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Credit with helping to write a PhD thesis
I am an undergraduate student doing summer research and I am helping a PhD student to write a portion of her PhD thesis and with a bit of editing here and there. I am wondering how would credit be distributed since I don't think a  PhD thesis can be co-authored. Also, when I apply to graduate school afterwards, how would I show the admission committee that I have done this work?
To clarify: I had two kinds of contributions to this thesis. There are parts describing research we collaborated on, but it was mainly me in that I collected the data and performed the analysis but she gave me advice. There are also parts that describe her research, that I helped to edit.

The PhD student would certainly fail her defense if you truly "collected the data and performed the analysis." You may think you have done a lot, but I am sure that the PhD student has done far, far more. Working as a tutor from a sophomore until after my own PhD, I have helped countless PhD students w/ 1000s of pages of research--enough to earn 15-20 PhDs of my own using your logic. But the truth is that at most my help was collaboration, something that is expected of all researchers. "Credit" is the wrong word. "Acknowledgments" in a dissertation are appropriate for help such as this.

hahhahahahah. "Certainly fail her defense." I love humor in science too much.

In some fields, almost all work is done as a collaboration. In these fields, it is not at all unusual for this collaborative work to end up in a student's thesis. However, the thesis text should clearly state "This chapter describes joint work with X" (e.g. in a footnote).
However, to really get credit for this joint research, you should prepare a manuscript and try to get it published, or at least release a preprint you can put online (if there isn't time to get it published before you apply to grad school).
For the editing assistance, the most you can get is a thanks in the acknowledgements, and help with editing is not likely to impress an admissions committee.

My answer is somewhat of an amalgam of previous answers, with a little softening.
As to the editing, there is no problem.  It is fine (and encouraged) for PhD students to ask others to proofread or edit their writing.  Out of courtesy, she should acknowledge your assistance in an appropriate part of the thesis (usually a special page near the beginning).  But you should be doing this either as a personal favor to her, or in exchange for money; other than that, there is nothing in it for you.  It isn't something that would likely interest an admissions committee (though you could certainly list that you did it, as it does give you a little extra exposure to professional writing).
As to the substantive research and writing contributions, there are possible ethical issues.  You should talk to the PhD student and make sure that she has told her advisor and her committee about your contributions, and that they are okay with it.  You should also ask about any special procedures that the university might have for including collaborative work.  (For instance, at my PhD institution, they would need a signed letter from you confirming which parts were yours.)  If you get any sense that she might not be following all the rules, or that she may be intending to pass off the work as her own, you should go to her advisor and explain everything.  (Ideally, you have already been talking to her advisor, since he or she presumably is the ultimate supervisor of your research work.)  The fact that some of the text was actually written by you will invite the most scrutiny, so be sure this is clear to everyone.
She should certainly describe your contributions, very specifically, in the acknowledgements.  If the thesis work is going to be published in a paper, depending on the level of your contributions, you might be entitled to coauthorship on that paper.  You should discuss these authorship issues with the student now (e.g. who will be first author, etc), but you might also want to talk with some other faculty member, since it sounds like you may not have enough experience to know what is reasonable or customary in your field.
In the short term, the way you would get "credit" for your work, for the purposes of graduate admissions, is to get a letter of recommendation from the student, as well as from her advisor or whichever other faculty member is supervising your research.  They can tell the admission committee in detail about what you did, and how they think it reflects on your research potential; that's likely to be even more helpful than being able to point to a part of a paper or thesis as yours.

For my MSc Thesis, I put the people who proof read and helped edit my thesis in the acknowledgements.
I think the admissions committee would care if you did some of the research, and if the PhD student was your primary advisor for that research, it would be good to get some form of letter of recommendation from him/her. A few people I know submitted 4 letters instead of 3, because a lot of the research they did was a PhD student and they thought a 4 letter from that student would help them.
If you didn't do any research, you basically edited and made suggestions, I'm not really sure an adcomm would be interested. Great, your a friendly dude who helped his friend, now show me what you've done yourself.
But I'm not really sure how the adcomm will look at "editing" someone else's PhD thesis.
If you did some of the writing for the PhD thesis, I think thats weird; all of the writing should be done by the PhD student.

There is a portion which is my own work and my own research. The parts where I edited are her part.

Then it's probably worth getting a letter of recommendation from her; she will have a PhD, and that is a credible source.

@Mat.S Did this PhD student collaborate with you for the parts that you worked on? If some parts are your work, and your work only, that material probably should not be in the thesis.

Yes, sorry for the ambiguity. The work that I worked on we collaborated but it was mainly me in that I collected the data and performed the analysis but she gave me advice.

I think you need to have some discussions with the PhD student, and perhaps even the PhD student's advisor. I have never heard of an undergrad's work going into someone else's PhD thesis.

