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Applying for PhD after a poor master's
I am attempting to apply for a PhD but made rather a mess of my masters. Advice from anyone involved in the process is appreciated.
I am applying in the UK, and have a good bachelor's, which is all that is necesary for funding. I worked for 2 years before doing a master's. My field is computer science or bioinformatics.
The master's went wrong - I failed about half of my modules, although I passed them on retake. I produced a good project, but did not impress my supervisor. He doesn't dislike me, I just just ended up looking flaky. Regarding what went wrong, on the one hand, my cohort had an exceptionally high failure rate, but on the other I didn't work hard enough, and got quite depressed after failing some of the first set of exams.
There is a reasonable question over whether I would be suited for a PhD, but you could say that about anything hard that I try and do next.
I need a bounce-back plan. What can I do to mitigate the damage? How bad is the damage? Do you accept candidates with less than ideal transcripts and so-so references, given a good work history and supportive references from earlier supervisors?

The answers here might be relevant: http://academia.stackexchange.com/questions/973/phd-opportunities-when-lacking-publications

Many votes no answers, although Bravo's link is useful.

RE Bravo, I should add that although I lack publications, in my field and country, it is not normal for MSc students to publish. But I have a few idea, and was thinking it would be a way to cancel the transcript...

Delay applying for a year and work on a new project, where you can perform much better (now that you have more experience). Get a publication out of that and work with someone new, who will write you a good recommendation letter.
I know for a fact that many labs are very interested in getting bioinformaticians, so it shouldn't be hard if you are not looking for a great salary (which you shouldn't be: this is a career investment).

Personally, I have seen some people that were very good in their Masters totally screw up their PhD. And other people are not doing very good in the Masters but doing a great PhD after and get an academic position. A PhD is long time, so be sure that you like the subject, be sure that you can publish within the subject. You have to be comfortable with the people you will working with. If you can work with the people that will offer you a PhD before starting the PhD, that is a very good point. That maybe out of the question but even after 6 months or one year, if you see that not doing it, that better to leave and try to find another PhD. You can do well on your second PhD and get an academic position, I know someone who has done this.
If you don't find a PhD that you feel is good for you it's definitely better to wait. Going back to work or doing an other Master, but in a related field. That gives you more experience and more time to find a good PhD subject.
When you start your PhD it's kind to be like in a tunnel, sometime you never really see the end. I think most of people get discouraged at one time in their PhD, even the better, you really need to believe in yourself.
The main problem by doing a PhD after a not so good Master is that you will have more difficulty to find a good PhD subject. You can definitely find one but you have to find a good one for you. If nobody wants a PhD subject, there is a reason. That's not mean that it's bad subject but you have to figure out why it's less attractive.
Some questions that may help you:

Did you mentor have previous PhD candidates and how did those PhD candidates end up? Generally when there is not a full transparency from the mentor there is a problem.
Are you comfortable with your mentor and the team that you will working with  (if there is a team)? Can you talk freely? If it's not comfortable when starting I don't think it's will going better with the stress of the PhD.
Is the plan of action of the PhD well defined?
When can you expect the first publication? For example if the mentor said you that there is a publication in progress and they can add your name to it that a good point.
Do you feel comfortable with the subject or does it look too hard? Especially if you have to write a program or build an experiment. You have to estimate the time that it will take you and if you can get publication from this. Some mentors don't hesitate to take a PhD candidate just for coding as cheap workforce.

Hope it helps, good luck!


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Incentives for professors to write recommendation letters
Is one incentive their ability to communicate their perceptiveness to people in their general community?
Are there other incentives?

Do you mean, 'do professors get anything out of writing recommendation letters'? Is that your question?

The principal reason for writing any letter of recommendation is to benefit the person for whom you are writing it.  If a student is talented, helping him or her get into a good program is its own incentive.  I can't imagine writing a letter with the motive of showing off my perceptiveness.
An additional motive is that others wrote letters for the writer once, and he/she can show gratitude by paying it forward.  From David Keyes' excellent essay on procuring reference letters:

Everyone in a position to write a career-changing letter of reference
  is there by the grace of earlier generations of mentors at school or
  work who poured their lives into today's writer and then wrote about
  the results in now dusty letters. The only gifts today's authors
  expect from today's candidates are those "in kind" or better to be
  delivered to tomorrow's candidates, in one-way cross-generational
  equity. Writers have their own rewards in the success of their
  protégés, and though they will moan to each other about the burden,
  they recognize that reference letters are key components of an
  imperfect system that nevertheless is on the whole effective in
  keeping their discipline healthy and growing.

As others have said, the main incentive is to help the students.
But recommendation letters are also a service to the departments who read them.  Your colleagues will read your letters to help them make admissions or hiring decisions.
Moreover, over time, faculty build up reputations for the kinds of letters they write.  Faculty that are known to write overly effusive letters (as an extreme example: "best student in five years!" every year) are not taken seriously.  On the other hand, a strong letter from someone who is known to write measured but accurate letters has a big impact.  So writing perceptive letters is not useful only to the present student, but to future students as well.
The reputation effect becomes more significant (but more entangled with research reputation) as you climb the academic food chain.  For graduate admissions, it's fairly subtle.  For faculty hiring, it's much more noticeable, because hiring letters tend to come from a smaller pool.  For tenure and promotion, where the pool of writers is even smaller, the reputation effect is quite significant.

I guess the best incentive you can give a professor to write you a good letter is to 1) develop a relationship with the professor so that he or she knows something more about you than the grade you earned in their class, and 2) impress them in some way so that he or she has something good to say about you.
I agree with David Ketcheson. My sole purpose for writing letters of recommendation is to help the student. Letters of recommendation are read by committees that read hundreds of them every year, and I want the committee to have a strong impression of the student after they read my letter, not of me.
That being said, my students don't automatically get the "best" or "strongest" recommendation I can write. They get the recommendation they earn. For example, I cannot justify describing a C student as having strong academic potential. I can't write favorably about an undergraduate who signed up for a research project and then never showed up. And, I usually cannot say all that much about students I don't know very well. No matter what, I will take what I know about the student's strengths and weaknesses and try to paint the best picture possible; it just might not be glowing.

Obviously the letter must be accurate, but I've always believed that if you cannot recommend a student, you should decline to write a letter.  A negative letter will typically kill any application.  I would never write a letter for a "C" student.

It depends what I am writing the letter for. I wouldn't write a letter for a C student for a Ph.D. program, but I might for a Masters' of Arts in Teaching (M.A.T.) program.

Right; fair enough!  I guess the potential scenarios depend on what kind of school you're at.

I'd be hesitant to write a letter for a C student under any circumstances.  First, like many others I am a generous grader at the low end of the spectrum.  For me a C is always below the median passing grade, often well below.  Second, students take a lot more courses than they need letters of recommendation.  If a C student asked me for a letter, I would explain to them that they should instead get a letter from someone else.  If they're still asking, it means they don't have more than a C in any relevant coursework, and I can't recommend such a student to anyone.

In addition to the excellent points others made, it reflects well on a faculty member and a department for their students to be successful.  While I primarily write letters for the benefit of the students, it's great to be able to say when recruiting other students, or when talking to the Provost, that our graduates are getting great jobs.

In addition to the other reasons that have been discussed by other answers, many of which are true, there is one more fairly distinct reason: They may some day need a letter in return.
For example, there are often nomination letters for awards, or promotions from students. I've been in the position to write at least three letters for someone who wrote me a letter of recommendation in the past, and while I'd like to think it didn't bias my letter, it certainly made it easier to justify the time and effort that went into crafting it.

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Citation to well-known results and reference to user manuals
There are some very well-known results and equations, e.g., Shanon Capacity formula, Erlang Distribution and Poisson Distribution, etc. Do we have to provide a reference for these results as well?
Also at times we seek help from a user manual while writing a simulation program or conducting a practical experiment. Do we have to provide reference for user manuals as well?

References to manuals are not common, unless your approach is based on what the manual suggests to do. It is more common to acknowledge the software package that was used than referencing its manual. Many software packages can be cited, especially academic ones such as R.

My first comment will be that it is better to add one reference too many than one too few. Reviewers or editors might suggest to remove references during the review process if they seem superfluous.
In some cases, it might be more useful to add references to quite basic concepts. One such instance is when papers are directed at least partially to people outside the field. In such cases it may be sufficient to point at a basic book in the field, as an example to point to a good book on statistics regarding the Poisson distribution (the book has to provide some good information on the topic of course). This can help people who may have a different background to get deeper into the topic.
In general there is of course a fine line where references are or are not needed and with time one learns to identify this line better. What you can do is to simply look at other papers that you have read and see where they place the line and try to follow their example. That will likely form a very good basis for finding the right level of referencing. But, be aware that the line is different depending on the audience of the publication where the paper is published and you should briefly check to see what is applicable in each journal where you publish.

