Reflecting bad experience with previous graduate program in statement of purpose I am applying to master program in computer engineering, but I have some concerns and not sure how to present them in my statement of purpose.

First, my undergrad was in computer engineering but after moving to US I pursued biology in graduate school. I had bad experience with my adviser. He moved to another university right when I started my research, but since I had a fellowship that came from a school in our university, I was forced to stay. He promised to help me, but didn't do anything after he moved. That being said, since I just started my research and we had a small department in which no one else worked on the same area, I couldn't make progress on my own.

But, then I started taking some online courses and became really interested in some new areas and also coauthored a paper in computer architecture. Now I want to apply to computer engineering for masters.

I also had to extend my graduate program in Biology due to some immigration related stuff, so now my graduate degree took more than five years, while I don't have any result in it. I was wondering how can I represent these stuff in my statement of purpose without hurting my chance of getting admission. I should also mention that I took almost all the PhD courses in Biology and have a very good GPA in graduate school.

It's tough to explain this, but here are a couple of things to note:

Explain the situation without being disrespectful to your adviser. If it were me I would not even blame him for anything, I would just make sure my writing leads the reader to that conclusion without me explicitly stating it.
I don't think that your immigration status issue would sit well with the committee as a reason for you staying in the program for five years. If you had the intention of finishing your degree despite your new-found interest you should mention it.
I'm getting the understanding that you will not be receiving any degree for your efforts over five years. I'm guessing that the school does not award M.S. degrees to PhD students who have not been able to conclude their research. However, if this is not the case, I highly recommend you try to get a master's degree. You mentioned that you completed most of the PhD coursework. You may be able to get a course-based master's degree even if your research has not progressed enough for a master's thesis. An SOP stating that you had difficulty with your research and ended up getting a course-based degree reads a lot better, especially since you seem to have a valid excuse for it.
Completing your PhD would disqualify you for being admitted to EE PhD programs at many universities (many schools do not award PhD's to people who already have one). I would assume if getting a PhD (in your new area of interest) became your goal at some point during these five years, this would be a good reason for you not to complete your current PhD, so you may want to mention this to justify not completing your degree. Again, if you are able to get a course-based degree, this will sound a lot more convincing.
Don't lie in your letter. Not that I'm implying that you meant to do this; however, it is usually pretty easy to detect an untruthful SOP.

Good Luck!


Clarification needed: Job market paper During my ongoing academic job search, I'm seeing that some universities require a job market paper as a part of application package. While I read a bit about the meaning of the term, I'm still somewhat confused about it and hope that more experienced people on this site will clarify that.

Question: What exactly is a job market paper? Is this term interpreted differently across disciplines and fields of study (and to what degree)? Is it closer to research statement or writing sample?

Note: my main discipline is information systems (a multi-disciplinary field of study with a focus on management science and other social sciences; in addition, my own current focus is computational social science, complex socio-technical systems and data science) and I do have both research statement and writing sample (a slightly abridged review of literature from my dissertation).

Elaboration on Above Comment

In economics and certain business school fields, a major part of junior academic hiring is the job market paper (JMP). The JMP is an original piece of research by the applicant that constitutes their best research to date. It is meant to serve as a signal of the candidate's potential for becoming a good researcher.

Bob Hall makes a number of nice points here, which I will condense and expand upon. Answers to the two questions posed by @Aleksandr Blekh after my comment are in bold below.

It should highlight the original contributions of the research.
Write "for a wide audience of highly trained economists" (replace "economists" with the appropriate noun).

Don't take this the wrong way, JMPs are a great place to showcase one's technical skills.
However, think very carefully about who might be on your committee.
Hall says to write for JPE or AER. More generally, think of the journal in your field that everybody at least skims through. Write as if you're submitting to them.

The JMP need not be published. (See also discussion in penultimate paragraph below.)

If you get a flyout you will probably be asked to present the paper at what is essentially a working paper seminar. Participants will not expect that it is complete. You can always substitute out a work in progress but it is far better to have one close-to-publishable paper than one publication and a half-baked paper (this is when all of the faculty who aren't on the committee will see you).
People are looking for good ideas, all of the finicky stuff that goes into a publication can be ironed out later (assuming your idea is sound!).

Hiring committees will probably only look at your JMP so that is what you should focus your efforts on.
Yes, do post your work to repositories where others in the profession will see it. This is probably a good way to gauge whether your paper is ready - are you willing to post it in a semi-official place like arXiv where you can't just take it down and post it back up willy-nilly?
For most people the JMP is their first publication. So, yes, do expect to publish the JMP in a traditional journal.

Some concluding notes about why economists bother with this JMP business in the first place (and a method to gauge how much this applies to your situation). Very few economists are coming out of grad school with publications. Ergo, hiring committees can't do the thing where they just scan down the list of previous publications and sum up the prestige (economists - of all people - would if they could). So instead candidates get one shot at wowing committees with their JMPs.

Therefore, if you can already signal to hiring committees that you're awesome (or not) in some other way (i.e. past publications), then the JMP may be something of a formality. This also motivates another reason for not using published work as a JMP: If you already published something in a good journal, the committee can easily incorporate that information into their deliberations. Using another paper gives them a second piece of information to go off of. I would also speculate that using a prior publication might be a negative signal in the sense that it suggests that the candidate is a one-hit wonder (of which there are many).

Best of luck! Let me know if anything needs to be clarified or amended.


Should I apply for a second masters degree (PSI master's program) after already having done a dual degree in physics? I am a master's student in India, supposed to apply for PhD applications this year. However, I am still unsure of what I want to pursue in my PhD program. Meanwhile, I came across PSI's one-year master's program which seems like something I would like to explore. Should I apply for it or another master in the same subject will be a drawback for admission committees when I apply for a PhD in the US? I am also a bit reluctant to apply this year for PhD because of the pandemic.
Also, while presently I am mostly interested in computational work related to general relativity, I want to explore more in the theoretical side, hence inclined towards the PSI program.

I would say if you apply and are successful then it would be worth taking, I think the program in general is well-regarded but if your worried about it looking weird to have two masters degrees you could refer to one as physics and the other as theoretical physics. The program is very challenging to get into but it covers lots of material in theoretical physics, though goes through this material very fast (and the entire lecture series is online).
You will also get to know all the other participants well which will be good for networking in the future, and you will get to meet a number of well regarded researchers in theoretical physics (and because of the reputation they will probably be more likely to keep an eye on people who participate in the program).
The only thing that comes to mind is that it is possible PSI may be looking for students who don't already have a master's degree, but I have no knowledge of that and it if it is an issue, then its not an issue with respect to your ultimate goal.


How can I start to write my final paper? How can I start to write my final paper? I have been doing nothing during the whole week. I just stayed at home and slept. I'm afraid to do anything even cooking. I can't focus and can't concentrate on work. I'm just afraid to write a single sentence. I don't know how to start. I mean that I know how to write but I just can't start. I am incredibly anxious and don't know how to get started. Can anyone  help me?

Getting started writing can be very hard—if it weren't, it wouldn't have a name: writer's block.

There are a lot of different strategies you could try:

Free writing. Just write anything that comes to your mind as you think about your topic. Don't worry about grammar or correctness or appropriateness or accuracy. Just put down something. (You can handwrite it or type it, as you see fit).
Mind map. Just put together a flow diagram showing how different things you want to write about are related.
Create an outline. Don't focus on writing the whole essay, or even whole paragraphs or sentences. Just try putting together a skeleton for what your essay should be like.

There are a lot of other ideas for how to cure writer's block, including walking or even spending time with people who make you feel comfortable.


Do grant proposals with no funds for faculty members have higher chances of being accepted? Some grant proposals mention that they only want funds for students and no funds for faculty such as summer salaries. Would this point increase the chances of being funded by some agencies? Specifically, if two similar competitive projects were proposed and one asked for faculty salaries and the other didn't, would this make the difference?

This of course depends on the kind of competition, agency, country, etc. Those agencies and competitions I'm familiar with, always rank applications based on merit and not on financial need.


Dealing with students who sent email with empty body but the homework attached I am responsible for the exercises for a graduate course. The students submit their solutions via email and all of them send a normal email: greeting me and telling that the solutions file is attached then (most of them) wishing me a good weekend as the due dates are Fridays.

One group sends me an empty email: just an attachment without any word!
I believe that this behaviour is odd, should I take an action or it is not my business?

I don't really think this is odd: they have been asked to send the assignment by email and they did.  There isn't really a need to say anything further and they didn't.  Maybe it would be slightly more courteous if they were to add a couple of words of greeting, but your job is not to be Emily Post.

If the assignments were submitted on paper, and they left their assignment in your mailbox, would you insist that they include a note wishing you a nice day?  No, that would be silly.

There isn't anything you need to do about this.


