? would you get their phone number to discuss things on the phone ?
Thanks

I do this all the time. This question is subjective and opinion based.

why do you have to judge the question ? just answer it !

Everyone judges questions here, actually. Don't be offended. I hope my answer is a bit more than opinion, but you are the judge of answers.

This depends on personalities. For some it is perfectly acceptable to be very informal. For others, such as mine, a more formal relationship was needed. But, even in a formal relationship, you need to have your questions answered and concerns addressed. But it is really a matter of "style" how you go about that.
So, the first thing to do is ask the advisor what they prefer and how frequently it is "good" to touch base. Even with a formal relationship, an advisor might want a progress report every couple of weeks (or more, or less).
But work it out initially. And, you want to have a good relationship so that they will be willing to support you after you finish, as well as during your degree years.
Of course everything was, and we hope will be, in the absence of a pandemic.

Note that different advisors rank different parts of their job differently. Some value their own research very highly, which can be a problem if they aren't as helpful as they should be. I often worry about untenured advisors for this reason (and once suffered because of it until I switched). But, I'd just guess that phone conversations with advisors are pretty rare (though mumble mumble pandemic).

And you might also want to look at my earlier question and its answers on this site: How do you build a healthy and productive relationship with your supervisor?

The most important thing students forget is: "... you need to have your questions answered and concerns addressed" (as mentioned in the answer)


text:
I forgot to click the link "Yes, I am affiliated" in the paper submission paper, will I lose co-authorship if paper is accepted?
If one omits to verify their co-authorship (at journal submission time) and if the paper is later accepted, could they confirm co-authorship then?

I think it's a good idea to write to the journal about this and ask whether they can change the selection.

That is very unlikely. Authorship is up to the authors unless there is some misconduct with the paper itself. If the paper lists you among the authors then you are an author.
If corrections need to be made they will be time for that as few papers are ever published exactly as submitted.
Note, however, that being listed as an author and verifying affiliation are very different things. If you are not listed in the paper itself, you need to work with co-authors to correct that.

I am listed as an co-author, But when the paper was submitted by my co-author, the journal in question asked me (through an email) to confirm I am a co-author (which I think I did not do)

Send an email back to that editor and clear it up. Not likely a big deal. Note that author verification is a standard practice.

I'd think that the editors might want either a "yes" or a "no", and not a non-response. But, then who knows what their default action might be...

It is good idea to write to the editor about the missing information and have your name included as co-author in view of contributions made towards the work. Good Luck.


text:
How common it is in the US to ask for technical help from the supervisor as a PostDoc in CS?
I want to know if it common to ask the supervisor about a technical question (in coding or in  the theory behind the code) as a PostDoc in computer science (in US or even EU)?
Is it seen as "normal" or would project a technical weakness and thus communicate a lack of confidence in the technical aspect of the work by the postdoc which would in turn lessen the reposed confidence from the supervisor to the postdoc.

It seems like this would depend entirely on the question asked.

I would much rather have a postdoc who admits they are stuck or confused, than one who pretends to understand things and then makes mistakes...

What would be the point of having a supervisor if you couldn't ask them questions?

I was asking about a specific type of questions. your comment is not helpful at all

Discussions on technical issues are very common. That is true about the supervisor or others in the field. The coffee room in large departments can be one of the most productive places of all. Big questions don't have easy answers. Different people have different backgrounds and different perspectives as well as different insights.
It would be a mistake (IMO) not to ask if some question is holding you up. Among other things, even things we know won't always be at the forefront of our thinking.
Such questions can also lead to new insights and new directions. Working alone in a cave is one of the least productive methodologies of all.
If your PI is overly grumpy, however, tread lightly with them, but not necessarily with others. If research were easy, no one would pay you to do it.


text:
are letters of recommendation always required for lecturer and/or postdoc positions in the CS field in the USA?
I want to know whether letters of recommendations are always a requirement for all lecturer/postdoc positions (across all universities) in the USA in the computer science field?
If not are there any universities that don't require these letters? if not, how to apply for such positions without the need for recommendations?

This sounds like an XY problem.

Pretty much any job in the US in ‘academia’ will require references. My lab does not require formal letters of reference, but I am required to call the provided references and ask certain questions. If you are unwilling or unable to provide references to contact you won’t be hired. Simple as that.

that's also a proof of your inability to make fair competency judgement without (a possible rigged) opinion from others.

@Sam - after hiring dozens of people over the years, I can look back now and say that my judgements were pretty darn good. Almost universally without needing to contact the references, but fighting against or lying to HR is just not a battle worth waging. But, if nobody wants to speak up on your behalf, well, there are some issues there that I'm not willing to take on in an employee. Good luck.

