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Doctoral stay in foreign university
I am a PhD student in my second year, and I am thinking about doing a doctoral stay in some foreign university with a group that works on the same topic as I am. I do know about some interesting research groups where I could do this kind of doctoral activity. However, I am unsure about how does some proceed to pursue this kind of research position.
Does one directly write to the group presenting yourself and what are you doing (also presenting some of your published work)? Do you have to follow a formal application at the target university? Does it depend on the country/institution?

Yes, maybe and most likely. Just contact the group you are interested in, they will let you know if you have to go through the university or not, as this depends strongly on the institution and group in question.

Any kind of contact will be easier if you are introduced by a trusted mutual contact (usually your phd supervisor). At the very least because professors get a lot of e-mails, a good deal of them exactly like that, and it can be difficult to separate random request from actual serious requests.

If you simply want to work with them and don't require either a formal position or funding then you just need to talk to the PI of the research group and deal with visas and such.
But if you need funding, it is a separate issue that might be handled by the PI (via their grants) or by the university. You might be able to arrange your own grant, of course via some agency.
If you desire some official position, such as formal matriculation, then that can only be granted by the institution. That will generate an academic record for your stay. Later in your career, the position of Visiting Professor might be open to you, but from the institution.
But you need to talk to the PI in every case. Give them your qualifications and your interests. Treat it like you would any application. Convince them of your suitability and likelihood of success.


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Is it usual to ask for several references for postdoc positions?
I have seen postdoc job adverts which were asking for as many as three recommendation letters, despite being supervised positions and inviting freshly graduated PhD students.  Is this practice common and reasonable?
As a more practical question, how should an applicant deal with this situation?
It seems to me that it is not unusual that the only person a student worked with extensively is their advisor. In fact it would even seem like a good thing to have an advisor who does not lead a large group and has time to work closely with all their students. Yet such students would find it rather difficult to obtain three recommendation letters.

In my experience in Mathematics, three letters is very common.
So who to ask for these three letters? The better your letter writers know you and your work, the more meaningful their letters can be. But this does not mean that you must have worked closely for an extended period of time with them. Perhaps there are others that are familiar with your work, for example because they are on your thesis committee, or they have invited you to give a talk. Depending on the types of positions you are applying for, you can also have a letter that focuses on your teaching skills.
Finally, an advisor that has plenty of time to work with you, does not preclude you from also working with others. In fact, the value of building a network of colleagues cannot be underestimated. This does not necessarily mean collaboration with others, but it is important that you get out there so that your peers become aware of you and your results. These are the people that eventually may have to decide to hire you or not, or could write a letter for you.

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How can we effect institutional change to make academia climate-compatible?
How can we create an environment in which academic institutions are responsible for the carbon footprint of the research carried out under their auspices?
For context, I am a postdoc working several thousand miles from home.  I try to mitigate my carbon footprint, but there is absolutely no incentive not to travel, other than personal conscience.  In fact, one actively harms one's career prospects by not travelling to academic conferences, for research visits, etc.  Currently I am using my own money to carbon offset every flight I take, but I cannot avoid flying if I want to retain my job.  I am certain that I am not the only academic unable to reconcile my love of my research with the entirely unnecessary environmental damage which it is causing.
The individualism of academia means that my university appears to take no interest in mitigating the climate impact of the research going on within it, and seems to consider any action on the matter to be my personal responsibility, rather than their responsibility as my employer.  This should not be a matter of personal conscience (or financial resources) for junior members of staff on precarious contracts.
I am aware of initiatives such as Flying Less, but these largely rely on individuals to risk their career progression by participating. It clearly is not enough to tell academic staff not to attend conferences or to travel to perform research that will further their careers.  How can institutional change be effected?
Some thoughts, which would likely need support from national-level funding bodies to implement:

Could carbon offsetting costs be factored into research grants?
Could carbon trading schemes be instituted?
Could universities cap the maximum air miles of their staff?
Could remote participation in conferences be incentivised?
Could conference funding be made contingent on climate mitigation measures being implemented?
How can we push institutions to create the systemic changes to our profession which are clearly required?

I am of course aware of the arguments that, e.g., academic travel is a negligible fraction of total air travel; air travel is by no means the largest part of the problem; we need more research in order to combat climate change, not less, etc.  However, it is my opinion that academia needs to be an exemplar of adapting to become sustainable.  If we as scientists cannot alter our own behaviour in the face of overwhelming evidence that it is actively harmful, how can we expect others to moderate theirs?

Why limit this so much? You should include the lights on when not needed, excessive use of water, poor buildings with excessive heating etc etc - if you really want to address this then you should do it properly.

A couple of related questions that have been asked: How to promote reduction of carbon footprint for conference participation?, and What practicable alternative do I have to not fly around the globe to present a poster/pollute environment?. The main difference seems to be that those questions focused on what can be done on a conference or individual level, rather than the central funding level.

I would very much like to do this properly, and I would hope that any action taken would also involve energy and resource conservation.  I chose academic travel as something conspicuous, and which involves large-scale collective effort to change, but I entirely take your point that there are many other facets of this problem to be addressed.

Here is a blogpost (disclaimer: co-authored it) with what I hope are useful suggestions: https://tcs4f.org/taking-action-against-environmental-crisis

You may also like this report allea.org/wp-content/uploads/2022/05/… from ALLEA (European group of national science academies) from 2022 which lists possible actions at many different scopes

I can think of two main ways to reach these goals:
Method 1: grassroot campaign
For example it could go something like this;

Create a group of researchers from various fields who share this goal.
This group reaches a consensus for a set of realistic measures that an institution could pledge to apply.
Reach to the most prominent scientists from various fields, ask them to:

publicly  support the pledge
lobby the institutions/organizations they belong to to sign it
boycott the conferences which don't sign it.

Keep the pressure from the scientific community until most major institutions are compelled to sign the pledge. At this stage extend the scope of target institutions to funding bodies and big industries.

Rationale for targeting the most prominent scientists: because they have the visibility and influence, they are on the board of the most important conferences, they can afford to boycott conferences and their boycott could destroy these conferences.
Method 2: patience
This kind of measures are going to be taken sooner or later, when the damage is too obvious to be ignored (recent research point to more death caused by air pollution than by smoking). At some point it will simply look ridiculous for academic institutions and funding bodies to insist on ethics in research while paying travel expenses across the globe for researchers. But that's going to take a while.

If you want to affect how universities do business in this or any other way, you have to get the policies changed. Those policies may be set by governments and/or boards of directors/overseers. To affect those changes you need to do things at that level. You can petition governments. You can elect better leaders. You can make public protests, etc. All of this requires collective action - organization. For private boards you can petition them at their (infrequent) meetings or you can try to push proposals upward from lower levels. Again, collective action.
These sorts of things can be effective, but big organizations have a lot of inertia. So, to move them takes a pretty strong force. None of the actors with power to change things like bad publicity, however. That can be an element of your collective action. Some people can be shamed into doing the right thing.
On the other hand, you can just ask individuals to behave better and to show them how to do it without disrupting their lives any more than necessary. Given the climate change potential disaster, a lot may be necessary, but individuals, like institutions have a lot of inertia. Make it easy to do the right thing if you can. Make it hard to do the wrong thing when you must.

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Should I acept my second choice?
I applied to a PhD program, and after all the interviews I got a firm offer for a fellowship let's call it PhD A, that I have to give an answer to before a deadline (next week), since they have
Now the lab in which I did my master's thesis, and in which I have been working since 6 months applied for a grant to finance a PhD student (me) but won't have an answer before a May. Let's call this PhD B.
Now my problem is that I would prefer staying in the lab I am at for PhD B, but, even though it might be small, there is always a chance that it wont get the grant, so if I say no to PhD A I would be left with nothing.
And on the other hand, if I accept the fellowship offer for PhD A and my lab gets the grant, I would prefer doing PhD B.
The real problem is this deadline, because the PhD A wouldn't start before October, and so if I also get an offer for PhD B after having accepted offer A, I would prefer not to burn any bridges by just leaving after having accepted.
So my question is what do you think can be done in a situation like this?

Possible duplicate of Offer for a pre-PhD visit, how to handle the situation with other PhD applications in the queue?

In this case, I would do the following first. Go to your present admin/PI and let them know what you have said here and ask them what would happen if they don't get the grant. Is there the possibility that you can be kept on with other funding, or is it absolutely dependent on the grant?
If you are valued enough where you are, it is just possible that they can make some arrangement to keep you. "I'd rather stay, but it seems uncertain, and I have this other offer. What can be done?"
I think it is probably worth asking the question.
But if it isn't possible to make an accommodation, then you need to decide how much risk you are willing to accept. That is personal. It would depend on the likelihood of other options, of course.

Thanks for the answer, I have already talked with my current PI and it is dependent on the grant since he doesn't have any other funding for the moment, but the process is fairly under way and he is confident that it will be successful. However there is always that slim chance that it won't work out.

Ok. And, good luck.

