What should I do if I realize there is a minor error in a paper I submitted? I have submitted a research article and later realized that it has a slight error.  The paper is now under review. I have proposed a few theorems; one theorem contains a slight error that can easily be removed. The methodology is correct. Would this cause the rejection of my paper?

In order to answer this question, we need to define some magnitudes of errors.

A small error does not affect the conclusions and if the manuscript was accepted as is could be fixed in the proof stage before the manuscript goes to press.

A minor error does not affect the conclusions but requires too many changes to be made that it could not be fixed in the proof stage.

A substantial error affects the conclusions and would require the manuscript to be re-reviewed.

If you have found a substantial error, you need to contact the editor and request the manuscript be pulled from the review process. You do not want to waste the time of the editor and reviewers. A small error can either be ignored or reported to the editor if you think that the correction will help save the reviewers time. Minor errors are the real problem. There is no easy way to tell the editor/reviewer what is wrong, but an unclear manuscript is likely to get negative reviews. I would suggest contacting the editor and explaining and apologizing for the problem.

The real question should be how did you find the error? What are you doing looking at a manuscript after it has been submitted?


Applying to masters program to further explore my interests, should I mention specific areas of interest in statement of purpose? I am currently revising my statement of purpose for several applied math master program. I wounder if I should mention some specific area of interests or specific name of faculty? The problem with me is that my undergraduate is rather "theoretical" , that I haven't taken many applied math courses and the purpose of my master is to further explore my interests. But the lack of specific interest on SOP seems a little bit odd for me.

Short answer: be honest and concrete.

It's not typically expected that you have very specific, highly focused interests for masters programs in mathematics.  For a masters, you won't get too specialized anyway (at least assuming you're not doing a thesis).  Read the application directions carefully to see if the schools are looking for anything in particular, but what I look for in SOPs is a sense of the applicant's goals, background, motivation, seriousness and maturity.  (And maybe other things in special cases.)

You should try to explain your goals as clearly as you can, but be honest about it.  So you don't need to say something specific like you want to do KAM theory for Hamiltonian PDEs, but if you can give specific examples of things that made you want to study applied math, that would be good.  If you can list specific topics in applied math that you would like to learn about, also good.  It's also not a bad idea to get an feeling for the strengths of the departments you're applying to and say why you're interested in them (e.g., strong in xxx, but you don't need to mention specific faculty, unless you're honestly really interested in workin with them).

See also here and here for other points of view.


Switching between active and passive voice I realize writing in active vs passive voice is a heated debate in academia, with arguments being made for and against both styles. My adviser prefers passive voice.. But is it acceptable to switch from passive to active voice in the same paragraph? What about different sections? For example, the intro and literature review in passive voice, but switching to active voice for materials and methods section. Is this a big no no?

"I realize..."

Active.

"arguments being made..."

Passive.

My point here is that it's normal to switch.  It's probably a good idea to favour one or the other, but I imagine you would have a lot of difficulty using only the active voice or only the passive voice throughout a paper.  Don't worry about it too much.


Is it possible to give too much praise in a reference letter that supports a green card application? I am currently writing a reference letter for a colleague applying for a US green card. Given that I don't know much about the process and expectations of the immigration bureaucrats who will handle the application, I asked around for examples of such letter. Obviously, they are all glowing, and I started writing in the same style.

Now, don’t get me wrong: she is truly a great researcher, I wish her the best of success with her application and hope to help as much as I can (at least, not to let her down). But… at the same time, as I finished writing my letter, I wondered: is it possible that I went over the top with praise? Is it even possible, in such a case? And if so, how can I tell? I mean, I did not  write anything factual wrong, but if read very literal (and outside context), it might sound more like the eulogy of a Nobel prize winner than the recommendation of a mid-carreer researcher (even a very good one).

Letters written for a green card application are very differently structured to letters written for other purposes. As was explained to me when I went through the process, the structure of a green card letter is usually

I am awesome
here are all the ways in which I am awesome
because I am so awesome, you should trust me when I say that this person should get a green card
and oh yeah, they're pretty awesome, which I can tell because I'm awesome.

I'm only slightly exaggerating here. The point is that GC letters are not read by academics - they are read by lawyers who don't evaluate technical skills so much as achievements and strength of recommender. So there's no way to go over the top really.


Gamification in Asian Classrooms I've been thinking about how to improve attendance in my classes as well as how to get my students do the expected work outside of class. I've tried a lot of sticks but the weak students care very little and I end up failing what seems like too many of them.

Lately, my mind has turned to gamification (that is, using elements of the gaming world such as badges, points, and similar things used even here on SE sites) to encourage student engagement.

While reading in English, a lot of what I found is about students in western countries. There has been plenty of research showing that there are significant differences introduced by culture, and to paraphrase Blaise Pascal, what is true in one country is false in another.

Since I teach in Asia, I'm wondering if anyone knows of any studies (or has any experience) using gamification in Asia to improve students' performance.

While not exactly an answer to your question ...

I should start by saying I am not an expert in the field of education or learning sciences, but it appears your gamificiation strategy is based upon extrinsic motivators. In my opinion, Malone and Lepper (1987) make a pretty clear case that intrinsic motivators are the way to go. Therefore, asking a question about how to optimize extrinsic motivators seems like a premature optimization problem. The framework that Malone and Lepper (1987) set out with individual motivators (challenge, curiosity, control and fantasy) and interpersonal motivators (competition, cooperation, and recognition) seems like it should be universal, although how to achieve those motivators, and the relative strengths of them, will likely vary with culture.


Funding is from TA - What to put for funding acknowledgment Most journals require you to state your funding sources. I am a current phd candidate, submitting a paper as sole author, and my funding currently comes from a teaching assistantship, which is paid for by the department, not my advisor. I feel that people usually list any grants/awards in their funding acknowledgment. What am I supposed to put? "Supported by department X in X university?"

A TA doesn't directly fund your research. It funds you, personally and allows you to be a student. Your research hasn't been funded specifically other than the fact that you may have an office, etc. There is probably a tuition waiver, which is a sort of general funding.
You could list the department and university generally as you suggest. You could probably also list "none", but the department might be the better option.


About Ph.D application to US Suppose a student currently doing Ph.D in an institute wants to leave the institute and apply abroad for Ph.D. Should he/she mention the name of the institute he/she wants to leave? If the universities call the current PI, they will never get a positive feedback since the current institute will never want to lose their student. But the student wants to mention that he/she has work experience. What is to be done in this situation? Can the US universities reject the application based on the current PI's feedback in spite of the candidate having excellent grades and recommendations from previous PIs?

Should he/she mention the name of the institute he/she wants to leave?

Yes, absolutely.  The application will typically ask for your complete academic history, which would include the institution where you are currently studying.  Leaving it out would be an extremely serious ethical violation that could jeopardize not only your chances of admission but your entire academic career.

  If the universities call the current PI

They normally wouldn't call your current PI.  But one of the requirements to apply to a US graduate program is to have letters of recommendation from people who have known you academically.  If you are currently in a PhD program, they would usually expect that one of those letters would be from your current supervisor, since that is the person who would be most familiar with your most recent work.  If you don't have a letter from them, an admissions committee might make the assumption that your current work is not very good, and so you didn't request a letter from your supervisor because you knew it would be unfavorable.

You can mitigate this somewhat if you have a letter from someone else at your current institution, especially if their letter explains why you could not ask the PI.  But your application probably still won't be as strong as if you had a positive letter from the PI.  If you have no letters from anyone at your current institution, that's likely to be a red flag.

Many PIs would have no problem writing a positive letter for a student wanting to make a move, and I think any PI who refuses to do because they don't want to lose the student is being selfish and doing harm to their profession.  But you know your PI better than we do.  So you're going to have to make your own judgment as to the relative risks and benefits of asking your PI for a letter, or seeing if there is someone else there whom you trust.

  Can the US universities reject the application based on the current PI's feedback in spite of the candidate having excellent grades and recommendations from previous PIs?

Yes, they can.  The admission committee looks at the entire application, and any piece of it could affect their decision.  At some very competitive departments, any significant piece of negative information on the application might be enough to reject it.  Other departments might be willing to overlook a single negative (or missing) recommendation if other parts of the application are strong.  There is no way to know in advance what any given committee would decide to do.


How to review bogus science without hurting feelings? I've been forwarded a four-page outline of some sort of "theory of everything" whose ambition is to explain just about everything in the universe in terms of particles oscillating in and out of some kind of hidden anti-universe. I've been asked to give my opinion on the theory.

It has all the hallmarks of bogus science written by someone with only the vaguest notions of quantum physics and cosmology (no equations, electrons being defined as the antiparticles of protons, cute drawings). Perhaps more telling is that most of the ideas are unfalsifiable, in the sense that I couldn't think of an experiment that would prove or disprove any of it.

I'd like to give my frank opinion about it without hurting the person's feelings. How should I go about it?

So, I see that you're conflicted by the desire to give your honest opinion and your desire to be nice. While some say you should let go of the desire to be nice, I think in this case it might be more productive to first look at how you can be nice. But first, let me briefly talk about 'cranks':

What are cranks?