I don't think there is any rule that applies to "every university" in the US. Not many anyway. But not requiring letters would be very rare. Very rare.
Most universities are bound by advertising rules for most positions other than "per-course adjunct lecturers". Those are probably available, but have no benefits (usually) and no guarantee of permanence. (Some are unionized, however, so a bit better.) But regular, even not on the tenure track  and postdoc positions are usually advertised and there are usually lots of applicants, leading to the problem of choosing the "best" candidate for the position. Letters of recommendation are one of the best predictors of success when they come from someone who can be trusted and who has nothing to gain from a good letter.
One possible path to a regular position, though not a post doc, would be to serve as an adjunct for a while, underpaid and under-appreciated. If you do a good job and make yourself known to the faculty over a few years, then letters might not be required, though you would still probably need to compete for a regular position due to the rules. Some of those rules at some places are enshrined in law in the US.

Even the private universities?

I can't find US regulations that require it, but the universities that come up in searching suggest that they make faculty searches as wide as possible. That is, they have their own regulations at least. If nothing else, this helps them show non-discrimination and also give a rich field of candidates. And universities that receive federal funds in various ways are more likely to be bound by regulation. There are probably exceptions among those that don't accept any federal funding, but one questions their reputation.

All universities in the US I've ever heard of use this system. If there are some that don't, they will likely have other ways of ascertaining a candidate's qualifications, and that other system will also rely on people who actually know you.
In other words, there is in all likelihood no way for you to avoid the scrutiny. Of course, the obvious question is why you don't want to subject yourself to the system as it is? Do you have something to hide? Or are you just on a quest to demonstrate that the existing system is stupid, at the risk of self-immolation?

Even the private universities?

They operate in much the same way. But like I said, even if they don't require letters per se, they still will want to have references they can contact to ask about you. What I don't understand is why that bothers you.


text:
Is it okay to give students advice on managing academic work?
My journey through academia has been a hard-fought battle against myself and all my worst traits. I'm now finishing my PhD and concurrently teaching courses in which I inevitably come across students who do things that remind me of my own mistakes. I find myself empathizing and trying to find bits of 'life wisdom' to impart, with the goal of being helpful.
I don't remember ever being on the receiving end of such an email. I'm also certain that my colleagues don't it, which, given that they're quite good at their jobs and I'm relatively new at this, makes me want to evaluate this tendency critically.
Here's an example:

Student missed a deadline for a makeup assignment. Class policy
(decided elsewhere) is that this forfeits their right to an exam
retake. So I send all the boilerplate emails, and they apologize,
saying that they didn't have the time or energy to get it done before
the deadline.
I totally get it, so I write back that I'm sorry, I understand it's
rough to play catch-up in these situations. Then I said that teachers
often have greater leeway to offer students who ask for extensions
before it's due, and that sending a quick email to a teacher explaining the situation upfront can be really helpful. I say that I
was totally oblivious to this fact when I was a student, so I try to
tell students this now.
Then, I explained that it was still really important to complete the
replacement assignment anyway, because it's easy to glance at it,
think you understand it, then realize during the test that there were
nuances in its application that you didn't actually understand.
Then I offered to look at the student's assignment if they could send
it within a few days, just to make sure there weren't any obvious
knowledge gaps.

It seemed reasonable as I was writing it, but afterwards I wonder if it's preachy and patronizing. Given that it's exactly the sort of advice I give my teenager on the regular, it makes me wonder if it's the sort of communication best left to their parents and not their teachers.

Are these school or university students? If the latter, are their parents really monitoring their work and exams that closely? Personally I would send emails with advice like this as it's not going to actively harm anyone and may help those struggling students a lot.

@astronat, these are undergraduate university students, largely first-years. I also teach some third-year classes and have had similar moments where I take what I'm now identifying as a very mom-ish approach to communication.

Glad you asked. Yes, do this!

Not all students are in regular communication with their parents, so one cannot rely on this.

You could probably setup a wiki/mock FAQ with such advice, and provide the link to the students at the beginning of the course.

I wish I'd had more teachers and their assistants like this in my classes when I was in college. This is a wonderful display of understanding, empathy, and helpfulness, mixed with fairness! By all means keep it up! Just make sure you don't accidentally cross over into giving students wiggle-room later to undermine class policies. I didn't see any of that in the example you gave, but something to keep an eye out for. Basically keep your empathy and helpfulness, without crossing the line between "I'm your caring helpful teacher and mentor" to "I'm your buddy". Anyway keep it up--it's great!

Within reason, this is a good thing, though you risk burnout if you constantly go out of your way to save struggling students.