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Using a number of equations from a paper, how to mention it in my paper
I am using a number of equations from a different paper. I am using those to derive another quantity.
Is it appropriate to just mention them one after another, without stating the assumptions behind the equations etc, since I am already citing the previous paper like
Equation 1 -- (1)
Equation 2 -- (2)
Equation 3 -- (3)
.
.
.
.
.
Equation 14 -- (14)
then state the physical meaning of each parameter in the above equations?
I tried looking at some example papers but couldn't find any in the particular journal I am writing for.
If it were 1 equation, it would be fine, but I am not sure how to handle so many equations.
Or should I just reference the main equation and state the rest in the supplemental section? I just read and it seems putting too many equations in a paper is not a good idea.

It depends on what you're writing. I normally write a brief paragraph beneath each equation which describes what the equation represents and the obvious things about it such as the parameter meanings and the reasoning for certain aspects of the equation. If I'm repeating myself in the paper I'll just refer inline to equation (1), and if I have to add MANY equations, I'll usually try to put "where the parameters \alpha, \beta, and \stuff" have their usual meanings. Unless I'm showing a set of three equations that you get at the same time from one derivation, I normally have at least some text.

@lafemmecosmique That's a good approach, and the one you'd typically see in papers. However, if alpha_989 really has 14 equations, and especially if they are not self-explanatory enough, putting them in an appendix sounds more sensible to me.

Oh yeah, 14 equations is appendix-material for sure. Somehow I missed the '14' part ;)

You want your paper to be clear and readable.  Do what makes it so.

Thank you @101010111100  for your comments. I think its probably more appropriate to move it to the appendix, and cite the main equation. It was a lot of work to find the relevant equations, and connecting the dots, so I kindof thought that maybe if I put all the equations in the main body, it would kindof show the amount of work that went into finding the equations.
But I guess a paper is judged not on the basis of the amount of work but on the importance of the results. Sometimes thats a hard pill to swallow.

@lafemmecosmique, yeah.. thats what I usually do when I have a few equations. I will write out the equations, explain the physical meaning of the parameters, and where it is coming from in a simplified fashion. But with the 14 or so equations I cited, it would take another paper to just describe what the meaning is. So maybe its best left to the appendix.
Its not completely cut and dry in the sense, i am using some equations directly, and then have to use some equations from another paper to make the connection between those equations and the previous equations I have derived in the paper.

So I will probably mention the main equation from paper 1, and the connecting equation from paper 2, and the equations I derived in my own paper. and leave the rest of the equations from paper 1 in the appendix.

@Kimball, Thanks.. You are right.. while I have written previous papers, those were trimmed and edited by my professors, and I didnt have to think about whether the paper was clear and readable etc.
For this paper, my advisor basically gave me free reign, and basically told me that I should write and submit the paper by myself as a corresponding authoer. So I am kindof trying to figure out the balance between explaining everything in a self-contained paper vs making it readable.

Yes, there's always a balance to be struck, and it's not easy, but this is part of the challenge in writing papers, and one can get better with practice.  A couple suggestions are: try something and draft it up, then (1) have other people look at it an give feed back, and (2) put it away for a week or so, then read it again.  I often realize that explanations that seemed clear to me at the time weren't anymore after I stopped thinking about it for awhile.

I'm not sure about the common practice in your field, but, as a mathematician, I feel that you have approached this thing from the wrong direction. You don't reuse equations from another paper; you reuse theorems. A theorem is a statement like

If A and B and C are true, then equations D and E hold, where the symbol F is defined as... and G is defined as...

Maybe the authors of the other paper did not formulate their result as a theorem, but it is one. It is a sloppy but common habit to throw the derivation of a result in front of the reader directly, instead of first stating it then proving it.
Another important point to note is that there are hypotheses and assumptions under which these equations hold; if you focus on equations rather than on the whole 'theorem' package, this information can very easily get lost.
So, my suggestion is: reformulate those results as theorems. It could be a single theorem with 14 separate equations as the thesis, if they are all related.
If the word theorem sounds too pompous, use proposition. If your result seems too simple to deserve this name, use lemma.

My suggestion is to use the main equation from the previous work and for the others refer the reader to the main paper.
About explaining the equation, if you give an introduction before formulating the problem, the reader would be prepared for your idea.
Moreover, you should illustrate the coherence of the equations clearly to get interests from the readers (and especially your reviewers). The recommendation is to use the graphs and plots (visual description) to notice the reader about your idea, proofs, and results.

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Publishing a letter: how much extension can I ask for?
I am attempting to publish a letter in a IEEE journal. The journal gave me 2 weeks to address the comments. It also mentioned that if I need more time, I should let them know as soon as possible so the editor can reset the dates. How much of an extension can I ask for?
I dont know how long its going to take to complete the revision, and frequently I find that I need more time that I originally think I would need. So instead of asking for extensions multiple times, can I just for say more that I think I would need at this point (say 2 months)?
Is that too much? First time publishing, so no idea of the protocols.

You can ask for whatever extension you like, but you should expect that the editor will say no.

For letter papers, and a minor revision (as you mentioned in your other question), I wouldn't expect the editor to extend beyond a week or so.

Is it possible that the comments from the reviewers could take more than 2 weeks? I don't think the editor might not have thought about it. I agree @MadJak, it can be max 1 week.


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Old supervisor not responding to email for reference
I have worked with my old advisor for 1+ year to produce my senior thesis. I'd say that our relationship was good when I left to do my masters (and he did write me a reference the first time around). I'd say he was satisfied with my studies if not terribly impressed.
I was fairly confident that he would write a letter this time around for my PhD application (1 year after our departure) but now I've sent him two emails without getting a reply. I feel that there is really no reason he would decline other than he is too busy or getting too many letter requests--this may be why he just didn't reply to my email without an outright refusal.
I cannot "ambush" him in person since my visa has expired. I do have contact info to one of his phd students and his phone number. Should I call him or contact his PhD student? Or keep sending more emails? What should I say in the emails? I really need his reference.

Try to call him, at least he should tell you explicitly he doesn't want to write a reference. (Your mail may have ended up in a spam folder, or he is on vacation or ill or something).

I agree you should call if he has not responded after a reasonable time (say a week or two).  If you cannot reach him, contact the department administrative staff, or the chair, and ask if they know of some reason why he is unreachable.  Do not contact the PhD student, they are not the professor's secretary and it is not their job to help people get in touch with him.

I think the answer of Bob Brown at the link cited by @NateEldredge is especially useful. Note that the professor may not remember you as he may have had a hundred or so other students since you last had contact with him and his focus has been there, and likely on grad students as well.


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OK to ask a professor at my institution with whom I have no previous relationship some questions relating to hobby-project?
I go to community college so our professors aren't busy with lab research. They're still busy people though and I wish to respect that.
I'm pretty much just working through some neuroscience textbooks for the sheer heck of it, but I often get stuck. It would take forever to ask every single question on the internet. Plus, sometimes a discussion with a real person is just better in many ways; it could lead to further questions and answers plus instant clarifications.
Thus, would it be weird/wrong to just ask a random professor (with whom I've never taken a class...just one with the relevant biology expertise) for help with specific questions about my side project?
I'm guessing it depends on the professor; but on a scale of 1-10 how weird/ intrusive would this be? I mean, some people would be ok with getting hugged by strangers, but that doesn't mean it's a good idea to try and hug them.

is it possible for you to take classes in your interest? I understand your question, but it seems you are seeking an alternative route to what is already being done at many universities/community colleges. By taking a class, you will have the material explained to you by an expert in your field while also having a person whose job it is to answer student's questions. In addition, more than likely most of your questions will be answered through the course being taught.

It's hard to do this and not come off like a crank. You'd be better off developing some rapport by taking a class from one of these professors first and then asking for their help.

These are some pretty specific topics i'm interested in that are not taught at 2 year community colleges. Plus, i think it would be more annoying to be in a class/office hours and take it off topic than to just schedule a whole separate meeting.

have you looked into online "MOOC" courses, through websites such as coursera and edx?

MOOCs and what i'm doing have the same "nobody to ask for help" issue though...

many MOOCs have forums where you can discuss your questions with classmates, who are viewing similar material so they have more context than a random person. In addition, you may be able to email the MOOC professor (or TA's) who will be receptive to student's questions.

there's also a cognitive science SE for what it's worth. I can't speak to its quality, but it might be a good place to ask questions about neuroscience.

"arbitrary professor" makes it sound like you closed your eyes, walked down the hallway of faculty offices, then opened your eyes and knocked on whatever door you happen to have been standing in front of  :)

Ah. Title like a true journal article. Ok sure let's have it be that.