Thanks Peter for your quick answer. What about reference to user manuals

It is not necessary to reference very well- and generally-known results. For instance, it would be reasonable for somebody to say "by Pythagoras..." instead of trying to find a reference to his original writings ;-) I imagine that the Poisson Distribution would fall into the same category, but not being in your field can't comment on the others. Ultimately, as others have said, this judgement depends on your field and your intended audience. If in doubt, cite.
Re user manuals for software: If you have simply used the manual to learn how to use the software, a reference is not necessary - instead, reference the software itself. However, it would be appropriate to reference the manual if you are quoting from it, or if you are explaining how the software does a particular calculation and your evidence for this is that the manual says so (and perhaps provides more detail than you are including).

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Does helping a PhD student with proofreading violate school policy in general?
I am proofreading and editing a dissertation proposal for a student for whom English a fourth language--cleaning up the language for clarity and grammar, etc. The student has asked me to paraphrase the information of some articles so that s/he can use what is most relevant to her research. Is this commonly against school policy?

Reading and understanding the articles is part of the research, so this should really be the PhD student's job. I believe proofreading the student's own words is acceptable, but you shouldn't be doing part of his job for him.

The question in the title significantly differs from the one asked in the text.

I agree with @NickKidman. The title question asks about proofreading, which is (probably) acceptable; the text question asks about paraphrasing other articles, which is certainly not.

The paraphrasing part sounds like a ghostwriting request.

@JeffE: The funny thing is that in my comment, I was refering to the old version of the title, which was about ethics.

I am proofreading and editing a dissertation proposal for a student for whom English a fourth language--cleaning up the language for
  clarity and grammar, etc. The student has asked me to paraphrase the
  information of some articles so that s/he can use what is most
  relevant to her research.

That is fine.

I am proofreading and editing a dissertation proposal for a student for whom English a fourth language--cleaning up the language for
  clarity and grammar, etc. The student has asked me to paraphrase the
  information of some articles so that s/he can use what is most
  relevant to her research.

That is abhorrent in two levels. First, the student had the guts to even ask. Second, the task itself involves significant amount of intellectual input that is not of the student's.
I understand you wish the student to do well, and the work would reflect on your mentoring ability. But this is just identical to parents helping children with art project the night before school. It can be a fun and educational experience for kids, but outlandish for a grown up PhD candidate.
At the very least, make the student do the major part of the work:

Highlight the parts that he/she feels relevant. The selection of articles and contents should never be done by you. Discuss with the student on the rationale of the selections, and use this as an educational opportunity.
Paraphrase 5-10 various statements and hand them to the student as a guideline/examples, ask him/her to replicate on a dozen or so, check and give comments.
Send him/her away with a complimentary copy of a thesaurus, or some URLs like  http://thesaurus.com
Identify the ESL center in your institute, and ask the student to work with the ESL staff along the way.
Recommend the student to identify an editor. His/her English standard will not become any better. Now you are helping with proposal, a couple years later you'll help with dissertation---vicious cycle.

Also, as how I define it, if English is my mother tongue, then all languages I would learn are my second languages. It'd only be a fourth language of this student if, say, he/she has Russian as mother tongue, then learned Chinese in Russian, then learned Thai in Chinese, then learn English in Thai. I don't think that is a very viable pathway, and you may want to hook the student up with a Russian English teacher/editor.
And lastly, where were you when I was working on my PhD?!

awesome example about languages, some sort of inception of languages, as if..

I would maybe like to add that since a collaboration is an important part of research, explaining or summarizing the articles you already read would be okay in my opinion.
When somebody new comes to my team and either has read something relevant to my research or is researching something where the articles I have read will be of help, we will often sit together for an hour or so, and the one who has read the relevant articles will explain the basic ideas, point out to relevant examples and/or results.
In my opinion, this is fine, since there's no point in duplicating the time invested. Of course, I always read the articles in question after such talks, and I hope the other people do to. But, the explanations help reduce the time it takes me to fully understand the paper.
So, to summarize, sharing the knowledge and research findings is okay and even encouraged in PhD level, but not researching and summarizing the relevant materials for somebody else; that is something I imagine high school professors would do for their pupils in the classes.
Oh, and as a sidenote, proofreading is completely fine and I would gladly do it for any of my friends and colleagues whose English level is lower than mine (provided I have time).

It normally comes under plagiarism to do paraphrasing for all dissertation. But if student does it by himself/herself it should be fine to proofread and suggest how to improve that.
Just noticed kigen wrote same thing in the comment.


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Contents of paper being included in a conference presentation by a co-author, first author is unhappy - why?
Recently, my student raised the following concern: She worked on project A, and she is the first author for a publication based on the previous paper from the second author. Now, this second author wants to include project A, and also some other results by themselves, to submit an abstract to a conference.
My student seems not happy with this, but assuming the student did not attend the conference, I did not see too many issues. I would see this as a good thing that someone helps to promote my student's work.
Am I missing something important here? The only potential issue I could think of is if my student also wants to attend the same conference and she also wants to present the project?
P.S. the paper is still using the same author list, my student is still the first author.
P.S2 My student already presented the project in a local conference and an international conference. I told my student if you feel uncomfortable, you can just say no.
Update: it turns out that my student misunderstood that student B wants to combine my student's work and her works into a single manuscript, which is of course also not acceptable for me. My student did not tell me her decision yet, but I am fine with both 'yes' or 'no',
RE: the reason of student B wants to include the works from A is that their projects are related, one is a theory development and one is an empirical work to validate the theory.

"The paper is still using the same author list, my student is still the first author. " I am not sure about the conventions in your field/country, but usually the first author is expected to be the presenting author.
Are you by any chance the second author?

The natural person to ask this "why"-question would be your student.

@EarlGrey No, second author is another PhD student.

The student probably feels like their work is being stolen. At least in my field, it would be inappropriate to repeatedly present the same work at conferences so it's not just this conference but any conference.
"Credit", whatever that is worth, tends to go to wherever you heard something first. Letting someone else get the first shot at presenting their work means they can't be the one to get that credit anymore.
If this is your student, it's your job to help them get opportunities to present their work. Don't just wait for her to suggest submitting to a conference, encourage her to present at specific conferences that you know will be valuable to their career. Fund her travel so she can go present. Be a mentor.
If the work is already published, then the other author can freely cite it and present results from it that way if it's necessary to build on for their other work, just like anyone else could, but they shouldn't present it as if it's their own individual work.

The post has since been edited to mention that this work has already been presented at a conference by the student. In that case, why is the other coauthor presenting it again? They should present what they have that is new. Any presentation of new information will of course include references to previous work that it builds on, but that's not the same as including it as if it's part of the work and does not require any permission, only attribution. The student can't say "no" to someone else citing her work. She definitely can, and should, say no to someone re-presenting her work as if it's new work of their own.

In math, at least, it's very common to present on the same work several times as long as the audience for each presentation doesn't have much overlap. Provided, of course, that one isn't submitting the same work for peer-reviewed conference proceedings over and over. Sounds very subject dependent.

@user176372 Yeah, there's a bit more nuance in my field, too, where presenting at e.g. a local conference or seminar or similar is likely not really considered "presenting"; it's even common to have local conferences especially for students where it is assumed that all the presentations will be work already presented at another conference. And in-progress work at various stages can be welcome. But the major conferences expect that work that is presented is in some way novel.

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Be a member of TPC of a low quality conference
Recently I have recieved few emails from conference organisers to become a member of conference technical program committee. Three of them are international conferences and going to held in China and Thailand. I am a fresh PhD is it good to participate in low quality conferences as TPC member?  it will have a positive or negative impact in my resume?

I get spam emails like this several times per week. Often, these conferences are in China and often they are very broad. Just delete and forget them.

I strongly suspect that these are fake conferences, ultimately designed to scam you, other researchers and/or grant agencies for money. Any voluntary association with such events is a sign that you are rather clueless as an academic, and should be avoided.
There, however, plenty of small, very specialized conferences with high acceptance rates. These serve more as meetings and get-togethers for their research community than as highly respected publication venues. Being asked to serve on the TPC here is essentially a statement by your community that you are a respected member of this community, and would be a nice addition to the CV of a recent graduate.

I am a fresh PhD is it good to participate in low quality conferences as TPC member?

No. It is never good to associate yourself with unreputable people and activities. Your reputation is determined by the things you do and organizations and people you associate with. If you want to attain high reputation, only get involved in reputable projects.

it will have a positive or negative impact in my resume?

Negative. To me, activities like this on a resume signal someone with poor judgment, and/or who doesn't have more impressive activities to report, neither of which are good.

It might be hasty to jump from "low quality" to "disreputable". While I agree that the OP probably is talking about a disreputable event, there are obviously events which are reputable, but amongst the reputable events, of comparatively low quality.

@Arno well, disreputable simply means "not having a good reputation". Thus, to my mind a low quality conference is by definition disreputable.