What effects (if any) do audited undergraduate courses have on graduate admissions? I'm an engineering undergraduate, and my university doesn't require me to take any math courses past the standard calculus sequence and differential equations. The field I am interested in entering in grad school is slightly math-intensive, to the point that it requires more math than what I have taken. At this time, I have two years left to graduate, and I'll be taking about 17-18 hours each semester until then, so it would be very difficult me to tack on an extra math course. I was considering simply officially auditing one, so that it appears on my transcript and so that I at least have some exposure to the subject.

My question is: will this have any positive benefits while I'm applying to graduate school? Or would the admissions committee assume that I didn't learn as much as someone who actually took the course, and take it with a grain of salt that I know the material?

On a related note: what about if the course I audited was on directly in my major? Would that be beneficial (if it were, say, a graduate-level course)?

My question is: will this have any positive benefits while I'm applying to graduate school?

I think you are asking whether it will make your application more competitive.  Answer: not much.  At many/most universities, anyone can audit any course at any time, and it doesn't certify anything more than that they showed up for class -- in some cases not even that.  I had an auditor in a course this semester who showed up
for the first half of the lectures and not for the second half.  My response: ok.  It shows up in my records -- so presumably also hers -- that she audited the course.  I am not asked to assign a grade of any kind.

  Or would the admissions committee assume that I didn't learn as much as someone who actually took the course, and take it with a grain of salt that I know the material?

They would probably not assume anything at all.  They would certainly not regard this as being evidence that you learned the material: getting a poor grade in a course certainly does not demonstrate learning of the material, and auditing shows less than that.

Of course you can learn things by auditing a course.  But you can also learn by outside reading and in other ways.  However most students at this level learn more by actually taking a course, and of course if you do well in the course then that knowledge gets certified (to an extent) and can be used advantageously in your graduate application.

Story check: you say that you have two years left of undergraduate study and can't find time to officially take one course that you think will be beneficial to your intended graduate study.  This professor who read graduate applications for several years finds that hard to believe.  In two years you should be able to work in the time to take one extra course, e.g. by (i) taking courses over the summer or (ii) getting excused from one course in a sequence, say by taking an exam which shows your competence.  This is something to talk to your undergraduate advisor about.


Is it okay to mention we're citing an article only because a reviewer told us to? In a recent review, one reviewer said we must rework the paper in light of two other papers.  One paper was a highly valuable suggestion, and we've enthusiastically taken it on board.  However, the second paper seems to be an ultra-specific paper (one example among thousands) and not applicable to our work.

I'm thinking of writing something like:

  There are many methods for XYZ (and an anonymous reviewer of this paper seemed fond of QRST [26]), and a survey was given in [15].  In this paper, we take the approach ABC for our specific problem.

(Here, I leave off "...since QRST does not actually apply to our problem".)

In this example, we (fairly politely) highlight that we're citing [26] at the reviewer's request.  But I'm a bit worried it would be perceived as a passive-aggressive slight.

Question: Is it okay to mention we're citing an article only because a reviewer told us to?

I'm also considering two alternatives:

Alternative 1:

  There are many methods for XYZ, such as QRST [26], LMNOP [4], and QRSTUV [5]; a survey is given in [15].  In this paper, we take the approach ABC.

But this seems like I'm adding even more virtually irrelevant citations.

Alternative 2:

  Acknowledgment
  A helpful anonymous reviewer suggested citing [26].

But while accurate, it might be considered provocative (and rude) and get the paper rejected.

This question is related to: How to deal with an unreasonable reviewer asking to cite irrelevant articles?  But in our case, the reviewer is not being unreasonable, maybe just fond of this particular paper.  And it's just one additional citation that's being requested.

Update: Thanks for everyone's help!  To let you know what's going on (and maybe this will help someone who winds up in the same situation):

(TL;DR: The reviewer's suggested paper is related to an "in-between" paper which is related to our work; we feel it's not off-topic to cite it while discussing this in-between paper.  It wasn't as off-topic as originally thought.)

We generally agreed with the advice in the answers (don't cite it).  We also found the editor's email specifically said not to cite irrelevant papers suggested by reviewers.  But we dug deeper to ensure we're not perceived as being dismissive.  What happened next:
Upon more careful inspection, the reviewer described it as an "example".  Eventually, we concluded that the reviewer was not giving us a list of papers to cite, but to generally say "look at papers like these".
This turned out to be a gold mine: it gave many papers which we could use to put our work into a broader context; none of our paper's predecessors do this.  In fact, we found a paper which almost identically states the motivation for our paper, but in a broader context (which empowers our justification for working on this topic).
We looked into the suggested paper's references and papers citing that paper.  We found another paper is a kind of "in-between" paper (related to both our paper, and the paper that was mentioned by the reviewer).  We now discuss this in-between paper in detail, and explain how our method deviates from it.  In the context of discussing this in-between paper, we feel it's not irrelevant to quickly cite the paper that was mentioned by the reviewer, without giving it undue weight.

(PS. In this particular instance, I feel this is not the reviewer's paper: other papers by the same authors (e.g. the in-between paper) are more natural to cite.)

As it turns out, not every comment or suggestion forwarded by a reviewer needs to be necessarily accommodated in your manuscript. Hence, as you seem to have a convincing argument against citing the suggested paper in your manuscript, in your rebuttal letter state that you have considered the suggested comment but you didn't find that paper to merit citation. (However, compose your argument politely, thanking the reviewer for the suggestion.)


Will my advisor regret taking me if I start slacking off? I just found an advisor, and the semester after that, I took a much harder courseload because I'm behind on my course requirements.  As a result I haven't gotten a lot of research done.  Is my advisor going to regret taking me or think I've somehow deceived him?

Communication is critical here. If your advisor knows what you are doing and why you are doing it, there is a much better chance that he or she will be patient with a low rate of progress.

You can communicate in a number of ways. A sit-down talk is obviously the most straightforward, but you can back up the message by putting in face time time in the office or lab, attending all lab meetings and relevant seminars and departmental events, and so forth. You can even ask for advice on how to balance classroom and research time. Sometimes an A- and research progress is better for your education than an A+ to the exclusion of everything else. (See also the threads about the relevance of your PhD grades going forward).


Is it wrong not to cite a bad quality paper when the literature on the topic is scarce? Should I cite a paper that I deem of bad quality just because it is among the only two papers that use the same methodology I'm using in my research?

I'm writing a paper that uses a relatively new computational tool. There are ONLY two studies that use the same tool in similar research contexts. One did it superbly (Paper A). The other didn’t (Paper B). I have to make the reader aware I am not the first using this software in my field, but the scope of my paper is clearly defined and does not include delivering opinions on the other two papers (both papers are in my same field, but their research questions are so different to mine that, on behalf of directness, there is no point in discussing their results and wasting precious space in an already dense paper). In other words, a plain sentence of the sort “Software X has been use in rocket science before (Cite A; Cite B)” must do. But I feel a little uncomfortable for not differentiating between the disparate quality of the papers, perhaps sounding like I am endorsing Paper B at the same degree I am endorsing Paper A, and implying that readers should view both as having equally meaningful information. As a clarification, I do not see any wrongdoing by the authors of Paper B; it is just a flawed paper that made it into a top journal.

Is it ethical to skip citing a paper that I consider of bad quality? To what extent does citing means endorsement if no further evaluation of the cited paper is included?

Consider that the problem is more nuanced that it might seem. If the software was of customary use, no citation would be needed, but these two papers and mine are the only studies using the software, and I want to make the reader aware I am not a crank for trying this approach.

To which extent citing means endorsement if no furher evaluation of the cited paper is included?

None at all.

By citing the paper as using the software, you are acknowledging that the paper exists, and that it used the software, and that is the only thing you are doing. Citation is not a sign of approval or agreement or endorsement; it is merely acknowledgement of existence and relevance.  Citations are not statements about the quality of any result, either positive or negative.  If you want to state an opinion about the quality of a result, either positive or negative, you must actually state your opinion in the text, using English words.

I suggest initially citing both papers, and then giving more details about how paper A used the software to derive interesting results, and then remaining conspicuously silent about paper B.


Additional correction after paper publication My journal paper has been published on IEEE Xplore website. I noticed a typesetting issue which I didn't notice when I was evaluating the proof version. Is there any chance to contact IEEE staff editor to modify that or it's now impossible to make any corrections? If yes would they change the "date of current version" printed on top of the paper?

A more serious content issue could be corrected with an erratum or corrigendum, but if it's a minor typesetting issue, there's no chance they'll make the change. It's simply too late. The paper issues might already be printed, the electronic versions already distributed.


What to do if your phd went well? I will soon be in my final PhD year and am about to start my job search. Suppose that for some reason I suspect that I did quite well, research-wise. My main question is:

  What is the optimal job search strategy/advice in this case?