If your school has any seminars in which said professors might attend, this might be a more organic way in which to meet them.  Then discussions might simply naturally arise.  Also, professors often like to go to drinking establishments, so an offer of a beer for a discussion is not out of the question (depending on the university and professor of course)

Yes, it is entirely appropriate, especially if you come to them in person and just knock on their office door when they're around and ask if they can spare 5 minutes to answer a question or two. If you are nice, polite, curious and fun to talk to (and you sound like all of those things to me) they may easily end up talking to you for an hour. Busy or not, professors are people and love to procrastinate just like anyone else. :-)
Email is a lot less likely to work, but again, I don't see it as inappropriate, simply less effective.
And don't overthink it. Knocking on someone's (even a stranger's) office door is not the same as hugging them, and not every decision in life should be agonized over and analyzed in minute detail. Just try it, the worst that can happen is... nothing.

Very good answer, especially the last paragraph. Systematically overthinking every decision is a great recipe for unhappiness in my experience.

This may depend on your macro and micro culture, but in Germany it may easily come off as rude to randomly knock on someone's office door without prior notice. Instead, you would talk to their secretary first.

@Stefan I have never in my life met a professor who has a secretary.

@Dan Oh, I had no idea that this wasn't the norm everywhere.

@Dan ...and not every decision in life should be agonized over and analyzed in minute detail  I could hug you for this.

@Myles Lol, apparently @Dan doesn't work so well when there's more than one Dan.

As a professor I would add only one thing to this answer: only approach the prof during his or her posted office hours. This is the reserved time to meet with students. Expect to get bumped if the professor's current enrolled students show up.

One of the perks of being a college or university student is access to the faculty for academic purposes.  Ph.D's become professors at community college particularly because they want to be engaged with students and their curiosity without the enormous overhead of excessive grant writing, etc. In short, they basically live to work with curious students like you.

Ok to ask random professor questions relating to hobby-project?

Yes, and if you show half the courtesy and respect in your introduction to the professor that you did in this posting, you can rest assured that the response will be solely a function of his/her current availability.

100% agree! All of my favorite professors were extraordinarily open to intellectual discussion even while they were very busy. Professors spend a huge amount of time preparing and marking coursework and lectures, so taking a short break to have a discussion with a curious student might even be the highlight of their day.

If he is in the topic, he might be interested. Be relevant.

If you don't ask, the odds of getting help are zero.
Admittedly, even if you do ask, you're unlikely to get very far—as you mentioned, the professor doesn't know who you are, and therefore would be very unlikely to respond unless the email is written in such a way as to grab her interest.
However, if you're a student attending the same institution as this professor, asking to set up a meeting might be a more productive route, so long as you show genuine interest in the professor's work. Most professors will take the time to talk to someone who's interested in their work (we're human, and we usually like the attention!).

yes I'm part of the institution, but our professors don't do research work (at this school...who knows what they cook in their garages). They are all lecturers and only teach classes. I'm also not doing "research"; just reading some complicated books I need help understanding.

I was about to give much the same answer, well worded email from university email asking for meeting over just asking for help. @Flurpy, if you want the professor's help it would behoove you to research what his/her research areas are as it shows effort (and we really do love to speak about our research - yes, many of us still research even at community college)

Absolutely agree with the last sentence. I would personally react more favorably toward a student who is willing to take the time to e-mail and set up an appointment, compared to someone who just make a cold call. (Besides, if someone just knock on my door about something that will likely take more than 5 minutes, I would ask them to e-mail me and make an appointment first.)


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How important are GRE Quant scores for a PhD applicant for B-schools?
I will be applying for a PhD in Management and Business in non-Math / economics related topics. I have been out of touch with calculus for a few decades and while I am studying hard, I am not sure that I will reach the top percentile in GRE in quantitative papers.
My question is: How important are GRE quant scores to the Academic committee of Businesses school PhDs? Esp. the top 20 schools in USA / Canada?
What if I have reasonably good work experience (25 years) across the world (Asia - Far East and London - does this make any difference?)?

Are you talking about the GRE math subject area test or the GRE general quant test? Given what you said about your intended graduate program, I would assume you are NOT taking the GRE math subject area test. However, you talk about calculus, which is well beyond the scope of the GRE general quant test, which usually does not extend much beyond one year of school algebra and one year of school geometry (meaning it even excludes, I believe, many precalculus topics such as trigonometry, conics, logarithms, complex numbers, etc., to say nothing of calculus).

Look up the schools on Grad Cafe and see what the reported GRE scores are.

@ Hobbes - Thanks a lot, I was not aware of Gradcafe.

@ Dave: Thanks a lot. Yes - that clarifies my question. I am only taking the GRE quant test (and of course the qual / verbal etc). Do forgive my ignorance as its been a good two decades plus since me or any of one near me gave a semblance of a GRE. its fun to be a student again, :)

Incidentally, depending on your background (what math you studied in high school and early college) and your exposure to math since then, you may (or may not) have MORE to "relearn" regarding the GRE quant topics than if it covered topics up through elementary calculus, such as mixture problems, distance equals rate*time problems, "simultaneously working together at their own individual constant rates" problems, geometry problems involving properties of circles and secants and such, percent increase and percent decrease, all sorts of data and table interpretation problems, etc.


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Using Google Trends diagram in a scientific paper to show evidence of interest in an area
I am preparing a paper for a conference. At some point, I want to show that one area is gaining more interest over another area. Do you think that using a google trend diagram as a supportive (not the main) evidence is a good idea ? My area of research is web information systems.

I feel like it may look a bit unprofessional just using a screenshot from google. I've done similar things in the past for a talk and I believe google has an api. I'd pull the data and make my own plot - would look a bit better.

Thanks, yes this is what I will be doing. But I was wondering whether it does really reflect the interest? because some people may argue that interest is not necessary connected to google searches.

I would check publications with certain search terms over time. Might give a better picture of interest.

Related: Is it common to cite the numbers of results a search engine yields as evidence for the prevalence of something online?

Yes, you can use it, but treat it like any other source of data.
I have been encouraged to use Google Trends data as supporting evidence by my professors.  You would need to explain the implications of the data, including caveats, just like any other type of data.  In the case of Google Trends, be careful not to overstate what it is saying.  It is only counting searches made on the Google platform, so what does this tell you directly, and what does it imply indirectly?

You can use it. There is no rule that prevents you from doing this anyway. But consider a few points.

Where are you going to include this? If this is part of the Introduction or Motivation sections, this should be fine, as there are (field dependent, of course) many papers that have introductions that are not-so-technical in the nature, and to build up the interest of the reader.

However, including this as part of a latter technical section such as Evaluation is a terrible idea, as it is not really technical.

If you are indeed going to include this in the "Introduction" or "Motivation" as above, make sure to use it appropriately.

For example,
Don't pay too much importance to the numbers (Search results). They mean nothing. Rather, discuss or point how they grew over time (Topic "A" appeared to grow exponentially in interest though it started with much lesser impact in the Internet compared to Topic "B" based on the Google Hits).

Space is very expensive in research papers. Most of the conference papers give you a limited space (such as 10 pages). Are you sure you are not wasting the precious space with not-so-useful diagrams?

My point is, consider whether there are better ways to utilize the space while proving your point (Topic "A" is gaining more interest recently compared to Topic "B").


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Lukewarm grade in proposed area of study?
I'm applying for study in a particular area of math.
To keep matters short , I was an undergraduate that took the graduate version of a particular class and ended up with a B+ . I had never taken any class on the topic before this.
The department received several complaints about the professor in the course and other professors in the department even acknowledged that the distribution of the grades was quite terrible , not expected for a graduate course.
Since the grade is in a class that is in my proposed area of study , should I mention it at all in PhD admissions? My supervisor and other professors in the department said they would mention that the class in question was terrible but I'm not sure if I should  talk about it myself.
I feel kind of strange not addressing the fact that my proposed area is the only course which I didn't do great in. For some context every other grade I've ever received are great so there is no pattern of doing bad or anything.

Possible duplicate of How do you get a bad transcript past Ph.D. admissions?

You've tagged mathematics. I think the cultural thing here is that they'll focus on the letters of recommendations most, so they will see this. If there's nothing you need to take responsibility about, then I don't see a reason that you need to mention it.

@CapeCode I don't see anything in that question or its answers that actually addresses the specific question "Should I address a single poor grade in my application myself, if my supervisors said they would mention it?"

@TK Which culture? The question doesn't mention any specific country.

@DavidRicherby Mathematics culture.

@TK There's a single mathematics culture throughout the world?

@DavidRicherby I may qualify this to EU and NAmerica.

A B+ is not a bad grade for an undergrad in a grad course.  I suspect that it will not raise red flags in an admissions process.  The discussion on "complaints" or "the class was terrible" has no place in your application package, especially coming from you, and it would make the applicant come off as a whiner.  You took a course, you got a grade.  Done.
If admissions slots were limited, and I had to make an otherwise equal choice between  two students, I'd opt for the one that looks more mature, and complaining in your application package about a course does not make one appear mature.

If you could get the distribution of all marks from all students in that class,from the secretary of study, for the semester you took the exam, you could mention that. But a not A is not a reason not to be admitted in a phd course.


text:
How important are citations when applying for jobs or promotions?