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Whether to seek correction after my paper is published when the order of my first, middle, and last names is incorrect?
My article has just been published in a reputable journal. I discovered that my name is in Last, Middle, First order e.g Bagud, F.M instead of Bagud, M.F which doesn't go with APA style. Do I need to raise a corrigendum or should leave it? Actually, the name was written as Bagud, Meas Ford and the copy editor asked me to identify the surname among the three in which i chose Bagud. Thereafter, my name appeared as Ford Meas Bagud (Bagud, F.M) in the published article.

Leave it. That's irrelevant.

Did you see the error in the proofs? If not, why not? If it was introduced after the proofs, then the journal should fix it.

I disagree that it's irrelevant.... it could confuse things like Google Scholar metrics. Is there an ORCID to uniquely identify the author? Then that may be sufficient .

I mean that by now it's pointless. If it's already published, even if only online, the journal can only publsih an errata, which does not fix, e.g., the Google Scholar metrics.

I can relate to the discomfort of having your name misspelled, however, I don't see how to completely resolve the issue.
First, if the mistake was already present in the proofs, then you're in fault for not noticing and there is nothing to be done. If the mistake was introduced after the proofs were accepted by the authors, then it's the publisher's mistake. But to my experience, there's little they can do to remedy the situation.
As anedoctal evidence to this, I recently had a very respected publisher re-order our list of authors after the proofs (second and third authors were switched in a four authored paper - order was initially alphabetical). The publisher offered to publish an errata, that is, a minor one liner in a forthcomng issue stating the correct author order of our paper.
Although not as reconforting as having a correction in the actual paper, it's not completely useless as you can prove (in your case) that it was actually a mistake and you are not simply claiming a random paper in your CV, but I don't think you will ever need to prove this. The issue is that your paper will still be published and cited with the incorrect name, and probably not correctly indexed e.g. in your Google Scholar profile.
TL;DR contact the publisher and ask for a correction, but expect no more than a published errata.

Small addition: It is possible to add the article to your Google Scholar profile, even with a mistake in the name.


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What information to share and what to hide?
Science and research is open knowledge. We should always share our knowledge with each other. However in current competitive world, scooping research is very common (specially in bioinformatics, methodology and medicinal sciences where research has immediate applications). This has further downstream effects like less chance of getting published in good journal, loss of novelty etc. I was wondering what kind of information generally people share openly versus hide. I know this will depend on kind of research you and your rivals are doing but still is there any commonality ?
To be more specific, I am looking for research in computational biology. Let's say I want to present a poster in a conference where my rival group (working on similar topic) is also presenting. Now how much information about my current research I should present?

If you can't patent it or productize it quickly, you should probably publish it.

It is not uncommon to not speak about unpublished results...

Given the focus on field, I have voted to reopen.

It depends on your state of development. I actually believe bioinformatics and computational biology could be more open about ideas safely, because dealing with the messy details of the data actually takes most of the time. I spent half of my day figuring a way to fill in the gaps in some structures... that have been manually curated and supposed to be examples of the best ones.

I have to admit that the concept of "rival group" strikes me as rather unscientific.

Post to the arXiv or bioRxiv and then don't worry about it.

I think that you have to consider and balance, at the very least, the following aspects:

Your overall career goals. I would argue that career-wise every researcher wants (and has to) establish themselves as an expert, if not in a discipline, in a particular area(s) of research. With that in mind, it seems pretty obvious to me that sharing your research is much more beneficial then hoarding it. The one potential exception to this approach is noted in my next point.
Your current research (that is, particular study's) goals and priorities. If your current research has a potential to be commercialized and you have desire to deal with that and you have financial means (or your institution's support) to do so (as you know, patenting is not cheap, and, as I imagine, patenting in such a complex field, as computational biology, is doubly so), then you might consider taking this route (should be decided on a case by case basis).
Impact on potential collaboration. Modern research in many, if not most, fields is highly collaborative. Thus, your decision to significantly limit sharing research results and other related information will most likely make you an unattractive candidate for participating in upcoming collaborative research studies and, therefore, will most likely have a serious negative impact on your future research portfolio and, consequently, research career.

Good answer, but I'll add these aspects: 1) Ethics: would you want other people in your field to follow the same rules of action that you are following, in similar circumstances? 2) Greater good: does your action promote the greater good of the field, both in its academia and business?

@MrMeritology: Thank you. You bring up good additional points.

Good points ! I guess many times it will be subjective.

If you are worried about showing your work in a conference poster session and then someone scooping your work, I suggest you:

write up a rough paper preprint containing/describing this work
put that on a public preprint server like the arXiv
make it very clear on your poster that you've published the preprint (include a link)

Then it's in the public record that you were first, and anyone trying to scoop you is obligated to cite that preprint and acknowledge you were first.
If it's then the case that someone tries to literally scoop your idea and write a journal paper on it, with no additional work/development from them, their paper would very likely be rejected (if they do the right thing and cite the preprint properly). If they don't cite the preprint, it's a clear case of plagiarism, so if their paper gets published you can contact the journal editor who will very likely have to retract their paper.

This is a poster, right?  Print some pretty pictures, give some general descriptions of your techniques, whet their appetite to learn more about your group, give some references to some published papers from your group.  Think of this as a PR opportunity for your group.
When individuals visit your poster and chat with you, you'll be able to gauge what the person's motivations are, and share accordingly.

The scholarly community today is more in favor of sharing and open data rather than hiding your research. Research is meant for the benefit of society and should not be kept hidden. The fear of being scooped is of course there, but there are ways to protect your research and your data even while making your research public. Apart from writing a pre-print and putting it up on arXiv, you could also consider hosting your data on public repositories like Figshare or Dryad. You would then get a DOI, and your data would be citable.


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How to mention one year PhD gap on a CV / Resume
I have 4 years' work experience as a software developer (industrial); then I moved to academia and completed one year of PhD study, with one publication. I want to quit my PhD and go back again to Industries because of lack of interest in the present topic. It is quite different to my previous research and work experience. I made a big mistake entering into this area. I am bit confused how to mention this (one year of PhD) gap in CV. Do you think is it good to put in CV or Just leave it as gap?
It would be great help and appreciate your valuable suggestions

Hello in Academia.SE! Please, do you speak about US (mixed masters with phd) or Europe (PhD after masters) or another part of the world/another system? Knowing your location and the degree of your previous studies could change the answer.

I did Masters degree after that I worked for 4 years. I am doing doing PhD now.

You can just mention that you quit PhD. You already has research result and people in industry will not care much, especially when you already had 4 years experience.
You can also list your PhD experience as Research Assistant. A PhD student is definitely a Research Assistant, but a Research Assistant may not pursue a PhD degree.
In many universities, including Imperial College London, Research Assistants are people in the research group, who do not hold a PhD degree, and do not pursue a PhD in the university either. However, they often have significantly higher salary than PhD students (and significantly lower than postdoc/Research Associate).
However, are you sure you really want to quit?

In some parts of the world, a PhD student calling himself a "research assistant" would be considered wrong, since a research assistant is an employee (hired through a hiring competition), while a PhD student is a student on a scholarship (obtained by being admitted in the study programme). So one should be careful!

Women who take some time off for family matters deal with gaps in the CV all the time -- it's not a big deal.  In those cases, I recommend acknowledging the gap in the cover letter.  I don't think that's necessary in your case.
In your CV, report the academic year under Education (two semesters of graduate study in [field] at [institution]).  If the reader chooses to interpret this as meaning that you planned all along to spend exactly two semesters to get some theoretical underpinnings, what harm is done?
If an interviewer asks you why you didn't continue and get a Masters or PhD, you may tell a small white lie:

The computer science courses were interesting, but I'm really looking forward to getting back into industrial software development, because that's what I like best. For example, (and then talk enthusiastically about some work project that was rewarding and that came out great.)


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IEEE submission vs ArXiv Version with missing IEEE-statement
I've just got and corrected my revised paper. I submitted the revision to IEEE and I uploaded a newer version to ArXiv. BUT I made a mistake and the IEEE-disclaimer statement was regretfully missing on the ArXiv version and I did not notice it. (the older versions DO have the IEEE-disclaimer.)
Now, I get the feedback from the Editorial Office that it is a quite serious problem and I should add the statement to my paper.
The question is:
Do you think that it is enough if I update the paper on ArXiv? Won't the fact be a problem that the older version (without IEEE-disclaimer) is still available? Or should I contact the ArXiv-support team? Could they make an exception?
Yes, I know that this is a stupid mistake, but it would be really bad if the IEEE Transaction wouldn't publish the work because it is really important to my PhD...

You are unlikely to be the first person to make such a mistake. So, go take care of it as IEEE requested.

Thanks, @JonCuster? So are you suggesting that I should contact ArXiv to change my last version? Our I should simply add the newer, corrected version?

Replace, per the help documentation. If you believe your situation warrants an exception, you should contact arXiv's helpdesk with a detailed explanation.