It's totally appropriate especially for first year students. Learning college level study skills is one of the crucial tasks of the first year.  Additionally, many students whose parents did not attend college (and even some who do have such parents) are totally unaware that they can do things such as attend office hours or email the professor if they need an extension or have a problem.  In fact the way you have structured this, you could even in the future think of developing such knowledge as a learning outcome.

Additionally, this topic (academic skills) would be a great topic to place in the syllabus and also to discuss during the first class when the syllabus is discussed as a way to inform ALL students and to give them a skillset which will be important throughout their entire academic career.

It looks like you give your advice because you care and this is all that is important. The notions of being "preachy" and "patronizing" may be applicable to the wording of your message in this case but not to the message itself. In any case, your advice makes no harm and can potentially make some good. As usual, a fool will ignore it and a smart person will listen and decide for himself whether it makes sense or not and that is all you can expect, but I wouldn't be afraid of "stating the obvious" if it once was not obvious to you. I would even put a few things like that in the syllabus.
Unfortunately (at least in the USA) we cannot rely on parents guiding our students because we are not even legally allowed to discuss their performance with them and guess what type of students are most prone to hide their achievements and problems from their parents.
So just continue what you are doing. It makes perfect sense. If you wonder why your colleagues are not doing that, just discuss it with them. You may discover that they have other ways to communicate such messages that they find more efficient. As to myself, I usually give advice like that in class rather than sending individual e-mails (so if I see that obvious thing that can benefit one student, I just tell it to everybody).

Advising better ways to handle academic life is not, IMHO, stepping outside of your boundaries as a teacher.  Sure, if you were meddling in their personal lives then, yes, it would be better to leave it to their parents.
A second point is that, from your message, it seems some students might get different conditions than others. This is dangerous territory and I would not recommend going into it. Specially since, with experience, you'll realize that these occurrences are the norm, not exceptions. In my experience, students that ask for more time (and get it) during their first year continue to do so until they eventually graduate. Also, some students might start pressuring other teachers to open exceptions and soften rules.
A strategy that I implement is to make these "exceptions" part of the rules. For instance, delivering assignments late (up to a certain point) deducts points from their grade as long as it does not make a passing student fail. So there is a consequence to delivering late (smaller grade), but it does not fail a student that has (eventually) achieved all the courses' objectives.
Another strategy I use is to allow for individual time extensions, but students must ask for it one week before the deadline and must also have at least X% of the assignment done. This one is great to communicate that if the student plans to do the assignment on the last moment and then something unexpected happens, it's the student's fault and they do not deserve more time. Shit happens in adult life and they should start taking that into account. Of course, we can throw a "shit happens" rule so students can deliver at most one late assignment without consequences.
I usually present all this upfront at the start of the semester, so student know what they will have to live up to. It can also be a nice way of bringing up the subject of how to handle academic life and help students that are struggling.

I appreciate this answer because the perspective differs and suggests why other teachers react differently. In this particular case, it's one of many workgroups for a lecture with hundreds of students. Because the goal is fair treatment of each student, there are specific rules with built-in exceptions, rigorously documented. Explicitly, little room is allowed for individual circumstances, but we are nevertheless responsive to people who ask. I think this speaks to a true nature of the "real world," biased in favor of those who communicate. Maybe communicating this fact helps mitigate it?

I think it is great that you care both about your students and about doing things rights. Having had similar questions and being myself a child of parent that did not have higher education on top of having to move to a different city to study, reducing my interaction with my parents, I fully share your concerns that some sudents may not have access to the information this kind of arrangements are possible from their family.
A core concern I have about this is: how are you making sure it is not unfair? To build on you example, some other students in similar situation may have been able to meet the deadline in a way damaging to themselves (e.g. poor quality assignment, overwork or even straight up giving up on university before getting your boilerplate emails). If I was in the second group I would be very upset about the fact that some other could get out of it by simply asking nicely, especially since I would never have imagined it was possible or considered acceptable in any way.
This is not to say that you should not give these kinds of advice, but rather that they are so essential that if possible you should distribute them to every students equally before they even need it. If universities had clearly layed out and broadly publicized policies about when getting an exception to a rule is possible and acceptable, it would probably be ideal and you would not have to be concerned about it yourself. Things being what they are, your inputs are unvaluable.

I'd suggest bringing it up during the lecture - so that the students who rushed poor quality work would know they they could have requested an extension as well.

"If I was in the second group I would be very upset about the fact that some other could get out of it by simply asking nicely"
Asking nicely is always an acceptable option.

