How can I keep my ideas of a new theorem safe? This post is similar to this one except this is a little bit of a special scenario, I have yet to graduate high school.

I know what you're thinking, oh THIS conversation again, check if it exists, make sure your theorem works, etc. etc.

I have gone through all of this, for over a year I have looked for my theorem online and nothing has come up. I have tried disproving my theorem for over a year, and I have contacted professors and have conversed about this and they all say that it is definitely publishable, but that I should prove it myself. My big worry is that due to my position my ideas can easily be stolen, and I am starting to get a little on edge.

How can I ensure that my ideas are not stolen, Can I provide direct proof that the idea is mine somehow? Should I just publish it without a proof, Can I even publish without a proof? I am kind of stuck at this point.

I have a document that has the theorem on it written in permanent ink, dated, and it is signed by a witness. But what more can I do?

EDIT:

For those curious about my conjecture click here, there are two pages so click next to see the other page.

Feel free to comment

The word "theorem" implies that there is a proof.  If you do not have a proof, you do not have a theorem.  Let's call it a conjecture instead.

  I have tried disproving my theorem for over a year.

That's a slightly strange thing to say: how long have you spent trying to prove your conjecture?

  Should I just publish it without a proof, Can I even publish without a proof?

It is possible to publish conjectures, but it is significantly harder to do so than to publish theorems.  I would not recommend that a young researcher -- especially, a high school student! -- try to do this.

  I have contacted professors and have conversed about this and they all say that it is definitely publishable, but that I should prove it myself.

It's no help if I'm not honest, so: this sounds fishy to me.  It is often not so easy for (even) a professional mathematician to know what is "definitely publishable": after more than a decade of submitting math papers I find that I still have some things to learn about this.  But anyone who is telling you that your mathematical work is "definitely publishable" if it does not contain a proven theorem is either giving you bad advice, or you are misinterpreting the advice.

  How can I ensure that my ideas are not stolen, Can I provide direct proof that the idea is mine somehow?

With probability extremely close to 1, professional mathematicians simply do not steal ideas in the manner you are worried about.  The "I did something great, but oh no I can't show it to anyone" train of thought is a sad one that amateurs often fall into.  Rather, if you do something great, show it to more than one person, and you're fine.  One way to do this is just to upload it to the internet in some public or semi-public location.  For instance, if you have an account on facebook, just post a scanned copy of the paper as photos.  Facebook posts are archived with date and time, so that's that.

I will extend to you the following offer: after you archive your paper publicly on the internet, send me a copy.  I will spend up to one hour looking at the paper and tell you one of the following:

The mathematical content of your work is such that you should try to publish it.  I will then tell you some places you might send it.
In my opinion your work is not publishable in a reputable, professional mathematical journal.
I am not qualified to judge whether your work is publishable, but I recommend that you send it to third party X.

You should understand that unless the work is very directly connected to my own I will not have the time to help you with it, nor to send more than one email.  (I simply can't: I have a lot of other people who are counting on me to spend my time on them.  In many cases I am being paid to do so.)  But I will give you a professional evaluation of your work so you can (probably) know where you stand.


Does working while you are studying affect your GPA? I am studying computer science and I have money to pay for my university study, but I do not have money to spend on entertainment such as going to cinema with my friends in the weekend or upgrading my laptop. I have applied for a job at McDonald's. My shift is 4 days per week with 7 hours per day.

I am scared this would affect my grades. How can I balance my studies with the part-time work I must do in order to improve my living standards or afford a social life?

This study suggests that employment outside the university (especially in excess of 25 hours per week) does have a negligible adverse effect on GPA, and a signigicant adverse effect on the probability of a student's continues enrollment. A second paper (here)  suggests that hours worked do have a significant negative effect on student grades.

  ...results show that an additional weekly work hour reduces current year GPA
  by about 0.011 points...

A personal anecdote: When I attended the mandatory freshman orientation seminar during my first semester as an undergrad, they recommended no more than fifteen hours per week, suggesting that anything more than that would tend to have a negative impact on our grades. I do not now recall whether they also provided references to back up their claims...

Of course, this is a general guideline, and an individual student may well be able to handle more. I know some students who were somehow able to juggle a full course load, a full-time job, AND major family responsibility, but those paragons are very rare!


Is my PhD programme a scam? Does my department only want to get PhD students as TAs for their recitation section? Next month (August) I am supposed to go back to the US to continue my math PhD programme in a Public State University. I hold a TA position as everybody does in my department. Nobody, I say again, nobody holds an RA position. My duties, as equal to almost everyone, are two recitation sections of 60 students each. Every section meets 3 hours a week, that is 6 hours a week for both, plus preparing material, grading a weekly quiz (120 for both) plus grading homework weekly (120) plus grading classwork weekly (120) plus holding office hours plus organizing and keeping grade records plus going 4 hours a week to a center called "math help room".

I saw many US students leave the programme. They get fed up. The vast majority of the students are Chinese and they seem happy with it but I do not. The workload is too heavy and there isn't much time for learning or research. I have seen most people get their PhD at my department with only one publication that even says "to appear" on the resume of the PhD graduates. All advanced PhD students at my department spend even more of their time on TA duties than doing their research, as opposed to my country (Mexico) where advanced PhD students do not have TA duties.

Is that normal? Is my math department a scam?

I was surprised and happy at first that I was accepted to a US university to do a math PhD. But I could not get admission to a PhD in my country nor Spain nor Brazil, which are not supposed to be as good as a US university. Is my reasoning ok? Why did my department accept me when lower schools rejected me? Do they only want to get staff for their recitation sections?

Is my reasoning correct? Or is the main objective of a PhD here in the US just teaching?

The idea that there is some sort of dichotomy between academic mathematics "research" and "teaching" in the U.S. is an incorrect over-simplification. It is true that there is considerable PR hype about "research" being the fundamental goal/criterion/status-generator... It is true that almost all math grad students in the U.S. are supported as TAs, not RAs. It is also true that sometimes the TA workload is unreasonable, and, often, people seem to find the TA work more immediately gratifying than their research, and if done inefficiently certainly takes more than 20 hours per week.

It is also true that some grad students from abroad are happy enough to be in the U.S. that working conditions are not an issue...

While it may be that many academic math jobs, particularly those with lighter teaching duties, are filtered on research, faculty still inevitably spend quite a bit of time on teaching and service. If teaching is extremely unpalatable, then academic math will be unpalatable.

Some people might say that any situation in which the "apprentices" cannot expect to get as good a job as the "master" are scams... but it's hard to find a situation in real life which works differently, I think. It's only a scam if someone makes a stupid promise to you that you'll eventually have a job just like your advisor, since, based on numbers alone, that's unlikely.

In my opinion, the true goals of graduate education in math are several: learn how to be an effective undergrad teacher, learn some advanced mathematics, learn how mathematicians make new mathematics, and practice attempting that.

In particular, research in mathematics requires mastery of so much prior work that it's very unusual for grad students to have genuine publications prior to the award of the PhD. This is very unlike lab-oriented engineering or CompSci degrees. That fact is not a sign of failure. If anything, it might be a sign of substance, that faculty insist on graduate education and more genuine research accomplishment than "papers" per se.

Also, in particular, again, the purported dichtomy between "researcher" and "lecturer", and a perception that the "goal" of graduate programs is to produce one or the other, is inaccurate. Graduate programs teach advanced mathematics to the grad students, and show what research is. The likely fact that they'll be doing a lot of teaching in their subsequent career does not affect the advanced mathematics... and the TA practice is helpful in becoming efficient and effective as a teacher.

There is sometimes a subtler issue, of grad programs which recruit international grad students who won't complain ... about workloads or anything else. That's not a good sign... but "even" domestic students are often pessimistic about the possibilities of change, and don't want to speak up for fear of retribution, etc. In the range of "generally reasonable", there are extremes, and there are abuses, indeed. Nevertheless, even then, it's probably not really a "scam".


Expectations for a research student at a Japanese university I have recently decided to enter a grad school in one of the Japanese universities (namely, TiTech). It seems that the general recommendation is to start as a non-degree research student first and prepare for entrance exam while being a research student. After reading this question, I still don't understand what is expected from a research student. On one hand, it is a first step before doing a masters degree, on the other - I find the explanation very confusing. After all, the word "reasearch" in "research student" is there for a reason, right?

My question is - do I have to come up with a research proposal before contacting my potential academic supervisor? I have found a professor doing a research in field I am interested in (inductive and abductive logic programming in AI), but the problem is that this is not something you can get experience with in undergraduate studies. It doesn't come up in an undergraduate curriculum, so I have only a general understanding of the topic. Starting a novel research (if that's what research student should do) without some background will be very hard. Yet I cannot get this background unless I get at least an Ms in AI first.

This is especially worrying given my background. I graduated from my university 10 years ago and was employed all this time as a software engineer. I have a good GPA (4.99 out of 5), and I lived and worked in Japan for 6 years and got a JLPT N2 certificate. However my bachelor thesis was about image processing, not about AI, and in any case it is not particularly relevant after so many years in industry.