Thank you!
Indeed, I was not the first person. Replacing the pdf was enough for the editor and finally our work got published :)

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
I have written one mathematical paper which I want to publish, do I need to give professor co-authorship?
I am an undergrad student studying in the last year of my bachelor’s. I have written one paper in number theory discovering one new elementary method. I want to publish it.
For mentorship I went to my mathematics department and asked for help, but the professor whom I met wants his name on my paper as a co-author. He has not done anything. I just asked him for guidance and to review the paper format. He even said that without the name of professors some journals don’t consider accepting papers. Is that true?
This is my first paper so I have no knowledge about anything. I desperately want this paper to get published. This is my five-year long research and could be a good paper which may change the perception of people working in that field. Can someone give some suggestions? Should I do as that professor says?

Somewhat related: Mentor says I cannot be first author of my paper because I am an undergraduate

@Wrzlprmft The question you linked is similar but asks about a paper in biomedical sciences. This question is about a paper in pure mathematics. Those two fields have very different conventions regarding authorship of papers. In biomedical sciences it is extremely rare for a supervisor not to be a coauthor.

@Stef: I know, hence related and not duplicate. Still, even the answers to that questions say that you do not need a professor as a co-author.

A principle of how copyright law works is that you can claim as yours some piece of intellectual contribution as long as you can prove that yours appeared first. So I would recommend that if this is novel work, then publish a draft in an online blog. The way mathematicians usually go about it, is first they publish a preprint in arXiv.org, and then they submit their work to a conference/journal. This has the benefit that others can comment on your work. Last time I checked, to open an account on arXiv you just need an institutional email address.

Also, by looking at arXiv publications in your field you can get a sense of the formatting that they need.

If you have written the paper on your own and another person has made no intellectual contribution to it, then they have no claim at authorship. I don't know of any journal that requires a professor to be the author of any paper, but I can't rule out that such might exist, but it wouldn't be true for most reputable journals at least.
Note that there are math journals dedicated to student work. You might consider submitting there.
But also note that you might be overestimating the importance and impact of what you have done. Advice from someone more experienced can be valuable, but this professor seems to be unethical about authorship, given what you say. If they help you with the presentation of the ideas then they might be due an acknowledgement, but the standards for authorship are pretty high and especially true in maths.
If you submit to a journal, you will get some feedback. If the paper doesn't meet the expected quality standards then it will probably be quick, but not especially valuable. If it is a good paper, then the feedback will take longer but be more useful.

Thank you. Actually, I want to get someone's mentorship especially for formatting my paper as I m inexperienced in doing that and yeah I might be overestimating as well. My research is at the elementary level and it's just about the observation which I did. But it seems so interesting and may result in future research and link between something more. can you recommend me some way to get mentorship or any formatting sources?

once I mailed one professor working in the same field and he asked me to send my work. Would you recommend me to do this? He is residing outside my country. I contacted him after reading his paper. I do have not much information about him. I just saw his paper in this field.

It is hard to recommend this without knowing the person. Not everyone is ethical. Most are. Someone local might be better and you can judge how they might react. It might also be helpful if someone local, but with some authority, is in the loop with you if you are sending things around. Don't worry about formatting too much. Editors will help you with advice for that.

Given that we only have one side of the story here, I think that you go a bit far in stating that the professor seems to be behaving unethically.  While I agree that someone who has made no intellectual contribution shouldn't be listed as an author, I think that asking someone to review a paper prior to submission is asking them to make an intellectual contribution (i.e. to check the work). If a student came to me and asked for a review of formatting, I would be worried that it would turn into a review of the mathematics...

Personally, I have the time to mentor such a student without compensation, but others may not.  It does not seem entirely unreasonable to say "If you want me to review your work, I need some form of compensation, such as co-authorship."

@XanderHenderson, here is a fairly typical ethical standard for authorship: https://www.bmj.com/about-bmj/resources-authors/article-submission/authorship-contributorship. Note the AND usage.

@Buffy I see nothing there which contradicts my previous statements.  A professor being approached by a student may assume that they will eventually be responsible for all four of the criteria listed in your linked advice for publishing in medical journals.

My point is that while the student might think that they are asking for someone to just go over the formatting, the professor might see this as a request to review the actual mathematical material.  To do that, the professor would need to become an expert in the material under discussion (in order to check the results), and would nigh certainly have to make some real intellectual contribution to the paper in order to fix errors (which almost certain exist---all works contain errors).  As presented, the actions of the professor appear unethical, but we don't have the whole story.

"you might be overestimating the importance and impact of what you have done" → Then again, what they've done appears to be good enough for the professor to want to be listed as a co-author, so...

I agree with Buffy that going through a paper does not constitute authorship immediately. However, I will defend the other case.
You can benefit greatly by including a professor in your paper. For one, by including him you will not be losing much. There are non-critical benefits such as bringing an established name (if they are known in the field) which could open opportunities to publish in better journals. They might be able to identify well suited journals which could save you time.
However, more important is once they are in as an author, they are duty bound to ensure your paper is factual, they might also identify representation and presentation issues, find problems with the writing and so on. While theoretical work and the idea are the most important parts for a paper, you cannot publish it, if it is not represented well. You cannot expect a professor to review your paper multiple times (my top review count is 12 for a single paper) without compensation.
I was in a similar situation during the first year of my PhD. I have decided to go to the professor of a lecture with my idea that I thought I would publish in a conference. We ended up publishing in a very good journal.
Finally, this might be the start of a fruitful collaboration.

additionally, it will likely get you an Erdős number

@ysth Depending on the definition, everybody has an Erdős number of infinity. A joint paper might bring this down to single digits.

@usr1234567: don't be silly! That would require an infinite chain of mathematicians.

@TonyK By definition, a person with no publications has an infinite Erdos number.

@CemKalyoncu  Playing devil's advocate, the downside of publishing with an established co-author (particularly if you are an undergraduate) is that many readers will assume that the established professor is responsible for the majority of the intellectual work, and that the undergraduate did very little.  In such a case, a sole-authored paper in a B-level journal might actually be better than a co-authored paper in an A-level journal.  Of course, everything else you say is spot-on (including the important point that one collaboration may lead to further collaboration).

@XanderHenderson: by definition, a person with no publications does not have an Erdős number. As any sensible mathematician would expect.

@TonyK The Oakland University "Erdos Number Project" would beg to differ:  "If there is no chain of coauthorships connecting someone with Erdös, then that person’s Erdös number is said to be infinite."

@XanderHenderson In my field, computer science, we generally assume the opposite. Most of the work is done by the student, especially if they are listed as the first author. But I can see that it might be different in maths.

@CemKalyoncu In physics the usual expectation is that indeed most/all of the work is done by the student ... but most of the thinking was done by the professor.

@CemKalyoncu Yeah... different fields are different.  I should have kept that in mind.  In my own field (mathematics) the general assumption is that the big name did most of the thinking, and probably also did most of the work, but handed the project to an undergraduate in order to fill in some details (the idea being that the student gets to put their name on a paper, which helps them apply to graduate school).

I do math by myself. I'm preparing a paper for submission, and I wanted to add a few things that others haven't fleshed out.

Examine the different kinds of contribuion in detail, to understand what must be referenced, what kind of work counts as contribution, coauthorship, etc.  Consider several different kinds of help:

commonly known results  vs.
material from a college course vs.
specific theorems I looked up in a book vs.
new published results

someone rewrites equations for me using standard methods vs.
rewriting equations for me using her judgment and knowledge to find a particularly useful form

general advice about how to tackle the problem vs.
help solving specific subproblems in the paper vs.
help clarifying arguments and organizing the paper vs.
assistance with layout and the submission process

To evaluate for ourselves the contributions to our work, we need to know standards of practice.  The details.  Ultimately, only you know how individual contributions were involved in the progress of your work. If someone else is making those judgments because they know the rules and you don't, and also have a vested interest in being credited that sounds bad for you.

Ask questions.
An answer like this may not mean what it seems.  I spoke to a professor who believed that these days it's impossible to finish a paper alone. He said if I think I have the arguments right start to finish, I'm fooling myself.  He said "you can't" but he meant something else.
What are the specific reasons your school thinks you won't make it to the finish line as the sole or principal author? It may still be unfair to you, but it might not.
For example, it may be school policy that a professor review student work to make sure it meets the standards for submission.  This may be valuable help, and -as mentioned by other posters- it would probably be wise to clarify you are not asking for assistance with the  result itself or its development... before accepting.

Get as far as you can without confrontation.
It's easy to imagine teachers overestimating their involvement in your work, or the amount of help you will need to reach publication. EDIT: a quick internet search indicates, as a general rule, the assumption that your faculty is by default coauthor appears to be false. Student work belongs to the student.  In an ideal world, that means it's up to them to justify their contribution, not your job to deny it.
The main thing is, to publish with a fair and accurate representation of how the work was done.  If your teachers are reasonable, they will take your word at face value, help you get credit for your work, and only ask for credit where it is due.
Give them a chance to recognize the originality of your work, and give yourself a chance to re-examine the contributions of others.  Only walk away if they don't cooperate in a reasonable and fair way.