You write that you are "helping a PhD student to write a portion of her PhD thesis".
Clearly from your question and comments this isn't a stapler thesis: this isn't a case where you and the PhD candidate have co-authored papers, where your work would be in the thesis and explicitly attributed to you.
In your other comments, you make it clear that you have written passages that are in her thesis. That goes way beyond just doing collaborative research. If it's in the student's PhD thesis as her own writing and her own research, then she is falsely representing that she's done the research, and she's falsely representing that the thesis is all her own writing.
In any university that I knew of up til now, that would result in the thesis being failed.**
I think you need to find out the rules of your university pretty quickly, because although the PhD candidate will get the worst of the enforcement, you could get hurt by this. This is now your responsibility to put right, for your own sake. That's because if it is against the rules, then you have unwittingly been complicit with the PhD student in what, upon submission of the thesis, would be the breaking of those rules. I think ignorance of the rules is unlikely to be taken as innocence in any ensuing disciplinary proceedings. At best you could make a case of being led astray by trusted colleagues, but that's going to damage your relationship with them. It is possible, as things stand, to extricate yourself from this situation without too much damage.
So don't go to the candidate or her supervisors to ask for their interpretation of the rules yet (if at all). Find and read the relevant rule yourself. They are almost certainly on your university intranet, if not the outward-facing website; failing that, ask in the university library.
Here, for example, is the rule for PhDs at University College London (UCL):

The work in the thesis submitted by a student must be their own work and the submission of a thesis for examination will be regarded as a declaration of that fact.

The thesis may include collaborative work, but this should be stated as such, and must be written up by the PhD candidate, not the collaborator(s).
If, as I suspect, co-authorship of a PhD thesis at your university is not allowed, then you need to insist to the PhD student and her supervisors that the passages you've written be removed from the thesis. Do it gently, politely, in a collegiate spirit, but do it unambiguously. As you've done genuinely new research, you'll be submitting the words you've written to a journal, so tell them that - that should be enough for them to be sure to remove it from the thesis. Keep the paper trail of all of this (including the emails or other records of when you've sent your material to the PhD candidate in the past), to protect yourself.

** though through the comments below, I've learnt that the University of California in San Diego does allow some co-authoring, providing advance permission from the Dean of Graduate Studies has been obtained.

We must have experience of very different universities, then, because at all the ones I know, it is perfectly fine for a thesis to contain collaborative work, provided that the collaborations are appropriately disclosed, and the committee is satisfied that the student's contributions demonstrate their research ability.

@NateEldredge the OP has written bits of another student's PhD thesis - have you seen that happen before? Can you say which departments, which universities?

As a simple example, I could cite "stapler theses" consisting of several papers, some or all of which had coauthors.  In such cases, it would be surprising if some parts of the coauthored papers had not been written by the other authors.  Would you like me to find examples?

@Nate: What you say is true, but there are all kinds of rules about it.  ("Even in mathematics" this comes up now and again: I have been on thesis committees where everyone has to check the rules and make sure they are being followed.)  One important rule at my university is that the PhD candidate must be at least a "co-first author" on any papers included in the thesis.  Another rule is that any published materials that are being included must be acknowledged and documented in a very particular way (which I think amounts to advanced vetting by some university officials).

@NateEldredge This isn't a stapler thesis though, is it: the OP hasn't co-authored a paper that is being included. So can you find a non-stapler example?

As EnergyNumbers points out, I think one should also make a distinction between including already published work on which the candidate is a first author (so in some sense they did write the paper, or are acknowledged as having that level of oversight of it) and simply having someone else do work and/or write text which will appear for the first time in a student's PhD thesis.  Indeed I agree that that would be problematic in many circles.

On the other hand, I mildly disagree with "This is now your responsibility to put right, for your own sake." Owning responsibility is never a bad thing, but it is really not any undergraduate's job to know the rules and customs of what constitutes an acceptable PhD thesis in some academic department.  That responsibility is that of the student, the advisor, and the committee.  The OP should not in any way hide his participation, and I think that a conversation with the student and/or the advisor addressing this issue would be a very good idea.  But this is really not the OP's problem to fix.

@PeteL.Clark I see what you're saying. But if it's against the rules, the OP is complicit with the PhD student in breaking those rules. I think ignorance of the rules is unlikely to be taken as innocence in any ensuing disciplinary proceedings. At best the OP might make a case of being led astray by trusted colleagues.

I wouldn't call the OP "complicit", because he and the student are not at all in the same situation.  Is there any written rule that says "Undergraduates cannot contribute to PhD theses"?  No: all the rules are from the perspective of the thesis.  Someone who is more academically sophisticated would know that he has been asked to do something strange, but that's not the same thing and I don't see why the OP would be expected to know this.  But I think this is kind of moot: I think the OP should talk or write to the candidate's thesis committee with their concern.  Once he does that, he's fine.

No, I do not know a non-stapler example off the top of my head.  But my PhD institution's thesis guidelines contain procedures for how to include co-authored material in a thesis, whether or not it has been (or will be) published.  See page 43 of this document; despite the heading "Using Published Material", the rules in that section are described as applying to coauthored material, even if unpublished.  It certainly requires extra scrutiny, but is not inherently impermissible.

@NateEldredge there is a big difference between perfectly fine and not inherently impermissible :)

I am helping a PhD student to write a portion of her PhD thesis.

Based on this statement, I assume that the thesis is a monograph. I think it is very weird for an undergrad to write parts of a PhD thesis. Although the work in a thesis can clearly be the result of collaborative work (in the form of co-authored papers or other publications), a thesis in essence must be an individual effort.

... and with a bit of editing here and there

The PhD student should describe in the acknowledgement section that you proof-read and/or edited parts of the thesis.