I was a research student at the University of Tokyo for one year.

As the answer to the other question states, a research student has literally no responsibilities whatsoever. The apparent point is to allow foreign students time to study for the entrance examination for the formal graduate program. They might give you as little as four months (roughly) or as much as a year before the exam is held.

Your advisor may or may not recommend that you sit in on classes and learn how the university works. If you are in the sciences, there's a good chance that you will be assigned to a research team in preparation for entering the college. If you are in the humanities, it's likely that your only responsibility will be to try to pass the examination. If you are already familiar with your field, you will have an extreme amount of free time.

"Research student" is actually kind of a misnomer. During my pre-acceptance year I did independent research on my own initiative (mostly because I was bored) and had two papers accepted for publication, but my advisor did not ask what I was doing, and my office did not know I had published papers until after I was accepted as a masters student.


What's the impact of former university's transcript on PhD application? I'm a junior majoring in chemistry and have a plan for applying Ph.D. after graduation. My current GPA is not distinct, just 3.65 out of 4 (Many people say 3.7 is competitive while 3.6 is like average if want to apply for top programs). My current school is awesome though and highly prestigious in Chemistry, ranks 10ish on USNEWS, I don't know if that helps when the GPA is not that top?

In addition, I'm a transfer student, which makes the things more complicated. Before coming to US, I spent 2 years at a Chinese university with an overall GPA 3.43/4.00 and rank maybe top 10%, which seems to be fine but not that satisfactory. The most serious problem is that I even got C for some important courses like Orgo 2 (well even I got an A in orgo 1...)and both 1,2 of p.chem. The average scores for these courses were around C and the failure rate was about 30% so luckily I at least didn't fail but just got an average score. That's terrible and I don't know if the past transcript will play extreme bad effects on my application. (Actually, I think I put more emphasis on some entrepreneur and voluntary activities, that was really time-consuming and meaningless...)

I want to do research in the biochemistry field. And it's a dilemma. The pChem seems to have no significant relation to my field of interest(ye, orgo 2 does...) but which are definitely important courses for a Chem major. And I'm wondering if sacrificing time to retake these courses is a better choice since I really want to take some grad level course during my senior year. If the good performance in upper-level courses can cover the bad grades in past?

And I know the research is extremely important for Ph.D. application. I did one in my former Univ. in my sophomore which is related to organic synthesis but was very basic. I didn't have some papers for this one I just started my second research last semester here at my current university. It's awesome the lab is closely related to my field of interest and the PI and Ph.D. mentor are really nice and helpful. But here comes the question, I think the lab is awesome and if I continue to involve there is possibility I can get some result maybe some publication? But the lab is very new and the PI just started her AP position here, definitely, she is willing to write a strong RL for me if I continue to work at her lab, but is the RL strong enough for a top program? (I know I'm greedy but... Everyone wants the best right)

I know it's a whole lot of questions and sorry for that...

Every field (chemistry vs. mathematics vs. history) is different and every PhD program at different universities you apply to is different. Also, who serves on the PhD admissions committee may change year-to-year.

Yes, many top-tier programs will look at your GPA. How much weight will they use to judge your application is variable. I can imagine a situation where the five professors on this years admission committee decide to stress class grades for incoming students.

Yes, many program will seriously consider any research you do, even if you never published anything. Simple being involved in an processor's research laboratory will most likely give you an advantage. I can imagine a situation where the five professors on next years admission committee decide to stress undergraduate research in incoming students.

My point is the following: You can't predict what will get you into a PhD program because it may change year-to-year.

What I would do: It would be nice to find a way as an undergrad to research something, but I wouldn't stress about it being publicly published. It may be enough to have a strong undergraduate thesis, similar to a senior-project, that shows your research ability. That with a good recommendation letter from one (or more) professors you work with will be the building blocks of a strong application.


AAUP standards for timing of recruiting/resigning a faculty position: Do they really mean anything? According to the American Association of Union Professors (AAUP),

A faculty member should not resign, in order to accept other employment as
of the end of the academic year, later than May 15 or 30 days after
receiving notification of the terms of continued employment the following
year, whichever date occurs later.

...

An offer of appointment to a faculty member serving at another institution
should be made no later than May 1, consistent with the faculty member’s
obligation to resign, in order to accept other employment, no later than May
15. It is recognized that, in special cases, it might be appropriate to
make an offer after May 1, but in such cases there should be an agreement by
all concerned parties.

The few relevant comments in this thread

http://chronicle.com/forums/index.php/topic,163851.15.html

(e.g. comments 23, 26, 27) seem to indicate that this standard isn't important/widely observed.

However, it appears that some universities do observe it (or some variant), e.g. University of Pittsburg and University of Louisiana and Lafayette.

My questions are

Is this etiquette widely observed? That is, would this be a reasonable barometer of what is "ethical", or is the standard dated (if ever relevant), as indicated by the commenters in the linked thread above?
should I let the existence of this AAUP standard modify the way I handle accepting a pending offer that would require me to go beyond this May 15th deadline?

I'm soliciting anyone with knowledge of these matters but information from deans, department chairs, or anyone who has resigned at this late stage would be especially valuable. Thanks for any info.

Note: Previous posts of mine give a bit more (probably not relevant) background:

I want to leave my tenure track position before fall. I have great prospects but no new position "locked up": when should I break the news?

Proper "notice period" for resigning a tenure track position?

The second one is closely related but is distinct in that this question specifically is about observance of the AAUP standard that I learned about today while reading the chronicle.

Note 2: Mine is an AAUP school but does not have any explicit policy like the two mentioned above.

I have seen faculty leave or take positions at all kinds of times during, before, or after the semester or even right after (or during!) sabbaticals.  The AAUP guidelines are nice, but, ultimately, everything depends on the schools involved.

If you are concerned about ethics, I would recommend being upfront with both departments (the one you are leaving and the one where you will be hired) and coming up with something that leaves both of them satisfied.


How many emails do professors get every day? When I was in academic publishing, I received about 50? emails a day. The bulk of these (~60-70%) would be semi-automated emails of the form "so-and-so has agreed to review this paper" or "the first proofs of so-and-so paper are now available at this internal link". There'd be a few (<5) internal emails about e.g. meetings, new hires/resignations, policies, and so on. There's the occasional promotional email sent by other publishers or conference organizers (I have no idea why they would email me, but not mine to reason why), and finally there are actionable emails: author corrections, complaints, questions, initiatives, replies from acquisition attempts, and so on (usually more than 1, but less than 10, of these every day).

What does it look like for professors? I've had one professor tell me that his inbox resembles a black hole, and I'm curious how black is black in this case.

i get well over a hundred emails per day despite fairly intense efforts to unsubscribe from lists and block spam.  Some are from students, some are from faculty colleagues, some are from research colleagues at other institutions, some are marketing junk, and lots are from administrators at my own institution.


What should be my prime focus for the next 2 years to improve my chances in securing an academic position? I am a 5th year PhD student in Materials Engineering in the US. My research involved simulating a 3D printing process. I was able to publish 1 paper in my field related journals (IF around 2) and 3 more are in preparation. My performance could have been lot better but I was struggling to find a definite research direction in my first 2 years. I also wanted to learn new methodologies to create better models.
My advisor did not have experience in my area of research, so I had to formulate questions and also had to look out for solutions when I got stuck.

Yes, I am ashamed about my PhD experience. I should have done many things differently. Yes, I should have worked harder. But, I really want to be in academia. And I don't have a good CV to support that. What should be my prime focus for the next 2 years and how can I make my CV attractive before I start applying for academic positions? Thanks.

Your feeling that you could/should have done more/better in your doctoral studies is, of course, completely valid and completely misguided, as it is true for just about everyone. Of course, you could/would have done more if you hadn't started the process as a novice, but rather as an experienced researcher.

You have a different perspective now, since you have gone through an extensive learning process and have gained skills that you didn't have a few years ago. That affects your judgement about what you are capable of. Yes, you are capable of quite a lot more now, but it is a mistake (logical, psychological,...) to project that back five years.

Your sense of "failure" would really only be valid if you now have the same naive views that you had five years ago. But if that were the case, you would actually be an imposter, but wouldn't have any way to recognize it.

This is classic imposter syndrome and many people at your stage suffer from it for exactly these reasons.

However, let me try to give some guidance on your question. First realize that the range of positions as an "academic" is very broad. Some of us are primarily teachers. Some primarily researchers with only a bit of teaching - mostly of very advanced students. There is a fairly smooth gradation between those extremes. So, first look at what sort of position you would like to hold. Then explore what such people do and what is considered valuable for such a position.

With that background, work to fill in your CV (and your experiences) that give you the expertise to do those things. If you want to be a researcher (my assumption, since you list post-doc as a tag) then you should work on getting things into the publication stream and also in building collaborative arrangements with other researchers in your field. Your advisor(s) can probably help you get "connected" to the wider research community as can attendance at conferences - especially as a presenter. But you can also get connected to other researchers just by serving on conference committees in some fields.