How important is citation count for fresh doctorates? Is this number more important for joining the academia than the industry?
What is the importance of citations for someone seeking tenure? Does this depend on the field, as papers in an esoteric area can be expected to have few citations?

In my experience, citation counts are considerably less important than recommendation letters, but they still matter, especially for tenure.  For fresh PhDs, high citation counts are definitely helpful, but they're not a hiring requirement for most fields in CS.  But for tenure, it's really hard to build a successful case without at least one high-impact (post-thesis) publication.
Smart committees know to gather citation counts, publication counts, acceptance rates, impact factors, h-indices, and other quasi-objective numerical data from reasonable sources and to compare them with peers in the applicant's field.  (For my promotion cases, for example, my citation counts were mined from Google Scholar, not ISI, and I was compared against other theoretical computer scientists, not other computational-geometers-who-play-with-surface-graphs.)  Alas, not every committee is smart.

@Abe: This is one such site for CS: http://www.cs.ucsb.edu/~almeroth/conf/stats/

I think you mean "...for networking (a small subset of CS)".

To answer the part of the question about freshly-minted doctorates, citation counts are not normally considered as a critical component, either for academia or for industry. Or perhaps I should state that the lack of citations for recently published literature is not a major obstacle, particularly in fields with long "half-lives" for research papers. (Some of my papers only got cited after a year or more following publication.) However, a high citation count for a paper indicates that the student is doing potentially impactful work, and that can carry weight with a professor or manager doing hiring in either academia or industry.

"Some of my papers only got cited after a year or more following publication." This is definitely field dependent. I just checked my personal records for probably my best known paper --- published in 2006; citations I know of are 2006 (1), 2007 (2), 2008 (1), 2009 (1), 2010 (2), 2011 (none), 2012 (1), 2013 (1), 2014 (3), 2015 (2).

You already got some nice answers, but let me share my personal experience. I am a fresh PhD and I got hired on aP position after 3 months of graduation. There was another candidate (my friend) who also graduated same time with me, he had 14 times more citations, 6 times more total impact factor, and almost 10 times the number of publications. But he graduated from a university ranked in 400 and I graduated from world top 20. He published most of work by collaborating with different students from developing countries, while my publications were totally focused on my thesis work. He had 100+ publications during PhD but no patent, my all publications were registered for  patent and 2 were bought by the industry. I was convinced that my friend will get this position not me, but the result was surprising I got hired while he was rejected. So, in my opinion sometime citations and number of publications has minimal impact and you may get hired based on from where you are coming and what exactly you did during PhD. Focused, well organised, and quality work with few publications and citations are better than low quality large number of publications with high citations and high total IF.

100+ publications during a PhD in journals with high IF sounds like there's a part of the story missing here.

100+ including conference papers. His SCI journals were around 30+, but yes its still something unbelievable achievement.


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Publication sponsorship for research conducted elsewhere
Do universities sponsor a student's conference travel and publication costs if the research on the paper has been done elsewhere? For example, a student may have published a paper during a master's at university 1 and may currently be pursuing PhD at university 2. Similarly will the second university bear the cost of the journal publication? Are there any caveats involved (eg., indication of university's name in the paper, related department, etc)?
On the other hand, will the first university sponsor one of its alumni for the travel? (This looks unlikely to me.)

In contrast with Anonymous Mathematician, in the cases I'm familiar with (American CS departments), travel funding is provided primarily by advisors rather than by departments.  And then it's really up to the individual advisor.
But as a rule of thumb (or as evidence of my confirmation bias), I suspect most CS advisors would be happy to pay for at least one conference trip stemming from earlier work, if only to advertise their own insight in recruiting the student!
Journal "publication costs" are almost completely unheard of in computer science, even in open-access journals, so the answer there is trivially yes.

In contrast to both Anonymous Mathematician and JeffE, I've had a fair amount of conference funding come from a University-wide funding source, and never had anything come directly from my department.
In that case, there wasn't actually a restriction on whether or not the research was done at the university, merely that I was a student there, and that I was presenting research (rather than merely presenting at the conference). As you have a very limited number of times you can apply for travel funding using that mechanism, and it seems the frequency of conference travel increases as you approach graduation (and understandably have more to present), I suspect they're content if a few "slip through".
In terms of @JeffE's statement that a lot of funding comes from advisors, I agree, and then it really is up to the individual advisor. Many I know would be happy to fund a student regardless of where the research originated (especially if the student hasn't had a chance to produce research from their lab yet) for the experience, networking, education, etc.
Publication costs are a somewhat trickier question - honestly, I've never had to publish in something with publication costs, so if I were the new supervisor, I'd argue it was an avoidable expense. If its not, then I'd probably say it's the originating university's problem - their faculty are presumably the ones who would be benefitting from the research hitting the press.
Regardless, I'd at least expect your affiliation to be at your new university.

At least in the cases I'm familiar with (math departments at US research universities), funding for travel is more likely to come from an individual department than from a university-wide source, so this would be a matter of department policy.  That's a little less true for publication costs, because some universities have started funds to pay for gold open access, but everyone is setting it up a little differently so I don't think one can announce a general rule.
At the department level, this really varies.  One department I used to be at provided a certain amount of travel funding to each student, to be used however they wanted (as long as it was for academic purposes, of course).  I think that's a little unusual, and many departments don't make a decision until the student applies for funds.
If you are in a field in which these costs are an important part of publication (not pure mathematics, for example), then this is probably the wrong question.  In such fields, the funding usually comes from the advisor's grants, rather than the university.

In India, all travel funds are managed only by the university. My main question is whether people will be willing to sponsor another research in general.

Well it really depends on the specific university. In the US, with department level funding, the department doesn't really care that much about the nature of the research and when it was done. They just have a limited budget, and often go by need (who can least afford it, who might need it to help with jobs/networking etc)


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How good are entrepreneurial opportunities for faculty members?

How easy is it for faculty members working at a reputable university to become entrepreneurs?
If the faculty member sees an opportunity for a great product and wants to set up a small office with a few engineers working with one or two students, will the university sponsor such a venture?
How enthusiastic or forthcoming will the industry and VCs in general be towards this?
Lastly, how common are such professor-run companies for, say engineering faculty in top US schools?

Who owns the copyright/patent of the research? Will the university claim ownership of the startup company?

This is quite common in American universities, and there are probably thousands of start-ups that have arisen out of university-based research. The question of financing such a venture is of course a challenging one to answer, but with the right contacts, is usually available.
I can think of at least four or five such start-ups in the department I attended for graduate school, and I imagine there are several more in the planning stages.
As for how enthusiastic industry and VC's are, well, I think it depends entirely on the strength of the idea, and how "market-ready" the concept is. The sooner it's ready to go, the more enthusiastically people will flock to it.

Who owns the copyright/patent of the research? Will the university claim ownership of the startup company?

Usually there's a patent- and revenue-sharing process at most universities. Typically the university will get some percentage of the total revenues, while the researchers get a substantial chunk (numbers I've seen vary from 30% to 70% of the total).

I think the main issue is that a lot of entrepreneural mindset is eliminated from faculty, but if the faculty has the right mindset there is no limitation to a venture, especially if the faculty has tenure.


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Different types of conference publications
Consider a conference publishing papers related to any EC/CS engineering field. What is the exact difference between different types of papers published in such a conference, i.e., main conference paper, mini-conference paper and workshop paper? Is it inferior to have one's work published in a mini-conference or workshop as opposed to a full conference? Are there any other such sessions within usual conferences for these areas?

This will likely vary significantly between fields, as conferences are structured differently (and have varying degrees of relevance to one's standing) in different fields. Could you edit the question to include your field of interest?

For the value of the publication, it will matter more how it is published than whether it's a workshop or conference. If the proceedings are published by a well-known publisher (i.e. with ISBN/ISSN), a workshop paper might be as "valuable" as a conference paper. If on the other hand there are no formal proceedings or just something like a folder, it would be less "valuable". That usually leaves the opportunity to publish the same paper elsewhere though.
Most workshops in CS don't have formal proceedings, so in general it would be better to publish at a conference. That said, in some cases the reviewing process for a workshop/symposium might be more stringent. As smaller events are more specialised, the feedback you get on your work might be better than at a bigger event.
I personally would always go for publication at a conference if I thought the content of the paper to be good enough.

Thanks @Lars. Some simple clarifications: 1) by formal proceedings, you mean an oral presentation followed by some questions, right? 2) In the last line, I suppose you refer to a full-conference and not a mini-conference.

I mean the way in which you get the papers, regardless of how they are presented. Formal proceesdings == properly bound book with ISBN/ISSN. 2) Yes, although if it's a very specialised topic, the main conference for the field may seem like a mini-conference when compared to others.

Miniconferences and workshops are usually considered to be satellite events to a main conference. Often, these are on specialized topics, and often what starts as a workshop becomes a spin off conference of its own.
So it's tricky to say that it's inferior, but depending on the workshop/miniconference it might certainly be more specialized.