@CaptainGiraffe I suspect it may be cultural. I can definitely imagine situations where asking for a favor would not be considered proper, even if it is asked nicely.

I'd like to chime in with some experience from my PhD time (as a student, we either had deadlines about which there was no discussion, or there wasn't any deadline as in, submit whenever you like, but there won't be a grade before)
My professor had a very good reputation for teaching. That is, teaching analytical chemistry. As a PhD student, however, there were a whole lot of points which I did not understand - not chemistry related, but more about the management of research and research politics and the like. Many years later, I can now see likely (and good) reasons why he said what he said, wanted me to do things the way he wanted, and acted the way he did.
I'd now say that after receiving a formal tertiary education in chemistry, as a PhD student I did an apprenticeship of learning by doing a 2nd profession: that of an academic researcher. Back then I had only the hazy idea that I did not quite understand what was going on.
And I'd also say now that he probably also never had the idea that - maybe - the profession of research (or group leading, academic management, lecturing, ...) could be taught in an explicit way like we teach chemistry.
With that in mind, I'd like to encourage you to go on reflecting also these "secondary" professions and then teaching it to your students, like you teach your field.
The same applies to dos and don'ts of how studying at university works.
(BTW, we were told as first year students e.g. that the failure rates are usually high [we performed as usual, with about 1/4 passing the 1st semester at the 1st time, and another ≈ 1/4 passing after re-doing 1st semester], and has always been so since university works quite differntly from school and most people need time to adapt to this.)
Like teaching your field, the question what to email or say in a one-to-one setting vs. bringing up a topic in the lecture is a decision that may differ depending on what the point in question is.

I wonder if it's preachy and patronizing

This is a valid concern, but to me the very fact that you worry about it indicates that you are much less likely to err in this way than others who never waste a single thought on it. :-)

This is highly insightful. I never quite paused long enough to see these "secondary" professions stand on their own. They clearly have plenty of enough impact on academic performance and the morale within the team that approaching them as subjects of their own importance seems like excellent advice to me. Sometimes just having such a mental framework enables to apply rational thought to some setting that could otherwise seem much harder to reason about. Even just having a name for common experiences leads to better outcomes.

I like the way you describe it as a "secondary" profession. I've been thinking about it as the academic "meta" but it's really much more than that. I think that I was quite blessed in my Research Masters program to have been taught many of these soft skills explicitly, but I wonder if they might have been better conveyed earlier. I guess it's either an oversight, due to lack of space in the curriculum, or... maybe because undergraduates aren't yet ready to receive the information? Anyway, thank you, I think this really is a helpful way to think about it.

Increasingly, late-stage undergrads are being recruited to do some mentoring to address similar concerns.  That indicates a need for it.
I suspect similar conversations happened face-to-face until recently, in tutorials or project-related discussions - I've had similar ones.  Transferring this to email communication should be easy enough, but some of the nuance is lost, making things harder.  It's also harder to spot problems early on when you're not meeting face-to-face.
Students need support, and it's good that you're someone who offers it.  You might want to check what else is happening, either to help you support them, or to avoid stepping on any toes.

I think this is a good point that I hadn't really considered, especially in situations where I sense that what I'm offering up may not be enough. My low-level mentoring might be like trying to put a Band Aid on a severed hand, and the student would be better served by communication that tries to establish what resources they need realistically.

@DanielleMcCool Any support is likely to be good support, and knowing there's someone supportive around can be a benefit in its own right

I am not a doctoral student, but the question seems weird. Is it okay to help someone with something you believe you can help them with.
Yes, it's okay, I would even say, it's a moral obligation to remove a stumbling block from before the blind.
Once you clearly voiced your advice, especially if the other person is mentally an adult, it's their responsibility to decide whether to follow your advice.


text:
academic job offers during Coronavirus
I signed a contract for an academic faculty position in the US in February. Now with the pandemic affecting universities, do you think it is possible that they rescind the offer? Is it appropriate to reach out to the dean or someone else and ask how the situation is developing in light of hiring freezes at some universities in the US?

What does the contract say?

it's a regular TT contract with all the info about job responsibilities, teaching load and salary. It does not say anything about contingencies and emergency procedures.

Once you have signed the contract, I don't think the offer can be rescinded - but you could still be laid off like any other untenured faculty member.  The procedures around that are probably in the faculty handbook or some similar university policy document.

Thanks. I'm more worried about it being rescinded at this stage since I stopped applying when I signed the contract. In fact, I rejected another offer then as well.

It is also possible the institution closes permanently.

Thank you. That's also possible although I'm less worried about that scenario at this point as it is a large well-established school.