But "academic" is probably too broad a goal. Narrow it and then work to fit that narrower definition.


Due to my depression, the department wants to kick me out of the graduate program. How to stay in this environment? This is the third installment of the series: What can I do if my advisor wants me to keep working, even while I'm on medical leave for severe depression?

So, many months were gone and I'm still clinically depressed. Medication helps just a little bit, but I don't know how could I live without it. I had a very bad day at the lab a couple of weeks ago, and I posted on my personal profile in a social media that "life sucks, I can't take this anymore, my life is a failure, I wish I were dead".... that stuff. I was on my personal profile, and I wrote something like this before when I got really stressed. Nothing out of this world.

However, some of my lab mates and grad colleagues saw my post and went to the Head of the Program (faculty and staff too) "worried about a suicidal student".

It didn't end well. The HoP called my adviser and asked her about "a troubling student" that she may be dealing with. My advisor tried to save my back saying positive things about me. But the HoP said if I continue causing trouble, my adviser should send me to her and "she will take care of this mess".

This is not a good thing. I heard rumours that the department thinks about getting reasons to kick me out of the program, because if I leave - and never come back - the program itself would be penalized with less government funding. That wouldn't happen if I get expelled. Apparently, they don't want to take that risk.

But I want to stay. So, how to deal with this kind of environment? My professor got my back (after all problems that we had, so I happy for that), but the "Witch Hunters" are lighting up their torches. How to deal with a department that wants your head??

Even if I stay, how to deal with the stigma about depression and suicidal thoughts in academia? Everyone here thinks I'm about to star the second season of the Netflix's series 13 Reasons Why. I am now the "crazy psycho guy."

I'm having some trouble with the way you're mixing the words trouble, troubled and troubling.

If a student shows some red flags for possible suicidal thoughts, it's a good thing when the people around him alert the department, in order for support to be offered.

On the other hand, targeting the troubled student and painting him as a troublemaker would not be good.

As you are currently not in as good shape, mental health-wise, as you would like, it's difficult for me to know how objectively you are able to be, currently, in your perceptions and interpretations.  That is, I'm not sure whether your colleagues are actually targeting you for possible removal from your academic program.

However, I will go ahead and do my best to answer.  I'm not sure what country you're in, or what the laws and regulations are where you are, so I'll write the answer I would give to someone facing the problems you described in the U.S.

People fear what they don't understand.  The key to acceptance of a mental health disability is education -- both of staff and peers.

In the U.S., I would ask NAMI, the National Alliance on Mental Illness, or a local disability rights group, or a county mental health association, to send a trained expert to give a mental health awareness presentation to the students, and a separate training session for staff.

Here is an example of a presentation that a college student gave about her neurological disability, Tourette Syndrome, to her classmates, with the help of a staff ally: https://youtu.be/zVY6B3ezY3k

I get the feeling from your post that you might not be in the right place at this time to give a presentation of this type yourself.  That's okay.  There are people who have experience giving presentations on behalf of a student.

Here is a nice website with suggestions for how to seek reasonable accommodations for a disability in the workplace (in the U.S.) -- I think this may give you some good ideas, and in general instill you with more of a belief that you are entitled to accommodations! -- Job Accommodation Network.

It would be great if you could participate in a peer to peer support group.  In the U.S., in order to find such a group, one can try to find such a group with the following techniques:

google
ask a mental health professional, since these providers often have an email discussion group through which they can query each other about such opportunities
ask a government information service (one reaches it by dialing 211)
ask a psychiatric ward at a local hospital
the campus counseling center may have organized some groups of this type
ask the county mental health association
ask NAMI
if necessary, take the initiative and form such a group


Cannot submit revision of preprint in bioRxiv (Current Version Status Closed) I went to the 'Author Area', and the first sign of problem was that the 'Submit a Revision' link had 0 papers. After that, I went to 'Author history', found the specific preprint. I noticed that the table's column 'Current Version Status' had entry 'Closed'. The preprint has 'Date of Original Submission' on September 2017.

Does anyone have any idea what is going on? I've searched in bioRxiv's site and in the web, but no clue of any rules related to closing of preprints to revision after some time since last or initial submission.

I contacted the bioRxiv Team. They replied saying that "The system automatically closes submissions if they are inactive over the allotted period of time. We can have this reopened, but first we need confirmation that your paper has not yet been accepted or published in a journal."

I then asked them "How long is the duration of inactivity leading to closing a preprint for revision, since I couldn't find any specification in bioRxiv's website."

They replied that "The timeline for closing a submission that is in progress is two weeks."

Thing is that I couldn't find any mention in their website about closing to revision after a two-week period of inactivity since initial submission; actually, their FAQ says that "An article posted on bioRxiv can be revised at any time, until it is accepted for publication."


Can a researcher get his full salary from a European Project? I would be interested in creating with some colleagues a FET Young Explorers project, in which I would be Work Package leader.
I've been involved in several european projects, but always as a postdoc recruited by a PI (or WP leader), and I don't have a permanent position yet. So basically, the idea of applying to this project would be to get my full salary paid by the EU project, but I don't know if it's possible.
Indeed, in the FAQ, they say that the applicants need to have a position somewhere. I don't think getting a position would be a problem, but only if I come with my own salary. The question in this case is whether the hosting institution still needs to pay some part of my salary?
EDIT: A precision on the question. From the Guide for Applicants, Section A3/Budget, p. 47, the part about the requested European Commission contribution:

The requested EC contribution shall be determined by applying the upper funding limits indicated below, per activity and per participant to the costs accepted by the Commission, or to the flat rates or lump sums.
Maximum reimbursement rates of eligible costs

Research and technological development = 50% or 75%*
Demonstration activities = 50%
Other activities (including management) = 100%

(*) For participants that are non profit public bodies, secondary and higher education establishments, research organisations and SMEs.

So, if the salary of a researcher is included in the Research and Technological development, then does that mean that it's possible to only ask for 75% of it to the EC? (assuming the researcher is employed by a university).

So, after quite some time spent on reading the paperwork and talking with helpful staff, I finally understood how this system works. There are different amounts involved:

S: the salary of the researcher, corresponding to the gross amount, i.e. before tax. For instance, 50.000 euros per year.
r: the overhead asked by the host institution, which basically corresponds to the indirect costs of hosting the researcher (renting the office, paying the admin staff, etc). This is an agreement between the host institution and the european commission, usually calculated as a percentage of the salary. For instance, where I'm working now, it's 67%. In some places, it can go up to 100%.
T: the travel and equipments expenses. It basically depends on the expected number of conferences to attend per year, the meetings organised for the project, etc. For instance, based on 4 conferences per year, 2500 euros per conference, that makes 10.000 euros.
C = S + rS + T: the total cost of the researcher per year. For instance, that would be 50000 + 33500 + 10000 = 93500.
Req = 0.75 * C: is the requested amount to the commission (assuming the host institution belongs to: profit public bodies, secondary and higher education establishments, research organisations and SMEs, 0.5 otherwise). So, for the example, we would request 70.125 euros per year.

Note that the request amount is 10.000 euros above the gross salary of the researcher (deducting the travel costs). In other words, one could consider that the 25% the host institution has to pay are indirectly paid by giving an office and proving staff support (who, in general, would be paid anyway, EU project or not), and therefore it does not necessarily mean that the researcher has to find another funding source for the missing 25%.


No proper reply from professor after acceptance I had applied for an academic internship after my undergraduate studies. The professor has accepted me for the internship. But since then he has not properly replied to my emails. I need his letter for VISA purposes. How should I write an email to him asking for the same? I had sent an email to him regarding this but he has not replied to the email. The problem is that I can't write a proper email and also he is the director of the institute and is probably very busy.

Could you please help me with writing such an email. Also I am taking a year gap for this internship, so this is extremely important to me. I also want to convey him that this internship is extremely important to me.

I think the problem is not with the content of the email itself, but rather with the fact that the professor is busy -> doesn't respond to emails consistently. Therefore, you should somehow try to attract his attention/the attention of others if he is unavailable. Possible options include:

Having a clear email subject (e.g. a reply to the thread where you discussed your acceptance; mentioning that your request is related to the visa application, etc.)
Trying to call/email the department to establish ties with them. They may be able to assist you with the process & in some cases even write the letter for you.
Trying to reach other people in the lab. They can tell you whether the professor is away and whether there is a better way to reach him. Some of the other lab members may be international as well and, therefore, can provide you with additional information regarding the visa & your life post arrival.

Finally, it is likely that the professor is currently conferencing/vacationing. If none of the above helps, your best bet might be waiting and emailing again toward the end of the summer. It's no fun but delaying the start of your internship is better than not having one at all. In all of your communications, be polite and patient. That's the key to getting someone to help you. Good luck!


How to know when its time to quit grad school, due to my own failings I am in my second semester of a MS in engineering.

While classwork is fine, research is not going well. I wrote the first few pages of my thesis and basically everything was wrong: formatting, writing style, poor graphs and figures. The results my codes are calculating show that my method makes no improvement to current methodology and sometimes its actually worse.