I agree with everything that has been said so far, but I'd like to add that one way to more quantitatively judge the "value" of a publication is by looking at the acceptance rate of the venue.  Many conferences in Computer Science are considered "terminal" publications because of their extremely competitive nature and low acceptance rates.  There are other conferences, however, that have 50% or higher acceptance rates.  Likewise, some workshops are very competitive while others have near 100% acceptance rates.


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How important is mathematics in engineering research?
In EE/EC/CS departments, there are certain fields that are theory-based (like the algo or complexity groups), ones that lean towards systems implementation (OS, programming languages, etc) and others have a component of both (like networking).
In such a field like networking, there are professors who work on hard-core math modelling (example) and people who work on implementation and protocol design (example). From what I glean from my own paper-reading experience, the natures of these papers are as different as chalk and cheese: the math papers seem to look for ways to cast the problem in a mathematical framework and try to derive their results from such a set-up, while the implementation-oriented papers conceive of some algorithm and a protocol (based solely on logical argument rather than any rigorous mathematical premise) and present the results of their software simulations.
While on paper people argue there is no divide between theory and practice, at least to me the approach towards research differs widely between faculty members in the same field and department. Now to my questions:

How important is math emphasis in an applied field like networking? Industry work is almost always simulation-based from whatever I have seen. After all, networks are there to be implemented and deployed, so why bother about probabilistic modelling?
When there are two modes of research in a particular field, will the PhD student's approach play a role in faculty recruitment?
Is there a widespread notion of one being superior to another? I know of professors and students who widely emphasise math and pooh-pooh "S-BAA: simulation based on arbitrary algorithm" type of papers.

I guess you'll have to distinguish between math and applied math.

why should an engineering department award a degree to a thesis where the problem has an engineering cause, but everything is simply applied math? — What do you think engineering is?

@JeffE: Ah well, that's worded poorly. I have seen theses where the problem is engineering just on the surface, i.e., the cause is phony and is simply a "pretext" to use math results.

How important is math emphasis in an applied field like networking?

Networking is an enormous field, which runs the full spectrum from pure mathematics to actual real-world deployment, with many shades of applied mathematics, algorithm development, modeling, simulation, and experimentation in between.  There are far more than "two modes of research" in networking, as you put it.  Mathematical emphasis is fundamental at the mathematical end of the field, useless at the deployment end, and somewhere in between in between.
To put it differently, it depends on what you mean by "networking".

Why should an engineering department award a degree to a thesis where the problem has an engineering cause, but everything is simply applied math?

There is no contradiction here.  I'd estimate that somewhere between a third and half of our engineering faculty at my university can legitimately call themselves applied mathematicians.  There was even a small but serious proposal a few years ago to move our mathematics department into our college of engineering.

Will the PhD student's approach play a role in faculty recruitment?

Of course!  Hiring patterns at my own university (in both CS and ECE) suggest that the networking PhDs most likely to be hired as faculty comfortably bridge the so-called gap between theory and application, speaking to both camps in their native languages, and applying techniques from both camps to Actually Make Things Work.  (Sylvain's answer is consistent with this observation.)

Is there a widespread notion of one being superior to another?

Of course.  Networking people are people.  As in any other wide-ranging field, many experimentalists think all theoretical work is pointless symbol-pushing, and many theoreticians think that all experimental work is mindless hacking.  They're both wrong.  Some theoretical work is pointless symbol-pushing, and some experimental work is mindless hacking, which is exactly as it should be.  Neither viewpoint is "better"; they're just different.
Not chalk and cheese, but chocolate and ginger.

How important is math emphasis in an applied field like networking?
  Industry work is almost always simulation-based from whatever I have
  seen. After all, networks are there to be implemented and deployed, so
  why bother about probabilistic modelling and research? In other words,
  why should an engineering department award a degree to a thesis where
  the problem has an engineering cause, but everything is simply applied
  math?

In these fields, math is a tool, as coding or lab experiment. Even if you have a full mathematical analysis of a protocol, you have to conduct experiments, because real life is not one of our - too simple - models. Why bother on probabilistic modelling? because we have to find ideas for designing algorithms, hoping that the performance in the real world will be somehow related to those in the formal model.

When there are two modes of research in a particular field, will the
  PhD student's approach play a role in faculty recruitment?

Yes it almost always will. You apply in a team, probably the team is inclined in some of the ways, and want either to make the team even stronger wrt an approach or, to the contrary, to open itself to other ways of thinking.
I also remember my own recruitment, where the fact that I am in the middle (maths + experiments) was a big plus for me- since people assumed that I will be able to speak to a lot of people in the lab, from theory to practical people (and that's what happened).

Is there a widespread notion of one being superior to another? I
  know of professors and students who widely emphasise math and
  pooh-pooh "S-BAA: simulation-based on arbitrary algorithm" type of
  papers.

At the end, only one thing is important: making things that work. You will always find people that think that the theoretical approach (resp. the experimental approach) is superior to the experimental approach (resp. the theoretical approach). Both are wrong, what we want is usable (in real conditions) algorithms with guarantees (controlled error, correctness, etc.), how we achieve this goal is interesting for us, but not the main point of our research (recall that the question is about engineering research).

Thanks! A couple of points: 1) For Q1, from what I have seen, the translation from theory to practice seldom happens in some fields - Results in many areas (info theory, space-time coding theory, etc) are so far removed from practice that it looks unlikely the latter will ever catch up.

The middle ground is sometimes very tough to attain: in an expt-based setting, you do not get to do many math courses; in a theory-centric lab, there are no more resources other than computers and furniture and so experimentation becomes infeasible.

Yep, I am currently in a huge lab where everybody (could) have access to what is necessary for the experiments (even real sensor networks for people in networks). This helps ;)


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How independent should an academic be?
I am a computational scientist and I often find myself much more productive when working with others with resonating mind. When working alone, my motivation level is lower, distracted more easily, and I feel the progress is slower. However, in academic jobs, I often hear that it is important to show that you are an independent researcher.

Q1. What are the defining properties of an independent researcher?
Q2. How can I show that I am independent?
Q3. I like working in
teams, is academia (esp faculty in research university) not a good
career path for me? (I could think independently, but I could do
better with others, so why be independent?)

Collaboration is generally seen as a major strength in computer science and computational science, not a weakness.  One of the biggest questions we ask about any faculty candidate in my department is "Who in the department/college will they work with?"  We do occasionally hire faculty that work alone in their cave and occasionally emit theorems, but they're rare exceptions (and even they still work with their students).
The most important thing is to establish a reputation as a leader in your collaborations, rather than a follower.  You need to establish your own research agenda, instead of just following someone else's.  More importantly, you need to be seen to have your own research agenda, instead of just following someone else's.  Your agenda must be visible in your publication record, in your recommendation letters, and (eventually) in your funding record.  To this end, it is very important to do a few things:

Limit your collaborations with more senior researchers, especially your advisor, especially between getting your PhD and getting tenure.  As I've suggested elsewhere, publishing at least one paper without your advisor before you graduate is a strong signal of independence, even if you have other coauthors.  Once you have your PhD, DO NOT publish with your advisor for at least a few years.
Do not always publish with the same set of coauthors.  It's fine to have two or three different groups of people that you always work with, as long as you can wind a consistent story that ties most of your work in those different groups together.
(Once you have a permanent job:) Get at least one grant as a principal investigator, not just as a co-PI.  Definitely join other grants as a co-PI, too, but you must have at least one grant with your name on top to get tenure.

I think I have a similar mindset. I like independent work, but I find that I am more motivated when working with others. However, I don't think that will hinder your ability to show that you are an independent researcher. As mentioned by @aeismail, the defining point of independence is that you are able to generate and pursue your own research ideas and agenda. If you do it alone or with others is irrelevant.
In a lot of cases, like when you applying for positions, etc. You will have reference letters to accompany your CV. Thus, the author-list is not the only place to show your independence. In the letters your coauthors and mentors can attest to your independence.
A research statement or cover letter also is a great place to highlight your independence. If you work with lots of different people, then you can show how all these projects tie into a broader theme which is distinctly your own. In computational science it could very well be a theme like "I like developing information theoretic explanations for neural and multi-agent activity" and then work with an auditory group, a cognitive group, and a population biologists can be great supporting evidence of the fact that your ideas and approach are unique and independent, not to mention widely applicable.
Taking a leadership and organizational role is another clear way to show your independence. A personal example: I prefer to read and discuss papers with others, so I organized a reading group that meets weekly (ideally). A bit of my time gets consumed in organizing and managing this group, but it is more than made up for by the extra motivation I get to stay on top of the literature.
As for the atmosphere; group-work is not an antithesis to academia. It is very important to show that you 'play well with others' and frequent collaboration is a great way to do so. Especially with the large push for multi-disciplinary work, being able to work with people of various background is a great asset. Further, as a faculty in a research university, one of the things you will be expected to do is supervise and teach students. This means you need experience in sharing and developing your ideas with others, something that working in isolation does not nurture.