I've seen no effect of coronavirus on hiring processes except that  the personnel committee will meet by video-conference instead of in person.  I don't see any way the coronavirus situation would affect offers that were already made, especially if they were already accepted. If the university spends a ton of money on the current crisis, it might limit our financial ability to make new job offers in the future.

Yes, it is appropriate to explore the situation. I doubt that the offer would be rescinded, but who can say except them. They will need the personnel now as much or more than ever.
You have a signed contract so they are bound as well in all but the most extreme situations.
But timing and such might be disrupted. And if you aren't already in the US, note that border crossing is very difficult if even possible.
But ask, and ask to be kept informed.

Thanks. I'm in the US so border crossing won't be an issue.

And you signed a contract, which binds them. Some emergency procedures might be used to change contracts, but I'm pretty sure nothing like your case.

It is possible, and not at all uncommon, for a US employment contract to not bind the employer at all.  A signed contract could very well leave "at will" employment in place, where either party can terminate the employment relationship at any time even without a good reason.


text:
My assessor is giving me spelling advice - but he's wrong
I'm writing the thesis on which I aim to graduate with a bachelor's degree. I've got an incredibly nice assessor, whom I sent part of it, and he gave a lot of helpful feedback on structure, relevant and irrelevant details, et cetera.
But he also suggested that a word is spelled wrong, when it isn't. Now, this isn't just any word; it is the name of the product I am creating as an IT student. Not the proper name, because that would be exempt from spelling conventions, but the generic name with which I refer to it very often; like, several hundred times, scattered over not just my thesis but all the relevant documentation.
This isn't a question about the spelling itself - the word is in Dutch anyway. But I want to know if I should be adopting his wrong advice because it comes from the person who is going to grade me; or engage in spelling debate which can come across as pretentious. It doesn't help that I'm a language nerd and that this isn't something to be settled with a single link to a dictionary; the term itself is a new compound, and there are specific rules for forming those that I consciously followed.

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

First of all: ask for a third opinion, just to be sure you are right.
Anyway, the nice thing about science people is that they are usually convinced by evidence, even when it goes against their previous thoughts. Write them a polite, respectful e-mail explaining why you think you are right, and pointing out reputable grammar sources to back you up. Show that you have done some additional research. There are good chances that this will work.

That's what I ended up doing. I got a compliment for it and an assurance that I can use my language however I want. Thanks for the advice!

I am glad I could help, and that you got a reasonable answer. Best of luck with your thesis!


text:
Progress to Ph.D. delayed due to COVID-19: How to convince advisor to let me finish degree without taking an extra year?
UPDATE: I completed all data collection and writing for my dissertation and have my defense scheduled for next month (January 2022).  I also still received satisfactory progress and funding.  Several months after the initial post, I think my advisor realized COVID wasn't going away any time soon, so I was allowed to propose my dissertation in Fall 2020 and collect all data remotely.  I will be staying in my current city in a remote industry job.
I’m doing my Ph.D. research in cognitive development using in-person experiments with children, which has stopped indefinitely due to COVID-19. I passed my preliminary exam last month, so I only need to propose and defend my dissertation.
I want to propose this spring/summer and defend by fall 2021 so I can stay in this city and get an industry job, but my advisor keeps pushing me to take a 6th year so I can publish and be more competitive for academia, despite me telling her many times that I want to leave academia. Now that in-person studies have stopped, my advisor is basically forcing me to take a 6th year and wants to push my dissertation proposal to this fall (which would give me unsatisfactory progress, thus possibly eliminating my funding). I asked about proposing a partially online experiment so I could gather data this summer, but she refuses to let me do any online data collection for my dissertation. I really don’t want to take a 6th year of a low stipend when I could be financially stable with an industry job, and I don’t want to possibly spend next year unfunded.
Is there any way I can negotiate with her so I can finish this degree sooner rather than later?

What do the other people on your committee say? Who at your institution have you asked for advice? In my experience, peer pressure is much more effective than any of your negotiating skills.

Perhaps helpful: https://academia.stackexchange.com/questions/114193/what-to-do-when-an-advisor-repeatedly-changes-graduation-requirements/114196#114196

Do the industry jobs you're aiming for really require you to finish your PhD?

A horrible advisor.

Is taking prelims typical in the fourth year for your program? That's very late for cog programs I'm familiar with

@Dawn, Thank you for the link.  I have not yet formed a dissertation committee because my advisor is not letting me do so yet.  However, I am going to meet with some professors/fellowship mentors who have served in my past committees to talk about this.  I mentioned it to them and we are going to set up a meeting.

@AzorAhai, Yes, that's typical for my program.  We typically take prelims during our 4th year and propose our dissertation in spring/summer after the 4th year.