The following quote from Nature is prominently placed on the Wikipedia article on cranks:

  A crank is defined as a man who cannot be turned.

Less cryptically, an important property of crank is the unwillingness to change their line of thought or accept being wrong (they likely admit to make 'unimportant' mistakes and will immediately explain what they 'actually' meant). This will become a very useful definition. Suppose for the moment that exactly one of the following is true about the motivation of your correspondent:

"I have a brilliant idea about the universe and by showing this to an expert, I'll get the recognition I deserve."
"I don't know much about Physics, but I think this is a good theory and want to know what the experts think."

Note that person 1 is a crank, for when you tell (1) that this idea is 'bogus', the reaction will be likely hostile, as (1) will refuse to be 'turned'. Any conversation with (1) is a waste time. If your know for certain that you're dealing with person 1, ignoring, aborting and running away in the most polite way possible is recommended. However, as you desire to be kind to your correpondent, I doubt you are certain that you're dealing with person 1. (Also, assuming 1-ness might be dangerous. Applying Hanlon's razor seems like a good idea.)

How to be nice to person 2

Now, is person 2 a crank? (2) could be a crank, but not necessarily. Perhaps (2) is simply a layman who always had an interest in physics, but never had (or took) the chance to pursue this interest with proper study and thinks this is how physics can be done.

For person 2, I think the best way to be nice is to not give your opinion on the  work, other than that it simply is hard for you to judge (2)'s actual ideas as they are very non-standardly presented. (This can be a lie. But I think it is a very useful lie.) It is important that you add the advice that if (2) has an interest in physics, (2) should learn more about physics so that (2) can properly present the theory. It is good to add some explicit method for (2) to do this, such as some introductory books, courses or videos.

In the best case, (2) will start learning things and eventually will realize that his theory is 'bogus' by themselves! In the worst case, (2) will show the inability to 'turned'. But thereby, (2) reveals to be (1) all along and you can therefore safely abort communications with your correspondent.

Conclusion

I think it is good you ask this question, because I believe there is a true dilemma here. You must choose at most one of:

Share your (brutally) honest opinion with your correspondent.
Help your correspondent by gently directing them to the path of learning.

Any combination of the two will likely act as a discouragement for your correspondent from attempting to learn, for your correspondents idea that they might be able to do some physics is likely crushed by the weight of an experts opinion.


A peculiar PhD situation, working full time in a government lab but getting my PhD from an unknown university because of formalities. Advice? I am involved in a peculiar PhD situation. I am working full time at a government lab that is fairly new (<10 years of existence), but has however attracted some strong names in my field (Computer Science and Data Management) as appointed researchers. Government labs do not issue PhDs, so I had to enroll at a university. The university that I enrolled at (not my choice) is among the top 10 in my country, but lies in the top ~1000 area worldwide. Furthermore, my advisor is not really involved in my work and is generally active in somewhat different research directions. However, I had very good funding so I decided to treat this as exactly what it is, i.e., a formality, as I can't get my PhD from the government lab.

During the past four years, I have been very productive and managed to create a solid publication record at A-level and A*-level conferences and journals, as well as a decent citation count (~150). I am first author in most of my papers, and some of the people I worked and published with are very established and acclaimed academics in this field.

Before starting my PhD, a obtained an Electrical Engineering degree and a Masters degree from top schools in worldwide rankings. Now my question is, do I need to somehow reflect this situation in the form of a justification of why I am getting my PhD from an unknown university? Or the fact that after two excellent school names, I have this third name in my CV that is unknown and overall a weird addition?

I think your stellar record speaks for itself (from my experience: 150 citations is something that is rarely encounered on a a PhD-level research).

And where would you like to put that justification? As an asterisk in your CV? THAT would be really weird.


Dealing with uncertainty when reviewing a paper I agreed to review a paper that falls within my area of expertise. However, I am not particularly familiar with one of the techniques used by the authors.  On detailed reading, their use of this technique feels wrong to me, but I am by no means certain. It is not a method that I have seen applied before in similar contexts. I can't put my finger on a definite flaw, but it just doesn't quite seem to "add up".

Given my uncertainty, how should I comment on this in my review? I have the option of simply stating “I cannot comment on the validity of [one particular aspect of the methodology] as it is outside my area of expertise.” Alternatively, I could raise my concerns, while making my uncertainty clear, but would this undermine confidence in my review overall? Is it unfair on the authors to raise an objection on the basis of my incomplete understanding?

Yes, it is fair to raise concerns when you don't understand a paper. It is the authors' job to explain in enough detail what they did. Especially if the method used is uncommon, then it needs to be justified. That justification needs to be done in a way that it is understood by the intended audience, not just the specialist within that audience.

Tell the authors in as much detail as possible why you think their method does not feel right. Maybe the method is problematic, and they will appreciate that feedback. Maybe they did not explain their method well enough, and they can use that feedback to pinpoint what was not clear.


Can a thesis contain preface? Usually preface is written in books and myself personally have not seen it in a thesis.

But, can a master's or doctoral thesis contain a preface?

Thanks

Note: This was going to be a comment, but then I realized it actually answers the question that was asked.

The following 2004 Ph.D. dissertation at Utrecht University has a preface on pp.
 xi-xviii, so the answer is YES.

Ideas and Explorations : Brouwer's Road to Intuitionism

However, the question you possibly want answered is whether a Ph.D. dissertation at YOUR university can have a preface. To find the answer, you can ask someone knowledgeable about the specific dissertation format rules at your university, or you could visit the library shelves where recent Ph.D. dissertations are shelved and spend 20-30 minutes quickly flipping through the first few pages of the 100-200 most recent dissertations, keeping in mind that for some universities the answer might be department-specific.


Career Paths for Mathematics and Physics I'm just looking at the Mathematics & Physics program at University of Toronto (I think it's like Mathematical Physics, correct me if I'm wrong), I'm wondering what career paths I can choose if I take this program.
Would this allow my to work in either field or just in the physics field? And would this allow me to go to grad school for either one I want, or is it restricted to one of the two fields?

If it makes any difference, here's a link to the university's program calendar:
http://www.artsandscience.utoronto.ca/ofr/calendar/crs_mat.htm

Thanks.

For grad school applications, after making it through GRE cuts, the biggest decider will be the research that you've done. You'll want to develop programming skills in multiple languages, even if they don't cover them in class. For math and physics, MATLAB, Mathematica, and R are the most commonly used languages. If you don't find any research opportunities at Toronto, look for REU programs in the summer elsewhere. A math/physics degree can get you into grad school for math, physics, all manner of engineering (I went from astrophysics to aerospace engineering), chemistry. There are probably others as well.

Outside of grad school, the options are pretty varied. Again, if you can program that will open many more doors. My friends from undergrad in physics went on into banking/economics, General Electric, CERN, Seagate, Boeing, Lockheed Martin, the air force, and NASA. The majority, however, went to grad school. That keeps all those former options open, but also opens up the academic track (becoming a professor or a research scientist at all kinds of places like NIST or NOAA, but there are hundreds).


How to read an article? I have searched the literature and I'm now have all the papers I need.

I'm reading the papers at the moment in order to write a lit review. I would like to know some strategies to read them, should I read them from first page to last page? or should I read specific sections only?

The objective of reading/review academic papers is to critically analyze research studies.

Critical reading is basically a process where you ask yourself questions as you're reading, such as:

What was the objective of the research study?
Did the researchers accomplish this?
Why or why not?
Why is the study important?
What are the implications of the findings?
How does this paper contribute knowledge to society?
Do I want to borrow an idea from this paper?
Do I believe something can be improved?

Answering those questions will help you figure out what you've read and why it was relevant to you and the research study you'll end up designing. It can also help you as you target each section, it's not always clear cut the order in which you'll read the paper critically.

Now that you know what to look for, how you organize those notes is up to your individual preference. There are many options available: hand written notes, digital notes, laptop, ipad, etc. I personally like to use a matrix format with different fields, such as objective, method, findings, theoretical model, etc.


When do most students publish in a European PhD? in US PhDs, it's typical to start publishing (first author or not) in their latter-half years. How does that work in the EU? Since EU PhDs are shorter than US programs, is it common for EU phd students to publish in their final year or so? Or do some people not even make that and wait till their post-doc or something?

Probably, you have an incorrect picture of European PhDs.

There are significant differences in the paths that lead to a PhD in the US and in Europe. Several of these differences have been already covered by other questions, but let me highlight those I think are the most important for what concerns your question.

First, however, the usual disclaimer: Europe is not a single entity, and there are large differences among European countries. What I'm going to say below applies to many countries around here, but not necessarily to all.