Also, when I apply to graduate school afterwards, how would I show the admission committee that I have done this work?

If there is a scientific or research value to your contribution, some or all of it could end up in a publication, of which you can ask to be a co-author.

I don't think a PhD thesis can be co-authored.

No, and again, I find it very strange that you are actively writing sections in the thesis. Furthermore, most academic institutions will ask PhD students to sign a document stating "I am the sole author of this thesis" when submitting their thesis.


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Can I attend a PhD program with the intent to transfer my PhD credits to an MS and after 2 years, apply to a better university for a PhD?
I have been admitted to a PhD program at a  US university in the department of physics. The  department ranking is 100 (according to the US News ranking). In the PhD program, most of the students in physics study the fundamental principle in order to be prepared for doctoral studies. It takes around three semesters.  The  department I have been admitted to, also has an MS course.
My intention is to  transfer my PhD credits to the MS in order to gather more research experiences (2 years study) and later apply to a better university. Is it possible to manage this with my graduate supervisor? How  positive is my case? And how do you think my supervisor would respond to this?

If your intention is to get masters, then you should apply for masters.

I have admitted into PhD program

If you switch to a master's, you may lose your funding or get reduced funding.

As far as I can tell, you are essentially trying to transfer from one PhD program to another. When you apply to these "better" universities, you'll still be enrolled as a PhD student. Therefore Is transferring an option for an unhappy PhD student seems like a duplicate.

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Soft money tenured profs in schools of medicine
I am a PhD student focusing in psychiatric genetics, hoping to become a professor someday. It is my understanding that a lot of the PhDs in my field end up working in schools of medicine in positions that are 80-100% soft money (even though they are tenure-track).
That sounds... terrifying. You're not a clinician so you can't make up salary with patient care, you're in a school of medicine so there isn't much opportunity to cover part of your salary with teaching... it sounds like you would have to spend your entire career living in fear of a grant dry spell, even once you had tenure (no grants = no salary).
Am I misunderstanding how this works, or is it really that bad? How do people survive in that situation?

What you describe as "terrifying" is the typical level of job security for, say, most non-academic employees in the US (probably better, in fact).  They survive somehow.

The reason I think it's so terrifying with professor jobs is because the hiring cycle for getting another one is so long (if you can get another at all, being forced out due to lack of grants would not look good in an applicant!), and you might have to move halfway across the country for another job in your field. With most non-academic positions if you are laid off you can start applying for other jobs in your field immediately, there is less stigma to layoffs and it probably won't count against you as an applicant, and you probably wouldn't have to move.

For soft money position, especially NIH funded one, there are a number of things working in your favor. You might be PI on 2 or 3 grants and CI on another 1 or 2 which means that no grant has more than 30 percent of your salary. Since NIH grants are generally 5 years long, it means you write a new grant every year.
The amount of time between getting an NIH grant and starting it can be 12 months. This means you have lead time before you run out of money. The NIH also allows you to get a no cost extension, which allows you to stretch what money you have.
Universities also will often allow you to either front pay or back pay your salary while you wait for a grant that has been awarded to start. This again allows you to cover gaps.

"Since NIH grants are generally 5 years long, it means you write a new grant every year." That's the part that's working in your favor?  Ugh.  Makes me glad that my money (what little there is of it) is hard.

@PeteL.Clark some people are on soft money where grants are 12-36 months long.

Thanks for the reply! It's good to know that the risk is at least spread across a few grants instead of having all eggs in one basket. What happens if you are going to come up short though... how common is it for that to happen, and what options do people tend to use (colleague adds you to their grant? just take a 30% pay cut for a year?) when it does happen?

As someone who looked at a number of these positions: Basically, the answer to your question is: "Yes, this is just as daunting as you think it is."
There are however some caveats to this, both good and bad:

Recognizing this, there are many schools that will not put a PhD in that position by not allowing them to apply on tenure track. This was the case with one position I looked at - they were fairly frank that the reason was exactly what you suggested: if my grants all went away, as I couldn't make up it up with clinic hours, they wanted to reserve the right to be able to fire me. Similarly, there are many medical schools where tenure is extremely rare.
While @Jim is correct that there are minimum salaries, they are low, and there are myriad other ways that the school can penalize someone whose grants have fallen through. For example, cutting down on their lab space is a common one.
Many institutions do have bridge funding for the unexpected gaps in funding, which can help smooth out minor funding problems.
As @StrongBad noted, not all the grants have to be yours. At an old institution of mine, it was fairly common for a considerable %-effort for new faculty to be covered by incorporating them into large, existing, fairly reliable grants.
Because it's so common, the NIH is organized around the assumption that PIs may be claiming significant %-effort in their grant, unlike some other funding agencies.

But yes, a 100% soft money position does have some very real pressures behind it.

Medical schools have minimum salaries, even for faculty, so even if you have 0% effort on grants, you will still be paid a salary (although a low one--think postdoc salary). Faculty are typically incentivized to meet the % effort goal set by their school through a yearly bonus. The bonus will be the first thing to be cut if you don't meet their goal. If your gap looks like a temporary one, the school will likely cut you some slack for one or two years, especially if this is a tough year for funding (think sequestration), and not reduce your salary. But the pressure will be very high to get a new grant.
There are things you can do to cover a temporary gap. Even in a medical school, you can teach and get a little funding that way. You can also work on the side as a consultant. Finally, you can change your effort allocation on your remaining grants to cover for the budget shortfall. NIH allows you to increase your effort on a grant if the project requires it.
The biggest impact your funding situation will have is on your chances of getting tenure. If you can maintain stable funding during your assistant years, usually it is a good indicator that you will be able to continue to do so once you get tenure.