Generally, I can think of two options that are "better" than a regular postdoc:

A fancy fellowship or a named postdoc position
A tenure-track (TT) position

First, do I have to decide between postdoc and tenure track before getting an actual offer? That is, is there anything special I need to do when applying for tenure track besides pressing buttons on mathjobs.org? (Also, is there an option I missed?)

Second, I have questions about each option.

Option 1: Is there a comprehensive list of "really good" postdoc fellowships? Or can we combine a list here? I know that there is Clay fellowship, Miller fellowship at Berkeley, Society fellowship at Harvard, Veblen instructorship at IAS. What other well-known similar positions come to your mind? How do they compare between each other, and to a regular postdoc or a tenure track?

Option 2: Since this depends on many random factors, it seems like if I apply two times, that is, apply next year and then (if I only get a postdoc) apply after my postdoc ends, the probability of landing a nice TT job increases. On the other hand, the quality of a TT job offer I can get after a postdoc will likely be higher because I will have better publications. So I'm not sure whether it is even worth it to seek a TT position now as opposed to settle for a postdoc right now and just apply for TT in 3 years after it ends. Although I've seen people switch between TT jobs, I don't know how common that is. Also, how much of a blocking factor here will be not having lots of teaching experience? (I have some but not as much as most postdocs.) Finally, I understand that when applying for postdoc, I should prefer schools where my area is represented best, but this seems not too crucial when applying for TT, right?

--

To be specific, the field is pure math, the country is US, and I am not eligible for NSF.

A couple of other disclaimers: I understand that the answer depends on my priorities, so let's say the top priority is landing the "best" possible tenured position I can at some point in the next ~7-10 years (which includes not having to teach too much before getting a TT job offer; money is not too important to me personally at this point). I also understand that it's very hard to tell objectively how good my research is, but for the sake of argument let's assume that it's good enough, comparable to other TT job applicants.

You’re overthinking things (but not by much, and in a way that is both typical and understandable given your current situation and vantage point on the job market for academic math positions).

The main things you need to know are:

You don’t need to make any decisions until you get an offer.
You don’t need to do anything “special” when applying for jobs other than follow the application instructions, and there isn’t much else you can do to gain an advantage, other than obvious things (like proving a major result, winning a major award, and having strong visibility in giving talks at various places, especially departments where you’ll be applying).
Your chances of getting a tenure track offer straight of your PhD at a very good (say, top 50 R1) US university are pretty low, assuming you are an average person who meets your description of yourself in the question.
Your chances of getting a tenure track offer at one of the top math departments in the country (like the one you mentioned in the comments) straight out of your PhD are extraordinarily low, again assuming you are an average person who meets your description of yourself, and even assuming you are quite a bit above average. Of course, there is a possibility that you are a person for whom this is a realistic prospect, but if so then I would say you have been rather modest in your description of yourself.

The bottom line is that at the moment your optimal strategy is the obvious one, which is to apply to any place/position where you think you have a realistic chance of getting an offer (and if it doesn’t embarrass you too much, even places where you don’t think you have a realistic chance). Once you get some offers, you may or may not be faced with a minor dilemma of the kind you seem to be worried about. But there’s a good chance that won’t happen (e.g., you’ll get a few postdoc offers and it will be fairly obvious which one is best for you). And even if it does, I think it will become fairly clear in due course what is the right choice. Trying to preemptively make strategic decisions of the kinds you are thinking about long before those decisions are even applicable and when you don’t have all the information is pretty much a waste of your time and mental energy.

Good luck!


Uncommon order of authors names? In my field (theoretic CS) it is very common to list the authors names alphabetically on papers.

I have been working on a paper for quite a long time with three other researchers, which is almost complete, and in the last week or so we consulted another researcher who made a non-negligible contribution to the paper by pointing out (with a proof he thought of after considering the problem with us for a couple of days) some direction we were working on shouldn't work and suggesting considering a different direction - the final version of the paper will not include his ideas but we probably wouldn't finish it on time without realizing we are following a dead-end.

So, he deserves being listed as an author if he wishes, but the problem is that if we list the names alphabetically his name will be first - is it acceptable to put our three names (alphabetically ordered) before his, breaking the common alphabetical order? If not, what is the usual practice in such cases?

Thanks.

In fields (like pure math and TCS) in which the convention is to list authors in alphabetical order, it makes a very jarring, striking statement to put authors non-alphabetically.  The most common instance of this in my experience is when one author is very senior, enough to perform a power play on their very junior coauthor.  Unless the reasons for the non-alphabetical order are carefully explained and seem logical to the readers, this could make a widely negative impression.

Non-alphabetical ordering is almost never used in pure math and TCS to signal importance of contribution: the convention, for better and for worse, is that the authorial contributions are not disclosed to the reader.  As a result of this, unlike many other academic fields in which being a fifth author may be understood to mean very little contribution, in pure math and TCS there is a cutoff phenomenon: you have to decide what level of contribution merits coauthorship, and there will certainly be many cases in which a positive contribution does not result in an authorship.  People who are not coauthors but made intellectual contributions to the work should be acknowledged for this.  If you read acknowledgments on papers in this area, you will find that people are sometimes acknowledged for things that are clearly significant contributions: e.g. for providing the key idea of the project, or for providing correct proofs of key technical results needed by the authors.

The general conventions are to be generous and modest.  Namely, the coauthors should err on the side of generously offering coauthorship to those whose contributions were positive, even if they were lesser in magnitude than the other coauthors.  On the other hand, one should be modest in responding to coauthorship requests: if what you did feels like helping out a colleague rather than doing substantial, original work, then probably you do not want to be listed as a coauthor.

Of course in practice there is a lot of subjectivity here.  In the case at hand, another answerer says that because your colleague's contributions "did not actually make it into your paper", then they are not sufficient for coauthorship.  I don't completely agree.  Telling people what not to do and setting them back on the right track can be an invaluable contribution.

Recently a junior colleague found a key mistake in a draft of a work of mine in which she was not an author.  The coauthor and I withdrew the paper immediately and were able to fairly quickly recover the main result of the paper by arguing in a different way.  The paper was then accepted.  I think it is quite likely that if not for my colleague's contribution, the original, erroneous version of the paper would have been published.  In principle we would have fixed it eventually, but in practice: yikes -- she deflected a bullet.  I offered my colleague coauthorship...and she declined.  In this case the offer was essentially mandatory, whereas both accepting and declining it seem reasonable.

If the OP feels that the contribution to the work was sufficient to make it plausible for the contributor to be listed as an author, I would recommend that the coauthorship offer be extended.  If you know your colleague pretty well, I might follow the offer with an offer to discuss the situation: that's a good way
to make sure that you reach an outcome which you are both comfortable with.  I don't think your colleague's last name has any role to play in this discussion.

Added: Here is the American Mathematical Society's 2004 "culture statement" on coauthorship.  It says that more than 75% of coauthored math papers with at least one American author use alphabetical order, and that this percentage is over 90% in pure mathematics.  I think that for publications in more mainstream and prestigious journals, the percentage is even higher.  For instance, I checked the last 100 multiply authored papers in the Journal of the American Mathematical Society and found that alphabetical order was preserved 99 out of 100 times.

The cultural statement also says: "Joint work in mathematics almost always involves a small number of researchers contributing equally to a research project." Unfortunately I do not completely agree with this statement.  For one thing, the number of coauthors on papers has been rising so sharply that even a statement from 2004 seems a little out of date: I remember that 10 years ago, seeing a math paper with more than three or four authors was worth a raised eyebrow.  That is really not true anymore: a substantial minority of papers has a long enough list of authors -- with such widely varying expertise -- that it is not plausible that all are contributing equally.  Moreover, unlike alphabetical order, I don't know how one can gather statistics about whether authors contribute equally.  To me this statement reads like an aspiration rather than a description of reality.  In my experience, there is a cultural push for authors to contribute equally, but there are other cultural pushes as well.  Listing authors alphabetically essentially always in confluence with the reality that sometimes the contributions are not equal seems to me to an underacknowledged problem of our profession.


When submitting a journal article, can I cite a paper which cited my arxiv preprint? I had uploaded an arxiv paper about 4 months back which developed an algorithm. After uploading the preprint we got some good feedback from a colleague, following which we have added additional simulation results and a more detailed discussion.

In this span of 4 months, the paper has been cited a couple of times. The original work was primarily theoretical, whereas the papers which cited our work successfully applied our algorithm (with minor modifications) to power systems. Hence, when submitting to the journal, I would like to cite these papers to show that our methods have practical application.

My question is: would this form a citation loop which is undesirable? They have cited my work, and I cite their work. Is this firstly even allowed?

Field of research: Intersection of applied mathematics, engineering, and computer science. The paper is likely to be submitted to a SIAM journal.