My adviser and I keep having miscommunications, and I keep disappointing compared to what I originally showed when we first starting working together. He won't ever tell me directly that I am failing but I can sense his attitude while we talk.

Due to my job, classes, and thesis work, I have no hobbies and I only sleep every other day.

Is this a normal amount of struggle everyone goes through and I'm overthinking it. Or is this an indication that grad school is not for me?

If I do quit, I will not be able to get a job at a good engineering company due to an average GPA in undergrad.

EDIT: This is an edit for anyone else who might have tendencies to get stress paranoia and start spiraling down negative paths.

I entirely overestimated the situation, my adviser was perfectly chill about everything, and the issues I thought I was going to get reamed over, were discussed and resolved in about a minute. Instead of criticism, he helped explain a math issue I had, and even let me know some higher-level industry folks he knows were interested in my work.

PSA for people like me (who probably are going to be like me and still worry over everything), making mountains out molehills in your own head is not a wise course of action.

The results my codes are calculating show that my method makes no
  improvement to current methodology and sometimes its actually worse.

For a master's degree, there is usually no requirement that your research produce a successful result. One can make a contribution to science by showing others what doesn't work. But you may find that your new method is an improvement under certain circumstances. Or you may get an idea (after you get some sleep!) for improving your method. That's exactly what happened to me.

Given your lack of sleep and your state of mind, I'm not sure you should trust your impression that your advisor is disappointed in you. I recommend you have a heart-to-heart talk with your advisor, being as open as you can about all your concerns and fears, including that you are stressed out and not sleeping. It's very common for students to feel like failures at some point during a master's degree, and your advisor should be ready to help.

  I wrote the first few pages of my thesis and basically everything was
  wrong: formatting, writing style, poor graphs and figures.

Academic writing is a very different beast than the types of writing you've done before in school. No one is born knowing how to do it. Expect to have to do a lot of rewriting as you learn this skill.


When to use "I" in a master's thesis A similar question exists here however I don't feel that answers my specific question. Other questions on this topic seem to explain why "we" is primarily used in academic writing, which I understand.

However, one part of my thesis is reviewing work I studied during the first half of my master's year, not the research I did. In this context I feel I should use "I did this..." or "I read..." etc. Not we, like I use in the research part.

So should I be using "I" when reviewing the subjects/topics I studied? As opposed to introducing the research I did in which case I use "We"

The answer is to ask your supervisor. Theirs is the only opinion that matters. It is unlikely that anyone except your supervisor and maybe your committee members will read your thesis.

I prefer "I" but that's irrelevant. I'm not your adviser.


Do I have to wear academic regalia to a student's graduation? I have been a postdoc and including occasional lecturer for the last several years. A former student just invited me to his graduation. Would someone at my career stage at an American research university typically be expected to wear academic regalia at a graduation ceremony? I have not seen any specific guidance for this.

It sounds as if you are going to be seated in the audience as guest (e.g., sitting with the family or as if you were friend or family), so just wear 'regular' clothes. It still is a very nice thing to do and to show support.

If you are seated with the faculty (in those universities which have the faculty march in with the students), then those faculty who are part of the ceremony would wear regalia. If you are sitting with the faculty, you probably wouldn't be asking your question, as it is usually arranged in advance to do so (both to make sure there are enough faculty showing up, and to help with renting the regalia for those faculty who do not have their own. And - depending on the size of the university, there will need to be a lot of instructions of where to park, where to mass up and what time to show up in order to march in.).

If the student is asking you to 'hood' him/her (for PhD in many US universities, the advisor can come up to put the PhD hood on the candidate) then talk to the department to find out how to get included in the 'faculty' who are formally seated in the ceremony.


I submitted my own code on someone elses account I was flagged for plagiarism on a programming assignment. We get 3 submissions a day for the ~3 weeks that the project is open. I finished my project in about 1 week, but on one of those days I used my friend's computer to submit my assignment to the autograder (so I really got 4 submissions in one day). The undergraduate Honor Council at my college found me guilty of cheating on the assignment, and I'll have to report to another Honor Council with 5 professors evaluating my case and asking me questions to determine my ultimate punishment.

In all honestly, I just submitted on my friend's account to see if it would work (I was curious if they checked on submitting on peoples' accounts who weren't in the class). I still had ~2 weeks worth of submissions when I submitted my project for the final time, so I don't really think I had an unfair advantage over my peers.

Is this really a serious offense? The undergraduate council recommended to the official council that I get a 0 on the project (I actually got 100 on it), which would put me at a <= C- in the class (which is failing) given how heavily weighted this assignment was, but this seems rather ridiculous given it was all my code.

Given that the student Honor Council has already found you guilty of cheating, maintaining that what you did was simply out of curiosity does not seem like a good strategy.  I don't find that explanation so convincing myself: your "curiosity" got you an unfair advantage in the grading of the assignment.  Your position that this advantage was not relevant to the final outcome is really not the point: many if not most students who cheat on assignments and exams could have reached the same outcome honestly if only they had been more patient (and honest!).  If you were really "just curious", you could have asked about it, and you certainly could have submitted only the allowed total number of submissions in a single day.

The real question is whether you deserve the punishment you've thus far been given, of a 0 on the entire assignment.  Generally, when students don't follow all the rules of an assignment, they can reasonably expect to be penalized for it in some way, but the penalty need not be the entire value of the assignment.  I think your position should be that you agree that you did not follow the rules and that you did this out of a combination of curiosity and stupidity.  You can make a reasonable case that you did not violate any fundamental principles of the assignment: all the work you turned in was your own, and you got it 100% correct well before the final deadline.  So all in all you did more good work than bad.  You did exhibit poor judgment and agree that some penalty is reasonable.

I would suggest that you ask to be given the score that you got on the last attempt before you submitted on your friend's computer.  This score is undeniably legit, and giving you that score for the assignment seems like a nice compromise between giving no penalty for breaking the rules and ruining your entire course grade.

On the other hand, all this is to answer your question "Is this really a serious offense?"  (TL,DR: probably not too serious, but you did do something wrong.)  What I suggested above is really more a suggestion for what I think a just outcome of the faculty deliberation would be.  Depending upon how your system works, you may or may not have the opportunity to suggest a punishment.  As others have said, your real strategy here is to remain calm, explain all the facts as clearly as possible, accept that what you did is wrong and convey the impression that you are nevertheless a good student overall.  What they decide is really up to them.


What should I do if a coauthor, who has contributed the most among my coauthors, declined to be listed as a coauthor? For a paper with coauthors, what should I do if one coauthor, who I feel has contributed the most among my coauthors, declined to be listed as a coauthor and wished only to be acknowledged in the acknowledgements? The reason he gave for declining was that he did not think he has contributed significantly. The other coauthors knew this, but didn't say anything.

This happened once in the past, and at that time I did as requested by the coauthor, i.e. I removed his name from the list of authors and acknowledged him instead. The other coauthors still had their names as authors of the paper. I felt uneasy about it because I didn't think that it was right. I mean, if my second author did not think that he had contributed enough, why should the third and fourth authors stay? Of course the reader wouldn't know this, but I knew, and my third and fourth authors knew.

Now I am facing the same situation again.

I have previously asserted that a co-author has the right not to be recognized as a co-author, if that is her preference. If she is amenable to publication (as would appear to be the case here), then you may proceed with publication. (If not, then you would need to remove her contributions entirely, and then see if the paper is still salvageable in that form.)

However, you should make sure you have a written documentation of the coauthor's declining of credit. You should also make sure that you have explained clearly why you feel she should be co-author; perhaps you can include a list of the contributions of the other co-authors.


What's the editor's benefit in setting deadlines for manuscript revision? In many journals of my field, upon acceptance of a manuscript for publication with minor revisions, the editor sets a deadline (4 weeks, in many journals) for submission for the revised manuscript.

While I usually resubmit these papers as fast as possible, I don't see the benefit for the editor to set a deadline. After all, once a paper is “almost accepted”, the authors are motivated enough to get it over the final line, aren't they?

Editing a journal is a non-trivial exercise, something which tends to drag on forever and requires lots of pushing of reviewers and authors to complete their tasks on time. It is time-consuming. Without deadlines, reviewers and authors will submit their work arbitrarily late, making it very difficult to get each issue out on time.

Authors may well be motivated to get over the final line, but when there are other things to do and the possibility of delaying one piece of work yet another day, then it is easy to delay that work.


Career advice about a short stint at a mathematics institute as a postdoc I'm finishing my PhD, and am about to take up a postdoctoral/visiting professor position this Fall. I do have the option of taking leave for six months to attend a Mathematics institute, which is having a thematic year in a field of my interest.

It's clear that I need to be as productive as possible in the next three years to get a tenure-track position. Since I do not have a very specific problem that I'd like to work on with people at the institute, I'm worried that I'd be wasting six months of my time at the institute. On the other hand, its always nice to meet new people, make connections and learn new math.