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How to study for the exams which are mathematical in approach but subjective in nature?
Predominantly whenever we are to face objective questions we generally tend to practice more and more objective question papers and sort of "remember the mistakes that we make while solving them".  However when it comes to subjective papers this approach doesn't seem to work for me anymore.  The more subjective questions I study the more I tend to deviate from whatever I need to retain for the approach.  Any suggestion about this will be highly appreciated.  I am particularly speaking with regard to semester examination of an Undergrad/Postgraduate course in Material Science & Engineering.

Could you give an example of the kind of course or exam you're wondering about?

The exam is predominantly a semester examination and the course is an undergraduate/postgraduate course in Material Science and Engineering.

It's hard for me to understand why a course in Material Science and Engineering is subjective.

Do you feel the questions are more subjective because you will be asked to synthesize information or do more design work?

Is is sort of like "How does concrete make you feel?"

@mkennedy It is asked to synthesize information which makes it all the more boring.

@JohnColeman Not really it asked questions like "Why is one particular dislocation glissile and the other sessile?"Justify/Substantiate.

Perhaps by "subjective" you simply mean "not explicitly computational".

@JohnColeman Absolutely correct.You just read my mind.

I don't know why you find such questions "boring". Computers can compute stresses, but they can't yet synthesize information in any genuinely conceptual way. You just need to show that your understanding of material science goes beyond what can by easily programmed.

Let us continue this discussion in chat.

Thank you for a good laugh! As an MSE PhD, you chose an example subject that could easily be held up as the perfect reason to ‘get a feel for’ what might happen. If you doubt me, find a copy of Hirth and Lothe’s book on dislocations and see just how mind boggling hard it is to try to calculate almost anything to do with dislocations.

Learning math, science and engineering is to a certain extent about learning a collection of computational techniques that one can improve at by rote practice - integrating, differentiating, solving equations etc. But to a much larger extent it is about acquiring a conceptual understanding of the key ideas and concepts of the science you are being taught. This is a higher lever skill, and one that is ultimately much more important.
What you call “subjective” questions are precisely those questions that are designed to test your understanding. They are the questions that, ever since I started teaching, I have been hearing students (even well-intentioned, hard-working, eager to learn students) describe as “trick questions”, “unfair”, “not in the book”, “impossible to study for”, and so on. They are the questions that students dread and loathe and complain about and seek to find ways to avoid and bluff their way through. They are the questions that really test whether you have learned the main thing we wanted you to learn.
To be fair, subjective questions are indeed hard, and I completely sympathize with your frustration about them. They are characterized by the fact that there is no mechanical practice procedure, like “solve X problems from section Y in the book”, that is guaranteed to prepare you for them. Learning how to study for them is probably the single most valuable skill a student can hope to learn in their time at university. If you have learned how to study for subjective questions, it means you have learned how to learn, and that’s a wonderful thing to know.
So how do you study for them? In some sense that’s something each person has to discover for themselves. But in another sense the answer is blindingly obvious: you study the material, and you think about it. That’s it! But what I mean is really really study the material, and really think about it: that is, you think critically about each and every sentence of each and every section in the book/lecture notes and each and every thing the instructor said, trying to identify what conceptual meaning it is trying to tell you. You try to probe into every nook and cranny of the theory by criticizing it, and asking “what if” questions and “does this make sense?”, and reading Wikipedia and textbooks and watching online videos. You solve problems, and solve more problems, then go back to the theoretical part of the textbook and read it again and think about it in the context of the problems you solved. And watch more videos and read more books and forums and talk to your friends about the material. Etc etc. - note that this process has no natural end because no one understands everything, not even your professors. But at some point you’ll probably feel like you understand things at a reasonably good level for the exam you are about to take.
And then you move on to the next subject and start all over again. :-)

By solving more and more problems do you mean the computational part of simply the subjective ones?

@gateprep - he means actually think about the material. What about a material influences what? If a dislocation is glissile in an fcc material, how does it behave in bcc? OK, how about hcp, what is different? Monoclinic? At the heart of it, what factors do you need to consider, and why, to attack the problem in some arbitrary material? You can’t memorize and plug-and-chug through real world problems (or at least not at the salary point of a materials engineer).

@gateprep both. Try to think holistically about all aspects of the material, and solving any sorts of problems you can get your hands on - even invent your own problems. Solving a computational problem might also reach you something conceptual if you think about the meaning of what you are doing, and conversely a subjective problem might help you think of a trick that will be useful in doing computations. The distinction between the two types of problems is in any case a bit arbitrary, and many problems will be somewhere in the middle between those two categories.