This depends on what the journal's policies are. But in general (i.e. unless the journal overrides this), there's no requirement that the paper you submit be exactly the same as the paper you put on arXiv. It's often the case that the last round of edits you make prior to publication won't be reflected in the arXiv version, and you could consider the addition of citations to be part of that round of edits.

I have seen citation loops in the past, and nobody raised an eyebrow about them. In fields where posting preprints on arXiv is common, it's well understood that this can happen.


How to get ready for a visit to a lab where I would like to do undergrad research? I am a senior physics major and I recently applied to a national lab that is associated with my university. I applied for a student research position through their website (uploaded my resume and wrote a cover letter etc.) I was contacted by the PI of the research team to come for a 'visit' for an hour with him and his team. He went through the hassle of giving out the visitor pass for me.

More about me, I am a senior but I have no research experience. I don't have a strong GPA and I admit I am not that 'smart' like other students. Should I have to explain about my GPA?

So my question is what should I prepare myself prior to my visit? Do you think it would be some sort of an interview? What sort of questions (academical/personal) should I prepare? Also, should I take an updated resume (I don't think it has really changed since I applied)?

You should treat it as an interview unless you get information telling you otherwise.  Yes you should bring a resume, but you may not need it.  You should read about the PI's research, lab, and team.  Usually there is some information on the national lab's website.  Typically undergraduate researchers are not expected to know how to do research, so you might be questioned about your motivations for learning to do research.  If your grades are not good you should be prepared to say what you are doing to improve them.


Work for college affecting assignment For an assignment, I was paired up with a professor who also has an administrative role within my college. The assignment was unique to me, with a competitive process to be chosen for the assignment (or put on to a different one). The assignment was to produce some software for the college.

The assignment did not require me to completely finish the software. The assignment has now ended, and the professor has informed me that he expects me to receive a good grade.

Outside of my studies, I make a living doing the same work that was required of the assignment (hence why I took it). The professor has asked to meet me to discuss completing the software to the college's specification. The professor is also the one currently marking the assignment. He has offered me an extremely modest sum of money for this - I would never work for this low rate under any circumstances in my job.

I'm concerned that refusing to work for such a low rate will jeopardise my mark as there is a conflict of interest. I do not have any feelings either way for the college and do not feel that I am obligated to complete the software, other than to appease the professor, and the college is very wealthy and so could afford to pay me a reasonable rate. Furthermore, during the course of the work I will graduate and no longer be a student of the college.

I am looking for advice on how to approach this. Would you suggest that I complete the work for, basically, free? Otherwise, how can I sensitively reject the work without affecting my grade?

While the comments already provide some advice, let me add a bit with some possible options. First, you should be properly compensated for your efforts. Sometimes that can include course credit. Sometimes it can just include relationship building with a professor - looking toward the future. Compensation need not be monetary in all cases. This is likely why you did the project in the first place. So, you might examine what it is "worth" to you to do a favor for the university, or just for this professor.

But there are other options. Telling the professor what your normal rates are for such work is valid. If you need that income to live and the time the project would take would lower your income if not compensated, then he needs to know that.

But there might be a possible way to just step away from the project. For example, you could suggest that some other student(s) might benefit from carrying on the project and may not need to be compensated financially for their work. The experience itself can be valuable for them, where it is less so for yourself.

But, if the university really needs professional level work done on this project, then they should expect to pay professional rates to get it done. The fact that you are also a student, in addition to being a professional, shouldn't give them reason to exploit you.

I'll add, however, to address your main concern, no ethical person would blackmail you into doing something by holding grades over your head. If that is how the university behaves you should work to step away as soon as possible.


What is the difference between a college and a university? What is the difference between an institution calling itself a "college" or a "university"? For example, take the "University College London". Is it a college? A university? Both? What does it mean?

Some colleges are universities: The Imperial College of Science, Technology and Medicine, London; University College London; these award degrees in their own right.

Some colleges are listed bodies of collegiate universities: Merton College, University of Oxford; Churchill College, University of Cambridge. These do not award degrees in their own right; the parent university awards the degrees. Some teaching occurs in college. Some teaching and research staff are attached to a college, and to a university-wide department; others are attached only to a department. All undergraduates are members of a college, and of the parent university.

Some colleges are residential bodies of collegiate universities, e.g. Bowland College, University of Lancaster; Halifax College, University of York. Teaching does not occur in college, and the parent university awards the degrees.

Some colleges are independent and part of no university: Ruskin College, Oxford; Working Men's College, London. These tend to make awards other than traditional degrees.

This is the situation for England. Other anglophone countries may have different arrangements.


Where to start for a Topics Class I am teaching my first non-examinable graduate course this Winter term. This course is for students ranging from Masters' students to PhD students in Pure Mathematics and is a course for students to see a topic that is a bit more specialised than the typical qualifier type course.

Since it is a bit more specialised, I am having a bit of an issue figuring out where to start. I can start with a bit of background at the risk of boring some of the more advanced PhD students working in my field, or I can tell the students that are not as adept where to find that material to catch up. I am leaning more towards the latter so that I can have more students taking the course, but the course is only 16 one-hour lectures and I want to get to some interesting material that can help someone starting to work in this field. I am also concerned I might be being overzealous in what I can accomplish in this time and might speed right through details that would be useful. (My imposter syndrome is acting up and making me feel like a lot of this stuff is trivial when maybe it's not!)

The question is this: How do you in a topics course balance giving general theory and also the more specific information that is relevant to the current research trend? I'm afraid if I spend too much time on general theory, I may end up not touching on what research is being done today. Would this be bad just spending the last lecture or two in a topics class just punting the question "What's happening nowadays in this field?"

Thanks in advance!

One concept/approach, which is what I try to keep in mind in addressing a heterogenous audience in a not-required more-advanced course, is exactly to not try to be "systematic", much less "complete". As noted in the question, it would be easy to use all the available time for "general theory", without ever getting around to the points of interest that motivated the course in the first place. So, instead of "laying a systematic foundation...", I try to get to interesting phenomena as directly as possible, and then back-fill "general theory" as relevant. For that matter, "general theory" is more widely available in textbooks and on-line notes than are interesting examples (since the latter tend to be written in "research papers" aiming at more-expert audiences), so students can more easily do further back-fill themselves if desired.

For that matter, some "general theory" is somehow over-hyped as a big deal, when, in fact, the introductory parts of it are really very elementary. For example, in an introduction to modular/automorphic forms (my interest...), one could position the thing as having prerequisites of "Lie theory", "algebraic number theory", "representation theory", and/or "algebraic geometry". It is certainly true that all these things are relevant and useful, but (I claim) it is not the case that one must have "systematically" studied all these things prior... For example, "Lie theory" at the entry level can be simply a study of behavior of two-by-two real and complex matrices. "Algebraic number theory" at a basic level is just about integers, or perhaps Gaussian integers, and so on. "Representation theory" (infinite-dimensional unitaries, etc.) relevant to automorphic forms will not even be found in "basic" representation theory books (which tend to do finite-dimensional and more combinatorial things), but can be approached in a down-to-earth way (for real rank-one groups) as Bargmann and Wigner did, by looking at asymptotics of solutions of second-order ordinary differential equations. (Indeed, the later work of HarishChandra and Casselman-Milicic might be construed as adapting those classical asymptotic techniques via Deligne's PDE version of the old ODE asymptotic results, as in the appendix to the C-M paper about it.)

In particular, to my perception, far too often students think that they have some moral-professional obligation to be "completely expert-prepared" in the alleged background material before starting the next stage... which is (to my perception) substantially misguided, since that way one has no inkling of what the use of the "background" might be. Trying to short-circuit this impulse a bit by directly drawing attention and explicating the applications is a good anti-dote.

And, to repeat, one has no obligation to "prove everything in class"... That's a recipe for not getting anywhere.


How do I ask for an extension to revise a manuscript submitted to an Elsevier journal? I have submitted an article to an Elsevier journal and received the manuscript with reviewer comments and a "revision response due date" within the Elsevier evise system.

I am unable to meet that deadline and I need to ask for an extension. I assume it would be the most usual way to ask the editor, and I have done so about a week ago and not received an answer yet.

Now I wonder if there is any way to do this within evise. But if I click on "Agree to Revise" from what I understand I'm asked to submit the actual revised version already (see screenshot). I don't really dare to click the "Confirm" button to advance but may that be the way to ask for an extension also?

What would be the usual way to ask for an extension?

Write to the editor. This can be either via the system (see if they have a "send email" function) or simply reply to the decision letter email. It's likely the editor will say yes so you don't have to wait for a response to start revising your paper.

About the "agree to revise" button, clicking it tells the editor that you will be revising your paper after all. Some authors abandon their papers after a revise decision - I don't think they abandon the paper entirely, but they stop caring about the submission to this journal. It's good practice to remove these dormant papers from the system; otherwise it'll get cluttered. If you do not agree to revise, then after a reasonable length of time (several months, say) the desk editor might remove your submission. Since it's only been a week, you don't have to worry yet. There's no need to agree to revise for now: in the unlikely event the editor does not approve an extension, it's a (minor) administrative hassle to change the article's status again.