I'd like to hear the community's experiences so I can make an informed decision. Thanks!

I did precisely what you're discussing (attend a semester program at a mathematics institute immediately after graduating), and I'd strongly encourage it.

You say you're worried about wasting six months of time because you don't have a specific problem to work on with the people there.  Unless the only work you're expecting to do in the next six months depends on someone who's at your postdoc institution, presumably you can expect to be at least as productive at the institute as at your postdoc.

But as a newly minted PhD, you want to be productive, but not just by continuing to work in the exact speciality you carve out in a thesis.  So you don't want to only be working on the specific problems you're already thinking about right now: you exactly want to encounter other perspectives and other problems and get some work done on those.

Which is basically the point of a thematic program.  Even if you aren't going in with a specific problem in mind, you may well discover one.  Someone may want to work on something with you, or may mention something as an open problem, or it may just come up while talking to people.  And even if it doesn't, and you end up doing most of your work by yourself in your office, you'll still get a lot of exposure to the broader state of your field.

Also, of course, you'll meet a lot of people, which may pay off down the road.  Even if you don't end up working on something with the person in the next office while you're there, you'll hear a lot about they're specialty, and perhaps a year from now suddenly realize that they're the perfect person to ask about something.


Face-saving way of asking whether audience is familiar with specific topic Sometimes I give a talk for a limited number of persons (typically well below 15). Here, the audience consists of persons from different subfields of the same fields. Consequently, I am often not familiar with the background of all persons in the audience. In the past, I sometimes was unsure whether all the attending persons are familiar with a specific topic that is considered basic in my subfield but might not in theirs. I then asked directly, whether they are familiar with the specific topic. The answer was almost always "yes" although later it turned out that the topic was not so clear to everybody.

How can I rephrase this question in order to get an honest answer?

When I give talks in similar situations, I typically assume that at least some of the audience members will be unfamiliar with much of what I think of as basic.  Your job is to "remind" them, without spending excessive time on the topic.  A good place to use this technique is with definitions.  For instance: "... a polynomial, for example 3x4-5x2+2x+6."  (The best way to teach most things, particularly definitions and algorithms, is with examples.)  You can do this fairly unobtrusively, so that those who don't recall the definition are reminded, while those who do are still not offended.

Another point to remember is that generally, it's good for some of your talk to be a refresher.  You might say something like "most of you are probably familiar with this, but just to make sure we're all on the same page..."  This material shouldn't be the majority of your talk, but 5 or 10 minutes of this is often very appropriate, say in a 25 minute talk.

In most talks I start by saying: "If you have questions as we go along, please ask."  If you get many questions on material that you think of as basic, be ready to slow your pace.  A variation on this is to have some worked examples early in your talk.  Give the audience time to think about a question, then ask audience members for the answer before revealing it on your slides.  Their responses (especially nonverbal) can give you a good sense of who knows what.  Typically, I talk with slides, but answer miscellaneous questions on a whiteboard.

A final option is to get to the room early, and try to talk one-on-one with the audience members, as they arrive.  If you ask them then, you may be more likely to get an honest answer.  Another version of this is to ask the seminar organizer (or whoever schedule you to give the talk) what knowledge they think is reasonable to assume of the audience.

To summarize,

Make educated guesses beforehand about what your audience knows (typically less than you would think), asking them (or the organizer) if possible.
Make liberal use of examples and "parenthetical explanations".
Plan for 20-30% of your talk to be review.
Adapt the speed of your presentation based on the feedback you get during the talk.


Should I post publications in preparation (or just submitted) on my CV? If I have works that are almost submitted to journals, or are in journal review, is it appropriate to include these on my CV?

Don't put anything in your CV you cannot justify if asked. A CV is not just a list of your accomplishments, it's a list of material you can provide to a recruiting committee in order to help them make a decision.

In a same way that if you claim to have a given degree, you should be ready to provide the corresponding credentials, if you claim to you have a paper under review, you should be ready to provide the submission.

In other words, you can list in your CV your submitted work, but not the pieces of work that are "almost submitted", unless you're ready to provide the draft if asked (the question is: if the draft is not submitted, that probably means it's not ready, therefore can you provide it?). If it's possible with the journal/conference policy, you can even put your submitted version on a pre-print site, such as arXiv.

On going work can go into the "research statement" part of your CV, where you can explain the different ideas you're working on, and even give the key concepts.


Should I finish my PhD? I have one more year until finishing my PhD. I feel that I will have a mediocre PhD thesis, at best. I feel like quitting, and I had this feeling even from the start of the PhD. I felt even from the beginning that something is wrong and I should not continue but I continued anyway because I was very passionate about the subject that my thesis is supposed to be focused on. (Of course I did not get to do exactly what I thought I would do, but still... the things that I worked on belonged somehow to that area of study that I always interested in). I struggled a lot during these PhD years, and that's mainly because I did not get much help. Now I feel exhausted. I don't have any energy left to continue. I really feel that the reason I got into this situation is because people that were supposed to help me think very low of me... And they just left me to deal with my problems all by myself. Probably because they think I wasn't good enough to deserve much of their attention.

I have a few publications. In principle, I have all I need in order to finish. But somehow I feel like it is worthless. I am aware that it would be very stupid to quit right now. I don't know what to do. I don't know whether I will continue my work after the PhD graduation.

Your mental health is the most important factor in this equation. PhD's are hard, and demotivating, and exhausting. But the best PhD is a completed PhD! It sounds like you've got everything you need to finish, you just need to full together the threads that make up a thesis.

Often people get most of the way through a PhD and have not taken a holiday in years. When was the last time you took a holiday or just some time off?

Make a plan of exactly what is needed to finish. What are your publication requirements? Structure out what the thesis will look like and define any loose ends that need to be finished. Make a list of these things and plan out - week-by-week when you want these completed by. If the end is in sight, you'll find that motivation will return - like a marathon running who has hit the wall but can see light at the end of a tunnel. These feelings are so natural - almost everyone I know who did a PhD experienced it!

And with regards to you thinking your thesis is mediocre at best. EVERYONE thinks that! I'm not going to tell you that it's better (because I don't know). But statistically, half of PhD graduates wrote a thesis that is average or worse than average. I know mine certainly was! Who cares? If you do enough to pass, then it really doesn't matter. And the saving grace is that very few people will ever read and understand the thesis enough to work that out!

You've got this! Remember to prioritise a good work-life balance as in the long run, it will serve you far more effectively than if you crammed for the next year!


Situations where changes in advisor/lab interests makes you feel lost I'm currently enrolled in an MS/PhD integrated program in a school in Korea. I was originally planning to study in the US, but I wasn't confident that I'd get funding and the lab/advisor that I'd met at my home school fit with me well.

After having a meet up session with the advisor, things were great for the past year or so. I was able to study and do research (mainly help PhD's with their projects while thinking about what I want to do). All was good but recently the professor has become more of a businessman than a researcher. He's hardly at school and is always attending meetings or networking events. There is barely any supervision or guidance. I read this Quora answer and it reminded me of my advisor.

I'm not here to judge another person's personal life choices, but I feel like I need some insight into what to do in these situations because it's been quite distressful as myself and many others in the lab are being forced to work on projects that bring in funding, which are usually irrelevant to our own interests.

Many of my peers have brought up how they're thinking of changing advisors to other professors within the same department, some have outright said they're thinking of dropping out and looking for a job. It was manageable before, because we would just be able to take care of tasks and do our own thing. However, the funding situation of the lab has recently become a bit more dire and hence the desperation on the professor's side.

I don't want to quit, I love the environment of a lab and school. How should a graduate student approach his advisor regarding conflicting research interests? I've tried to talk to him about it before, but it didn't go too well (he was mostly reluctant to let me do my own research). Is there any particular way that I should be approaching this issue? Thanks in advance.

Just for some background information, I'm enrolled in computer science and do research on machine learning/deep learning.

The desirability of such a situation varies from person to person. Some people, but I doubt many, would love the independence. But others (most?) need more guidance, especially at the start and possibly near the end.

But if you need more guidance then you need to find a way to get it. A co-advisor? A different advisor? Something.

But just going along as you are is probably counterproductive.

An outside possibility is that, provided the advisors "business" interest has research potential, that you could get involved with that as a source of ideas and research opportunities. I don't know if this is actually possible or desirable, of course.


How to cite papers where the names are sorted? I have a paper with autors A, B, C and D. Their names appear sorted by last name, so the order of the authors does not really say anything about their role in the paper.

When I cite this with the style that I currently use, I obtain “A et al, 2014”. This is logically, but B was the speaker and D is the professor of the workgroup.

Should I now cite this as “A et al”, or change the order of the names and make it “D et al” or “B et al”? The second version only works since I know the roles in the workgroup. With other papers, I would not know how to do this.

I could also just cite it as “[1]” and not worry about that at all …

What would be a good way to deal with this in general?

If the authors are listed as Adams, Brown, Clinton, Dylan, you cannot cite it as Brown et al. The standard thing is to simply cite Adams et al.