I disagree on your point about leadership and organizational roles. They aren't treated as evidence of academic independence at any level of which I'm aware. Instead, it's usually an "expected" contribution that you will participate in so-called "service" activities—at least if you plan to remain in academia at a serious level.

I agree with @aeismail.  Leadership experience (not just "service") is definitely a good idea; all else being equal, that can break ties in hiring decisions.  But it's definitely a low-order effect.

The issue of independence is an important one, but it doesn't obligate you to work in isolation. Instead, what it means is that you are capable of generating and pursuing your own research ideas. This can be done in collaboration with others, but there's still needs to be some evidence that you can lead the effort.
Some ways to show independence are to have some collaborative efforts where you are in the "leadership" positions—first or last author. If you can do this across multiple independent collaborations, preferably in multiple disciplinary areas, that will show that you have some lateral flexibility, which is among the hallmarks of an independent researcher.
I don't see, in this day and age, the desire to work in teams as ruling out a career in academia. I might not lean towards it as a first choice—instead, I'd probably steer such a person into a research institute like a Max-Planck-Institut here in Germany, or a DOE lab in the U.S. Those offer more collaborative environments which would be a better "fit" for someone who prefers to be a team player than a team leader.

At least in my field (mathematics), there are people who do almost all their work collaboratively.  Academia can be a good place for such people, but:

It varies a lot, not only by field, but by subfield, so you'll want to take that into account when choosing a specialty.  (Math has a lot of single authored papers, while the lab sciences have very few.  I gather CS is somewhere in between, and that it depends on the area.  Even within math, it depends on the particular subfield, sometimes for reasons that have more to do with culture than anything intrinsic to the subject.)
If you're in an area where single authored papers are common, you'll eventually be expected to produce some, just to demonstrate that you're not be carried along by your co-authors.


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What to do if you are assigned to TA a course you are not qualified to teach?
I am a PhD student in an Applied Math program. Recently, we received our TA assignments for the next quarter. To my surprise, I was assigned to TA a graduate-level class that I had never taken before which covers material I have very little experience with. I wrote an email to the DGS to ask if this was a mistake and if I could maybe switch to another class I'd be more comfortable with TAing, but he responded that the department currently has a TA shortage and some graduate students have been assigned to TA courses that they have not taken before. He also mentioned that all TA assignments are final.
So it seems like I'm stuck TAing a class with material I have little knowledge of, and I'm really nervous about the upcoming quarter. I do not think I'm going to be very helpful to the students in this class unless I put in a lot of effort to learn the material and spend way more hours than we're supposed to be spending on TAing each week. I am also not confident in my abilities to correctly grade assignments, but I suppose this will be something I need to discuss with the instructor. Does anyone have any advice for someone in my situation? Should I escalate this to someone higher or just accept that I will have to TA this class?

You will be surprised about how much of this material you will be able to understand well enough to teach!

As an incoming graduate student, I was asked to TA a course I had wanted to take! It all worked out in the end.

I've had lots of classes (in both computer science and math) where the TA was a student who had never taken the course before either. Their trick was to simply stay one week ahead with the material. Additionally, they received sample solutions from the professor. For the most part, it worked out okay. We students knew about the TA shortages and accomodated to the fact that we could not ask questions beyond the current assignment. We all turned out okay ;)

@AndrewJaffe: That is a completely unprofessional and inappropriate quip.

@einpoklum: Absolutely not! (Or at least not intended as such.) The happy fact is that graduate students have already shown their ability to learn mathematics at a very high level, and are very likely able to master this new material with relative ease.

I would even claim that those courses that you still have to learn yourself (or are not an expert in) are the most fun to be a TA. That was my experience so far.

This is only a problem if you think teachers are supposed to be subject matter experts instead of or in addition to being didactic experts.

Who is DGS?
4 more to go...

@VladimirFГероямслава most likely "Director of Graduate Studies".

"Director of Graduate Studies" sounds reasonable. For a particular university: "The Director of Graduate Studies (DGS) serves as the coordinator of graduate studies within a program. Together with the graduate program faculty and department and collegiate leadership, the DGS shares responsibility for guiding and improving graduate education within the program(s) under the DGS's jurisdiction."

Yes, discuss the duties with the instructor. For some TAs the work might only include grading according to a rubric provided by the professor, which should be do-able. If you have to lead small groups, however, you need to be more creative. In particular, don't present yourself as the source of all answers, but perhaps, the organizer of discussions.
You may actually need to attend the course lectures to make a good go of this, but that isn't necessarily unusual. You will certainly be expected to review course materials.
But, I asked a question on another site here and the answers given may help, though it was directed at instructors, not TAs: How do you teach something when you don't know it yourself?.
As a professor (hopefully in your future) you will occasionally be put in such a situation. If you are honest with the students (and your instructor) you can come out ok.

(+1) [awarded 30 minutes after my answer] My answer was originally a comment, but I decided I answer too many questions in comments as it is, so I decided that since it had been 8 hours since the question was asked, with no comments or answers, I may as well put it as an answer. After reading your answer 30 minutes later, I realized how much more I could/should have said. FYI, I was in this position myself once, but it was "advanced math for physicists and engineers", and I'd already taken complex variables and PDE's (both mostly attended by engineers), so it wasn't much of a stretch for me.

I've been in the same situation as the OP. Having mostly studied the science of zoology I was assigned to be the TA of a course called "Man and Environment" which contained sociology, politics and in fact everything from bicycle lanes to epidemics. But it was in the Zoology department. The best way to learn about something you don't know is to teach it!

Your TA position is for X hours a week. The professional thing to do when you are given a work assignment, even one  you feel unqualified for, is to enthusiastically say you will do whatever is needed to perform the assignment competently, including spending time acquiring the skills and knowledge needed for the assignment, within the limitation of X hours a week. If you have a concern that that won’t be enough, express it clearly and let the people making the decisions make whatever decision they want to make in such a situation. Since you have documented your concern, they will also be the ones responsible if any problems arise later.
I suggest sending the DGS an email along the following lines:

Dear [name of DGS] (cc [name of course instructor]),
Thanks for your reply. I understand that my assignment is to TA the underwater basket-weaving class, and that you are unable to grant my request for an alternative assignment.
To be clear, I am excited about this opportunity to broaden my mathematical horizons, and will do my best to perform this assignment within the X hours a week allocated to my TA position.
However, to reiterate the concern I expressed earlier, I estimate that because of my lack of familiarity with the course material, it will take me about Y hours a week just to learn the course material at the level needed to competently work on TA duties like grading. I am concerned that this won’t leave enough time to actually finish those duties, which might create an awkward situation for [course instructor]. However, as I said, I will try my best in any case.
Best wishes,
weighted sum

I really appreciate this email template! I will definitely send a similar email to the DGS, thank you.

Hmm, I can see your point, but I'm not convinced whether it's in @weightedsum's best interest to really write such an email. I think there's a considerable chance that the main outcome of the email could be that both the DGS and the instructor are seriously pissed off (I'm not claiming that this would be an appropriate reaction by them - but it might still be a very likely reaction).

@JochenGlueck “they will be seriously pissed”, even if true, does not imply “it’s not in OP’s interest to write the email”. To the contrary, OP has a professional duty to make their concern known and documented even if it pisses people off.

I think this is company professional but not phd program / university professional. Most universities expect you to work around the clock; which you do not have to do of course, but one shd be cautious to talk about it. The first rule is: you do not talk about not working around the clock. Maybe the culture of this specific varisity is different, we dont know.

@lalala you are wrong. The unprofessional thing is the attitude you describe of departments expecting TAs to work around the clock, and TAs not knowing and standing up for their contractual rights. At my university (well, at my department at any rate, and many others on my campus) we are very careful to respect our grad students’ rights and I am confident the email will be treated, if not with great enthusiasm, at least with respect and the understanding that its writer is behaving maturely and professionally.

@lalala I also believe you are wrong that “most universities” have the unprofessional norms you’re describing. This is the attitude in some places, of course, even many places probably. But in the US today at least, in serious, highly ranked universities, there is generally an attitude of respect for the labor rights of employees, and a growing awareness of work-life balance, the mental health needs of graduate students, etc. I hope OP’s university is one of those, otherwise they might have bigger problems to worry about than this TAing assignment.

If I had no one to turn to, I might have written something like this. But I would avoid starting out with the individual approach and try to get others involved in this situation (see my answer).

I would just try to connect with the instructor as soon as possible and be honest with them about your concerns. I'm sure they have dealt with having TAs that haven't taken the course before and so they will have a good feel for if you will be able to "survive" or not and what you might need to do to prepare.
I was in a similar situation and ended up being ok without it taking more than my 20 hrs per week I was supposed to be working on it because the instructor had good grading rubrics, I could typically just tell students if I didn't know an answer and research it and get back to them, and for the discussions, like Buffy said, I was really just as a facilitator and not there to give the students the answers.
Connecting with the instructor as soon as you can will hopefully remove some of this stress and worry! Also, you likely are qualified to teach it...you are a PhD student in the department!