@AlexanderWoo In almost all cases, yes.

Interesting. I'm sorry you're caught up in this, but it seems like we really won't be able to make decisions for a month or two more.

You really need to work this out locally.

"I only need to propose and defend my dissertation" -- there's an elided "write the dissertation" step in there, right?

Very sorry to hear about your situation. I know of others, like yourself, who've had their research stalled as a result of the COVID-19 situation. I must say, I was taken aback shocked to hear about such inflexibility on part of your supervisor:

I asked about proposing a partially online experiment so I could gather data this summer, but she refuses to let me do any online data collection for my dissertation.

If you haven't yet already, then you should really have a heart to heart with your supervisor and explain to them how you're feeling. Try and see if it is, in fact, the case that they are fixed on this issue. Should collecting data online be a feasible means for you to collect data for dissertation and defend by the fall, it would be very unreasonable on your supervisor's part to not allow you to do this. So if your supervisor is firm on this position, I'd recommend consulting with your department's ombudsman or even head. It is definitely not fair that you should be held back if that is not a necessary outcome, and merely reflects your supervisor's research motivations.


text:
Are journals biased towards more famous authors?
Say you are an independent researcher, with no affiliation and no famous co-author. Assume that you have authored a paper, which you believe is decently written and reports a method that is at least comparable with state of the art. Some reviewers at a  reputable journal read it and acknowledge the merits of your work, suggesting only minor and addressable corrections. However the editors reject the paper. You attribute this to bad luck.
Then you submit to a few other journals with lower impacts, and the editors desk-reject it, providing a terse comment or two. You know the work you've done, so you don't find the terse editor comments fair and unbiased. They sound more like a made-up excuse to you.
Do all these rejections have anything to do with you being an independent researcher, not affiliated with any academic institution and above all, not having any famous co-author?
Is there another reason behind the curtain? Like the editors asking among themselves "who the heck is this guy?! Where'd he come from?! Who is he to have his work published by us?!"
Final edit: I voted to delete this post. It seems to have caused more mayhem than I intended. And I kinda got my answer anyway. My speculation was probably right. Many thanks to everyone who took part and apologies for any inconvenience.

When you get "minor revisions" from the reviewers (and you revise appropriately) but get "reject" from the editor, do they tell you  why? Some papers are just a bad fit or hit at a bad time for a journal.

Normally the reviewers tell the editor their overall assessment confidentially. They can write something to the editor that is not in the Comments to Author. This means that you can't really be sure from the comments that the reviewers recommended minor revisions, they may have had an overall more negative opinion. Of course it is better to write comments to authors so that the author knows better what the reviewer thinks, but exceptions exist. Another thing is that from your question of course nobody here has the slightest idea whether your work had good enough quality to be accepted.

I voted to close because this is a complaint, not a genuine question.

Also possible duplicate of https://academia.stackexchange.com/questions/3010/does-one-need-to-be-affiliated-with-a-university-to-publish-papers

99% of published authors are not famous.  Bias is everywhere.

Does this answer your question? Does one need to be affiliated with a university to publish papers?

Thanks for the help. Truth is I had already gone through this post and a few similar others before posting my question. I couldn't find the exact answer I'm looking for there. I already knew in theory anyone can submit. But in practice, can you really publish if you're a lone, independent and not-so-famous author? What will the editors make of your work? Will they give you a chance, or prefer to work with the authors they already know so well? To me the answer seems to be a vehement no. Anyway I guess I'll delete this post myself. Some of the replies are poisonous and missing the point.

@User32563 You may not need an institution to publish, but it sure helps to have an advisor who can guide you in the research process and let you know when the rejections you are getting make sense and how to improve your work to not get rejected. That's something an institution usually provides you access to.

Journals are biased toward experienced authors.  I've reviewed many articles that read like an undergraduate report.  In many cases, these 'articles' are not even at the level of a good undergraduate report.  In other words, it is obvious that the authors do not have a PhD or if they do, a very bad one.

Opinion-based, voted to close. FWIW here’s my take: there are several effects here. First, journals probably are a bit biased towards famous authors (not in the unethical sense of “who the heck is this guy”, but in a more sensible sense of being more confident that papers from established researchers are what they claim to be). Second, famous authors are famous because they, well, write very good papers. They also have a lot of experience and are better at communicating their results. So, the odds are in fact stacked against you as an independent researcher, but not for the reasons you think.

... And this is nothing special about academia. In every field of human activity, the established players enjoy entrenched advantages compared to the upstarts. But everyone plays by the same rules, and every established player was once an upstart and managed to climb their way up the ladder of success. So complaining about this won’t get you anywhere. Hard work and persistence will on the other hand. Anyway, good luck!