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How to acknowledge funding
This question expands a bit on my previous one Acknowledging funding.
I am unsure how to write proper acknowledgments at the end of a research paper. The wording that I read most often is Author XY is [partially] supported by..., which does not correctly describe my situation unless one stretches the meaning of these words.
More in detail, here are the two sources with which I have trouble:

a foundation that used to give me a postdoc grant. I did part of the work of this paper while living off this grant, which expired six months ago, and part of it under my new employer. How should I write this? If I write is supported by, I give the impression that I am currently being paid in full by the foundation; if I write partially supported I give the impression that I just got a smaller grant.
a research institute that paid my travel expenses for a conference. While this funding is not directly related to the paper, I met my co-author there and had a chance to discuss its state. And, besides that, it is basically my only occasion to acknowledge this grant. How should I write this? Is partially supported the correct wording, or is there a better expression?

It seems to be fairly common to phrase it "... was supported in part by ..." instead of "... was partially supported by ..." I think the former version is better, as it puts less emphasis on "in part".

If I write is supported by, I give the impression that I am currently being paid

"Work by this author was partially supported by the Hitchcock Institute and by the Norman and Norma Bates Foundation."

if I write partially supported I give the impression that I just got a smaller grant

Nonsense.  Unless the institute was your sole source of income and equipment during the entire research and writing process, "partially supported" is correct.  Also, it's standard idiomatic language; nobody will think twice about it.

However, if you use 'supported in part', you get the extra benefit of sounding like an NPR radio spot.

All your answers are useful; too bad I can only accept one, so I went with the most voted.

"And even though Tom and Ray Magliozzi thank God they gave up tenure whenever we say it...."

I found https://us.sagepub.com/en-us/nam/funding-acknowledgements and https://www.aje.com/arc/editing-tip-writing-acknowledgments/ to be useful supplements to this answer.

First: check if the institution who provided the funding requires a specific sentence for acknowledgment. Some do! Otherwise, read on…
Many large research projects nowadays are supported by more than one funding source, especially if you include the institutions you are affiliated with (although, being already listed as affiliations, they need to be acknowledged specifically). Saying “partially supported by” does not have any negative implication to me, and saying “is supported by” does not imply that this is the only support received.
But if you want to avoid this particular phrasing, it also common to simply say:

Acknowledgements
  We thank the John Smith Institute for funding, along with the William and Melinda Bates Foundation for post-doctoral fellowship (to F. P.).

The second part of the sentence makes it clear what was the support, while the first part is more ambiguous. Frankly, noöne cares! That is, except for the funding agencies: they want is their name mentioned for their statistics, but probably don't care how it is written.

"if I write partially supported I give the impression that I just got a smaller grant."
Not necessarily. It can mean different things like one of the co-authors was funded by them or  your situation in which they funded some of it before.
I am not sure if I would mention the research institute that provided the travel expenses. If you feel like you want to do it its a different story. Then I would write that the "collaboration between the co-authors would not have been possible with out the financial support from research institute blah blah blah" or "The co-authors would like to acknowledge the support of research institute blah blah which resulted in blah blah blah".

I agree that there's no stigma to partial support.  At least in mathematics, it's the default: you would leave out the "partially" only if you were 100% paid by the grant (with no university funds at all) for the entire duration of the research project, and that's pretty rare.

On the other hand, I'd suggest mentioning the travel expenses.  Until you reach a ridiculous number of funding acknowledgments, there's very little downside to adding more, while institutes and funding agencies really like it.

@AnonymousMathematician I haven't done it so far for travel expenses but I think you have a valid point. There is really no downside...

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E-mail address to use in publications
It is customary to use one's academic e-mail address as contact address in publications; I have seen once or twice an @gmail.com address being used instead, but it simply looked unprofessional.
However, I already experienced personally twice that system administrators love to deactivate e-mail addresses when people leave the institution. In a time when serving 1 GB of data costs one cent, apparently it is too demanding to set up forwarding for a few old users.
This leads to "e-mail rot" in many published papers, also for addresses that are explicitly designated as contact addresses. If one happens to have a popular name, it might become difficult to identify them using a search engine after the e-mail address becomes invalid.
What is your proposed solution to this problem? Should we (well, the ones of us that have tenure and power) put pressure on system administrator to change this practice? Should we use in our publications a different, more stable e-mail address than the academic one? Should we maybe get rid of the e-mail and contact address in papers overall? Should we insist that the journal publishers set up an alternative contact system (good luck with that)?
Related question: Changing mailing and e-mail addresses as corresponding author--which to include?

I'd have to disagree with "serving 1 GB of data costs one cent"...enterprise drives are far more expensive than the one in your desktop.  And you need backups.  And per user licenses (sometimes per user, per year).

On a side note, check out "E-mail Address Harvesting on PubMed—A Call for Responsible Handling of E-mail Addresses" See: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3068898/

@Grant you need none of those things (well, maybe per user licenses, but that's an argument for using a different kind of server if so) to do forwarding - he was talking about bandwidth costs.

"system administrators love to deactivate e-mail addresses when people leave the institution" - as I have recently been explained, they actually hate it, but feel forced to due to legal ramifications: In some jurisdictions, apparently, the moment the university provides an e-mail address to someone who is not formally a current "member" of the university (and having studied or worked there in former times does not count), the university does not act as an employer or educational institution that internally provides e-mail addresses any more, but as a public e-mail provider. ...

... Unfortunately, in some jurisdictions, this implies conformance with different legal requirements than if it were only an internal e-mail service for employees and students, such as conducting the data retention for security agencies, etc. This seems to be the case at least in Germany, and possibly elsewhere.