Most European PhD programmes require an MSc degree for the application. Therefore, the common European PhD student has already done the coursework (or  most of it) that a PhD student in the US has to do during their first years.
Students in the US usually fund themselves through teaching assistantship, which keep them away from research for many hours a week. Most European students, instead, are fully funded by their institution and can work on research full time. Some institutions allow them to work as teaching assistants too, but with a lower workload.
If I got it correctly, US students are allowed during their first years to "wander" a bit to decide what topic they like most. European students are usually not allowed to do so: they start working on a specific topic from week one of their PhD.
European PhDs are shorter than US ones, but not that shorter: though in many European countries the canonical duration of a PhD is 3 years, the real duration is frequently longer, 3.5-4 years.

Given the above differences, you should not be surprised to discover that many European PhD students start publishing from their first or second year.

For your last point:

  Or do some people not even make that and wait till post-doc or
  something?

In some cases this would not be possible because some PhD programmes require students to publish at least one journal paper before the end of their PhD.


What is special about the MDPI special issues? This question is related to this question, but specifically regards the special issues by MDPI. They seem to have a quite high number of special issues for every journal per year and as far as I understand, they are only different from the regular publications by having a dedicated topic and an associated editor.

One thing that confuses me is that papers are already published before the deadlines (this special issue with the deadline in October already has 4 papers published).

Is there anything else that is special about these special issues?

There really isn't a fundamental difference between their special issues and other publishers' special issues—it's just a "themed" issue.

As for publishing papers before the deadline, that's a relative feature of digital publishing—there's no need to wait for a deadline if a paper is ready to go earlier. The collection can be "built" as papers are ready, rather than presenting everything as a single fait accompli.


Why some universities don't require GRE AWA section? I've been rereading the admission requirements of the universities I've chosen and stumbled upon the fact that only Verbal Section and Quantitative section have certain threshold that has to be reached, however, nothing is said about the Analytical Writing Assessment, also known as AWA.

Is the AWA score is merged with the Verbal score or is it irrelevant to some universities (since nothing is said about that particular section)?

It's only a guess but as an admission committee member I have weighted AWA lower than the other two as well for the following reasons:

The range of the score is pretty narrow (0 to 6 with 0.5 increment) and according to the guideline, it appears a good tool to find out who can't write, but not who can write well. Anything about 4 is kind of hard to tell.
Verbal and Quantitative have algorithm that is carried out by machine. AWA is graded by hand, thus can make admission committee feeling doubtful about the objectiveness or specificity to their program ("GRE's thoughtfulness is not our kind of thoughtfulness!!"). And I'm not to say algorithm is perfect, but it may still beat grading by hand (for instance, you can get locked into a low-score path just because you got the first question wrong, making the first few questions more determining than the rest.)
Most of the writing skill and thought process can be gleaned from the personal statement. (Of course, conspiracists can also argue that the statement may be written by someone else. But they should also know that all GRE writing topics are publicly available (1, 2). Two of them will be randomly selected and presented in the test. In a way, the students could have also gotten external help on this part prior to the test as well.)


Is there a test equivalent to a bachelor's degree? Like the GED, which is equivalent to a high school degree, is there a test that you could obtain that is equal the a bachelor's degree? Which states in American can you take it? And what are the requirements? Is there a website? Please leave the link. Or is there some kind of online test that is equal to a bachelor's degree? If not, what would be the quickest way to get a bachelor's degree without going to college/University?
I want a bachelor's degree in Science, space science. I want to get a bachelor's degree quickly cause I feel as if I've wasted years of my life and want to get back on track. I want the bachelor's degree so I can go for a Master's degree.

No, there is not.

A bachelor's degree isn't a generic thing like a high school diploma.  For example, it makes a big difference what institution it's from and what your major was.  Unlike high school, in the US there aren't government-specified standards for what should be taught or tested for a college degree; each institution makes its own rules (usually under the oversight of accrediting organizations).  So there's no way that a standard test could substitute for a bachelor's degree in general.

There are some reputable colleges and universities that offer online degrees, but it involves a lot more than a single test.  You'd do roughly the same coursework as if you were physically attending the university, and you should expect it to take multiple years.

There are some disreputable "colleges" which will offer a degree based on a single exam, or your life experiences.  These are scams and their degrees are worthless.


Double blind review: anonymise data source? Apologies if this has already been answered: but I could only find questions relating to paper citations and grants in relation to double-blind reviews on academia.

If you are submitting a paper to a double blind review, are you permitted to talk about the source of your data-set at length if it is not publicly available? This may include, for instance, mentioning the company name and/or country of origin.

For instance, imagine being given a data-set by IBM in its European wing and you make your paper based on this data. Is it legitimate to name the origin if you are not directly identifiable?

A dataset may not be publicly available, but there is no way for anybody but the owner to know who the owner may have chosen to privately share that dataset with.

As for the owner of the data: I would expect anybody who was closely involved enough to know who the data was shared with to have a conflict of interest and to therefore not be used as a reviewer.  Certainly, as an editor, if I saw a paper used a proprietary data-set from IBM, I would not invite a person from IBM to be a reviewer.

As such, I would judge there to be no need to blind the origin of a dataset.


As a student, how much time should I spend helping other students with research? Assume that one has a skill (assume, programming) and is one of the very few in the department to have it. The other students need a bit of this skill for their projects and you help out when you can.

Where do you set the limit for how much effort/time you spend on helping others this way?

Pros:

You get insight into other students' work.
It's a welcome break from our own research
Maybe earns you a second/third author for setting up the experiment
Networking !

Cons:

Effort/Time spent
You don't necessarily improve your skills (For instance, coding in Python for someone else doesn't augment my Python skills by much. What I do might be really routine)
You tend to have a soft commitment towards that project. For instance, if I start working on it as a favour, it doesn't really come off well if I leave 'em midway.

EDIT: I do enjoy the work so long as it is at least a little challenging. I often get really n00bish questions and that is when I start reconsidering my stance on helping people.

You forget one consideration: do you enjoy using that skill? To take your own example, I enjoy programming, and even though I might not learn or get anything technical from it, I enjoy solving someone's else problem with some lines of code :) Of course, one should be careful of the time spent and the reward you can get from it, but doing something you enjoy is very different than doing something you can, but don't particularly enjoy doing.

For instance, I can probably install a server and manage a website (with a CMS) for someone, but I don't enjoy it, so I would be very explicit about the benefit (I do that for you if you do that for me). But I could do some cool coding on my free time.

On a completely different aspect, it also depends if you intend to stay in academia: it's a very small world, and the person you're doing a favor to today might be the one sitting on your tenure committee in 20 years (if you work in the same department and all stay in academia, it's quite likely that your paths will cross again at some point in the future).


What tense should we use when referring to a paper or experiments from other researchers? While writing the literature review section, I am confused about which tense should I use (past, present perfect, or present) while referring to other people's work.

I understand that established facts are presented in the present tense.
Work done is presented in past or present-perfect tense.
But in what tense should I define their (i) system model, (ii) experiments, and (iii) results so that the overall picture remains coherent and it does not seem like I am jumping from one tense to another?

What is the basis for using any of these tenses?

I present established facts in present tense, indeed. Other people's work that has led to these facts is presented in past or present-perfect. So for example: "Snippert et al. established a confetti mouse-line, and after doxycyclin administration showed that intestinal crypts tend towards clonality."


An important information is missing from my paper under review I have a paper under review (Second round) after a minor revision. The journal has limited page length and I contacted the editor to ask whether I can add additional pages but he said that it is only possible after acceptance. One information which I thought less important seems very crucial, where other researchers asked me about it after a presentation of my research. In addition, the lack of this information in the implementation will completely deviate the experimental results.

I am wondering how I can add it after the acceptance of the paper. Should I inform the editor for another review round?

Since it is a crucial piece of information that alters the content (and possibly the result) of the paper, the most fair would be to contact the editor and explain the situation so that the reviewers (which seem that did not catch the missing piece) make a better and more informative decision.

The new version should be refereed. I think just adding supplementary material on an accepted (but possibly flawed or at least weaker) version is not suggested.

So: Contact the editor. S/he probably let you submit a new version which will go to the usual review channels, probably with the same reviewers. As for the page length, probably you will have to squeeze in everything, which means a lot of re-writing.


Why is the Grievance Studies affair considered to be research requiring IRB approval? I'm reading about the Grievance Studies affair and there's one thing I don't understand. Portland State University (PSU) initiated a a research misconduct inquiry against Boghossian for conducting a research on human subjects without IRB approval. I assume that PSU considered the hoax as a research project, the human subjects being reviewers which received the papers.

It's not clear to me why such an approval would be needed in this case. What exactly makes such a project subject to IRB approval:

actions classified as "research", as in "contribution to generalizable knowledge"?
project funded by the university or the government? (AFAIK not the case)
being paid by the university while the project is under way?
publications or plans to publish? (again, AFAIK no official research papers were published)
affiliation with the university?
something else?

As an extreme example, if a university professor tells their colleagues a joke and counts how many people laugh, and later writes a post about it in social media, do they risk similar sanctions if the university doesn't like their post?

This article in NYMag answers pretty clearly most of your questions. I won't quote it all, you can read it on your own. Here are relevant excerpts.