It can certainly be helpful to have a famous co-author on an article.  For example, if one referee accepts the paper and then the second one will recommend revisions instead of rejecting if they see a famous name amongst the authors.  Not saying thats good or bad, I'm just saying it happens.

Arguably, you have got it backwards. Authors become famous by publishing stuff that other people read and reference. They weren't born famous!

@alephzero: That people becomw famous by publishing stuff does not at all imply that journals aren't biased against already famous people.

@BryanKrause there's now a paper (mentioned in this question) that definitively answers OPs question using data. Could we reopen it?

@JonathanReez I think the title question here is fine ("Are journals biased towards more famous authors?"; the original was "Is being an independent researcher frowned upon?") but the body of the question is about OP's papers and instead reads "did my papers get rejected because I'm not famous". The question was closed for the latter, not the former.

@BryanKrause can I open a new question with the title "Are journals biased towards more famous authors?"?

Correct me if I am wrong, but your previous experiences with publishing are only the one paper you published before, together with your former advisor? Then, you might lack the experience necessary to know about the typical mistakes that lead to a (desk) rejection. Your results may be very good, but this alone does not make a good paper. Being proficient in scientific writing takes time and requires practice. Your former advisor is a few steps ahead and you might not even have noticed some small corrections from her/his side that made publishing of the previous paper much more likely. Famous researchers usually are particularly good when it comes to presenting/writing about their results. They make it easy for the reviewers to like their work. Beginners often make it easy for the reviewers not to like their work. This does not result from bias, but from scientific writing skills. And the editor also needs convincing, so pay attention to your cover letter.
If you decide to go on alone, you might have to learn the lessons the hard way by facing a few rejections. An experienced person might be able to help.
And please stop making the mistake of calling the replies you get after peer review "stupid". This is also a typical beginner's mistake. Sleep over the replies until you can look at them in a rational (not emotional) mood. In my experience, virtually all replies can be used to improve your work.

Or in other words, a little more humility and a little less hubris may help you see their comments in a more helpful way.

Edit: since the question's been changed:
Yes, journals are biased towards more famous authors. Source

Another reason for the breakdown is the hypnotizing effect of reputation. When the names of eminent people and places appear on the top of submitted papers, says Florida physicist Hebard, "reviewers react almost unconsciously" to their prestige. "People discount reports from groups that aren't well known," adds University of Maryland physicist Richard Greene.

This is mainly positive bias however, because there are way more institutions and researchers in the world than anyone can keep track of. I don't know the details of your paper, but assuming you are right that it is novel enough, has been receiving positive reviews, etc, but is still being rejected, I will hypothesize that there is something you're missing which is causing the desk rejections, e.g. an omitted authorship. There're other strange things about your description of the rejections as well. This comment is especially weird:

A couple of other journals rejected without peer review, with stupid comments and excuses from the editors (I'm not one those scientist legends, but trust me, I know my field well enough to tell if a comment is a stupid excuse or not).

How can you know your field so well if you're a recent MSc graduate?

Fair enough. I haven't been in the business long enough. The correct phrasing is "I'm familiar enough with the related field to tell if a comment is stupid or not". About the supervisor, why would I include him when he hasn't done anything? Does he include me in his solo works too?

I don't know the details of your paper, so I cannot answer that question.

This is terrible advice. You seem to assume that reviewers treat papers as some sort of popularity game ignoring science. You are also suggesting phony authorship. You seem to believe that the only thing needed for good publishable science is to have a prestigious institution. I call BS.

@Buffy I don't think you read the answer.

Yes, I read the answer.

Whatever, then.

Your new source is but an anecdote of of scientific misconduct. It is just as easily explained by the (likely false) result being so new, unexpected, and potentially useful as any bias toward "fame" of the authors. One data point doesn't imply a trend.


text:
Publishing in Mathematics and Computer Science related journals
I have seen Elsevier journals offer Gold open access and Green open access options, when I was checking for journals related to Mathematics and Computer Science.
I have understood that Gold open access can be gained by making a publication fee. However they have mentioned that waivers are offered for countries eligible for Research4Life program.
Can someone help me to understand whether you have to be a part of some program to have this waiver? i.e. if you are in a country mentioned in the Research4Life program page in Elsevier, do you get free publication open access in Gold open access journals?
https://www.elsevier.com/about/corporate-responsibility/research4life
And do Elsevier and Springer offer reductions or discounts in Article Processing Charges for low income countries?
Can someone please advise if you are aware of this.
Thanks a lot in advance.