Strongly related: https://academia.stackexchange.com/q/96503/19627

Some Accademic institutions support life long email forwarding, this is cost-efficient.  Most PhD students will otherwise not be able to receive emails on their official adresses after a couple of years.

Since Piotr's answer and the discussion following it states the most important points (while an academic email address may become invalid, a private one provides no means to verify the author's actual affiliation, or even suggest the author doesn't identify with it), here's my suggestion:

Create a PGP key+ for your private email address

optionally add your academic email address as another identity

Have your key signed, e.g. by

colleagues
your institution's sysadmin
a key exclusively for your academic email adress

Publish the key, e.g. at http://pgp.mit.edu/
Ask the publisher to include your public key+ or at least the footprint in the publication

The online version should even link to the key entry to make verification easier

Now everyone can easily check your affiliation while you've made sure you can be contacted in the future - you can even add alternative email addresses to you key later on (the upload can be updated), and everyone will be able to deduce that should your original address not be reachable any more, you might be reachable via one of the other addresses associated with your public key.
As an additional benefit, now both you and your co-authors can sign the publication itself, adding another level of trust that this is truly authored (or sometimes rather endorsed, if you're so honest ;) by each of you. And since you now have PGP keys anyway, you can also sign and/or encrypt your emails, making electronic communication both more trustworthy and less prone to leaks. Also, it keeps the NSA out for a while.

+ In case you're not familiar with PGP:
You create a pair of keys consisting of a secret key (which you and only you shall ever possess) and a public key (which you are supposed to make as public as possible/required). The secret key can be used to put a signature on anything digital, like messages, files, protocols, papers or other people's public key, and anyone can use the matching public key to verify that this signature stems from that secret key, and thus (hopefully) from you. Reversely, anyone can encrypt data for you with your public key that only you can decrypt again with your secret key (messages can be encrypted for multiple recipients as well if required). Since everyone can sign anyone's key, you obtain the Web of trust, a network of keys that allows you to estimate how reliable the association of a key to an actual person is without having to exchange public keys in person. (The downside is, your email address is public and social engineering is possible, but we're responsible adults, right?)
A great open source implementation of the Open PGP standard is the GNU Privacy Guard

@CharlesMorisset well, those who are googling anyway shouldn't care about whether one used a private email address or not :-7 I don't think it's so much overkill, creating the keys and having them signed is a once in a lifetime (ok, make that once per institution maybe) thing which, due to the security shortcomings of email, should be encouraged anyway...

@CharlesMorisset Well, that's the great thing about PGP keys: You can add identities later on, i.e. even if your original email address is long gone (or email not used any more), the key will still exist and show your new address if you update it. But I agree that the sysadmin may not be too easily motivated to sign all academics' keys... Anyway I hope these thoughts at do inspire others to at least think about signatures and encryption a bit more

I like the idea in the abstract sense  of "the world should use more crypto", but it's not feasible in the real world.  Journals aren't going to publish or link to pgp keys unless you really push hard for it, and it's not worth pushing for in practice.  (For years I encouraged people to use the PGP key on my web page, but only one colleague ever did, and when I replied it turned out he had already forgotten the passphrase for his private key.)

@AnonymousMathematician Well, we've got to start somewhere, so signing each email (even to colleagues who don't yet understand the benefits) may encourage at least a few to follow your example. Maybe there even is a "bad example" story how things have gone wrong due to a lack of encryption or due to identity theft that somebody can share... There will of course always be others who will probably never understand, just like some folks still refuse to use email, but I'm thinking about the long run

Personally, I think that (in academia) sticking to official e-mail addresses is an atavism.
Currently, one's personal e-mail (say, ...@gmail.com) is better because:

usually more efficient/stable/etc,
lasts for longer than 1-4 years.

While names like mad_theoretican_666@... may sound ridiculous for professional communications (but it's rather a matter of taste than anything else), I don't see anything wrong with e-mails like name.surname@ or n.surname@.
However, I heard quite a few times that non-institutional e-mails sounds less serious.
But honestly, if someone builds his/her value depending on how his/her e-mail sounds (and doing it against very practical reasons), it is the thing that is ridiculous.

An institutional email address is a form of official affiliation.  Yes, it's stupid to judge a paper based on the authors' affiliation instead of the content, but people do.  (Remember, we're apes; we do apey things.)

@JeffE I understand. But a (full) institutional affiliation if one line above, isn't it? (Not even to say that it is easy to create a fake domain looking like a serious institute).

But a (full) institutional affiliation if one line above, isn't it? — Yes, with just enough information to be Googleable (or you don't exist).  The email address is ultimately redundant.

@Charles: The author states that he can be reached in the "personal@gmail.com". You would trust the paper, research, publication where it appeared, but in the author affirmation? hum...

@JeffE For instance, arXiv prefers you to use your official e-mail address because they can much easier verify it. (They simply consider having any email address from a university/research institute server as a proof that you are an academic.)

This being an international forum that happens to use English as its main language, I'd recommend keeping language simple and avoid terms like atavism, which most native English speakers, let alone non-native English speakers, wouldn't be familiar with.