At American colleges, are student evaluations of teaching subject to code of conduct? It is well-known that student evaluations of teaching tend to be spiced with language that is insulting, sexually harassing, sexist, or racist.

Most American colleges have a code of conduct that is would disprove such remarks if they were face-to-face or anonymous writings on the wall.

Does that code of conduct apply to student evaluations of teaching at American colleges, or are they considered exceptions? These course evaluations are largely anonymous, which is why students feel enabled to engage in speech they usually wouldn't utter. But this occurs via university media, not somewhere out in the streets or the dark web.

Yes, they are subject to the code of conduct.  However, they are usually anonymous, so there is no means of enforcement.


To what extent will your choice of PhD topic restrict your career? Obviously, if you choose to either do a PhD in English literature, or in mathematics, this choice will heavily determine the possible career paths you can later take.

But to what extent does the choice between two different topics within the same discipline influence your career possibilities?

Physics: Quantum computing vs high energy particle physics
Math: differential topology vs abstract algebra
Economics: business cycle theory vs industrial organization.
Psychology: Evolutionary psychology vs Neuro-psychology

Would such a choice significantly affect your future career, or is there generally such an overlap in the skills you learn doing different topics that you will be able to easily switch between these topics within the same discipline?

Very few people are static in their careers, in and out of academia. My PhD was in the area of molecular simulations in chemical engineering. My post doc was with a physicist working in computational materials, then I took a staff position in environmental engineering doing fluid flow and geochemistry studies, I have since moved into renewable energy applications and biomedical, with side work in algorithm development and kinetics.

All of this is to say, any limits on what direction your career can take are placed by the researcher, not the field of study. If you’re not willing to branch out, your choice of jobs will be limited. If you’re willing to explore, the options are as infinite as your curiosity and salesmanship will allow.


How old can references or sources in a thesis be? I have read that references in scientific papers should be no more than 2-3 years old, since such fields move fast, and no more than 10 years for arts or related fields:

  A good rule of thumb is to use sources published in the past 10 years
  for research in the arts, humanities, literature, history, etc.

  For faster-paced fields, sources published in the past 2-3 years is a
  good benchmark since these sources are more current and reflect the
  newest discoveries, theories, processes, or best practices.

However, I believe that's subjective, so how old is it for a reference to be "too old" to cite?

References can be as old as they need to be to cover the material.  I had some that were more than 30 years old. But if all of your references are "old," people are going to want to know why.

You must also be sure you cover the most current research in your field.  A few in my own dissertation were for material published in the same year as my own work.

The link given in the comments and the revised question seems to be directed toward undergraduate research assignments, and the "ten years" reference is a part of an example assignment, not a requirement given by the Shapiro Library. The key idea in the link is that references must be "somewhat current."

For a thesis or dissertation, one must cover the field, including both early and very new research.


Reviewer signs name on review. Should the editor censor? Say a reviewer writes something like

This paper is [yada yada blah blah].
Sincerely,
Professor John Smith, Big Name University

Should the editor just forward the review to the authors because Professor John Smith, by signing his name onto the review, is presumably willing to reveal his identity to the authors? Or should the editor keep the review anonymous by deleting the signature?

If the journal is structured with a blinded review process, as most are in my experience, I would censor the name as an editor.

Only if there is some sort of explicit journal policy allowing reviewers to unblind themselves would I consider not censoring the name.


It seems that almost all succesfull academics have had distinguished advisors. Is it really true that pedigree defines success? In his manuscript "The making of a scientist" [1], Hans Krebs highlighted the fact that great scientists are moulded for success by their renowned grad school advisors. Additionally, he talks about other things in the paper.

My question is, does the observation which Krebs made five decades ago still hold true? I was not lucky to get an inspiring PhD advisor during my PhD, in spite of my advisor having a really renowned PhD advisor. I did not learn anything substantially life changing (in matters of ethics, dedication, passion) from her apart from getting suggestions about my research. In such situation, should I just accept the fact that it is highly likely that I will never surmount to anything great in my future research career?

[1] Krebs, H. A. (1967). The making of a scientist. Nature, 215(5109), 1441.

I don't have a copy of the Krebs article, but I'm going to guess that he didn't mean to imply doom for every doctoral student who doesn't have a world renowned advisor. Your success is up to you and what you do, not some mythical inheritance from your legacy in academia.

Actually, I worry that if such a thing were true then scholarship would only  go down hill from wherever it started and never upward and outward. People who go beyond the the people who taught them are celebrated, actually, even by (especially by) those educators.

But, renowned people do have an advantage and they can pass part of that along to their students in some cases. If a person is a star in their field then lots of people want to work with them and they have lots of collaborative opportunities, even if they are often small ones. This means that there are a lot of ideas flying around in the presence of the luminaries and students can get into that sphere and exploit it. They can also exploit the contacts and build their own circle of collaborators.

But, it is also possible for people to form such rich research groups and seminars even when their own advisors are more modestly "endowed". Find ways to meet and interact with people who know more than you do and are willing to share it. In many fields, that means going to conferences and finding ways to participate there. You can also just correspond with people who might be able to help you put ideas together and focus your research.

But starting out with an attitude that you can't really succeed because your advisor wasn't in the very top ranks is something of a cop-out. If you really believe it, then it is a self fulfilling prophesy and you aren't likely to work hard enough to move upward in the estimation of your peers.

Work hard and swim in a sea of ideas, however you can make that happen. Luck helps too, of course. Others may have advantages, but that is true in everything.


When should a graduate student accept a peer-review request? I have recently published my first research paper and have already received a request to review a manuscript. The journal's impact factor is low, but it is open access, and the paper's topic is relevant to my field of study. What factors should I keep in mind when deciding whether to accept or decline the request to review? What level of expertise is typically expected from a good-quality review?

Writing peer reviews is a vital part of academic life and you should eventually partake in such service to the community. In order to write a good review, you need

time to actually read the manuscript and write the review;
sufficient scientific expertise in the relevant field;
some idea of what constitutes a good review;
confidence in your own judgement and in your critique of (potentially much more senior) authors.

Reviewing is always much easier and pleasant if the manuscript is good. When there are problems with the manuscript, that's where it becomes tricky (unfortunately, many submitted manuscripts fall in the second category).

You should definitely discuss this with your supervisor.


What is expected when "novel" and "innovative" ideas are requested as part of a research grant application? I am applying for a research grant which specifies that the proposed research should be novel and innovative. However without previous experience, it is not clear what degree of novelty is required. For academic publications the requirement is generally that the presented results should be non-obvious (novel) and making a significant improvement in understanding about the topic. For this reason straightforward incremental advances are liable to be rejected.

When considering grants, is a similar degree of novelty required, or is it expected that the proposed research is a new departure from what has has been done before? By way of example, say you have done research on a certain sample to investigate physical property A, would a proposal to investigate physical property B qualify as novel?

The purpose of adding words like "novel" and "innovative" is to weed out proposals that may be poorly researched and thus copying others or or involve repeating other works in a slightly different setting (or equivalent). The phrasings makes rejecting proposals easier since it provides a critieria (one among many) against which it can be judged. Funding agencies are also keen to see their funding go to research that can be judged to contribute "significant" results.

My experience says that what constitutes "novel" and "innovative" is difficult to assess in detail. In my field, environmental/earth science, some themes become "fashionable" or hot and signals these aspects, or rather absence means less likelihood to receive funding. These themes include finite element modelling (70s), acid rain(70s/80s) and climate change (currently). This can be seen as a communal will or interest to steer research in certain ways and so showing you can significantly contribute to these goals was/is more or less necessary to provide you with a good chance for obtaining funding.

So to define "novel" and "innovative" will be difficult. And, as a side point, your research either is or is not "novel" or "innovative", there are no degrees. You need to come up with ideas that are truly new (testing new grounds) or which promise results that are significantly advancing science but more importantly, you need to convince the reviewers in the funding agency about your case. This means to avoid "more of the same" proposals, to be sure your idea has not been worked on before (know your field).

A book, I strongly recommend for all is

  Friedland, A., Fold, C.L., 2009.  Writing Successful Science Proposals, Second Edition. Yale Univ. Press


What if my research does not give the expected results? I'm working on my Computer Science thesis. I have a two solution proposals until this moment, and I've been wondering about the following:

Sometimes you know that if you implement it correctly, it will work (eg. when building a website or a desktop app for some trivial purpose, etc), but some other times you try to solve your problem with some specific solution proposal. A few examples:

I will do some preprocessing, I'll represent the documents that way and use this metric, and then I'll apply this clustering algorithm. Theoretically, it should work.
I will use this computer vision technique for breaking the captchas, and then... In theory, it should work.

but when you implement it, you don't get the expected results (eg. bad text classification in the corpus you're using, low-rate successfuly captchas solved, etc.)