Did you email the journal editors to ask? What did they say?

The rules for Elsevier are stated on this page.  Essentially, as long as all authors of your paper work at institutions in countries in "Group A" then you get a full waiver.  If any author's affiliation is outside this set of countries, you don't (there is also a set of countries that get a 50% waiver).
It's unclear whether you can get a waiver if you don't have any institutional affiliation.  I suspect it may be difficult, since Elsevier is huge and the system is supposed to work automatically by detecting your country of affiliation.  If they don't even respond to an email to support, I wouldn't be optimistic.

Thank you very much @DavidKetcheson


text:
Can you use information acquired during the research (and listed in the appendix) in the introduction?
In some fields of research, e.g. ecology, it is common to describe the study area in which some field experiment was conducted. However, sometimes you find out some facts that might be of interest only during the field work itself.
I am currently not sure about whether it is ok to put such information in the appendix of a paper and reference the appendix in the introduction or methods section. The information was acquired entirely during the field work and is not available anywhere else (hence, some entirely new knowledge); however, it is not some result or output of the study but simple, basic facts. E.g., the number of tree species occurring in the area, or information about the climate that were calculated based on data from some weather station, in a study that tests some hypothesis not directly related to these environmental factors.
Maybe I am giving too much thought to this, but I have little experience so far and do not want to make some mistake.

At this point in your career, you should have read already many papers in your field. You should find examples on what you plan to do there.
Prima facie, you provide information that might be useful to the readers of your paper, who might be looking for a good area to study themselves. Putting this type of information in an appendix seems entirely appropriate. Once it is anywhere in the paper, your introduction can and usually should allude to it. If it is very short, you might want to describe your study area in the introduction itself.


text:
How do I salvage a 1-week old research internship offer, if possible?
I'm a pre-university individual.
About a week ago I cold-emailed university professors inquiring about interning at their biology research labs. A professor replied on the same day expressing possibility of an interview. He also made it clear it would be unpaid - which, after some thought, I've decided I'm fine with. Long story short, I was stupid and indecisive, and only emailed him back a week later, with an email looking along the lines of:

Dear Associate Professor X,
I'm really sorry for the delayed response; I’d hoped to get back to
  you sooner. I've thought about this. I very much am grateful for your
  kind willingness to consider and would be pleased to meet up with you
  to better present myself, and work something out together.
If it's not too late, when would you be free to meet? I promise not to
  dillydally again. I am free this entire week. Just let me know a time
  that works best for you.
Yours sincerely,
Las Nons

It's been about 2 days since I sent this reply, and he hasn't gotten back to me. When he first replied to me, it was on the same day I had sent him my first email.
Looking at my reply, I realize I forgot to thank him (for his time and consideration) at the end of the email. Ending my email off the way I did could have made me seem entitled/presumptuous.
Dear reader, was my reply rude/presumptuous? I'm really worried I've offended him somehow. I'm thinking of waiting a day more, then sending him a follow-up email that includes an apology or something. Should I?
Is this a gone case? What could I do to salvage this?
Thank you all for any input.

I think it is safe to just wait a bit. 2 days is nothing.

@Buffy Do you think I sounded entitled/presumptuous in my reply email to him?

I think it was fine. Saying thanks would have been better, but it sounds ok overall as you sent it. I don't think that trying to "fix" it with another email would necessarily be positive, actually. You did take a week to reply yourself, of course. Give it a few more days.

Since comments get deleted, I turned it into a proper answer.

The only thing rude about that E-mail is addressing the recipient as "Associate Professor X."  The correct term of address is always "Professor X," regardless of someone's technical job title

The message you sent has a sufficiently professional tone that I wouldn't worry about it. While it would be better in general to thank the person for their interest it doesn't seem like a big issue here. In particular since you were a bit self deprecating in your tone.
But a couple of days is nothing in academic time. That is always true, but especially now when people may be struggling with finding creative ways to teach without having student present. Since the offer wouldn't become "live" until August you have some time to wait.

Thank you @Buffy. This internship wouldn't start in August though; I'd be able to commit immediately and it would have to end by August. Right now I've finished what is the equivalent of US high school, and am an unemployed bum.  I know this seems trivial/OCD to many, but I really hope I haven't offended/made a bad impression on him.
In any case, though, my country just announced a one-month lockdown, so there goes my hopes and dreams, sigh..
Thank you again. Take care..

It may be country-dependent, but in the UK academic staff is now increasingly involved in research effort aimed at tackling the ongoing epidemic. With Universities restricting face to face interactions and closing down campuses, it is a good chance that all non-essential activities, such as internships, will be put on hold until the situation improves.