It's likely they felt a Ph.D. student should be able handle most any reasonably standard undergraduate course, regardless of whether the student had actually taken the course. Maybe you could try to find someone TA'ing a course they are also not comfortable with, but you would be, and see if you can switch courses with them. I don't see how the DGS could object to this, as it would not affect the issues the DGS is concerned with. [DGS = Director of Graduate Studies? Doesn't really matter here, I suppose.]

Yes, DGS stands for Director of Graduate Studies. I emailed him because he seems to be in charge of graduate student administration issues and I didn't feel like this problem was serious enough to contact the department head about.
In addition, by "upper-level class" I meant to say that this is a graduate course, although I suppose undergraduates with a strong-enough background could take the course. I think your suggestion to try to swap courses with another TA is a good idea. I will ask around to see if anyone will be willing to swap with me.

There's at least one advantage to teaching a subject you aren't yet familiar with. When teaching a subject in which you're already an expert, it's hard to judge how difficult various topics are to someone who's learning it for the first time (especially for those topics that are exceedingly difficult right up until you "get it", after which they're trivial).  But if you just learned the material yourself, you have an idea of what parts might give students trouble (admittedly, you know this from a sample size of 1, but it's better than nothing.)
And you may be overestimating just how much extra time it takes to teach yourself the material: a lot of what you need to do to teach yourself can be reused to teach the students.
I was once called on to TA a topic in which I had very limited experience (for first year grad students, if recollection serves), and had to take the approach of teaching it to myself and staying a week ahead of the students. Each week, I would teach myself the material, and then to verify that I understood the material, I designed toy problems that I could solve using the newly acquired knowledge. By writing programs to solve these problems, I had...

...verified that I did, in fact, understand the topic at least reasonably well.
...designed a set of problems that test the material. Thus, I could create homework assignments merely by writing out the problem specifications more formally (and I knew for a fact that someone who just learned the material last week is capable of doing these assignments, because I just did exactly that).
...written a set of tests and sample solutions for each assignment, which is prep-work I'd need to do for grading anyway.

So all that was left to do was answer questions (and the material was certainly fresh in my mind) and grade assignments. All in all, it didn't take that much more time than any other course I hadn't TAed before would have. Some adjustment to this approach will be necessary, based on the specifics of the course, but for applied math, something similar should be practical.

The first paragraph is spot-on.  An important skill in maths is how to check things as you go and how to find your mistakes (it is a lot like programming in that respect), and sometimes that is difficult to do if you know the topic too well.  As a TA you should be supporting the material taught by the professor/lecturer, rather than teaching it yourself,  so any advanced questions can be passed on to the prof to answer.

You write that the course is an upper level/PhD course.
You should check how much work you will have (esp. homework) with your professor, but in my experience with undergraduate courses, the higher the level of course the less the TA has to do.
The low level, introductory type courses are usually huge and packed with students from other majors who have no particular love of math and maybe not even much math background. That's a lot of homework that needs to be graded and a lot of students who need a lot of individual help (and often a large number of students who specifically do not want to be taking the class and can be very trying about it).
By the time you get to upper level classes, particularly in math after the first proofs class, all of the students have specifically chosen to be there and are at least somewhat proficient in what they're doing. The class sizes are usually a lot smaller, as well, so less homework (although homework can be more complex/nuanced).
In a PhD course that may not entirely hold, there may be some students coming from a non-math background who need more help, but they have at least chosen to be in that class and are willing participants.
Often all the help students really need is someone to talk calmly and provide very generic guidance. I got a lot of mileage out of phrases like, "I don't know, but can you explain what you're trying to do and I'll see if I can figure it out..." It's a sort of mathematical Socratic method (/rubber duck debugging, etc.) where there's a pretty good chance that by explaining the problem well enough they will figure out the answer on their own.

I was expected to be a professor of courses I had never taken.  Needless to say, it didn't go particularly well.  During the interview, one professor promised to help me.  From my POV, that didn't actually happen.
In any event, sometimes as a TA, all I had to do was grade homework.  On the other extreme, the TA can do everything, with only minimal supervising by the professor. So find out which is your situation.
As others have said or implied, probably, you will need to attend the course lectures, study the materials, and learn the course work. (See other answers and also comments on this page.)
Depending on your POV, this could be a positive learning experience!
Most PhD's are expected to do self-teaching at some point, but staying ahead of the curve while learning a course you are teaching IS a very real challenge!

First of all note that this is a labor issue. You are an employee of the university, given a certain work assignment which you are unable to properly fulfill, but expected to do so anyway. Even though the university cloaks it it the garb of "student" affairs.
Secondly, note that the university is linking your being a PhD candidate - a junior researcher - with teaching, to the extent that the junior researchers are, as they see it, obliged to teach whatever the university/department deems it necessary for them to teach. This is not problematic in itself - assuming you're not required to teach things you are not academically mal-equipped to teach; and provided your entire activity as a PhD candidate - research + teaching + administrative duties etc. - is considered altogether as your breadth of employment. In a typical US university, that is not, unfortunately, the case.
So now that we've established the scenario, the question becomes: What is a semi-uncrecognized, disenfranchised, employee for a large (academic) institution to do when demanded to perform tasks s/he cannot properly perform?
Unfortunately, many junior researchers bow their head down, swallow their pride and try to teach / TA the course as best they can. The result is a reinforcement of their collective servility, a deterioration in teaching quality, and indirectly also a push-down of employment conditions, since the university, when faced with lacking of qualified teaching staff, is under no pressure to offer better employment conditions so as to be able to recruit (especially on short notice).
Now, what I would like to be able to tell you is: Go see your academic staff union representative. The union should be raising hell on this kind of demand, calling out that DGS and threatening both collective action and initiating academic-disciplinary procedures against that DGS.
However, most US universities are not unionized, and even if yours was - the fact that this can happen means that the union is weak or co-opted (or both). So, what you should really focus on doing is unionize junior academic staff at your university. I know that is a tall order, and certainly it is not a matter for a single individual, but it is an absolutely necessity, and such struggles do succeed when carried out consistently.
Lacking a union - you need to find an officer or an organization which would be interested in putting counter-pressure on that DGS. Options could be:

The instructor in charge of the course.
The university's student union, or more specifically its departmental officers/representatives.
Your advisor.
Some Dean or vice-Dean in charge of teaching, as opposed to graduate studies.
A senior tenured professor whom you have a close relationship with.
Your cohort of junior researchers at the department.

These were not listed in order. The question of who to approach depends on your relationship with them, your assessment of their interest and willingness to act on this matter, their backbone, their ability to withstand pressure etc.
About the last option - it is the most relevant if there are multiple junior researchers who have been met with this demand. Try to locate a group of people in the same predicament. You would be amazed at the difference in effect of even 3-4 people coming to see the DGS together, to explain how they cannot ethically teach courses in material they are themselves not fluent in, relative to a single person coming to complain or ask for leniency. It would be even more powerful if that group could get a few more PhD candidates to tag along, fill up the DGS' room, and look seriously dissatisfied.

Actually, I doubt that most academics treat this purely as a labor issue. It would be if TAs worked in the bookstore or the cafeteria, or even in the library. But, instead, they are part of the educational process itself and gain valuable experience if their career is to be in academia. It is, in part, a learning issue, that helps assure somewhat more ready entry level faculty. Some TAs actually get to teach their own sections of a larger course, as I did once I got some experience with grading and such.

@Buffy: I agree that this isn't a pure labor issue. But the scale is tipped so far to the other side, that I need to emphasize the other end. As for the "educational process" - that's the same process that senior academic staff go through when they study a new subject. Almost everything can be presented as continued education. And in fact, that's true not just in academia - but in industrial settings as well: Much of one's time is spent studying new things.

As part of my PhD studies, I re-discovered a bunch of areas in physics that I thought I knew or thought I did not know.
All this thanks to teaching - that was a wonderful experience.
You can rest assured that you will always have that one weird student who already knows more than you on a topic. If you are lucky they will just go though. If you are lucky they will come to you directly during open hours to address a problem you have no idea how to address but at least you suffer alone.
And then if you are not lucky they will ask the question during your course and you will have to do some belly dancing to get out of that difficult situation. The experience is invaluable for your future career.
Oh, how much I miss teaching! (I am in the industry now and teaching was the best exerice I got from academia).