In those cases, is it a valid work? I mean, is it good to publish your work, saying that your solution proposal doesn't seem to be good when solving some specific problem?

I'm not sure what you mean by "theoretically it should work". The examples you refer to are cases where you're positing some kind of model for the data. That the experiments failed suggests that the implied model is wrong. The question then is: what is a good model, and what went wrong with the model you tried.

It's that kind of investigation that will set you on the path to a paper.


As a beginning graduate student, can you do without conferences in theoretical CS? I'm beginning my graduate study in theoretical computer science soon, and I've been admitted to two graduate schools in Northeastern Asia.

One of those makes it a rule to grant compensation for travel to conferences to graduate students who finished their master's thesis.  However, for beginning graduate students, they said they cannot be sure if they can fully afford their travel costs for conferences.

The graduate school requires the students little coursework and all I will do there will be do actual research.  As you may know, conferences are important in computer science and reputable conferences are usually held far removed from us in Northeast Asia.

Can I do with journals and preprint servers, and possibly without reputable conferences, in the field of theoretical computer science, as a beginning graduate student?

(By the way, the cons of the other school are that the professor supervises too many students and that he hasn't been nice to me.)

Conferences are very important in CS. Journals are also important, but they tend to accept more mature work, and therefore might be especially hard to publish into as a beginning graduate student (which, in your terms, seems to refer to someone who hasn't finished his/her master thesis yet). Nothing is impossible, of course, but you have to be careful not to end up with no publications after 4 years, just because you were aiming too high. In addition, some journals are very slow to respond, so you might spend half a year or even more waiting for a decision. In the mean time, you cannot send this work anywhere else.

You should ask students there how the official policy is, it might just be that they don't want to fund you a trip to a small workshop in Hawaii, but the question could be different if you were to get a paper at POPL. You should also consider that there are good conferences coming to Asia, and many conferences offer financial support to students (including reducing the registration fee, sometimes even helping with transport/accommodation). Finally, if you're writing your paper with someone else, such as your advisor, this person might be able to travel to the conference and present the paper (which would be a shame for you not to attend, but it still counts as a publication in your CV).

EDIT Some clarification: technically speaking, the only important thing is to produce good research, and to write good paper. What you plan to do after your PhD also matters, but if you'd like to stay in Academia, you will need at some point to get a job, and you will be judged on your papers (on other aspects too, but papers are very important). Now, to answer your question: yes, you could get a job with only journal publications, as long as they are good. Is that the best strategy? Probably not. Conferences are very important because they allow you to meet other people, to be exposed to state-of-the-art research, to confront your ideas with the community, to get published within a relatively short time period, to receive more frequent feedback, to construct your research project in a more incremental way (present your idea at some workshop, work on a good conference paper, present the extended version to a journal).

If I can give you one example, I've presented some of my work at a workshop with no proceedings (so it didn't count as a publication), and I met there someone who accepted to be one of my external PhD examiners.


(Psychology) Mismatch with Advisor's Research Interests A complicated story so I’ll try to keep it short. Basically, I was fairly young applying to PhD programs (in psychology) and got into a program where I thought I’d be a great fit. My advisor’s research interests seemed to match up with mine, but the more I started working in the lab I realized how much they....don’t. I’m realizing that we have really conflicting theoretical orientations, and I’m not in any way shape or form thrilled about the current research being conducted in the lab. I’ve been skirting by on the outer rim of their research interests, but I ultimately know for the sake of my future I should be working with someone who has more expertise in what I specifically want to work in. All that said, I can tell my advisor wants me to pursue my own interests and is trying to support my ideas (but it’s clear they are working outside their expertise). I actually have a great relationship with my current advisor and interpersonally get along fantastically with my lab. I feel lost as to what to do (switch labs and work with someone more related to what I want to do-not sure if that would damage any current relationships with my present lab, continue with someone who is very supportive but not in the area I want to be in, something else....). I would feel more comfortable working outside said advisors expertise; however, they are new faculty and I’m not confident they can support me very well in that domain. Honestly just looking for advice/thoughts.... I’ve subtly brought this up in our individual meetings but haven’t done anything drastic.

One statement in your question stands out: "I can tell my advisor wants me to pursue my own interests and is trying to support my ideas". That alone would suggest that, under certain conditions, it might be wise to stay. You have other supporting statements as well.

Some students can carry on their research with only minimal advice from advisors. Others need more continuing support, and even the ideas about what to study. You seem to be more in the former group than the latter, but you need to judge that.

If your advisor were hostile, or even indifferent, to your research goals, it would be better to leave, but in this case, perhaps staying is the best option.

But an advisor can be helpful to you in many ways other than just basic support. S/he can help with process and with keeping you within ethical norms of the field. They can probably also make a fair judgement about when you are done and ready to write up your findings. The general support also implies that they will sign off on the work and write good letters. That alone is enough, provided that you are self driven enough, and with enough ideas, to carry through the research relatively unguided.

You need to judge this, of course, but I would be hesitant to make a quick decision to go elsewhere, either at the same university or at a different one. Imagine what your situation would be if it were completely reversed: a hostile advisor who was very knowledgeable in your specialization.

Think before you jump.

However, there is also an opportunity to get the specific guidance you may want outside your institution. It is harder, but not impossible, to keep close contact. In the long term, you do want external collaborative relationships to support your future career and it isn't unreasonable to begin to develop them now. Your current advisor may even be able to put you in contact with a few people. Conferences are also good for making contacts in some fields.


How to get reference from lab I worked with, when lab head seems unlikely to help and I was advised not to ask postdoc I'm looking for PhD but I'm having issues with my referees. I did a placement year and for my second referee I was advised to use one from my placement. I worked only with 1 Post-Doc there but I was told by my uni tutor that I cannot get a reference from him as I need from somebody with a stable/fixed position, here is her reply I asked about that:

"You are normally expected to get the person who officially supervised your research work to write your reference. This must be a person who has a permanent position at the place you worked i.e. the lab leader (so never the post-doc, Ph.D. student or a technician i.e. anyone who is a colleague and not in official charge)"

I was quite surprised, I was planning to simply just use a reference from my Post-Doc. Now that leaves me with my placement lab leader. Well, the thing is she is very strict, moody and hard to please and we pretty much never really talked apart from maybe 1 or 2 short chats. She was away on conferences when I gave a lab presentation and when I had a short seminar. It's a shame, I wanted to show her that I really worked hard in her lab. Anyway, when I left I wanted to personally say thank you and ask if she would be willing to write a reference for me. Again, she was away on a conference so I ended up sending her an email. She never replied. I got too busy with uni and family issues and a month has passed. Now I really want to submit my PhD applications so I sent her another email and now I'm dreading what if she won't reply again? Maybe that was her answer? A 'no'?

Additionally, I got close to another lab leader who said she would be willing to write a reference for me. She also happens to be a very close friend with my Post-Doc supervisor. I wonder if that would acceptable? I didn't work in her lab but she holds a fixed position.

Please help me. On my CV I will mention my placement with my Post-Doc and the lab I worked in, wouldn't that be weird to not provide a reference from my placement lab?

I wonder how much this could affect my application?

One option is to ask the postdoc and professor if the postdoc can write a strong first draft that the professor would be willing to sign (and ideally edit). Most admission committees will probably know that the letter was written by the post-doc, but the fact that it is signed by the professor (in addition to the postdoc) means that the head professor agrees with the assessment.

This letter will likely be stronger than if only one of the two wrote it because (1) The postdoc will be able to provide detailed examples that the professor doesn't know about (2) The professor's name recognition, through the signature, adds credibility (3) the professor will typically have more experience writing these things and hence he or she may improve the letter by carefully recrafting a few of the post-doc's sentences. Note that (3) and (1) work synergistically. Without the examples provided by the postdoc the professor's experience in letter writing is likely to be less helpful because their letter will sound too generic.

Additionally, this option will also provide the post-doc good feedback for future letter writing (assuming the professor shares her/his edits with the postdoc). So it is really a win-win situation for everyone.


How should I facilitate a panel discussion? I've been asked to facilitate a panel discussion at a conference I'm presenting a paper at in a few weeks, and I'm thrilled at the idea, but I really have no idea what to do. I've never facilitated a panel discussion before, and I'm wondering:

What is it like?
Is this something I can (or should) put on my CV?
Are there any benefits to me for doing so besides exposure (which I'm assuming is already a big plus)?

Moderating a panel can be a lot of fun!