@CharlesMorisset It requires an (IT) child's ability to counterfeit an e-mail address so that it pretends to be an official e-mail. Moreover, I don't care at all if I get a valid answer from a Nobel prize winner or a prankster, as long as it is of the same level. And an e-mail address (in papers) is an additional information, not a validation.

@CharlesMorisset With receiving you can find a domain sounding similar as a real institute (so most people won't notice).

I totally agree with you, Piotr. I was going to post a comment "Use PGP to prove your affiliation while using your private email address" but got carried away into an answer... That also solves the issue of impostors, by the way @Charles

@CharlesMorisset: Google and gmail is now trying to move to an official educational/university oriented service, where students (and staff) can have their academic+google mail forever. See the initiative here

The American Mathematical Society had a email forwarding service for its members, which gives them a stable @member.ams.org address that they can update as they move. However, this email forwarding service is no longer available. Still, something like this could be a good solution.

And so does the Institute of Physics, as I've just discovered: http://www.iop.org/membership/why/page_38344.html

I think this is the best answer so far.  I personally think a university e-mail address is better than a "generic" address (for the reason mentioned by Charles Morisset in his comment on Piotr Migdal's answer).  But if the author is a member of a relevant organization (such as ACM, IEEE, etc.), then perhaps an address from here would be best (again, for the reason mentioned by Charles Morisset).

(1.) Your answer reminded me about IEEE email addresses. If you are a member of IEEE, IEEE will give you an IEEE.org address that you can configure to forward to your stable gmail.com address. NOTE: IEEE member does cost money per year. (2.) If you sign up for your own URL, you can use this as your email address and forward to gmail. NOTE: having your own URL does cost time and money per year. ||| Both (1.) and (2.) fix the social stigma associated with gmail/hotmail addresses and allow you to at the same time keep a stable gmail/hotmail address.

I find ieee.org or ams.org email addresses jarring for exactly the same apey reason as gmail.com addresses.  At some level, it suggests "Well, yes, that's my offical affiliation, but not really."

@JeffE But my view's the opposite: I see the paid-for subscription as indicating a longer-term commitment to the field than a uni email possibly associated with a one-contract that had already ended by the time the paper got published, and (still today) more professional than Gmail which I associate with the throwaway addresses used by spammers. :(

@LouKnee I see the paid-for subscription only as an indication that they have money to spend on a subscription. If I want evidence of professionalism, I'll look at their actual work.

@JeffE But you are looking at their actual work (the publication), and are hopefully impressed enough to want to contact them (by email); otherwise this question is meaningless.  Re. "Well, yes, that's my_offical_ affiliation, but not really." short-term contracts mean the affiliation a decade ago is nothing to do with contact details now, when you have questions about the paper.

@LouKnee That's why god gave us Google.

When I see a gmail address on a paper I think "this is an IT-savvy author who realises their current institutional email address will probably be gone in a few years and wants people to be able to contact them after that." It doesn't look at all unprofessional to me.
But if you're concerned about the appearance of such an address, one solution would be to register your own domain name and have an email address like contact@yourownname.com, which forwards to (for example) a gmail account. You can also put your own academic web site at this domain, meaning you can take that with you when you change institutions as well.
(Edit from years later: if you do this, make sure that you will be able to keep the domain name registered decades hence. I didn't receive emails from the registration company I used - ironically, because my email address changed - and consequently the domain now points to a spam site, and I can't get it back. So I'm kind of glad I stuck with gmail for my publications.)

...or to put it more succinctly, "The author is a student/postdoc."

@JeffE sure, but that's the majority of authors these days - I don't think there's anything wrong with giving the impression of being a student/postdoc if that is in fact what you are.

To me, if "their current institutional email address will probably be gone in a few years" that implies that either the institution is not a very good one (it's so bad that the author wants to leave it, or it's so bad that it's closing) or the author is not a very good one (he or she is so bad the institution doesn't want him or her).

@JoelReyesNoche I don't know anyone who went straight from a PhD to a permanent position at the same institution. At least in my fields (computer science and biosciences) and my country (UK), everyone does multiple 1-3 year postdocs, there just isn't any choice about it. It's not because they're bad researchers, it's just a sign of an overcrowded sector. Because of this, I've never experienced any stigma about being on a temporary contract.

@Nathaniel, thank you very much for the clarification.  I forgot to consider the case of post-docs (even though you and JeffE mentioned it).

@JoelReyesNoche: there are also cases of reputable universities where IT people make small changes to everybody's addresses every now and then, for no particularly good reason. When I was a grad student in Leiden (consistently ranking in the top 100 worldwide), addresses where @leidenuniv.nl; a couple of years after I left, they added a division subdomain, so my former advisors became @let.leidenuniv.nl; and a few years later, they renamed the divisions, so everybody had to start using @hum.leidenuniv.nl. Now there is a rumor that everybody will be @leiden.edu some time soon.

@Koldito, thank you for pointing that out, I hadn't thought of that.

+1 This is what I do. I'll add that it's easy and cheap (US$1/month).  My institutional address will be dead the day after I finish my postdoc.

I make a point of offering all of my papers for download from my website.  So if readers discover me via a paper I've written, it should be easy for them to find my website (just google my name and the title of the paper).  On my website I list my current email address.