For the purposes of Peter Boghossian’s case, three facts about IRBs matter a great deal: “study” is defined rather broadly in the federal guidelines; possible risks to humans — even ones that non-IRB nerds may view as negligible — are taken very seriously; and IRBs tend to look especially closely at studies involving deception. [...]
First, the definition of “study”: As PSU explained to Boghossian in a document it sent him December 17, the university determined that his work met the definition of “study” as defined by the Department of Health and Human Services in language that reads — this isn’t included in the letter itself — “a systematic investigation, including research development, testing and evaluation, designed to develop or contribute to generalizable knowledge.” [...]
Crucially, it does not matter that the hoaxsters didn’t attempt to publish their final results in a peer-reviewed journal. “Publishing in a magazine that’s not peer reviewed doesn’t matter if they’re reporting on their research,” said Celia Fisher, director of the Fordham University Center for Ethics Education. All that matters is that Boghossian is an employee at PSU, and that he conducted what the university deemed to be human-subjects research based on a plain reading of how that term is normally defined for this purpose.
[...] First of all, “if they believed that this was not human-subjects research, the process would have been to submit to the IRB an application that says I believe this research that I’m doing is exempt,” said Fisher. “And the IRB makes the determination if it’s not human-subject.” It’s not their call, in other words — it’s still the IRB’s. [...]
In the case of the grievance-studies hoax, the potential for harm came in the form of reputational damage and humiliation to journal editors and reviewers. And one decision the hoaxsters made — allowing accepted papers to actually be published rather than notifying the journals so they could be yanked before they were out in the world — neatly captures the sorts of ethical discussions often spurred by IRBs. [...]
Finally, as a so-called audit study [...] Boghossian, Lindsay, and Pluckrose’s scheme was more likely than a non-deception study to raise IRB eyebrows. “All audit studies require deception, and many social scientists who would like to see only a limited role for IRBs still consider IRB review appropriate when deception is required,” said Schrag. Deception is simply seen as an ethically fraught tactic, so even IRB critics aren’t necessarily in favor of them backing off entirely in situations where deception is involved. [...]
Pluckrose at one point mentions the impossibility of getting informed consent from journal reviewers — the implication being that to do so would be to blow the cover of the experiment. Again, though, that’s the point of an IRB: to gain permission to deceive, or to come up with some sort of work-around. The choice isn’t necessarily between obtaining informed consent in a manner that would blow the experiment and not running the experiment at all — plenty of IRBs have approved plenty of audit studies. [...]

The article was not particularly difficult to find (it was linked in one of the Wikipedia articles), and the way you phrased your questions casts some doubt about your good faith (it sounds like you have already attained a conclusion and only wanted validation, especially your last hypothetical question), but still, I think this deserved a good-faith answer. Now as for your hypothetical:

As an extreme example, if a university professor tells their colleagues a joke and counts how many people laugh, and later writes a post about it in social media, do they risk similar sanctions if the university doesn't like their post?

This is a systematic (albeit small scale) investigation designed to contribute to generalizable knowledge and the professor reported on it. It involves human subjects. If the professor doesn't inform the participants that their reactions are recorded and will be posted online, it also involves deception. I will let you reach your own conclusions as to whether it would require IRB approval. It sounds like you understood extremely well what especially was problematic with Boghossian's study, as you were able to construct a completely different hypothetical scenario that still presents the same three red flags.
You may find all this overblown or too cautious. But it isn't up to you (or a researcher carrying out an experiment with ethical ramifications) to decide. A researcher has a conflict of interest: it is in their interest that the study is carried out and completed. It is the role of the IRB to offer an external evaluation of this, to remove the conflict of interest. If the experiment is truly worth the risks, it will be approved.


Can a reviewer suggest references? I had submitted a paper to a reputed Computer Science Journal. The reviewer has a lot of constructive changes, in addition to that he also suggested citing a few more papers, all by the same author. Since this is a double blind process, we don't know each other's identity. So, is it common for reviewers to suggest references in this field or any other field ?

I'd say it is a common practice, and I have both been given reference suggestions in blind reviews and given reference suggestions in my own reviews. If you are concerned about a reviewer trying to promote his/her own papers by the suggestions, I'll just say that if the recommendations are apt (i.e., if you read the suggested papers and they do appear to be legitimate references), then it makes sense to cite the papers regardless of whether there is a seemingly disingenuous motive by the reviewer. Even if you don't specifically use the prior work, it makes sense to mention them in your "Related Work" section. If you don't cite the suggested papers, provide a legitimate reason in your rebuttal.

Indeed, if a reviewer is chosen well, he or she should be an expert in the topic of the paper, and most likely does have apt references under his or her name.


How do I prepare for the UK Research Excellence Framework submission? I want to strengthen my return for the UK Research Excellence Framework (REF). My publications are fine, but how can I improve my REF "impact"?

Necessary disclaimer: I have not had to be involved in REF. This is what I summarized from my experience of the recent French evaluation system. Reading the REF guidelines, it seems pretty similar in focus (although to be honest, for all their wordiness, I prefer the very detailed REF guidelines over the French way of not explicitly detailing every rule).

So, with that out of the way, I would say there are two ways to “improve” what is essentially one’s societal impact. Both are important.

On paper

This is the short-term way of improving your impact: just present it better. Peruse the guidance documents (and possibly other guidance, including documents your local university might issue in order to help its staff), write down the relevant keywords, list all items that can be counted towards “impact”. Then, brainstorm (possibly with colleagues or friends!) for ways to tie your already existing contributions to these items. Sometimes it is just a matter of remembering stuff you didn't think of (in my case, I remembered that we had some colleagues from an industrial company who showed up at a series of tutorials).

For real

Of course, you can also try to influence your plans to include more activities of clear societal impact. There are unlimited number of things you could come up with, and they depend widely on context (which you did not give). Keeping it short and generic, here are a few good examples that I can think of (some of them more applicable in some fields, obviously):

organize panel discussions on your favorite topic, open to the general public
open lab day
“cultural heritage” research
create visualizations of your research (pictures, movies, whatever), and publish it
interviews or other interventions in the media (even local)
being listed on experts registries: courts, journalism schools
all kinds of work with local artists
workshop or discussion groups involving academic and industrial communities
being a member of a standardization body

It looks like some sort of random list, cause I tried to list diverse activities. I'm sure others will have plenty of ideas to add!


Should I write IEEE membership in my CV? Does it worth to add IEEE membership to my CV? It seems every body can pay a fee and become an IEEE member.

Many CVs have a section for professional society memberships.  Mere membership doesn't necessarily convey a significant distinction, but it does say which groups you have chosen to invest in affiliating with and which judge you to qualify.

For the IEEE in particular, it actually does have fairly strict membership qualifications.  Most people cannot qualify for IEEE membership, but pretty much any practitioner of the field can, because that is what it is designed to select for.  Thus, putting an IEEE membership in your professional society memberships section of your CV is entirely appropriate.


Want to get MS in Computer Science but in a predicament due to low GPA and lack of references I have a BS in computer engineering from a state school with a GPA of 2.56 (out of 4.0). I had a pretty serious and unmanaged illness from the second half of freshman year of undergrad to one year after undergrad graduation. I went from doing physical training for ROTC with no problem to throwing up from doing 7 jumping jacks. It practically happened overnight. When you look at my transcript, I have had probation over two semesters due to extremely low GPAs and a leave of absence due to illness. Yes, I could have taken a longer leave of absence while figuring out my health problem but I was told that I would lose my financial aid and would not get them back. I was advised to just plow it through since it would be the best course of action for me.

A lot of courses I took had attendance integrated into the final grade. I would often get A's on exams but end up with C or B as the final grade. I tried explaining to professors that I was not physically able to get to the class to attend the lectures. Even with doctor's note (although it said "reason unknown/severe pain" at the time). Some professors even scoffed at me and told me to "take Tylenol and man up."

I had the option of retaking some courses before graduation to improve my grade but that is when the state started cutting the budget so a lot of courses were canceled. I was stuck with F's in some instances without being able to remedy them.

After graduation and finally being able to manage my health problem, I was able to refocus on education. Since I knew getting into a grad school with my academic record would be near impossible, I even considered going back to school for a second bachelor's degree in computer science. That proved to be a challenge since not many schools would accept me since my degree is too closely related to the major I am applying for. A lot of classes I should take to prove my competency for grad schools are not available to non-degree seeking students. If they are, those are only offered during work hours.

Now I have 2 years of experience as a software test engineer (more like DevOps) and 1.5 years of experience as a software engineer. During my professional career, I learned a lot. And fast. I taught myself a lot of computer science topics since those courses weren't available for my major in undergrad (thank you 2008 financial crisis). I did not get along with managers at work due to differing opinions on how much/fast I should learn... Managers didn't like that I became de facto tech lead for some projects under a product as one of the most junior members in the company.

Now that my background story is over... How do I approach grad school applications with my GPA? It seems near impossible to make up for the GPA while working. And how do I approach the letters of recommendation problem? I'm only able to secure one from a professor in undergrad days. My former colleagues at all levels are more than eager to write me letters. None of my direct managers nor other professors are willing to write me a letter. Managers from a different organization within the company are willing to write me one. Do those carry any weight? The ones not from direct managers/supervisors?