First: are the panel members already chosen, or do you get to choose them?  If you get to choose them, then look for a group of people with diverse backgrounds and viewpoints.  For example, different camps of scientific thought, different career stages, academia vs. industry vs. government, different subfields.  Try to pick people who you think will both have interesting thoughts to share and who will be willing to stop sharing them---one blatherer who insists on telling a ten-minute anecdote every time they talk can ruin a panel.  Also try to look for panelists who will be respectful to one another, even when they violently disagree: a fight might be "fun" but it generally less productive and interesting than a respectful argument.

It is also critical to be aware that due to the availability heuristic, your first thoughts on who to invite are likely to be biased towards socially dominant groups (typically: white men from Europe and America).  To avoid being racist and sexist in your picks, also make a list of people who are not members of this group, and ask yourself who in this list would also be a good panel member.  You may be surprised how many qualified people there are with more diverse backgrounds than you thought of at first.  Then, from your set of qualified people, pick a mixture that is significantly closer to the diversity that you want there to be in the field, rather than its current average.

Once the panel is running, as moderator, you have three responsibilities:

Get the panelists to start talking about the subject at hand.
Keep the discussion at least vaguely related to the subject of the panel at least much of the time.
Make sure the talkative panelists don't keep the less-talkative panelists from contributing.

A good technique to support all three of these responsibilities is the prepare a list of open-ended questions related to the panel topic.  You can start things off by throwing a question out to the panel to break the ice.  If the panel starts running down or (badly) drifting off course, you can feed another question into the mix to keep things going on track.  Let them drift a while first, though: the purpose of a panel is interesting scientific discussion related to a topic, and drifting a bit may get you somewhere important. Finally, if somebody on the panel isn't getting enough chance to talk, you can inject a question targeted to them: "The next question, I want to start by hearing from Prof. Quiet."

Some panels also are expected to start with mini-presentations, in which case you also have a session chair job, to make sure that the panelists keep their presentations short enough that there is time for a good discussion.  If they are giving slides, collect them onto one machine beforehand, so that you don't lose time to A/V changeover.

As for the benefits: sure, you can put it on your C.V. (it doesn't count a lot, but it doesn't hurt).  The primary benefits, however, are exposure to the audience,  networking with the people on the panel, and the fun of running a nice event.


Can a response paper agree with the initial paper, or must it disagree? A paper describes a computational method for solving a problem, and we made a significant improvement to the method and applied it to a new case study. Is it appropriate to publish a response paper?

Most response papers I've seen dispute the findings or methods of the paper they are responding to. Is it reasonable to write a response paper which agrees with the initial paper?

EDIT: It wasn't very clear when I first posted this, but the "response paper" I refer to is a specific mechanism that journals have for responding to an existing paper published in their journal. This is often called a comment or discussion paper. At Nature, they're called "brief communications arising". I might be the only one that calls it a "response paper," actually...

In general, 'comments' can be comments in support or comments in disagreement. Usually people tend to only submit comment when they are moved strongly to point out  a disagreement.

But, as question specifically referred to Nature's "brief communication arising" (BRA)  the answer is NO.  The BRA  notes that "Submissions should challenge the main conclusions of the Nature paper and contain new, unpublished data to support the arguments.". (i.e., pointing out errors, reinterpreting conclusions, coming to a different end result, comments to refute). Showing that there is an alternative method that is better than that presented in the paper doesn't seem to fall under that 'challenge' to the paper. (Unless perhaps you can write it as challenging some final conclusion that their method is the best possible ever? )

They offer the option to add extensive comments under the paper on the website. But then it will be difficult for others to be able to cite or even find your work. It sounds as if you should find a journal and submit your  your method as improvement in XX algorithm/method, citing the original Nature paper.

For comments and criticism there is a brilliant new service of pre- and post-publication reviews called Publons. For example, a recent and very harsh criticism of a sensational paper in Nature. Each review is assigned a DOI, so others may easily cite your comments. Also, it is well covered with Altmetric, which provides quite a visibility to your comment. Yet, no official impact factor for you reply publication.


How to stay motivated when working on projects by yourself? My advisor told me that I needed to be an independent researcher, so I came up with a project by myself.  But I don't really work on it because there are no deadlines and no one else is involved with the project.  Also I stopped having regular meetings with my advisor, so he is no longer there to kick me in the butt when I don't do any work.

I spend most of my time procrastinating, working on coursework, and being a TA.  TAing and problem sets are things that actually do have hard deadlines and involve other people, so I end up working on that stuff instead of my research project.

How can I stay motivated to work on my research project?  I have barely done any research for months.

In my experience doing an independent research project, one of the most helpful things has been to remind myself why I thought my project was worth doing. If you can periodically re-excite your interest in the project, you may find yourself wanting to spend time on it. Those have been my most productive times.

Also, meet up with your advisor on a regular basis, even if it's only once every quarter or something (more is preferable). If it will help light a fire under you, set a meeting a few weeks in advance, decide on something you'll show them/discuss with them at the meeting, and use the meeting as a mini-deadline.

It's all about carrots and sticks. Remind yourself why you're doing it; remind yourself that it won't be so nice if you don't do it. Reward yourself for meeting milestones. Make yourself keep milestones.

Also, if you're experiencing any health issues (mental or otherwise) related to this, don't be afraid to seek help. There are often resources nearby, and you're better placed to do good research if you look after yourself.


APIs or databases that allows one to retrieve the works that a book cites Are there APIs or databases that allow to retrieve the works that a book cites. Eg. I give it an ISBN, and it returns all the works that it cites (not those it is cited by).

APIs or databases like Microsoft Academic Search usually only contain citations of journal articles and papers, but not books.

Mendeley has quite powerful database on all kind of sources.

http://dev.mendeley.com/

Also, you should check Elsevier's developer portal, as they provide a number of APIs for their services:

http://dev.elsevier.com/

Where ScienceDirect API is especially relevant for you:
http://www.elsevier.com/solutions/sciencedirect/support/api

As you probably know, Elsevier is one of (if not the) the biggest publisher(s) of academic publications, including books.

In case you might want to query your own instance of Mendeley Desktop - check my blog post, for few starting points:

http://blog.veles.rs/mendeley-desktop-http-api/


Turning down a scholarship...with the hope of getting more funding? I recently applied for an intensive language program at my university; the program's relatively expensive, but many students get full or partial scholarships to cover some of the cost. I just got a letter confirming my acceptance into the program, along with a modest scholarship. I'm thrilled, but, unfortunately, there's no way that I can afford this program based on the scholarship they've given me.

I have to write back to the program executive, who I've spoken with several times throughout my application process, either accepting or refusing the scholarship. What I'm wondering is: is there some way that I can refuse the scholarship while also hinting at the fact that the only thing keeping me from attending this program is money? I've had a lot of friends who have written letters along the lines of "I would love to enroll in University X, but University Y has given me a larger scholarship", and have gotten larger scholarships from law/grad schools. I'm wondering if sending an email like "I appreciate this opportunity and would love to attend, but, unfortunately, cannot afford the tuition" would have a similar effect, or does it seem... I don't know, slimy? Is trying to subtly manipulate my way into a larger scholarship inappropriate and/or a futile effort? Should I just politely reject the scholarship offer instead?

Any previous experiences/advice anyone has would be a huge help!

"I appreciate this opportunity and would love to attend, but, unfortunately, cannot afford the tuition" - that's pretty much the situation according to your description. It's not flattery, it's not manipulation, it's the fact, isn't it? It sounds just right.

It gives the commission full discretion to decide whether they consider you worth being helped over this hurdle.

Just don't decide to join, after all, at this support level without having a very good idea how to justify where your suddenly newfound riches have come from.


Do postdocs in the United States generally get annual raises? Do postdocs in the United States get raises in general? (Is this different for postdocs hired under specific grants vs postdocs hired through departments, such as in mathematics?) If there are raises, how are they determined?

From my experience in the US, it is typical for a postdoc to be on a fixed "short term" contract where there are certainly no "promotion" raises, but might or might not provide cost-of-living increases.

A one-year contract will almost certainly contain no salary increase; for a 2- or 3-year contract, they will be minimal at best.


What are the key points in short descriptions of research experience? When writing short descriptions of research experiences as a student (undergrad or postgrad), what are the key points that professors, potential collaborators and admission committees would like to see?

These might be very short descriptions in a space constrained academic CV, or slightly less short descriptions on an online profile or research statement. What are the key essentials (in the CV case) and the additional points (statement/website case)?

In a one-sentence statement, I want to state as precisely and concisely as possible as much relevant detail about the project I was working on. For instance

  Analysis of Widget Manufacturing

doesn't tell me much about what you did. On the other hand

  In-situ XYZ Experiments and Numerical Modeling of the Parametric Influence of Temperature, Humidity, and Cooling Time on the Strength of Widget X under Load-Bearing Conditions

tells me much more about the problem you're working on.