Document yourself
At the same time, document your process and interactions.  Those notebooks filled with scribblings as you work... keep them. Date them. Write out a timeline of your paper.  Do you remember any details about how and when you solved certain parts?  Write it down before you forget.  And keep a log of your conversations with your faculty.  Record their exact objections; respond to them, and keep a log.  Then IF something goes wrong, you can point to specific dates and say, "No, I spoke with you about X on this day, and made it clear what really happened, and I have the work to prove it right here".

I've never heard of a journal requiring that a student author include an academic co-author though my field is the biological sciences. Nonetheless, I see little downside to simply submitting your paper to an appropriate journal. Follow the instructions (if you can do original research in math, I full expect that you can follow formatting instructions) and send it in. If your work has merit, the reviewers and editor will provide the guidance necessary to see it published. There aren't many academics who'd claim that the process is perfectly straightforward and there are plenty of examples of good work that doesn't get published or only after excessive efforts. There are certainly many more examples of papers that are submitted with serious issues ranging from fundamental flaws to inadequate citations to atrocious writing. Frankly, your professor/mentor probably could help you avoid most of these...and co-authorship, while not strictly necessary, may not be unreasonable. Your post suggests that you don't think your professor's efforts merit co-authorship, but accepting his/her advice and taking them on as a co-author may be the most expedient way to getting your work out there.

For the first, there is no journal that requires to have a Professor as a co-author. However, if you want your paper to be published... this will be extremely difficult. You've asked for guidance, have you? I am following just what you are saying - that  you are new in that, in publishing articles, right? So that's why I am saying that it would be extremely difficult for you, because you are already asking the others what to do.
When I was young, I tried to send my first article to the highly reputed journal, and I did not ask anybody how to do that! And I won - I received three positive references at once and got published!

FYI, I didn't downvote, but the earlier part of your answer seems to suggest asking others for advice to avoid a bad outcome, whereas the later part of your answer seems to suggest not asking others can lead to a good outcome. Of course, "can" is not the same as "will definitely" or even "will probably", but I don't see how the later part of your answer builds on the earlier part of your answer. Maybe include something between these two parts, such as: "Nonetheless, in rare cases one can be successful without seeking advice. For example, when I was young ..."


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Why are some journals with low impact factor indexed in Web of Science while others with a relatively higher impact factor are not?
I'm a researcher in mathematics. While looking for journals in my field, I found out while some journals with a low impact factor are indexed in Web of Science, another Springer journal with a higher impact factor is not.
Journal indexed in Web Of Science (lower impact factor)
Journal indexed in Web Of Science (lower impact factor)
Springer journal not indexed in Web Of Science (higher impact factor)
I couldn't find an explanation, except that the Springer journal hasn't requested to be indexed in Web of Science yet. Is there another explanation of what makes some journals get indexed by Web Of Science while other journals with relatively higher impact are not?

There's an official answer: https://clarivate.com/products/scientific-and-academic-research/research-discovery-and-workflow-solutions/web-of-science/core-collection/editorial-selection-process/editorial-selection-process/

There are no journals with a relatively higher impact factor that are not indexed in Web of Science. That's because you need to be indexed in Web of Science to get an impact factor. Note the impact factor is calculated by Clarivate, which is the entity that owns Web of Science.
You could calculate your own impact factor (which is not too difficult, because the methodology is both simple and known), but it won't be the impact factor.
I don't know where you got the impact factor of the Springer journal, but if it's not indexed by Web of Science, it doesn't have one. Springer is (honestly) not reporting an impact factor for that reason. See here for an example of a Springer journal with an actual impact factor.

A number of BMC and SpringerOpen journals have impact factors and some journals are being tracked by Clarivate Analytics and will receive their impact factor in due course. For any journal to have an impact factor it must be tracked by Clarivate Analytics for two years (for more information on how impact factors are calculated, please see here).

Source


text:
PhD in computer science and work as a mathematician
I want to ask if it is possible to be a mathematician (while also being a computer scientist reseaching in a mathematical related field).
I really love mathematics, specifically analytic number theory. For example I would like to create algorithms to solve problems in number theory and I already talked with my professor who supervises my PhD (which is in computer science field) about this. The professor seems okay with the choice. I would like to ask if it is possible or even okay to be both a mathematician and a computer scientist in this sense.
The mathematics part that I would like to go deep into are mathematical theorems about number theory. That may include finding large primes (from the use of an analytic approach) in computer part, and also maybe the study of the proof or the calculation to verify the elementary theorem involving Riemann's hypothesis.(This one is what interests me the most)
I need to further study about mathematical theory that may not have any application in the real world (even in computing). So I am not sure if it is a good choice to start and if it is possible to be such a person by attending a PhD in computer science as I mentioned.

What exactly do you mean by 'working as a mathematician'? From your post you are currently writing your PhD thesis in a computer science department. You can definitely write a very math heavy thesis, especially if your advisor supports it. You can also submit papers to mathematical journals, provided the topics of your articles are suitable. Journals care for the content of your papers not your academic credentials. You can also collaborate with mathematicians, do joint projects and write joint mathematical papers.
Once you have your PhD thesis you can apply for postdoc or lecturer positions in math departments. If you research fits to their needs a computer science PhD will be just as good as a math PhD. It might be a little less obvious why you would be a good fit for a position but if you can argue that you are they wouldn't exclude you because of a PhD with a different title.

Thank you. Actually I mean what you mentioned (which I forgot to cover). The publication in math journal and working with other mathematicians, etc. that you provided.

The professor seems okay with the choice.

This is very important, but I think there is an equally important issue you need to pay close attention to. To successfully do a PhD in a topic X,  especially at the level that would position you to pursue an academic career, it is really really important to have an advisor who is not just “okay” with your choice but who actually has the knowledge and expertise in topic X so that they are able to guide you towards good research problems and successfully completing work on them.
So, if you want to specialize in analytic number theory (even if it’s mainly computational aspects of number theory), and your advisor is not an expert in this subject, and you don’t have anyone else aside from your advisor who does have that expertise and who is able to mentor you in a way that involves a significant time commitment (for example as a co-adviser), then your plan is not a good plan.
Summary: yes you can be a mathematician with a specialty in analytic number theory, and whether your formal PhD is in computer science or math is in a sense immaterial. But what is a lot more critical is if you have access to a mentor/advisor who has the knowledge to train you in this specialty. If you don’t, then even if you were in a math graduate program I would advise you to rethink your plan.

Actually, during the discussion he seemed interesting about the topic and a sketch proof. Your point is my primary concern indeed, as it is CS department so there might not be so many experts in the field.
There was a mathematician who taught at the university before, in the math department in the field I interested but he left to other university and other country.

Though I am not sure if he had students teahing there or even I can access to them.
May be I need to contact the professor together with my advisor if this is possible.

Actually, anyone can "work as" a mathematician. You don't need any degree at all. You can also publish as degrees aren't required for that. But if you want to get paid for that work then you need to get hired into an appropriate position and while CS overlaps with math, the overlap is actually quite small.
Unless your CS education, generally, was unusual in some way then there are probably vast parts of mathematics that you don't have any experience with. This makes it less likely that you have general insight into math, though it isn't impossible.
If you only want to work in those parts of math that are covered by the overlap, then getting hired for a CS position will serve about as well as any other, and you can, as an intelligent person, expand your understanding of the rest of math - which is a vast landscape. People do change fields and some are competent experts in more than one.
Going the other way is a bit easier, actually, since a deep understanding of math gives an equally deep understanding of some important parts of CS, such as, say algorithmics and computability. Much of the rest can be learned.

So, I'm not sure I understand you correctly but maybe you suggest me to get hired in the CS position and then expand my understanding of math myself?
I do agree with your point about anyone can work as a mathematician, even without degree. I think I can learn math more by myself, but the lack of professional network and decent collaborations or disscussions may be the big obstacles.

So, I suppose that it is okay to work in CS department with the publications on the small overlaps with math together with even unapplicable pure maths (maybe with some collaborations) that you recommended?

I recommend you get the job you can. I think CS is more likely to have a home for you. Note that the market at the moment is especially tight and you are competing with a lot of highly trained mathematicians for any math position. Just don't neglect applying for CS openings.

Note that the "small overlaps" aren't unimportant.

Thank you. I didn't treat it as unimportant. Actually, they are very meaningful to me and I really want to work on these (and other pure ones as I mentioned).


text:
Would recommendation letters from the chemists in the industry lab I work in be helpful?
A little background info,
I'm currently working as a lab technician in a drug lab which focuses on clinical chemistry and toxicology. I wish to eventually, within a few years tops, go back for my upper level degrees. I didn't have any close relationships with professors of mine as an undergrad, and as a result, I'm currently lacking possible grad school recommendations.
Would anyone recommend using recommendations from chemists, with PhD's, who work in the industry as beneficial grad school recommendations? They both serve as my employers/ bosses, and I'm 99.99% they would give high recommendations if asked. However, would these even help me on my applications?
Also, if anyone has any possible actions I could take that would help me strengthen a grad school application, that are possible with the time window mentioned above, 2-3 years, that would be very much appreciated.