I think your experience in industry will appeal to master's degree admission committees. Your application/cv should describe your technical skills. Get letters from your coworkers that speak to your competence with them and your ability to learn.
.
Your cover letter can talk briefly about your health problems as an undergraduate.

I don't know whether the absence of letters from your direct managers will matter. If I were interviewing you for a job it would matter to me, but for a master's degree I might well want to take a chance.


application to be a reviewer Can anybody post a template letter on how to ask a science journal to serve as a reviewer. Here's what I have..
I would like to serve as a peer reviewer for manuscripts submitted to your esteemed journal, XXX. My areas of expertise are XYZ. I have published n articles in this field and have reviewed manuscripts pertaining to these subjects before.
My CV is enclosed for your perusal

The best way I've discovered to become a reviewer for a journal is to submit a paper there. In my experience this is almost always followed a few days later by a request to review a relevant article.

Edited to add: I did my first reviews while a graduate student because my PhD supervisor was the editor of a journal. He would send me things occasionally because he considered it part of my training. So, another way to become a reviewer is to know an editor.


Paper was rejected for high similarity with parts of my own dissertation My PhD thesis consisted of two published papers and one submitted paper embedded in some additional framing. For completion of my PhD, I had to upload my thesis to the servers of our academic library, where it is now publicly available.
However, afterwards, the third paper from the thesis was rejected after peer review. I performed substantial changes and submitted the manuscript to another journal. They returned it back to me, stating that I exceeded by far the allowed index of similarity (40 % similarity with 35 % similarity of a single source). I spent $100 for a plagiarism check only to find out that the source from which I was accused to have copied a majority of my work, was my own publicly available thesis.
As my thesis contains my third (unpublished) manuscript, it naturally has a high similarity with the version I was about to submit.
How can I solve this?

Most publishers I know explicitly permit (pre)publication of papers as part of a thesis. For example the copyright policy of Elsevier (the publisher you used as a tag) states:

Authors can use their articles, in full or in part, for […] [i]nclusion in a thesis or dissertation (provided that this is not to be published commercially)

Going by this, everything is fine with your submission.
More generally, you did not attempt to sell a work previously published in another journal (or parts thereof) as a new publication, which would be the typical case of self-plagiarism.
For all of this, it does not matter whether you modified the respective chapter or included parts of the frame, as long as you stayed away from the already published chapters.
However, the rejection of your paper may not have taken this into account, either because it was automatic or somebody did not connect the dots.
I thus advise to consider the rejection to be an unintentional error or their side.
I would therefore simply write to the journal explaining that you suspect that your paper was mistakenly identified as plagiarism due to similarity with your thesis, which is fine as per the above rules.
In general, it is a good idea to mention upon submission that parts of your paper have been previously published, be it as a preprint or thesis to avoid exactly this as well as potential clashes with journal policy.
Finally, to address some of your concerns:

I feel like [writing to the editor] may be conceived as begging for permission to be allowed into a reviewing process

I would not worry about this.
First, what you are challenging is not a judgement call (e.g., a desk rejection due to lack of relevance).
The journal stated a very objective argument for rejection (plagiarism) and you have very objective arguments that this argument is erroneous.
It’s a simple mistake; it can happen; you are asking for it to be fixed.
Furthermore, even if this should be considered begging, you have little to lose: Right now the journal considers you a plagiarist (which you might want to set straight even if you decide to submit to another journal).

The copyrights of Elsevier allow me to use articles published under their flag in my thesis. My case, however, is the other way round: I want to publish something that has been part of my thesis in very similar form. The thesis is published, but it contains a part that is not peer-reviewed and has not been published as an article.

Copyright transfer to journal exists because the journal’s business model is selling your paper and they want to have some exclusivity on this.
For this, the order of events doesn’t matter.
My point with linking these policies is to demonstrate that Elsevier is generally fine with papers that are available as a thesis.


Independent Research and institutional review boards? If I am conducting independent research (ie no university affiliation), do I need to worry about institutional review board (IRB) approval, if I am working in a field where it is normally required?

This issue actually got some press recently with the case of uBiome, a citizen science startup that raised over $350,000 in crowdfunding.

This startup received a lot of negative attention for not getting IRB approval before raising the money. You can read some of this criticism here, here, and here.

A statement from the founders of uBiome says they were advised that they don't legally require IRB approval if they aren't receiving federal funding, don't plan to publish, and don't plan to apply for FDA (U.S. Food and Drug Administration) approval:

  Before we started our crowdfunding campaign, we consulted with our advisors at QB3, the startup incubator at UCSF, and the lawyers they provided us. We were informed (correctly) that IRBs are only required for federally funded projects, clinical trials, and those who seek publication in peer-reviewed journals. That’s right — projects that don’t want federal money, FDA approval, or to publish in traditional journals require no ethical review at all as far as we know. (No, that doesn’t sound like a great system to us either.)

In the end, they went through a private IRB firm (Wikipedia says it was this one) and got their protocols approved. The founders say:

  This is the same institution that works with academic IRBs that need to coordinate multi-site studies, as well as private firms such as 23andme and pharmaceutical companies doing clinical trials.

This incident raises the question of what you plan to do with your independent research (assuming the kind of research you are doing is generally subject to IRB oversight):

If you plan to publish your research in a traditional peer-reviewed journal, you will usually need an IRB review
If you plan to develop pharmaceuticals that will require FDA approval, you will need IRB review
If you plan to get federal funding for your work, you will need IRB review. If you plan to get other funding for your work, it'll be hard to get without IRB review.
If you plan to create a startup around your research, you may not require IRB review, but not having it can engender quite a bit of criticism (as per uBiome's story)


Do details of my undergraduate title matter? I'm a third-year undergraduate student yet to experience the graduate world.
Currently, with the course choices I made, I can choose between two degree titles, namely “BSc Mathematics” or “BSc Applied Mathematics”.

I will be taking the same courses regardless, but I'm wondering if it matters to have a different degree title.
E.g., might one of the titles benefit me or does it not matter at all (in terms of job prospects, continuing to my master’s, …)?

Moderator’s notice: Do not take this as a shopping question as to which of these specific titles is better (you can use them as examples though). Instead, focus on the relevance of such differences in the title in general.

In the long term it won't matter at all. There might be a small effect in moving to your next position depending on whether you go to grad school or to industry, but after a few years no one will notice anymore. You will be responsible for your own reputation and people will look to that, not to the specific degree you earned - especially its title.

I also studied math, but in the US. Here we have a very broad undergraduate education, studying many things beyond the major subject. At graduation I had qualified for either a BS or a BA and was given the choice. I chose BA as it seemed to me to be more "interesting". I had taken extra courses both in math and in other subjects. But it never mattered. Literally no one cared. For entry to grad school the transcript shows what I had done.

But, you might use the opportunity to think about what you want to do for the next ten or so years. Grad school and academia, or industry.


Thanking a professor for their effort Some time ago I had emailed a professor regarding the original data of an experiment they'd conducted almost two decades ago. He replied today to apologize as he had unfortunately not found the data after looking for it for a while.

How can I thank the professor for his efforts without coming off as condescending? Something like "Thank you very much for going to the trouble of finding the data" sounds to me like I still expect something and simply saying "Thank you for your effort" comes off as condescending to me, but this may be because I am not a native English speaker.

It would be fine to simply write

"Dear Professor X,

Thank you for taking the time to look.

Best wishes,

JansthcirlU"


What does it mean to be "former PhD student"? I saw the term "former Ph.D. student" in some article -- does it suggests someone accepted in a PhD program but did not get his/her PhD degree eventually?

That would be a valid interpretation provided the statement is about oneself. More likely they attended for some period of time and left before finishing. There are many reasons for leaving, some personal and some academic. You can't draw conclusions about why they left from a simple statement. But, most likely, they have no intent or no possibility at this time of returning.

However, as user JeffE notes, if it is made about another it is more likely to mean that the other person was once the writers student. In this case it is most likely that the person did finish the degree successfully, though it is possible not.

A third possibility is that a person starts their study at University A, but completes it at B. Even in discussing themselves in a conversation about A, they might use such phrasing.


What are the ways a professor in top R1 public universities can increase their salaries (through research)? I understand that professors can pay themselves +2/9 of the 9-month salary to cover summer.
Are there other ways to use research grants (private or public) to increase salaries (working in research)? Here I am asking for top R1 public universities in the US.