If you have perhaps a paragraph, then I went a short summary of your work. You should provide: a motivation for the problem, an overview of what you did, and a summary of the main methods, results, and conclusions of the work.


Why do professors obfuscate their email addresses on their websites? I've always wondered why professors write their emails like this:
john dot doe @ harvard dot edu
I am trying to figure out some benefit of this but I can't think of one. It is definitely not more clear. It is more work if you are actually trying to email the person. Why not just write your actual email?
I come from math so maybe this is just a math thing? I have no idea.

It's most likely to avoid Email address harvesting. There are bots that scrape webpages to pick up email addresses for spam purposes. An easy way to avoid this is write your email in a way that's harder to read for a bot that's scanning for email addresses.


Is it legal to upload preprint on ResearchGate? I have few papers already published in certain journals which cannot be uploaded on ResearchGate due to copyright issues, now is it legal to upload my own version of the paper formatted in LaTeX or in other words the manuscript I sent for publication that was not typeset for journal publication?

As one of the other answers says, typesetting is completely irrelevant--the question is whether or not you are authorized to upload the content.

The RoMEO website has documentation on the precise legal authorizations of every major journal publisher, and of an extensive list of journals. You can consult it to quickly confirm what exactly the journals you've published in authorize you to do.

Their information is not always 100% accurate, but it's above 95% accurate. I've sent them corrections and they are quite conscientious to update their information, and they usually have direct links to the publishers' copyright statements so that you can verify what they say.

I will note though, that a very large amount of the time, it is not authorized to upload to general repositories like ResearchGate, Academia.edu, SSRN or arXiv (depending on the journal). If you want a safe place to load your articles, the most commonly authorized places are your personal website or your institution's open access repository.


Mentioning non-academic pre-PhD work on one’s website? Does mentioning non-academic pre-PhD work on one’s website help or hurt one on the academic job market?

I’m a graduate student in political science approaching the end of my PhD and preparing to go on the job market next year.

When I began my PhD program I created a website, and in the personal section I briefly describe my pre-PhD work, which includes working for some well-known political figures in well-known organizations. At that time, I felt like my prior work was a big part of my identity and therefore included it in my bio.

I know this may be minor point, and the quality of my academic publications and dissertation is much more important than a paragraph of my website bio, but I’m asking because this could make a marginal difference when I apply for jobs.

For example (not real): Before starting graduate school, I worked for Bill Clinton as international policy advisor from 2006 to 2008. From 2008 to 2011, I worked in the office of President Barack Obama as multilateral affairs advisor.

Your professional website should reflect your professional identity.  That obviously includes all of your scientific work, but may also include other aspects of your life that you choose to share broadly with colleagues.  For example, some people put bits of their hobbies or family life on their page; others (like myself) choose not to do so.

If your political involvement is something that you feel is relevant and that you want your possible future colleagues to be aware of, then by all means keep it on there.  If you feel it is likely to be distracting (e.g., you were campaign manager for a famously corrupt and now-indicted politician) then removing it might be better.


Should a citation be included when answering a question regarding a specific source? For example, "How do the six types of shenanigans relate to the ethical use of a flux capacitor according to Smith and Smith?"  (Smith and Smith are authors of the textbook).   For this type of question, where there is a specified source that must be used, is it necessary to re-state the source in the answer?

The question is posted in a discussion board.  Only students of the course and the instructor are the intended audience.
Also, the chapter of the book is directly stated in the subject line of the posted question.
Ex. "Chapter 2: Electric Boogaloo"

If it is a discussion board the audience are only the course instructor and the students of the course, whether or not you repeat the citation in your answer is not going to have any important or lasting effect. That said, while a very strict instructor might complain if you do not repeat the citation, I cannot imagine any way in which repeating the citation could have a negative effect. If you are in doubt, just cite it again.


'Expert' interviews of academics - Consent and Ethics I am conducting a research trip to another country where i will meet with academics (individually and as groups), industry professionals and other experts to explore different aspects of a particular issue. The meetings will take the form of semi-structured interviews. I will be writing an article on my return analysing my findings. As the research is overseas, my University requires I go through an Ethics Approval process, which includes consideration of informed consent and of participant anonymity.

I want to keep the consent process as streamlined as possible and I am trying to determine an appropriate process that works for both industry experts and academics.

I can see that industry professionals might prefer any references I make to anything they have said to be anonymized, either to "a spokesperson for xxx company" or to "a senior industry figure" or "a customer services manager". Or they might be happy to have their contributions on the record. And academics are more likely to prefer to be named.

So, in asking for consent to record interviews and use the information for my research, do I need to ask each participant whether they want their contributions to be
a) attributed
or b) anonymized?

I should note that when other academics have visited my research group for discussions and to find out about our research, no one has ever asked for participants to give their consent for the discussion, and it seems odd in the context of an academic discussion.

Could I justifiably apply the consent procedure only to non-academic interviewees?

If you've had to go through ethics approval process, you are bound by the protocols that you come up with them. We've carried out interviews with other academics and are bound by ethics, and when I have been interviewed by other academics, I have gone through the ethics process.

I would be skeptical if somebody was carrying out a research interview with me without obtaining formal approval from me.

As for your question:

  So, in asking for consent to record interviews and use the information for my research, do I need to ask each participant whether they want their contributions to be a) attributed or b) anonymized?

Your ethics board will probably approve the protocol you want to use. But yes, when I obtain permissions from interviewees, I usually ask three questions: (a) do they of their own free will agree to the interview; (b) do they agree to be interviewed; and (c) do they agree to have quotations in the paper that are attributed to them/anonymized to them/etc. (the last part depends on the study)

Sometimes a study has a mixture of anonymous and named participants.


Can co-authors check the status of a submitted manuscript with various publishers? Inspired by the question How can co-authors check the status of a submitted manuscript in Elsevier Editorial System?, I would like to broaden the scope of the question and apply it to various publishers. In general, I feel that by default, coauthors cannot track the progress of a submitted manuscript during the review process.

Are there exceptions to this rule of thumb?

(probably more suitable as a comment, but I lack the reputation for that)

"Are there exceptions to this rule of thumb?"

At least some publishers that use Manuscript Central allow this. I am a non-submitting, non-corresponding author on some RSC and ACS papers and can view the basic status of (and download copies of) these manuscripts. It uses email addresses/ORCIDs to link these to your account, and you may have to have created an account with the relevant publisher prior to submission for this to work.


"Required Reviews Completed" "Required Reviews Completed" Is that normal that this status lasts more than one month after Major Revision?
Thank you for your contribution

"Required review completed" means that the reviewers who were assigned to review your paper have all submitted their reviews. The next step is that the editor who is handling your paper should take a decision based on these reviews such as "accept", "reject", "minor/major revision", or invite more reviewers.
It is a bit unusual that it takes 1 month after the reviews are completed. From my experience (as author of more than 200 papers and as editor-in-chief of some journal) it is usually more like a few days or a week but it can vary depending on the journal. There can be various reasons why there is a long delay such as the handling editor being very busy.
What you should do is to send an e-mail to the editor to let him/her know that your paper is waiting with that status for over a month. Write a polite e-mail and ask gently to check what is going on with your paper. I did that recently for a paper that was in that situation for 3 months... The editor told me that he was busy and since he was only a guest-editor he did not handle the job quickly, but after my e-mail, he processed it quickly. Don't send more than 1 e-mail because editors are usually very busy.


Is it "fair use" to use figures from a publication in monetized educational material? Is it considered "fair use" (i.e. legal) to use figures and/or images from a journal/conference publication, in educational material (possibly for a lay audience) that is monetized or monetizable, assuming proper referencing is done?

Example: suppose someone has a Youtube channel that discusses science, and wants to cover some immunology. Can they display a figure from a Nature review during their video (say for a 2 minutes in a 30 min video)? Such channels do make money (or can, at least) from advertising.

In some sense, this is similar to science journalism I suppose.

My thought is that the safest thing to do would be to ask the publisher (since I think that usually the author is not the legal holder anymore). But would that have to be done, say, for every video and every figure in each video (using the example above)?

I am not looking for formal legal advice, just whether an academic doing such a thing is uncommon, if people have some experience in such matters, whether one should feel confidently safe (or not) to do such a thing, etc...

Edit: I'm mainly interested in the USA and Canada.

That is very problematic. Even if the author would allow it, the copyright is usually owned by the publisher and they are usually not interested in sharing. And even if they would allow it in principle, they are certainly not interested in answering letters from people that want to make Youtube videos.

Things are differently if the material is published under a less restrictive license, for example Creative Commons. Then you just have to follow the rules of the license. But even if the paper is published under Creative Commons, that does not necessarily hold for the pictures and secondly it only holds for very few publications.

That said, there are rules such as "Fair Use", but you have to consult a lawyer to get to know if these apply in your case. Have a look at Can I use data and images found online in my project report, under the fair use clause in copyright law?