Assuming you're applying for Ph.D. programs, the basic question admission committees usually need to answer is "Is X capable of becoming a good researcher?" If your supervisors, both of whom have Ph.D.'s, can answer that question successfully, then there's no reason not to use them—particularly if they know your work more closely than someone who only taught you in courses.


text:
Why can't universities work around the proposed reclassification of tuition remission as taxable income, by not charging tuition?
There has been a lot of press about how the new tax proposals currently being considered by Congress could hurt grad students because one of the plans would treat remitted tuition as taxable income.
I understand why this would be bad -- grad students who receive tuition remission would have to pay a lot more in tax.
But if this became the new law, couldn't universities simply change the way they handle tuition for funded graduate students?  In most top Ph.D. programs no grad students pay tuition because it is always remitted.  Instead of remitting it, couldn't the universities just not charge tuition at all, or pay it through a grant rather than through remission?
I'm asking because I'm wondering why grad students are so worried about the new tax plan.  I understand why it would be bad if universities didn't change the way they handle tuition and students had to pay tax on all that extra "income." But as it is, tuition for many Ph.D. students is just a shell game because it is always remitted. If the goal is to allow students not to have to pay tuition, it would seem that there are other ways to do that that would get around changes in the tax code.  And I can't think of any reasons why giving students remitted tuition is more beneficial to the university than just not charging them tuition in the first place.
Am I misunderstanding something about the way tuition remission works, or the new tax proposal?

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

This is a great question! I decided to write an answer to test my own understanding of the (rather convoluted) forces and interests at play. Assuming my answer makes sense, I hope it will help further the debate on this new proposed taxation rule.

Why can't universities work around the proposed reclassification of tuition remission as taxable income, by not charging tuition?

We don't know that they can't -- I guess we will find out if this proposed new rule becomes law. But with that said, I think working around the rule would require a lot more than just relabeling "tuition" as something else or some similar cosmetic change. The reason is that there is something pretty honest and logical about the current arrangement, which makes me think that changing it would lead to an illogical, dishonest situation, which would be problematic from multiple points of view and create all kinds of undesirable distortions.
My understanding of the current system is as follows. There are four parties involved in the exchange of funds and services when a student goes to graduate school:

The university.
The student.
A funding entity (e.g. a public or private funding agency or an internal university grant).
The government, acting on behalf of the interests of the rest of society (yeah yeah, I know how naive that sounds).

Each of those parties has its own interests and has something to gain from the transaction, and provides some benefits to the other parties in return:

The university provides the student with an education and professional training, a costly good to provide (requiring physical infrastructure and lots of human capital). In return, it gets the tuition money (from the funding entity, or in some cases from the student him/herself) and the benefit of the research and other intellectual output of the student.
The student gets an education and valuable professional training that is likely to translate to a happier, more fulfilled life with improved employment opportunities. In return, he/she does research and other intellectually taxing work that benefits the university and the rest of society.
The funding entity provides funding to the university to offset (part or all of) its costs of educating the student. In return, it gets nothing, except the knowledge that it has fulfilled its mission of facilitating this process. (After all, funding agencies are set up precisely to be the entities in charge of giving away money to fund research.) This knowledge is used by it to justify its continued existence to the higher-level entities that are the source of its funds.
The government and society get the benefit of the student's research and other intellectual output, and the multiple benefits associated with a more educated populace. In return it gives a tax exemption to the student from paying taxes on the tuition money, which is after all a material benefit provided to the student by the funding entity (except for those rare students paying their own tuitions). This tax exemption is in effect a subsidy or incentive for people attending graduate schools. Of course, as readers of this site are well aware, going to grad school in the US is quite an expensive proposition (in both real costs and opportunity costs) already, to an extent that even deters some people -- probably a lot of people -- from pursuing a graduate degree. Going to grad school still makes economic sense for lots of people, but certainly not for everyone, and requires a lot of sacrifice and patience even from people who do end up benefiting.

Now imagine what happens if the tax exemption in item 4 is eliminated through a unilateral decision by the government, which is only one of the four parties. This will result in a net flow of huge sums of money back to the government. The whole set of incentives of the other parties will be drastically impacted. It is very hard to predict the exact consequences, but likely there will be an equally huge drop in the number of people wanting to go to grad school. Universities will have to go begging for more money from the funding agencies to offset that and restore equilibrium to the system, but the funding agencies don't have more money to give, or they would be giving it already. So: a big, big problem for everybody.
Now, you are proposing that universities simply eliminate tuition to forestall this flow of money back to the government. But then how will they offset the high cost of the education and training they are giving to the students? Charge money from the funding agencies, you say, but just don't call it tuition. Well, the funding agencies have to agree to this. How would the money be charged? By what logical name would you call this transfer of funds (it is after all a subsidy by an external entity of the student's education, which is a benefit to the student and therefore taxable as income under the new rules, at least if it is called "tuition"); and how will you prevent the government's taxation agencies from coming and saying -- quite logically in my opinion -- that this is effectively a form of tuition subsidy whether you call it that or something else, and that the applicable tuition taxes are therefore due? These are all tricky questions. As I said, I don't know if the universities will be able to find a work-around, but it is far from obvious to me that another equally viable arrangement can be found under the proposed new taxation regime.
Finally, I should add that the current arrangement works well not just because each of the four parties gets something in return for what they give, but because each of them gets back much more than what they give. There is a very large net gain of utility to society from the existence of higher education (and graduate schools in particular). That is why it is a resource that is subsidized, in one form or another, in all advanced countries.

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

Instead of remitting it, couldn't the universities just not charge
  tuition at all, or pay it through a grant rather than through
  remission?

It may not be possible to not charge admission. Things like that are sometimes controlled by the state legislature, which is not always a friendly body. Beyond that, the difference between remission and "No tuition" is that someone is paying for the remission (or has been allocated a set number) whereas no tuition is just...no tuition. And often that someone is a grant.

But as it is, tuition for many Ph.D. students is just a shell game
  because it is always remitted.

Accounting shell games come about for reasons. For example, the university might have a fixed cost of credits for graduate students (keep in mind Masters, Law, Medicine, Vet, Dental, etc. students are also grad students), and you may need a certain number of credits to be considered a "full-time student".
Which in turn can impact things like your insurance, loan repayment schemes, visas, etc.

If the goal is to allow students not to have to pay tuition, it would
  seem that there are other ways to do that that would get around
  changes in the tax code.

They may not be possible, and they may not be possible by the time your taxes are due.

And I can't think of any reasons why giving students remitted tuition
  is more beneficial to the university than just not charging them
  tuition in the first place.

The CDC pays my institution many thousands of dollars for my graduate students' tuition. Zero tuition would mean they pay zero dollars. That's bad for a university with very little financial wiggle-room right now.
It can also impact university finances. As I mentioned, there are other types of graduate students, and right now one of the major sources of revenue for my college is agreements we have with several states to take their students (we're the nearest vet school). Setting that to zero would be a financial disaster.

This is probably the better answer - fairly arbitrary rules that are specific to the US and which are bureaucratically hard to change. Dan Romik's answer fails to explain why universities in other countries can do exactly what the question proposes.

@MSalters which countries? And when you say those countries “can do exactly what the question proposes”, do you mean “work around the classification of tuition remission as taxable income by not charging tuition”? Or do you simply mean “not charge tuition”? That’s an important distinction: some countries might indeed not charge tuition, but I suspect their taxation and funding environments are so different from the US as to render their budget models irrelevant to OP’s question. And to clarify, my answer was written with a US context in mind, even if the description I gave is a high-level one.

@DanRomik: Actually, in the Netherlands the universities do both: pay PhD's and not charge tuition. The pay is real and taxed. A tuition remission would be taxed, but simply not charging tuition is tax free. Not that strange: PhD candidates are getting to the point where they're doing independent research, although they're still inexperienced in that.  University funding is a mix (direct government, funding agencies, industry) but misses the large alumni contributions common in the US.

If business gives away free goods or services, the recipient will not in general be required to pay on tax on them.  If, however, a business gives free or excessively-discounted goods or services to someone in exchange for work performed, the IRS will often regard that as a "barter" transaction, requiring the worker to pay income taxes taxes on the value of free goods or services, or the amount of discount, received.  It isn't always necessary for the worker to pay taxes on the full retail value of the goods or services, but discounts must be justifiable as something other than a reward for the work performed.  If, for example, a bakery allows workers to take home unsold bread, a 100% discount could be justified on the basis that the bread would be unsaleable the next day.
While there may be some opportunities to game the system slightly, the IRS is apt to be skeptical of a business that charges an employee far less than retail for goods and services that could otherwise have been sold, at a higher price, to someone else.  Tax-law treatment of barter transactions is sufficiently hostile that it's generally best to avoid anything that the IRS might view as one.