Although the NSF won't generally allow you to receive more than 2/9 of your 9 month salary from NSF grants, other federal agencies (ED, DOE, ARO, NRL, USDA, etc.) don't have such a rule, so it is possible to get +3/9 summer salary from such grants.
It's also possible to use a "buy out" to pay part of the 9-month salary out of grants in exchange for a reduction in teaching load.
Beyond that, the regulations forbid taking more than 12 months salary from federal grants.  Of course, the institution can give a very successful researcher a pay raise so that they can take more salary from their grants.
Here are some other ways to earn additional income:
Consulting.  There are usually restrictions on how much consulting you're allowed to do during the academic year but no such restrictions over the summer.  You can charge what the market will pay (e.g. I charge for consulting at an hourly rate that is more than twice the hourly rate that my institution pays me.)  However, you'll also be responsible for all of the legal and tax complications that arise (you may need professional liability insurance, you'll have to pay self-employment tax, etc.)
Royalties.  If you write a best selling textbook for a lower level service course, the royalties paid to you can be a substantial addition to your faculty salary.  However, there's a lot of work in writing a textbook and in most cases, the royalties won't amount to much.
Patents.  At most institutions in the US, faculty work under intellectual property agreements that lay out how the profits from a patented invention will be shared.  Depending on how generous your institution is, you might be able to earn income from patents.
Start your own business. In some fields, it's possible for faculty to spin their research off into a start-up company.  There are usually intellectual property agreements with the university that require ownership and/or profits to be shared with the institution.


PhD at the same university as master's I received my bachelor's and master's degrees from university A. I was then supposed to do a PhD at university B in a different country but relocating did not work out (I did not start in the program). Some time later, I took a temporary research assistant position at university C. I was hoping to do a PhD also there but having considered the topic/group I think it is not a good fit for me.

I have discussed about returning to A but not signed a contract yet. Would it be disadvantageous to get all degrees from the same university?

I had very high expectation for the PhD since I was a very good student at A. However, I have now had two attempts going elsewhere and neither succeed. I am not sure how much support I would get for further applications.

Should I stay at A and try again after the PhD? The thing is, A is not very well-known university.

The most important part about where you do your PhD. is not so much about the standing of the university, but about the reputation of your PhD. adviser. Your name will be (forever) linked to his name and his reputation. If he is a well known researcher in your field, then you will carry this positive reputation with you. If he is not well known and he has issues getting funds, then in this case this might make your PhD. harder. If I were you, I would not worry about the reputation of University A., but about the reputation of your research group.

On another note, sometimes it can be problematic if you have done your Bachelor, Master and PhD. at the same institution. In this case, you will have experienced research in a single environment and this can be detrimental to your candidacy when applying for faculty position or etc. However, if you do a post-doc in another research group later on, you can mitigate this aspect. Like I said, if you feel the research group of University A has all you need and you like the work environment there (which is crucial to succeeding in your PhD.) then go ahead :)!.


Will a paper published in an unrelated/other sub-discipline matter for graduate admission? My question is similar in spirit, though different in context (I think) to the question posted here.

My professor and I recently submitted a paper on arXiv (submitting for publication soon) that falls in the domain of quantum physics. Here's the link. I really liked enjoying working on the project, and I found it to be a valuable learning experience.

I, however, don't wish to apply to graduate school in physics and specialize in quantum mechanics -- and the study of open quantum systems etc. Ideally, I'd like to join a mathematical physics research group, working of such topics as quantum gravity etc. with a mathematical focus or working on the mathematical aspects of various sub disciplines (quantum mechanics, topological insulators etc.).

I'm aware that being able to demonstrated the ability to do research prior to the graduate level is highly valued at US universities. My question is how will the graduate admissions committee(s) view this (potential) paper? It's already hard to get a spot in various mathematical physics research programs. Will they consider this publication as having no value to them, since the paper doesn't directly coincide with their sub-discipline? Or (if I spin it right), is it possible/expected that they'll view this as an indication of the student's ability to work outside of classroom, work on a project etc.

Edit -- How I intend to spin it. I'd like to use this paper to convince the graduate admissions committee follows: I come from a non-physics background ( major), and I have been studying physics/mathematics (in class, out of class etc.) for the last 2-3 years, and I wish to apply in 1-2 years. I started working on this paper after 1 year of studying physics in class. My first year was quantum mechanics (QM) heavy (three courses). The professor suggested the problem, which mostly used ideas from QM and some basic ideas from quantum information. I worked on the project with him and given my experience of having made the transition, making the first year of transition QM intensive and then working on a QM related problem and producing something with/with the help of a professor (regardless of its impact), I'm thinking of selling it as an indication that I can work outside of class, even when I (had to) make the transition; more importantly, given a problem related to the material I had covered after making the transition, I could produce something.

I know I'm more of "selling it" rather than "linking it with my future research interests." How does this sound in terms of having an impact on the committee and how they'll evaluate me (and my unusual situation).

Evidence that you can complete a research paper is a definite positive.  Many good students are not cut out for original research, so this should help make you an attractive candidate.  As you suggest, it is up to you to explain how the existing work does or does not relate to your intended research program as a graduate student.

NB: I am in the social sciences.


What to do with long equation-heavy solutions? I am writing a paper about a problem that involves solving a certain equation. The problem is that the solution is very long and there are a lot of terms. My question is: Is there a way to present the solution in an attractive manner instead of just typing the solution, which is about a page long? Also, would the fact that the solution is long and looks unattractive affect whether the paper get accepted or not?

This happens not just in mathematics but in many other disciplines as well: modeling of biological systems, for example, often involves a vast number of terms in the equations.  The best approach that I have found for these sorts of situations is to look for the structure in the system and to build your presentation around that structure.

In most cases that I have encountered, it is not true that there are simply a bazillion essentially unrelated terms.  The true story of the equation, then, is not the expanded mathematical form but the process and relations that generate it.    This opens up a number of approaches for factoring out the equations in order to make them more tractable to present, including:

Abstracting sub-structures as variables (e.g., X^2+XY+Y^2, where X and Y are complex terms presented separately)
Separating variables from parameters (e.g., a reaction network where each reaction uses one of several standard Hill equation models, with the parameters of the models presented in a table)

These sorts of factorings also lead to a much more informative and interesting presentation of the equation as well.  In fact, the Big Equation itself may often end up being relegated to an appendix, where its page-busting form is of little concern.

There may be, of course, certain systems in which such factoring is impossible---and that fact is quite interesting and worth clear discussion!


Letters of recommendation -- from postdoc or professor? Both? I am an undergraduate studying pure mathematics in an American university with a top-10 graduate program.
I am applying to PhD programs and graduate fellowships this year, and I have a dilemma about who to ask for letters. Maybe this question is too specific for academia stackexchange, but actually I think it is abstractly a somewhat common issue.
I have four potential letter writers. Two are very solid (very famous professors who know me well from reading courses / research) as far as I know, and I will ask them. Call the other two potential letter-writers "Prof." and "Postdoc"
"Postdoc" is a postdoc whose graduate-level course I TAed; I also took a graduate topics course with her and produced something semi-original (a new proof of an already-known result) for the final project. She is originally from Europe and did her PhD in the United States at a top-10 graduate program.
"Professor" is a very famous professor, though not in the same field as the other three (who are in the field that I will apply to graduate school in). I took an undergraduate course and a graduate course with her; I did very well in both courses and produced a very thorough (and long if that counts for anything) expository final project for her graduate course. I also know she is very serious and enthusiastic in general about writing letters for undergraduates, though I do not know if she actually read what I wrote in my expository final project.
For graduate programs, I have the option of including 4 letters. Should I include all 4, or just choose one of {Postdoc, Prof.}? Should I expect one of those letters to dilute my application and make it less strong? In my view, there are reasons why either letter could do that: for the postdoc, either because she is a postdoc (so some people might completely disregard her letter), or because she is very young and European (so might not be very good at writing letters yet, especially in the American style). For the professor, there is the potential downside that she is not in my field (though could it be a strength to have some diversity?), and that I didn't do anything even semi-original in her graduate course (though my understanding is that for pure mathematics this can be OK?).
For some graduate fellowships (e.g. the NSF GRFP), it seems like I can only submit three letters, so I must choose one of the postdoc or the professor to exclude (regardless of whether I ask both for PhD programs). Given this information, is there a clear choice of which one to exclude?
Apologies again if the question is too specific. However, I think there are some general themes in letter-asking embedded in my question: (1) asking postdocs vs. professors, (2) asking professors who I haven't done anything original for, (3) "dilution" of letters and whether to ask for 3 or 4 of them, (4) asking a professor whose research area in pure mathematics is different from the one I am applying for

Realistically, your acceptance into a good doctoral program will depend on an assessment of your probability of success in research. Funding might depend a bit on other things as well, but not the acceptance itself. Normally that would suggest professors are to be strongly preferred.
In your case, however, the post doc has some knowledge of your research potential and that is very important to get on the record.
If you can send four letters, then send them all. If you can only send three then you need to balance what people are going to write so that you can get a complete and positive picture of your research potential. Whether "diversity" helps or not comes back to what they will say about your likely success with research in your own field. But there is little downside when people praise you and your work.
The fact that you have some experience as a TA will only give them some confidence that you will work out as a TA provided you are accepted. It will have little effect, or none, on the acceptance potential.