If you are one of the authors and you cite it.
Let's say that you are Brown and you now have an article with Eldridge. Then you can write the following:

  ... as was shown by the first author in collaboration with Adams et al. [ABCD14].

This way you cite the paper properly and at the same time, you make it clear that you are one of its authors.


Why don't publication venues systematically make the LaTeX source of papers available? I wonder why most publication venues don't systematically make the LaTeX source for published papers available? (which implies systematically asking authors for the LaTex source)

LaTex source are more machine readable than PDFs, and make it easier for humans to reuse part of it (e.g. math equation or figures), amongst other advantages. I fail to see any downside.

(I am aware that some authors write their publications using other tools such as Microsoft Word: let's ignore it.)

I suspect that this is a solution in search of a problem. Most likely journals aren't making LaTeX versions of papers available because they don't see a demand for such a service from the side of the readers; this would take effort to implement and maintain; and some authors would object to the idea of making it easier for others to reuse (read: plagiarize) their papers. In other words, publishers simply have (or at least think they have) better things to do with their time and money.

It should be noted that arXiv does make LaTeX source code available, and in fact will only accept submissions in the original source code rather than as PDFs (for papers that were written in LaTeX), so in those areas of math and physics where uploading preprint versions of one's paper to arXiv is the norm, this "problem" (such that it is) is already solved.


Status of submitted paper changed - why? Two months ago, I submitted a (mathematical) paper to a journal. On the journal's website, there is a status concerning the paper, e.g. "Rejected", "Awaiting reviewer selection" and so on.

About two weeks ago, the submitted paper's status was "Awaiting reviewer assignment", and then it changed to "Awaiting reviewer selection". This seems more like a backtrack in terms of statuses rather than a step forward to get the paper reviewed (correct me if I'm wrong).

Now my question is:

What could be the reason for that step back in terms of statuses?

(I always thought that if somebody declines to review the paper for some reason, then it will be rejected?)

What could be the reason for that step back in terms of statuses?

Without knowing the journal in detail, there is no way to know. Based on the names of the statuses, it seems possible that the editor has previously asked a few reviewers, but too many declined and the editor is now again on the hunt for more reviewers. This is not at all uncommon, and says nothing about the quality of your paper. Based on personal experience, at least 50% of all review requests are declined, and that is for reviewers that I know personally. When I have to ask reviewers that I as an editor do not personally know, the acceptance rate for reviews is closer to 20%.

That being said, for many submission systems the various author-visible statuses are just not very useful. I suggest you stop checking the status of your paper in the system and instead wait for mail from the editor.

  (I always thought that if somebody declines to review the paper for some reason, then it will be rejected?)

No, why would this be? Reviewers have not actually read the paper when they decline the review. And, as I said above, many or most review requests are declined, usually because the prospective reviewer simply does not have the time.


How to create incentive for students to take surveys? I started to do questionnaires and surveys to assess my teaching methods and the learning gain of my students. How to convince the students to participate in these surveys? Is it OK to give small course credits for taking these surveys (say 1%)? otherwise, what are the incentive for the students to take these survey?

I think that giving some small course credit for a survey like that can be a good idea. Taking the IRB protocols as a model, you might give course credit for the survey, and also some alternate assignment for a student who has some point of principle that makes them not want to disclose personal info like that. Then you've really covered your bases.

In my own case, I give a study survey like that after the first exam. Since this happens to be in sequence and in the same format as three earlier quizzes, I think many students assume that it's for credit and complete it without me saying one way or the other (it's not, and has a different title, but it serendipitously works in my favor that way).


Licence that converts to GPL after publication but is copyrighted prior to publication I would like to post an repository on github that includes data and analysis code in R. The analysis and data forms part of a journal article submission. I'm happy for people to view the code and data prior to publication (in particular, it might be an easy way for reviewers to examine the code). However, I do not want anyone publishing  analyses of the data prior to acceptance and publication of the journal article. After publication, I want to encourage people to re-analyse, re-use, re-publish (e.g., with a GPL licence with an encouragement to attribute).

Obviously, I could just keep the data and analysis code a secret until after publication, but I thought an appropriately worded licence might be more appropriate. I thought about just writing in plain English that the work is copyrighted at this time, and will be converted to GPL at a later date following publication.

Is there a standard way of licensing data and code so that people cannot republish the data and code until the corresponding publication has been published?
Or is it better just to keep the data and code secret until after publication?

UPDATE: I suppose there is a legal perspective to this, but I know that academia has its own norms and conventions regarding attribution and respecting the wishes of authors. So I'd be particularly interested in answers framed in that context. I.e., My broader aim is to be the first to publish my own research, generally get attribution, but also allow others to build on that work. So I'd be interested also in what is considered good practice when you are in the situation of wanting to share data and code while an article is being peer reviewed, but not wanting to lose your right of first publication.

Honestly, I doubt that copyright protection is of any use. The copyright on the code itself does not* extend to data produced using the code. Similarly, the copyright you would hold on the paper submission covers* that particular presentation of the data, but not the data itself. So as long as someone is physically able to view your data, I believe there is no legal avenue to prohibit them from doing their own analysis on their data.

However, for another researcher to take the output of your code and perform their own analysis in an attempt to scoop you, when they know you have your own paper doing the same analysis pending, is ethically very questionable. If it came to light that something like this happened, I think the academic community would strongly frown on it. That's a very strong incentive for any other researcher not to do this, and so I personally wouldn't worry about it.

Besides, if it does happen, the other researcher will have to cite your code anyway so you still get credit. This can actually be a good thing. I would recommend including in your code a notice of the form

  Please cite the following reference if you use the results of this code in a publication:

  [reference to paper or code]

(see this example from my own publication history) If you're worried about someone else abandoning all pretense of ethics and just using your results without citing them, rest assured that it is very difficult to pull that off, and it constitutes academic fraud, which is a career-ender if it's discovered.

And finally, as a practical matter, you have a very large head start on anyone else who might want to publish an analysis of the outcome of your code. Don't underestimate the time and effort it takes for someone else to go through your code in enough detail to learn what it does and figure out how to use it enough to generate original results, and then to write and submit a paper and have it reviewed, typeset, and published.

One more point worth mentioning:

  So I'd be interested also in what is considered good practice when you are in the situation of wanting to share data and code while an article is being peer reviewed, but not wanting to lose your right of first publication.

You don't have a right of first publication. Not legally, anyway. If you want to ensure that you are the first one to have an opportunity to publish a paper based on some result, the standard practice is to keep the result private until you are close to publishing the paper yourself. But keep in mind that "publishing" in this context doesn't have to be peer reviewed. For instance, in physics it's very common to put a paper on arXiv before submitting it to a journal. That establishes the authors' claim to the result before it enters the peer review process.

*informed layperson speculation; see a lawyer for a definitive statement


Editor assignment pending after "review competed" I submitted journal in the field of psychometrics about one year ago.  Three weeks ago, the status was changed to "review completed".  However, today it is changed into "editor assignment pending".  I am not sure what this means. Can you help?

It's not certain what it means without knowing the particulars of the journal's internal handling, but a likely meaning is that the paper has been handed off from the associate editor who has been handling the reviewing to a senior editor to finalize the decision.  In many journals, an associate editor provides a recommendation for the decision, but a senior editor actually makes the decision; if there are multiple senior editors, then a brief gap before one of them takes up the paper would create the observed behavior.

Bottom line: you are likely to see a decision shortly.


Correct way of referencing equations, figures and tables inline? What is the correct way of referencing an equation, figure of table inline?

I would currently say something like:

  It can be seen from Equation (11) that . . .

or

  Inspection of Figure (3) shows . . .

Is this method—capital letter for Equation/Figure/Table and the actual reference in round brackets—acceptable?

As far as I know, the standard in mathematics is:

Put parentheses around equation numbers; don't use the word "Equation" unless after a period.
"Figure/Table/Algorithm X", with no parentheses. Parentheses are reserved for equations, and square brackets for citations.

Example:

  This follows from (11). Equation (12) does not hold in this case. See Figure 13 for further information.

In your LaTeX source, use from~\eqref{someref} and Figure~\ref{someother}, with nonbreaking spaces and \eqref for the equations.

(The standard in mathematics is LaTeX; Word is often frowned upon.)

That said, as already stated in aeismail's answer, every journal has its own house style, which may override the standard.

EDIT: see also the answers to Referencing non-equations as to why adding "Equation" is not a good idea: not all numbered formulas are equations.


How do I write a white paper for a research plan? I will be starting my second semester of my master's program in a couple of weeks. I've been going back and forth with a professor I want to do my thesis under and he has asked to me to write a white paper outlining my research plan.
While what he's asking seems pretty straight forward on the surface, I'm not sure how to even get started on writing one. I've read through other questions on this site as well as articles on google, but I'm rather lost as this is a bit new to me. Any advice on how/where to start is appreciated.