This is all quite interesting, but can you explain more precisely the relevance to OP’s question? You seem to be saying something along the lines of “if universities try to get smart and change the word ‘tuition’ to something else, it may not help them in the eyes of the taxman” (similar to what I was saying in my answer) but I wonder if that’s what you meant or there’s more to it than that, and don’t really understand the barter angle.

@DanRomik: My point was that there are tax rules for the specific purpose of limiting the usefulness of such things, by classifying them as "barter" transactions.

"If business gives away free goods, the recipient will not in general be required to pay on tax on them." Uhm, can you give an example? If you win sweepstakes you have to pay taxes on them as far as I know... I know food samples and "gifts" that you get along with purchases don't really seem to warrant paying taxes, but I'm hard pressed to come up with much else of nontrivial value.

@Mehrdad That's because companies usually don't give away things of nontrivial value for free, unless it's to employees in the sort of "barter" transaction that is mentioned in the post.

@Mehrdad: Companies often give away free samples of merchandise, or free trials of services, in the hopes of attracting customers.  Recipients of such goods or services have no obligation to regard them as income.

@supercat: If the "sample" had a nontrivial value (like say a $10,000 diamond) would that still hold true?

@supercat Assuming they have no relationship with that company. But if, for example, that company is their employer, then they do have to regard it as income. This is why tips are taxable and why most benefits are taxable.

@DavidSchwartz: If the company offering the sample had a justifiable belief that it was likely to net a profitable sale, yes.  If a company's products are readily identifiable, and it believes that a celebrity who is given a product would use it on camera even without any obligation to do so, it could take a chance on giving an expensive item as a gift.  As Mr. Schwartz notes, however, if the donor and recipient have any sort of sponsorship relationship, however, then the item could become taxable.

@supercat Those are not gifts! They are taxable to the recipient. If the business gave them in the ordinary course of business in the hopes that it would net them a profit, it's not a gift for tax purposes. For tax purposes, a gift must be given out of generosity. When Oprah gave everyone in her audience a car, that was not a gift for tax purposes because it was given by a business for publicity. Those are taxable to the recipient. See this link.

@DavidSchwartz: If any affiliation exists between giver and recipient, such as the recipient granting permission for the use of their name and/or likeness, that could create the basis for a taxable transaction.  If a company sends someone a product totally unsolicited, however, I don't see how that could create a tax obligation on the part of the recipient, especially if the recipient has no easy way of knowing the product's value.  I think a company wanting to write off such a transaction as a business expense would be required to either show that a relationship existed (which would make...

...the item taxable for the recipient) or else that the transaction netted the business money (e.g. if the recipient then placed a $500,000 order).  If the transaction didn't make any money for the business, and it hadn't established any affiliation with the recipient, the business would required to treat it as a non-deductible loss.

@supercat The giver has an obligation to disclose the value so that the recipient can properly pay taxes on it. The recipient always has the choice to refuse it. There is absolutely no question that it is not a gift since it was not given out of generosity but instead in the ordinary course of business with the hope of making a profit. See here.

@DavidSchwartz: As I noted before, Oprah's guests had an affiliation with the show.  If someone receives unsolicited a nice looking ring in the mail from some jewelry company, how should they be expected to know whether it's a $100,000 piece of fine jewelry versus a nice looking piece of costume jewelry, likely worth $100 or less.  Obviously if the person included the ring in an insurance inventory with an assessed value of $100,000 that would suggest that they were aware of its value, but if they keep the ring in a box with other costume jewelry the fact that it happens to be worth...

...hundreds of thousands of dollars shouldn't make them guilty of tax evasion.  If someone who saw the ring and suggested they assess it, and the recipient of the ring subsequently discovered it was worth $100,000 and sold it, I'd expect the person to pay taxes on the difference between the sale price and the $0 cost basis (whereas no taxes would be due on the sale if taxes had been paid on the $100,000 earlier) but I wouldn't expect someone to know that $30,000 of taxes should be due on a ring believed to be worth $75.

@supercat Oprah's guests had no "affiliation with the show". They just went to see the show. They were there, that's it. As for your hypothetical, it has no effect on what taxes are due -- the fair value of the ring is taxable income if the ring wasn't given as a gift out of generosity. Whether it's reasonable for someone to know what taxes are due has nothing to do with what taxes are actually due. Your entire argument is a massive non-sequiter. These are not gifts for tax purposes, they are income since they're not given out of generosity but in the ordinary course of business.

@DavidSchwartz: The audience members had the "job" of appearing on camera in the role of audience members.  They received cars in exchange for performing that service.  That would strike me as creating some level of affiliation beyond that of someone who receives an unsolicited product in the mail.

@supercat Maybe, but that's not how the tax code works. The tax code says a gift if it's given out of generosity and not if it's given in the ordinary course of business with an expectation of a financial reward. For example, say you buy a used chair and find $50,000 hidden in the lining. That's taxable income because nobody gifted it to you out of generosity.

@DavidSchwartz: When I've received free samples of products in the mail, I've not generally noticed any information indicating any value for tax purposes.  If one partially consumes a product and decides one doesn't like ti, how should one figure taxes on the consumed portion?

@supercat Again, your entire argument is a non-sequiter. The law doesn't have to make sense or be easy to apply.

To address specifically:

But as it is, tuition for many Ph.D. students is just a shell game because it is always remitted.

At my institution (which guarantees tuition support for all its graduate students), many PhD students are covered by internal university grants, and the "charging" of tuition in these cases seem to be little more than accounting.
However, many students are funded from external grants or fellowships, and in these cases the tuition charged to the student is funded by the grant and fellowship and represents real income for the university.
If my institution were to drop tuition to $0, it wouldn't be missing out on "income" from internal grants, it would just have to figure out a different accounting method (I don't know what this might look like, not an accountant), however, it would be missing out on real incoming money for those students on external grants and fellowships.

This is important, but it's also worth noting that external grants or fellowships do not necessarily pay the total claimed tuition price. For instance, at my university, tuition is technically 50k/year, but external funders only pay 10k/year, and the rest is remitted.

One thing that I have not seen mentioned is that not all grad students (or people who take graduate-level courses) are from the simple "being a grad student is really a research job" cookie-cutter.  For instance, I did most of my grad work part-time, while employed in much more remunerative industry jobs.  One fellow student was a multi-millionare, another a retired gent in his 60s.  Dropping tuition to help the full-time RA-type students would mean we would all be getting our grad school for free.

The university is under no obligation to charge the same amount for every student. For example, one university charged non-matriculated students without a masters' degree 2/3 as much per credit as non-matriculated students with a masters'. They could simply charge part-time students.

@Sorcha NicEalair: IANAL, but I think that might cause all sorts of legal trouble.  If nothing else, the IRS could argue that not charging tuition for some was the legal equivalent of tuition waivers, so that the uncharged tuition would be subject to tax.

Currently some sciences receive tuition in proportion to graduate student salaries that covers some fraction of nominal tuition. If government were persuaded to give block grants to universities to run graduate programs in specified fields, no individual student would be tagged with the taxable income. Fields without subsidies (Law, Medicine [at least in many cases], too many humanities) could continue to charge tuition. The distortions, potential subterfuges, and potential for loophole exploitation are mind-boggling.
Nevertheless, there may be a simple, if expensive, work-around.  Suppose a current graduate student gets $20k in salary and a $50k tuition waiver. Tax on $20k isn't much (and depends on number of dependents and other variables). Tax on $70k is a lot. So if the salary is boosted so that ($20k + increment - tax on the waiver and the salary increment to cover the extra tax) = ($20k - old tax), the student is whole. This transfers the problem from the students to the funding agencies. It still cuts the number of graduate students. It discourages foreign students from attending US universities because they too pay tax and, in many cases, tuition even when the US students get waivers.  To cover the higher costs of teaching assistants, undergraduate tuition would increase. By making education more expensive, we can be sure we'll get less of it. There's a lot not to like in the House bill, but this particular taxing of the not-yet-wealthy or offspring-of-people-of-various-wealth-levels is about as destructive as one can imagine.
There's a part of me that says, "let's snap back ALL tax laws to where they were 1/1/99, when we were headed into a year of balanced budget and start over." That would raise a LOT of taxes. But it would sure help the deficit!