Submitting to a journal as an undergrad but lying about academic status on bio As an undergraduate I submitted a paper of mine to a reputable journal. Fearing that I would be desk-rejected for simply being an undergraduate, I stated in my submission bio that I was a PhD candidate. It turns out the paper is going to be published and I am curious if there are any long term repercussions or ethical concerns to be worried about on my end. Is it worth issuing a correction or is it statistically unlikely the EIC will even care at this point? Equally as important: would relaying such information result in the paper not being published?

It's maybe too easy to offer advice on such matters when one doesn't have to live with the consequences, but for what it's worth: for your own peace of mind, and to minimize the risk of long term consequences (while possibly increasing the short term risk, though not by much I hope), I think you should send a contrite email to the editor explaining what happened and apologizing. Although there is no telling for sure what the editor would do, considering that your bio status is immaterial to the acceptance decision, I doubt that this will cause them to unaccept the paper. In any case, it's the right thing to do. And if you decide to stay silent and keep your deception a secret, you will have to spend the next few years worrying that it will be discovered, with potentially worse consequences for your career. Nip it in the bud is what I suggest. Good luck!


Can research publications or paper acquire University credit? Or a degree? I've seen and been with people with a master's degree that haven't gone to any Universities. They acquired a degree by submitting a papers correspondingly to their field of interest. How is this possible? Where is it possible to publish those papers? How can one publish those.

Perhaps you are thinking of a "PhD by publication", which is a different thing. See, for example, https://blogs.lse.ac.uk/impactofsocialsciences/2018/08/20/a-phd-by-publication-is-a-great-way-to-build-your-academic-profile-but-be-mindful-of-its-challenges/


My co-author has not responded my email I am a postdoc in mathematics. I read a paper of a Chinese mathematician some time ago and I found out that I could extend it. Therefore, I dropped an email to him, and then he told me if I could do it, it would be an interesting result. He also told me " I would be happy to know if you have anything to share with me," I thought that meant he would like to work with me. So, I wrote an email to him that contains all of my ideas. Now, I found out that my ideas work and everything correct.
My problem is he hasn't replied to my email after two weeks and I might be pessimistic but I am scared he steals my ideas and whatever I explained to him.
Even though I am a postdoc, he is a well-known mathematician. Moreover, we both use university emails to contact each other. What should I do now? Thanks in advance.
I have been writing it, but what I can do if he published it before me

Just go ahead and publish. The Chinese mathematician has not contributed to your work in any way other than saying that your results would be interesting. In fact, in my eyes it would be entirely inappropriate for this person to be your coauthor.
I would suggest though to also discuss this with your PI to make sure she/he agrees.


Working on other stuff (side projects and activities) without permission from the professor and department I started a postdoc in a new lab a few months ago.
In my former lab, people worked on a variety of activities all the time. By these I mean activities other than the funded project and teaching, e.g. reviewing papers, grant writing, participation in working groups/editorial boards/societies/etc, (co)authoring papers on other topics, meeting researchers from other departments for informal discussions, and so on. Of course to a reasonable extent that it doesn’t conflict with the main activities for which the researcher is paid.

I was thinking that is the norm in academia, however in my new lab people seem to work only on their project and don’t do anything else. While I am not prohibited to work on these things, I am uneasy and puzzled to continue, but also I am not sure if bringing this topic to my professor is the best idea.

Should I continue working on these without an explicit permission? It is really important for my career to do other work too, e.g. I am currently finishing a paper I have been working on during free time, but it has nothing to do with my current project (which is good for my cv).

Can I have repercussions if I publish a paper on a topic that is not part of my funded job? Can I just say I worked on it in my free time or during weekends?

I was thinking that is the norm in academia, however in my new lab people seem to work only on their project and don’t do anything else. While I am not prohibited to work on these things, I am uneasy and puzzled to continue, but also I am not sure if bringing this topic to my professor is the best idea.

I agree that the norm in academia is, and should be, that staff on all levels need to have sufficient freedom to pursue their own interests in addition or within the funded project(s). As a postdoc, this is particularly troubling, because you need to use your postdoc time to diversify your research themes, skills, and collaborative network. Basically, if you are a postdoc and sitting in your office all day working on a single project, you are doing it wrong (and hurting your career big time).

I don't think that sneaking a little side project here and there by your professor is sufficient. As a postdoc, you should be able to dedicate significant work time towards progressing your own career. I suggest you bring this up with your professor, and, if they don't appear to understand or accept your concerns, I would start brushing off the CV and get back onto the job market.


What is the procedure for citing a source with incomplete information? If it matters, I am specifically asking about the IEEE referencing style, but I'm happy to learn about other styles as well.

One of the more frustrating parts of referencing is that every book publisher and journal has their own standards for what information they give you. I've come across some books that don't have a city of publication, for example, and some journal articles where the specific volume is not clear.  When citing web pages this is a particular challenge, since sometimes it is not possible to find, say, when the web page itself was published.

In cases where information is simply not available, how do you cite a source correctly?  Is there a way to indicate that the information was not available?

If you are in computer science (or anything IT related or IEEE), bibtex download (from ACM or IEEE sites) will be your friends.

Apart from that, if you still need more information, try your best (include everything you know) and it's ok.


How to get a postdoc without publications in "top" venues? I am a Ph.D. student in computer vision at a North American university. I have a very hard and limited problem in my thesis and I could not publish in top conferences such as CVPR, ICCV, PAMI,... I published 3 IEEE conferences and I submitted 1 journal (under revision) in PRL. I was very autonomous (99%).

I am looking for a postdoc in north America, Japan or Singapore. I remark that all positions demand that the candidate should have published in top conferences or top journals.

So, can I have a postdoc opportunity or I have to forget it and  look for an industrial post?

If your CV is weak and you are worried about being filtered out based on that, you can ask your advisor to contact people and recommend you directly. Additionally, you could try contacting senior scientists that you met in conferences and were excited about your work.


I have stack-exchanged through my undergrad math program. Am I likely to succeed in mathematics PhD programs? I'm currently a third-year mathematics student at a top-20 private research university in the US (though mostly known for the humanities). We have a small undergraduate mathematics department, but we were offered the option to take many graduate courses. I’m always passionate about studying pure math, specifically algebra, and I’m very seriously considering pursuing a PhD degree in mathematics. Nonetheless, I’ve not been able to participate in mathematical research of any kind so far – getting undergraduate research experience is impossible due to personal status issues, and my department has no resource committed to undergraduate research.

Indeed, as of my course load, I’ve finished the three-semester algebra sequence by my second year (i.e., group/representation, ring, field/Galois, category theory, commutative algebra, and homological algebra). Though I started late, I'm also working my way through the analysis and topology/geometry sequence, taking differentiable manifold and complex analysis now. I maintained all As in the graduate courses I’ve taken.

Regarding this, I do have one important confession to make, and it is in fact the reason why I’m asking this question. Math SE is a very robust community with respect to algebra. This worked very conveniently for me as there are very few peers at my school to discuss math with. As a combined consequence I actively seek ideas on SE whenever I get stuck on homework. (Please note that I'm not in violation of any collaboration rules set by my department: I understand and then proceed to write every proof myself.) This happens in about 30% of the assignments. I have no problem with exams since they are usually much easier than assignments.

Only after having recently talked to graduate students and professors at a conference, did I realize this is a terrible approach. I vividly remember one said something like: “unless you went through a textbook and attempted to prove every theorem yourself first you won’t truly understand the subject”, which is, the exact contrary of what I’ve been doing. I’m seriously in doubt about my aptitude over these subjects, fearing that I will be subpar on the level of understanding as well as the ability to conduct research, to approach open questions when I reached graduate school. I fear I never try/explore “hard enough” to come up with proofs like others have suggested. I managed to do most just by familiarity of common methods/tricks and theorems, but those things can be forgotten over time.

So here comes some specifics of my question:

Is searching SE for homework problems common for math students?
How will doing so affect a student’s understanding of the material?
In what ways does doing so tie to one’s ability to do research?
What are some possible ways to remedy this, besides completely re-learning the material?
How much do I have to pay in the future for stack-exchanging through my courses?

Yes! In fact, I think you're well on your way to doing better than your peers! Taking longer to understand something isn't something to be proud of! There's no need to reinvent the wheel. If someone can help you understand something, you would be well-advised to make use of them. In the same way, you would be well-advised to attend the lectures, thereby getting help from the professor, instead of staying at home with the ZFC axioms and attempting to derive the whole of mathematics from scratch.

My experience asking questions on Stack Exchange also indicates that simply writing the problem in a form which others can understand is a great help in clarifying my own understanding of the problem. Indeed, I've solved some of my problems simply by beginning to write a (never asked) question.

Of course, this doesn't mean you should outsource your understanding to others. You should make it so that you can explain the concept to next year's students without help (answer some other SE questions while you're at it!). But even then you should feel free to ask for help with next year's problems.


How to search for one phrase in the title and a different phrase in the body of the paper in a single Google Scholar search? Google Scholar is a very good source of knowledge especially with its advanced search, but the options in the advanced search is either search in the title or in the whole paper. How can I search for a word in a title and a word in the paper itself?

e.g. I want to search for papers that title contains the word "meta analysis" and the body contains "Alexandria". Is there a regular expression to do this?