Anecdote time: I was asked a question during my PhD defence, from the public. The sociologically impaired asker asked something of which I understood all the words, but not when they were all together in one sentence. My shirt got wet from the sweat and I had to say I have no idea. The president of the jury sighted into the microphone and said

This is very sad, Mr WoJ, that a PhD candidate does not know this. I am disappointed.
Dr IdiotWhoAsksSuchQuestionsDuringADefense, please explain to Mr WoJ the answer

To what Dr IdiotWhoAsksSuchQuestionsDuringADefense said

ah, I do not know, I though he would

The room was roaring with laughter and I finally got my PhD (that was one of the most crazy defenses in our department, but this is a story for another time. It involves mud, tongs, a wandering magnifying glass and the words fucking notes said in the microphone)

authors: Vladimir F Героям слава


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Replying a professor for not applying to PhD program
A few months back I had an email conversation with a professor of a German university regarding a PhD position. She told me about the details for PhD admission procedure and I replied that I shall apply when the application window opens. Before the opening of the application window, I  received a PhD offer from another university in the same field of study in another country in Europe. Should I let the her know that I am not applying for the previous position? Almost 3 months have passed since our conversation. I am afraid whether this will lead to any bad consequence.

Applying to a PhD program is not a commitment to take the position if offered. Not applying to a PhD program and merely showing interest is even less of a commitment.
I don't think there would be any harm in contacting someone via very brief email in this circumstance and saying something like "Thank you for talking to me about graduate admissions at (university). Since our conversation, I've accepted a PhD position at (other university), so I won't be applying to (university). Thanks again!" I'm in the US, though, and don't know what sort of formality a German professor might expect.
I also think there's very little harm in saying nothing. Nothing about your conversation established any commitment or expectation that you would join this professor's group, and it's unlikely they're waiting impatiently for your application to arrive.


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How to refer to the work you are presenting in a scientific paper?
I am co-authoring a scientific paper. In the related works section, we discussed how our work addresses some of the limitations not evaluated in the literature.
To keep style more formal, we structured the sentences to be impersonal when referring to the work we were presenting: "In this work", "In this paper" and NOT "in our work" etc...
One of my colleagues used the form "in the present work" a lot.
One of the reviewers asked to discuss the limitations addressed by our work more, so I am afraid that "in the present work" was understood as a reference to the literature instead of to our work. I'm not a native speaker, so I don't know if this could be the case.
Do you think "in the present work" is a correct way to express the concept in English? Are there other ways I didn't think about to avoid always using "in this ..."?

I think your usage is fine. But I think the reviewer is just suggesting that "the present work" doesn't sufficiently place itself in the larger context of the field.
You probably need to say more, probably in the introduction, how this work "fits", and why the current state of the literature has gaps that you fill with "this work" or similar.
I doubt that the reviewer thought that "the present work" was a reference to the larger body of work in the field


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A few questions about properly citing resources according to the APA format
I recently finished writing a monograph but I am having some slight misunderstandings about how to properly cite the resources I used.

When mentioning the source of figures, should I write the author's name, title etc. in English or the language that I am writing the text in? I'm writing in Farsi and I write details in Farsi under the figure, should the source be in English? For example, if I'm using the figure 9.2 from page 506 of Zetilli's Quantum mechanics, should I write "[details in Farsi]. N. Zetilli, 2014, p. 506. Wiley" or should I write the equivalent in Farsi?

Am I allowed to use figures that I found in textbooks or should I ask for explicit consent of the authors?

I am using numeric citations for citing in-text, like "The magnetic field splits the energy levels [4]" and then mention [4] in the end, is that ok?


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Professor is not publishing my work. Should I try to publish on my own adding him as a coauthor?
I went to do my postdoc (organic chemistry) in ICCAS Beijing, although I also had offers from other places. As soon as I arrived there, I was informed the professor had many unsubmitted works. After a lot of thought I stayed there because I had a good fellowship and the quality of the work impressed me (probably a wrong decision). I worked really hard for more than 2 years and completed a work (I thought) after which I had to leave for some family reasons. I wrote the manuscript and S.I and sent it to my professor but he is yet to publish the work. He always says he is very busy and some works needed to be done. I also suggested to perform any further experiments in PhD guides lab. However he does not do anything, publishing his PhD students work because he had to. And now he is saying- "very sorry" for the delay but still not doing anything. In the mean time I checked with many senior colleagues, all of them agreed the work is of good quality and should be published as soon as possible. I sent the work to my professor in early 2018 now its 2021. Should I try to publish it on my own keeping him as a coauthor? I was waiting till now because the issue of "recommendation". But, now it seems to me, my career in chemistry is over and want to publish the work for validation only. what should I do?

Have you asked the professor if you can go ahead and publish the work with their name on it (so that it does not cost them any time)?

@Sursula Yes, I did several times. The only time it yielded a result when I added my Ph.D. guide as a cc in the email.He only forwarded the email to one of his student. And since then nothing.

Is arranging an in-person meeting to hash things out possible?

@nick012000 I am in a different country. So an in person meeting is very difficult...also Prof . always says he is busy, though he published several review papers in the last two years.

Would arranging a Zoom meeting be possible, or has the Chinese government blocked it? If so, is there a Chinese remote meeting program you could use to schedule a meeting?

As I said a meeting is pointless..he told me several times that he is sorry for the delay, he is very busy, will publish it soon and then nothing happens. This is the story if past three years.And now my opportunities are all gone.

What do you mean by "publish"? Do you mean the professor should "write up the manuscript", or "read and give comments on a first draft", or "rubber stamp a mature draft for you to submit to the journal", or "take the existing manuscript file and submit it to the journal"?

First, I don't understand why it is the responsibility of your professor to publish your work. Perhaps this is a local requirement, but it seems odd.
Second, you can't just add someone as an author without both their proper participation and their agreement.
Normally, though, if the work is yours then you can submit it. If it is joint work then all authors must agree, but any of them can actually do the submission.

I'm sure a busy prof who has no time to write a paper covering your work would welcome the opportunity to have someone else write it.  Doing so isn't simply a matter of writing it and sending it in with the prof's name on it, but handing the prof a manuscript, asking for edits, revising, ...

You are asking them to devote not insignificant effort to what is clearly fairly low on their priority list. Yes, they've agreed to that, yes, it's long past due it goes one way or another... But some people are just terrible at time management (including myself). If that prof is anything like myself, don't read much into it - it's not malice or anything, it's just every time you remember to address that there's something even more urgent and important waiting in the backlog. And working on writing, while can be done quickly by an experienced person, requires a particular state of mind. Getting into that state of mind is valuable.
And honestly, if someone walked up to me and said "here, I've done some research, all you have is to publish it and you can have all the credit" - why'd I accept? It's not helping me further my own research and takes away valuable resources.
If you actually want it published at this point, handle it yourself.

It is important to quantify whether your ex-PI has done enough to justify a coauthorship, or whether they should be placed in the acknowledgements.
To be a coauthor, your ex-PI must fulfil all four of the following criteria by the Vancouver Convention:

Substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data for the work; AND
Drafting the work or revising it critically for important intellectual content; AND
Final approval of the version to be published; AND
Agree to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

Some journals and some universities have variations on these.
You will note that, actually, PI's should not qualify for authorships at all much of the time. I would suggest looking at point 1 closely. Did your PI make substantial contributions there? Did they make a substantial contribution to the conception of the study, data acquisition (i.e. lab work), analysis or interpretation? If they did not, then points 2-4 resolve themselves, because they are dependent upon 1.

I've seen the Vancouver Convention's criteria mentioned before, but never endorsed in my field (mathematics). I suspect the reason is the possibility that a perfectly good paper might have no authors at all under these rules.

Maths has some interesting conventions. My friends who are mathematicians tell me that in pure maths it is gauche for a PI to put themselves on one of their students papers, and that normally papers are single author - the student. I know that some have been turned down for grants etc. on the basis that their H-index was too high. I believe in applied maths it is a bit different.

Publish it on your own. You only have one life to live, so stop worrying about what your professor might think. You're not doing anything wrong. You've worked so hard and that deserves recognition. Don't be ashamed to shine. So go ahead and shine!

Please add further details to expand on your answer, in particular explaining how this is nothing wrong by academic authorship standards.


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References for a tenure track position
I am going to apply for a position as assistant professor (anthropology) and I have a question regarding the references I have to present. Should they all be from professors? One of my references is a laboratory coordinator and in charge of department collections (permanent position but not professor). He knows very well how I work, better even than professors who could write the reference letter, but would talk about me in a more generic way. What would be a better option?

You’re applying for a position as a professor. With rare exceptions, go for letters from professors (exception examples: you can’t find 3 to recommend you w/o reservation, you come from industry). You really don’t want to be recommended by a lab administrator not involved in research and teaching, if you can avoid it.

It depends on the nature of the position, actually. For most people the important aspects of the job are teaching, research, and service (in some order of importance). If the third person can support any of those, or any particular aspect of the position not covered by them, then it would be fine.
Otherwise, it would be better to align your letters with the nature of the job.
However, you also need people who know you well and can say positive things about how you will fit the position. You should choose the best among them.

'...say positive things' -- this part of the process is quite meaningless in a way.  Who would include negative letters?  Usually, referees who would say something negative will not accept to be a referee to ensure a person finds a job.

@VitaminE, it isn't necessary to be negative. A non-committal or neutral letter can be devastating. "The candidate took my course and did well."

I wouldn't offer to write a neutral letter for exactly the reason you pointed out.