The definition of a "white paper" seems rather loose: see here and here, for example. I would check with your supervisor to make sure of what he has in mind, so that you don't write something overly detailed or overly brief. My guess is that the difference between a white paper and a proposal is largely formal: the latter has to be structured and formatted according to the requirements of the institution you are submitting it to; the former gives you a bit more leeway. Regardless, based on my experience and on this book I would structure it as follows:

Abstract - I find it useful to draft it at the beginning, for your own guidance, and re-write it once the rest of the proposal is
completed so that it reflects the proposal best and it really
"pitches" your research project.

Introduction/Background - a summary of the state of the art in your research field, leading to...

Statement of need/Problem - where you define a gap in the existing knowledge that you want to address, or something that is
considered correct but that you want to challenge for whatever reason
(to be stated).

Objectives/Aims/Research questions - your goals, hypothesis to be tested and/or research question(s) to be answered.

Approach/strategy - similar to the "Material and Methods" of a research paper.

Significance/Impact - why you think your question is worth for you to research, or your goal to pursue, and for an institution to finance your effort.


What are some examples of famous scholars with low h-index? The h-index is often used to measure a 'quality' of a scholar, and it is also often criticized as a lousy measure, since there is more into quality than just the number of papers and citations.
What are some examples of arguably great and famous scientists with low h-index?

You can find a lot of historical examples, from people whose careers predated the publish-or-perish culture. A striking more recent example is Peter Higgs, who was awarded (among other honors) the 2013 Nobel prize in physics. Whether that makes him a "great" physicist is of course arguable, but he clearly did important work. However,

Peter Higgs, the British physicist who gave his name to the Higgs boson, believes no university would employ him in today's academic system because he would not be considered "productive" enough.
The emeritus professor at Edinburgh University, who says he has never sent an email, browsed the internet or even made a mobile phone call, published fewer than 10 papers after his groundbreaking work, which identified the mechanism by which subatomic material acquires mass, was published in 1964.

This article estimated his h-index to be about 9, but I've seen estimates of around 11 too. Either way, it's a very low number for the field by today's standards, for an established professor. To wit,

Speaking to the Guardian en route to Stockholm to receive the 2013 Nobel prize for science, Higgs, 84, said he would almost certainly have been sacked had he not been nominated for the Nobel in 1980.
Edinburgh University's authorities then took the view, he later learned, that he "might get a Nobel prize – and if he doesn't we can always get rid of him".


Non academic career for PhD in Biology This question has asked previously for PhD in mathematics and computer science in this StackExchange forum. However, the situation will be completely different for Biology graduate because of the skills we learn during our PhD. Math and CS graduates have lot of open options (?) looking at their quantitative reasoning skills, which are not enough for biology. We learn lot of logic, reasoning and statistics, but is that enough to survive in a highly competitive world?. So I was wondering: is there any alternative career option for PhDs in biology?

P.S: There are few options I am already aware of, like teaching in school/university, quality control posts at various firms, R&D in pharmaceutical companies. I was wondering if there are any other options which are not very obvious from our skills.

Update (18 Sep 2015)

After reading comments and answers, Following more options have raised

Science communication
Librarian
NGO and firms for data analysis

There have actually been some studies (if I recall Mike The Mad Biologist's blog covered them awhile back) suggesting that biology graduate students are somewhat less happy than their peers because many of the specialized skills they pick up aren't immediately transferrable. For some aspects of "biology" this isn't true - for example, a mathematical biologist is likely just as qualified to exit into a quantitative field as an applied mathematics student, some fields of biology involve code, etc.

Failing that, some other options colleagues who are biologists have pursued:

Government positions. Some of these are "academia-lite", some of them are markedly different, but there are several branches of government that hire biologists in some form.
Teaching at the high school level. You're likely overqualified, but that's not a bad thing, and there are private high schools that very much value "X% of our faculty have PhDs..." as something to tell parents.
As you mention knowing exist already, there are biotech companies that exist, and employ biologists in many capacities.
Conservation organizations, private foundations, etc. may be of interest, especially if you're more ecology oriented.
Depending on your research area, what you did, etc. you may be able to brand yourself as a "data scientist" - at the moment it's pretty vague as to what exactly that means.
Science communication - university offices that do outreach, news organizations, etc.
With the addition of an MLS, a career as a research librarian is also potentially an option.


Should systematic reviews be submitted to journals as original or review articles? In the Information for Authors of several (health) related journals, manuscript types may include original research and review articles, among others.

I thought systematic reviews (whether quantitative or qualitative) should be submitted as review submissions, as opposed to, for example, original studies with novel findings based on data collected or analyzed by authors. However, the guides in those journals say a review requires an unstructured abstract, as in narrative reviews.

In this answer, review articles can be considered original observations. So why do some journals distinguish between review articles and original research? And, under which category should systematic reviews be submitted to these journals?

I can see a good case to be made on either side:

A systematic review, unlike a more traditional narrative review, is often an explicit numerical meta-analysis of prior data.  Its systematicity allows it to be an actual experiment with objectively verifiable conclusions, and thus it may be reasonably considered original research on a new data set drawn from the literature.
Systematic reviews still, however, are organization and analysis of other studies, and so could be grouped in with other reviews.

Since both of these are reasonable, I suspect that there is no way to tell which perspective a particular publication subscribes to without reading their guidance to authors or asking their editorial staff (who will no doubt be happy to answer the question).


Two figures are redrawn and merged into one. Are reproduction permissions required in this case? I have two questions regarding writing of survey papers

Firstly, if one of the technical papers reviewed has a number of figures. Take for example: Figure 4 is "Data model" and Figure 8 is "Mechanism structure". In the survey paper is it enough modification (for a waver of official permission) to merge these two into one figure and cite. Say, Figure X: Data model and Mechanism Structure adapted from [ref]?

Secondly, in the case when author A proposes "Data model" and "mechanism structure" in paper [30] and [35] i.e four entirely different diagrams. Is it sufficient as modification (for a waver for official permission) if in a survey, all four combined in one figure.

Thanks in advance

Combining other people's published figures to create a new figure does not allow you to waive requests for permission to reproduce a figure. Each individual component is someone else's intellectual property, and they have the right to be credited for the work. Note that many journals have simple mechanisms for requests to reproduce, and usually it's just a matter of asking for the necessary permission.

Simply redrawing someone else's figures for a part (a) and (b)-type figure does not spare you from requesting permissions. If you have completely redrawn and combined figures (for example, to illustrate how the two figures are more closely connected than in the originals), then you are creating a new intellectual contribution. You need to cite the original work that you've adapted, but you would not be reproducing the figures, and therefore would most likely not need to secure reproduction permissions.


Is it appropriate to ask for a $220k piece of equipment on an ESI R01 application to the NIH? I'm an early stage investigator (ESI) working on an NIH-R01 application where I am proposing a good amount of experiments that necessitate this piece of equipment that costs $220,000. This piece of equipment exists on my campus, but it's located a couple of miles away from my lab, which requires me or someone from my lab to carry cells by car or on public transit. Since the equipment is used to measure cellular metabolic function, I've always been wary about carrying my cells all the way there. Anyhow, I'd like to buy this piece of equipment in my first year of the R01.
The good thing is that adding the $220k to my year 1 budget doesn't exceed the $500k limit/year.
Now I'm wondering if it's appropriate to request such an expensive piece of equipment as an early stage investigator. I am thinking that the reviewers may comment on the fact that I already collected a significant amount of prelim data in collaboration with another lab... so why not continue to do so? Why the need to purchase the equipment?
Do you think such request could tank a grant application?
Thanks for your input!

Get the tool that helps you do the job properly and efficiently.  Your previous experience and history of using another instrument makes your case stronger, not weaker.  Shows you will use the machine.  It's not some new angle, for you, that might get abandoned.
I really doubt NIH gets into the minutia of where competing machines are located.  If you get any static from the school or NIH, just put on a confident face and say "I need it...it's a workhorse machine for my lab."  Don't be bashful.  Fortune favors the bold.
The one thing is I would think about if you will be able to maintain it properly.  E.g. if you're a synthesist, probably not best to buy an SEM.  You almost need a technician or a group of SEM only types to keep it aligned and the like. But if you think you can handle running it and keeping it going, go for it.  Maybe mentally budget some ongoing costs for techassists from the vendor.  So if you are going to struggle with it, or it will be a waste since you have a hard time keeping it operating, then pass and use the remote facility instead.


Should I still consider this person as an advisor? I was discussing some matters with a potential MSc thesis advisor. However, when I pointed out a mistake they had made, they kept on stubbornly denying it and just dismissed my claims. This annoyed me as I had spent a lot of time verifying that
 it was in fact a mistake and building up strong evidence, and this professor didn't even seem to make an effort to listen to my arguments. In the end I had to give up because I was not making any progress.

In your opinion, should I still consider this person as an advisor? The thesis will take up 2 semesters of work. I fear that if my advisor is not able to admit their own mistakes, this could seriously compromise my work. Should I interpret this episode as a red flag that tells me not to work with this person? Or is it possible that as time goes on they would start trusting me better and consequently be more willing to accept my remarks? Keep in mind that aside from what I just said, this person seemed the ideal advisor for me right now.