One (but not the only one) of the reasons is that graduate employees (= researchers and teachers) are not unionized and therefore cannot exert collective pressure on their universities to address this issue.
In fact, the problem is not only the tax itself, but also the fact that this hit by the federal government is borne by the graduate employees exclusively, rather than in part by the universities as employers. Suppose a university has a grad employee union which is infinitely strong, and that it has no other concerns or interests but to avoid the reduction in their effective income. In that case they could have forced the hand of the university to give them a raise amounting to the exact amount of the levied tax - and thus transferred the burden of paying the extra tax to the university.
Now, of course these assumptions don't hold, so a grad employee union might not be able to repulse much of the burden; or if it's stronger, it would probably reach some agreement with university management and split the bill, so to speak. But even beyond that - graduate employee salaries, or salaries-disguised-as-stipends (/fellowships/scholarships/whatever you call them) - are extremely low in the US. Any half-decent such union would have already increased these salaries to a level where the extra tax might have hurt, but would not have been nearly as painful.
Now - unionization is always difficult; and university managements are typically quite ruthless; and an inherently-precarious workforce with employment lifetimes of 3-6 years in most cases makes it even harder. But it is certainly critical to set up in order to face challenges such as this one, collectively.

Suppose the university increases the stipend to cover the cost of the tax (which they probably would have to to some extent if the government started taxing remitted tuition). You still have real money going out of the university's coffers into the federal government's. This hurts grad students, faculty, undergrads, and everybody else at the university. It doesn't solve the underlying problem, even if graduate students aren't quite as bad off as they would be otherwise.

@PeterShor: You're absolutely right, I was talking about sharing the burden. However, when university management can easily depress the wages of some sector, it is less likely to resist budget cuts. So it's not quite a zero-sum game.

There are a number of graduate student unions...

@Fomite: 1. They're still the exception rather than the rule 2. Even those are mostly not recognized, or have not even demanded recognition, to be representatives of the graduate researchers, as employees in research (I mean, as opposed to representing people as students only and/or as teachers).


text:
Is it possible to apply to a PhD program, then transfer a year later to a higher-ranked program?
Is possible to apply to a PhD psychology program, and if accepted, then transfer a year later to another program that is higher in ranking?

See Is transferring to another university an option for an unhappy PhD student?

It may bear repeating that there is really no notion of "transfer" between grad programs in the U.S.  That is, you'd need to (re-) apply to the other program, and hope to be admitted. The fact that you'd been accepted to the other one already gets you almost nothing, certainly not automatic admission.

It might be possible, but I would not recommend it unless there are very special circumstances. For example, if your advisor is moving institutions, it might be appropriate to follow them if you have their backing.
The higher ranking program is going to wonder why you were unable to complete your studies at the original institution, and will question your ability to play well with others. They will have many, many applicants that are as qualified or more qualified than you that lack the uncertainties you will bring ("will they stay?" "why did they leave?" "are they being totally honest?"). Further, there is almost nothing you will be able to accomplish in your first year of graduate school that will distinguish you to the point that a school that originally rejected you will suddenly want to drop everything to have you.
Two more pieces of advice: first, the ranking of the school you do your graduate work at matters less than your choice of advisor and ability to thrive in the lab you join.
Second, if you feel like you need more experience or to improve your resume to get into the school you want, you will be much better off getting a research job for a year that is not part of a graduate program - this is very common, and will not be looked upon as strange by an admissions committee. Changing universities after a year will.

In theory, your PhD application should be your "last stop."
The idea of transferring to a better program might work if you "woke up" late in your academic career, say in your master's program or the senior year of a bachelor's program. Then if you get "top grades" in the first year or so of a middling PhD program to overshadow worse grades earlier in your academic career, that might enable you to transfer to a better program.
My own experience, and that of several of my PhD classmates was the opposite; that if you get into the best program warranted by your earlier grades and can't "hack it," the transfers are "downward."


text:
Research supervisor is easily distracted in meetings with me
I don't think my research professor takes me seriously. I have noticed that in several of my meetings with my PI, he gets distracted very easily.
Now I know of people my age who get distracted (in their 20s), but he insists it's something natural... and he's way older. For example at our last meeting, he was advising me on what I should do for the next part of my project, I was writing all that stuff down, and then he spaced off. I was looking through my notes to see if I understood everything correctly, and he stared up at the ceiling. Next, he asked me if I knew what the ceiling material consisted of. When I said I had no idea (I was trying to brush off the question because there are more important tasks at hand), he made me look it up on the spot. At the moment I thought he might have become bored, maybe there was an awkward silence, but now that I've been thinking about it more, this is not the first instance where this has occurred. He does this in front of my other classmates as well.
Is he just joking around? Trying to lighten up the mood? Am I awkward? Am I not important? How do I address this to him?

"He does this in front of my other classmates as well" - he gets distracted when he and I chat about my project, while other students are around.

It sounds like he has an attention problem. There doesn't seem to be any indication that it's about you.

Unfortunately, there doesn't seem to be a question here that we can answer for you (we don't know him). Just sounds like an attention issue or something else psychological. I've had meetings with people that had far worse issues. Learn how to work with it.

@ff524 is right.  Attention problems are less common in older people but they are not rare.  Also, any professor will have attention problems at a 4 PM meeting if they have been working since 6 AM.  Or if they worked until 6 AM.

@AnonymousPhysicist - good point.  Then the question still is, how do these two people figure out how to work together comfortably and productively?

So, what was the ceiling made of?

Why was this question closed?  I'm not saying it should or shouldn't be, I'm just surprised there was no explanation given.

Most people can concentrate better when they are still fresh, so my suggestion is try to schedule a meeting with him early in the morning, or as early as possible. Like the other answer has suggested, try to keep the meeting as compact as possible. Also, you might also have to try to keep him occupied on you so that he don't have any time to start thinking of something else. This can be done by keeping the discussion on. You have to learn to write while thinking and talking at the same time.

I have a few practical suggestions for you, to cope with your advisor's distractibility.

Set the scene.  For example, if squirrels or interesting people outside his office window are drawing his attention, tell him the light bothers you and ask permission to lower the blinds.  If he gets mesmerized by his screen saver, ask if it would be okay to turn off the monitor, or position yourself so that his back will be to his monitor.  Etc.
Ask permission to tape record your meetings.  Write down your notes later.  Keep things moving in your meetings, so that he doesn't have a chance to get too interested in the ceiling.
Bring along a couple of quiet fidget items, and put them in on the edge of the desk or table, where you can both reach them.  For example, one of the modern forms of silly putty.  The little donkey who takes a bow when you push up on the base.  Etc.
Observe how many minutes it takes for him to get distracted, subtract 5, and try to wrap up your meetings in that many minutes.
Have some of your conversations while on a small hike together.
Give him a yoga ball as a gift, for sitting and bouncing in his office.  Tell him you heard it's recommended for optimal back health and concentration.
Observe what time of day seems to work best, and schedule your meetings accordingly.
Bring along a high-protein snack to share.
Allow yourselves a 25% failure rate.  Be philosophical about it.  As mentioned in a comment -- don't take it personally.

I have experience collaborating with people with ADD and ADHD. Not all of the above ideas are guaranteed to be helpful with any individual distractible person.  Experiment.

I'm not sure all these suggestions are appropriate for an advisor/advisee relationship.  Maybe you should add why you think these will work.

@AnonymousPhysicist - I can say why I think they might work.  Because the advisor is a distractible person who is nevertheless capable of good work, no?  So with the right environmental accommodations, he should be capable of doing good advising, too.  //  All my suggestions came from living with a distractible person.  The idea is, see what the student can tweak, so as to get the best out of the advisor.

I understand that you like to talk about the things you do for your son. He's very fortunate that you invest all these efforts to take care of him. This being said, this situation has nothing to do with you taking care of your son. I'm sure you know of support forums for parents where that kind of content might be helpful. Bringing a puppet monkey to a meeting with one's advisor is rubbish advice.

@CapeCode - Puppet monkey?  Do you mean the donkey fidget?  Hmm.  Have you ever tried making a fidget available to a person like OP's advisor?

Puppet donkey then. "yoga ball" and "high protein snack to share" are equally silly ideas. This is two professionals meeting to talk work.

@CapeCode - Pardon the question, but have you ever tried to work closely with someone with ADD or ADHD?  If you have, and have some better ideas to try, I would be very glad to hear them.  //  Note, my list was offered in the spirit of brainstorming.  I do not mean to say that everything on the list will work in all cases.

It is a parent's job to care for their children and help them deal with  AD(H)D. It is not a student's job to care for their advisor or help them  deal with AD(H)D.  The advisor is an adult professional; they are responsible for their own treatment and behavior.

Also, nobody here even knows if that person has any kind of attention disorder.

@aparente001 I might very well have, how would I know? I don't ask medical records of people I work with. Even if I had, I wouldn't be giving advice here for many reasons, the most straightforward one is that it would be completely off topic on this site.

@CapeCode - Sorry.  I should have said, have you ever tried to work closely with someone who is very distractible.

@JeffE, It used to be thought that children with ADD outgrow it when they reach adulthood. It is true that as the brain matures, things can get better; also, as the person gains experience, he (hopefully) gets better at using coping mechanisms. At any rate, the bottom line here is that the OP could (a) take it personally and feel offended, (b) try to sand with the grain, so to speak, to get the most out of this advisor, or (c) choose a different advisor. I am not recommending against (c) -- that is a very personal choice. My answer is, if OP wants to do (b), here are some ideas to start with.