You can use intitle: to search for phrases in the title (no space after the colon) and similarly you can use intext: to search in the body.

intitle:"meta analysis" intext:Alexandria


How to set up lab rotation when commencing a PhD? I'll be starting a science PhD program in the fall, and I'm required to do at least three lab rotations. I haven't received any instructions from the program as to when and how I should secure a spot in the labs I want to rotate in. I did contact some of the PI's I'm interested in working for while I was applying, as well as during interviews, but obviously nothing was finalized. Should I be contacting them and trying to meet with them now, or is this generally done at the beginning of the school year?

Have you even shown up to orientation yet?  I think you're getting ahead of yourself.  But if you're already in the department wandering around lost then my advice is:

It obviously varies by department but there should be some sort of form you fill out with your top picks.  You have a few options:  contact your graduate advisor and ask; go talk with a perspective PI and bring it up during your conversation; or ask the other students in your program if they know what to do.  The third choice is by far the best.  It seems like you're just sitting there in a vacuum wondering what to do.  You will quickly die if you do that.  You need to meet the other students and you need to work with them to make it through.


As a freshman BME interested in graduate school and academia, where do I begin? I'm a current freshman biomedical engineering major going into my second semester, and am interested in graduate school and possibly a career in research (however, not a set decision, and could change).
One thing that bothers me is that I don't really have a specific question or focus that I would like to work on. I have contacted a variety of professors, a couple of whom responded positively to me starting out in their labs, in various BME-related fields. I am entirely not sure that their fields are ones that I would like to specialize in later on; I decided on who to contact out of broad interest alone. In the case that I later decide to focus on a somewhat different field (say in sophomore or junior year), does it matter that my first research experiences were in a separate one?
Also, would non-research based industry summer internships help my grad school application in any way? What about informal research project/competition teams on campus (eg. iGEM)?
I'm somewhat lost right now on what exactly to do.

When you're a new undergraduate, you can't make real statements about what you want to study. It's simply too soon. Saying you want to work in [field] doesn't carry much weight if you have no idea what working in [field] is actually like.

At this point, don't worry too much about what kind of research you're doing. Just do something, anything, and figure out what you like. If you end up doing research in many different fields before deciding on something, that's fine - most other people do the same.


Professor asks me if I have other options (to apply). How should I answer? A professor who agreed to advise me asked, "Have you found any other options?" I interpreted this as him asking if I have applied to other schools. I think he knows that I should spread my application to a range of schools, so telling the truth would do no harm. However, since we have had some trouble in the application process* and I need him to help me, I don't want to take a risk. I'm worried that he will lost a little interest in helping me.

How should I react to this?

*The problem may be off-topic, but I will put it here in case it's important. His school doesn't have a PhD program, and he has to advise me through another school. However, when I emailed the other school, they said that I could not have an advisor from the outside. I think this is a mistake and he thinks that too. He has sent an email to them and we are waiting for them to reply.

It sounds to me like he is just making sure that you will have other options if it turns out the school won't admit you with an outside advisor. I don't think there's any harm at all in telling the truth. If he wants you as a student, the fact you have other options shouldn't make a big difference to how much he is willing to help you in the admissions process. In fact, sometimes having other options can even make you more desirable, as it indicates other people/schools think you are valuable too. (In my case, having other offers allowed me to negotiate a slightly better package at my top choice grad school.) If you're worried that he will be less interested in helping you with your application if he knows you are also looking elsewhere, you could always say that you have applied to/been offered place(s) elsewhere, but that the opportunity to work with him remains your top choice.

Regardless of how you reply to him, however (and as I said, I don't see any reason not to tell the truth), I would say that it's always a good idea to apply to a range of schools. Hopefully you will get in to the school you want and be able to work with him, but if the school has indicated there might be a problem with this (even if you and the professor think they are wrong), you may want to have other options.


Disclosing hidden disability to employer I'm doing a project-based postdoc in an European university.

I have serious ongoing eye conditions that significantly affect my reading speed and as a result it took me 5 years to complete my PhD in a country where a standard Ph/D/ is only for 3 years.

I have been selected for this postdoc position, I think, mostly because of my particular fieldwork and user engagement experience, which is essential for this post. So I still got hired despite my very weak publication record. And because the interview was via Skype, the PI did not discover my hidden disability, nor did I disclose it.

However, as I've been working in the position for several months now, it becomes apparent that I'm falling behind other colleagues of the team. Despite working extremely hard, I couldn't finish the work designated by the PI on time and I think I'll need a thorough explanation for that.

The question is, will disclosing a hidden disability ruin my employment? This is a 3 year position and the initial contract is only for 1 year. Given this is an externally funded, project-based postdoc, I'm really worried that my contract will not get renewed at the end of the first year.

And also how do I explain this to the PI and the university? For example, the choice of terms, hidden disability vs. chronic illness vs. long term health condition? Do different terms imply different levels of legal protection for employment?

In most European countries, it is usually against the law to fire people because of disabilities. So long as you're capable of performing your assigned work with reasonable accommodations, you should not be afraid of being terminated. However, you will probably need to have documentation of your disorder to provide as evidence to support your claim.


How formal should figures in a thesis be? I am currently writing my masters thesis. I include in it a screenshot of a webpage, in which I want to point at some components and explain what each of them does. What I did so far is that I draw circles around the components and an arrow from the component to a one word text saying what it is, I intend to go into details under the image.

Is that sort of “labeling” formal enough for a thesis figure? Or is there another presentation that would be more appropriate?

Images in a thesis should be of the same quality as images in a peer-reviewed publication. Hand drawn circles and arrows are not formal enough. Circles and arrows drawn with programs like TeX, GIMP, Illustrator, or Powerpoint are formal enough.


What kind of help can I request from a terminally ill professor? I am a student in Mathematics. There is a field I'm interested in (possibly enough to make it my main research area) which is not studied in my city. I've read a lecture notes on this topic a few months ago and sent the author a list of typos/inaccuracies I'd found. He responded in a positive way. When I was looking him up I found out he is terminally ill which, besides being extremely tragic, prevented me from asking for his guidance.

Since then I brought him up in a conversation a few times and people told me that it is very important for someone with terminal illness to know they are appreciated. I am thinking about requesting some help with my study of the field from him. However, I believe, the author was a great professor and mathematician so he probably has a lot still going on and I shouldn't bother him. Thus, my first question is: is it okay to ask him for help in this situation?.

If the answer is yes, what should I ask of him?. For example, would it be appropriate to inquire if he knows a colleague who could potentially become my adviser? Or perhaps I can ask about current research? I already used the opportunity to ask for some literature in the first letter.

To state it more clearly, is there a favour/question I can ask that is

Appropriate for the level of contact we had;
Easy for him to do and hopefully would make him feel appreciated;
Would be helpful for my own studies/career?

The last (and least) issue: in his email he thanked me for the list of typos and said that because of illness it would take him some time to implement the changes. It's been two months and the text is still in the first version. Should I offer assistance with this?

Edit: note that my original answer below addresses OP’s original version of the question, which has now been edited.

To address the current version of the question: yes, it is okay to ask for help, but your motivation should be wanting to get help, not artificially creating feelings of “being appreciated”. If you want to let someone know they are appreciated, just tell them that that’s the case. And if you don’t know what questions you should ask, to me that is a sign that there isn’t really anything that you particularly need help with, so the best thing to do is to not ask any questions.

Finally, the fact that you know the professor is ill shouldn’t change anything about the nature of the questions you should ask him. Just ask what you want to know, whether it’s an easy or difficult question to answer. I am confident that if the professor finds the question too burdensome to answer given his illness, he will either not respond or will simply tell you that he is unable to help.

My original answer:

Maybe I’m misunderstanding your intent, but the way your question is phrased (particularly your statement “my main goal here is to make the professor feel appreciated” and the slightly absurd list of hypothetical questions you are thinking of asking the professor) I get the impression that you’re thinking of inventing a fake request for help, that is, a question whose answer doesn’t actually interest you very much, out of the belief that the professor will feel “appreciated” when receiving the question.

If this interpretation is correct, my strong advice would be: no, it’s not okay, so don’t do it. The reason is that this would be dishonest (and somewhat transparently so, for some of the questions you proposed - not to mention that you’re publicly posting your plan here using your real name...). I can’t claim to know what it feels like to be terminally ill, but as a general rule people don’t appreciate other people being dishonest with them, so I think your question could end up having quite a different effect than what you intend.

Here’s an alternative suggestion however: if you want the professor to feel appreciated, why not simply tell him that you appreciate him (assuming that’s correct)? And certainly I think it’s okay to offer to help him in any way you can — again, assuming the offer is genuine and you intend to follow up in case he takes you up on it. It’s also okay to ask him a question if you genuinely want to know the answer, but you should be asking it because you want to know the answer. Please don’t invent questions solely for the purpose of making someone feel appreciated; I find that idea patronizing, offensive, and highly misguided, despite the fact that the intentions behind it are good.