You might want to talk with people who worked with the person and try to understand if he tends to overlook remarks from others or situation spesific reasons led to this particular problem for you. You can not jujge someone with only one behaviour but I think you can not ignore it eather. I would say just try to learn more about the person.


Common grade curving or scaling techniques I'm working on a small application which would hypothetically allow instructors to perform a variety of grade transformation techniques on a given distribution. (I don't intend for the application to actually be used)

What are some of the more commonly used transformation techniques assuming a distribution is ~normally distributed? Online resources on the topic are somewhat sparse.

It's not perfect, but I often use a piecewise linear transformation.  Specifically, I fix some cutoffs (typically the cutoff between a B+ and an A-, between C+ and B-, between D+ and C-, and between F and D) and then scale all the A's linearly with their range, the B's linearly in their range, and so on.


How would you write to your in-class team, that you are going to drop the class, leaving no hard feelings? We have a project to do with them but I don't have the time and am not sure if this email is appropriate for them. What do you think? I would greatly appreciate your advice.
Here is what I am thinking of sending them.
Hello guys,
Hope you having a good weekend
I’m writing to you to let you know that unfortunately and for personal reasons, I have to drop this class. I have sent an email to the professor, so he should be aware of it very soon.
I hope you understand, and I wish you guys all the best on the project.
Sincerely,

Your suggestion looks fine.  I would consider making an offer to bring them up to speed on anything you have been working on that could help them out.


About Acknowledgements part I had a research stay abroad in an Institute 2 years ago. A short while after leaving institute (about 1 month later) I submitted an article related to my work there to a journal. Recently my article has been accepted to publish.
As I had an email address belongs to hosting server of the institute where I was working there, I want to write that as my email address. Is it right to write email address and the name of institute as the contact address for my article whiles I have left there? In addition,

This may vary from field to field, but in my experience (chemistry) it is always the case that you list your affiliation as the institution(s) where you performed your work; where appropriate, you can list more than one affiliation. In the case that an author's affiliation has changed since the work was performed, the convention is to add an additional "Currently at" or "Presently at" affiliation - your publisher would be able to give the details of how to do this for your article.

For an example of a publisher's take on this, see this excerpt from the ACS publications author guidelines:

  Institution Address: The author affiliation(s) listed should be the institution(s) where the work was conducted. If the present address of an author differs from that at which the work was done, that address should be given in an Author Information note


Using up grant money before a deadline I am aware that grants often only provide the earned money over a certain period of time. And if the money is not used up by the end of that period you lose access to it. Are there ways to effectively spend this money so it does not go completely to waste?

Note: A previous version of this question asked about setting up shell companies, which is why some answers address them. That part of the question was removed.

Things to do (to the extent allowed by the terms of the grant)

Buy work laptops or other equipment.
Visit someone, send a student to visit someone, or invite a guest.
Depending on how quick the "quickly" is, go to a conference or organize a small workshop, or a summer/winter school.
Hold a networking event with your research group, or together with another group of possible collaborators, possible or actual.
If you have suitable publications, buy golden open access for one of them.

Things not to do

Try to get the money to yourself (except NSF grants in USA and summer salary). Try to keep it for later. Try to use it on something out of scope of the grant, like personal benefits without scientific value.


I made a mistake of staying with my PhD even when I had lost interest in it. Should I continue with my academic dream? I had lost interest in my PhD topic during second year of my PhD. However, I continued. I thought, I shouldn't leave something halfway. My topic is "numerical modeling of shot peening process". Example publication (: paper)
I was involved in simulations only and not experimental work.
In my naivety, I thought, I shouldn't leave my PhD after 2.5 years and I should focus on getting published and return back to my home country for academia.
It took me 5 years to submit my thesis and now I just have 3 papers and no postdoc job offers. My PhD is not rigorous and though I can publish many more Q1 papers on the topic, I don't enjoy the topic. I love doing research though.
I want to try for academia. For that, one needs at least two years of postdoctoral experience. Should I continue with a postdoc in a similar topic as my advisor has offered me one? Is it common to not enjoy one's own PhD topic?
I am just frustrated with myself for not leaving the PhD earlier and now I am stuck with a poor CV. I don't know what I am doing with my life.

I'm not a personal or employment counsellor, but you should probably visit one.
However,  I think the only big mistake you made was to be born in the year you were, leading up to finishing your degree in a period that is very difficult for academics generally with an unfavorable job market and, then, along comes the pandemic. It isn't you, of course. Being depressed is pretty natural as long as it doesn't reach the level of a medical condition.
But, and this is employment advice, I guess, do what you have to do to (a) get through this period with short term or less-than-ideal employment and (b) use whatever opportunities you have to move your research to an area that you are happier with. Develop contacts with people who do interesting things and who can potentially help you move on.
You can't have the past back to do over your previous life. But you can take opportunities to move to a better place. It won't be easy, but the failure is with the general systems, not with yourself.
I was one who also finished up at a time of turmoil in the academic market and had to compromise drastically to stay in academia. But it worked out over time, and not quickly. I was able to find a job that worked, if not ideal, in a place that I enjoyed and developed some contacts and relationships that helped me move to a better situation. Make do for a time so that you can make better later. Really, it is about all one can do.


How will failing a PhD qualifying exam affect admission to other PhD programs in the future? My son, 25, just got notified that he didn't pass his qualifier the second time around so he's been dropped from his PhD program.

As a parent, I only want my child to be successfully happy, both in his personal and social life.  It's disheartening and heartbreaking to know that all his hard work and countless hours of studying and burying deep in papers can all fall apart just like that because a committee wills him not good enough for them.  He wasn't even pursuing a PhD.  He was working on his MS in EE and one of his professors saw potential in him so she encouraged him to pursue a PhD with full funding.  He will leave the program with a terminal MS (which he had already earned before entering the PhD program).

On the exterior, he says he's fine with the outcome and can't wait to get into the real workforce.  However, internally, I can sense he is battling with disappointment and alienation from his advisors and department, preferably the people he works with.  I can only advise him to rethink his future 5 years from now where he'll be an accomplished Engineer with loads of work experience under his belt or a recent PhD graduate looking for a job.  On the phone, I assured him, "you didn't fail, they failed you."

My son will remain with his department until the end of the academic school year.  However, how will being dropped from his program affect his transcripts if he should want to reapply at another university?

Just because your son failed a qualifying exam for university X doesn't mean he's not qualified to get a PhD at all.

The chances of this affecting future PhD admissions are slim as they would only consider the current qualification and skill-set of the candidate.

  ...you didn't fail, they failed you.

This reminds me about Thomas Edison Mother's Letter. You said the right thing to your son! Because, more than anything else, he shouldn't lose his self-confidence.

You believe in your son and so does his MS advisor. However, whether he has the potential or not, talk to him and find out whether he has the passion for research. PhD requires more of perseverance than skill.

If he still got the interest, then by all means encourage him to apply again to another university.

My best wishes!


How can I thank a senior faculty who's written me a good reference which helped me land a desirable job? I recently got a good job and I want to thank a very senior professor in my department, who spent time to write me a very good reference.

I am thinking maybe to give him a thank you card when I go to see him before leaving the department.

I come from a culture where gift-giving is considered obligatory if someone has helped you to achieve something major. I'm not sure this is appropriate in the UK context.

Any ideas?

A thank you card is definitely a good idea and I cannot see that it would be considered inappropriate. If you are from abroad, a little something typical of your country of origin may also be appropriate. Like a small box of traditional sweets, a little traditional doll, a fan, or something like that. I have had this kind of little things given to me by students.

Also, the university will probably have a policy on gifts which you may be able to locate on their web site. The general idea is that it should not be something worth a significant amount of money.

Rather than asking a classmate, I would ask a junior faculty for what goes as the norm. A classmate may be as inexperienced in this as you are, because the rules in academia can be significantly different from other parts of society.


What does non-exclusive publishing rights mean? I have read on open-access journals that some of them allow non-exclusive publishing rights. What does this mean exactly? Is there a general open access policy or consensus about what these publishing rights should be?

Does this mean that I can publish my article in other journals too? Wouldn't that be considered plagiarism, or at least reduce the citations to the original article in the first journal? Does this mean that the author(s) is/are allowed to only self-archive their article on a repository website but cannot publish it elsewhere?

I have also seen this term on the website of Directory of Open Access Journals. So, I suspect that this has to do with open-access policies.

I suspect you're seeing "non-exclusive distribution rights", which means the journal gets the right to distribute the paper, but it's not an exclusive one. Other venues, such as arXiv or ResearchGate, can also distribute it.

If you have an open access paper, presumably it uses the CCBYA license, which means any use, distribution and reproduction in any medium is permissible (i.e. you can publish it elsewhere) as long as the original authors are credited. Journal licenses that only allow the authors to self-archive are more restrictive and usually indicate that the paper isn't open access.

This doesn't mean you can publish your article in other journals. Most journals will have policies that all submitted content must be novel, and if you've already published the paper it's no longer novel.