+1, I've seen quite some abandoned websites of people who changed institutions, and more often than not there was no information on where to. But I assume you mean your private homepage and not one hosted by your institution

@TobiasKienzler Yes, I mean my personal (but professional) webpage hosted by the school, typically at: http://www.math.schoolname.edu/~myname .  Whenever I'm about to change institutions I move my webpage to the new institution's site, then replace my old page with something like "Dan C and his [link to new webpage] have moved to [link to new school]."

One's name is no safe harbor. There is a non-zero chance of someone with a similar or identical name to be internet famous and your webpage will be burried deep because of the google's search optimization. This is quite likely if your name is a common one. I have met with 3 different people with same name + surname and I am quite young.

Should we use a stable email address?
I agree that seeing @gmail.com, @hotmail.com, @yahoo.com in email addresses for academic papers is somewhat jarring. That it should be the case probably says more about our assumptions about the author than it should (why doesn't he/she have a proper email address?). The benefits of having a stable email account - for those of us still moving frequently from post to post - is undeniable, but we choose not to use it for these reasons. Will that attitude change? Not impossible, but don't count on it.
Should we put pressure on sysadmins to maintain forwards on our old emails?
I'm not a sysadmin but I doubt whether any sysadmin would look favourably on maintaining indefinitely forwards in this way. After two or three hops, your email chain starts getting long and vulnerable.
Should we get rid of addresses altogether?
Probably not. We need some way of being contactable.
Should we insist that the journal publishers set up an alternative contact system
I like this idea but appreciate that getting the publishers to do this would be difficult.
What if there was a third party site which stored up-to-date contact data and was linked to by the journals? A freely accessible, central repository of author contact data. The authors would be responsible for maintaining their contact information.
Users of the repository would themselves have to log in to prevent massive downloading of users' data by spammers.

For your last suggestion, Mathematics is one step ahead of you :)  Behold the Combined Membership List!  (Well, ok, it only covers North America, but it's something.)

Eventually, if ORCID (discussed also in this answer) takes momentum (and it seems it will, since it is backed by the most important publishers), it could solve this problem: the paper contains the ORCID number of the author, and points to an online profile which the researcher themselves can update.

In the end, this is similar to Tobias' solution, but with the ORCID in place of the pgp key and the orcid server in place of the MIT one. You lose the other benefits of having a PGP key available for encrypting and signing, but it will be much easier to set up since journals will do almost all the work (also for the non-tech-savvy researchers).

8 years since this answer was given, It seems ORCID hasn't taken off. Nobody has ever given me their ORCID and I don't see it in publications in my field.

@einpoklum It's likely field dependent. In physics, it's common to see an ORCID symbol next to at least one name in the author list of a paper. I think it helps that some key journals have encouraged people to adopt it.

@einpoklum I agree with Anyon, just check out recent publications in Physical Review journals (who encourage authors to add their ORCID).

@Anyon: Point taken, but - you're describing one field, in which, still, only a minority of authors publish with their ORCID number. Are there many fields where it's at least this popular, or some fields where it's more ubiquitous?

@einpoklum I don't know. That could be a good question for the site.

In the age of search engines and relatively high mobility on the side of researchers, personally I see no reason to include an e-mail address on research papers. Whenever possible (i.e., the published/editor does not explicitly ask for it), I do not include it at all and if I must, I use the currently valid one. The reason is exactly that it becomes invalid quite quickly. The e-mail address is not useful even as a means for author identity disambiguation. For lucky guys bearing a name like "John Smith" in various languages (I am such a case as well), it's relatively common to encounter a guy with the same name, or initials working at the same university, or sharing part of academic history.
A complementary issue to the original question posed is this:
How many times in the last ten years did you used an e-mail address stated in the paper as a means to contact the author(s) of the paper?
I did so exactly zero times and know of nobody who did so more than that (and yes, I asked several colleagues about this in the course of the last few years).

I did at least twice in the last 2 years. And I've been contacted that way about twice as well (though I don't know for sure whether it was via the published email address or via googling for me which would lead to the same email address).

@cbeleites: so maybe I am wrong in my answer if there is a significant number of people who do that. Well, one of the assumptions I made in the answer is that one has an on-line presence set up, that is a personal website hosting a collection of downloadable published papers. That completely removes the need to list an e-mail address in papers, but of course there are differences between cultures in different research fields.

One of the reasons I don't tend to use the email address from the paper is that, if it ends in .edu, I know it's likely to fail anyway.  When I see an address with more (presumed) permanence, I am likelier to give it a try.

I use email addresses on papers all the time. I mean, ok, not every day, but when I want to contact the author of a paper, I use his/her listed email address before trying anything else.

While I like Tobias' approach I agree that it is overkill. However, I wonder whether it would just be a rather simple solution to give two email adresses of the corresponding author: the institutional and the stable personal one.
On the other hand, while I do sometimes contact authors using the contact email address, I consider this a convenience rather than a necessity.

It is usually quite easy to track down the author even if he moved on. People at the old institute usually know where he went.
If the author has been moving on so often that the old institute doesn't know any longer where to find him,

usually that means that he (or the institute) moved to a different field,
and this happens mostly for papers that were published quite a while ago (but if he has continued working in that field, you usually find newer work with newer contact address)
consequently, there's a high probability that he anyways doesn't remember the details I want to ask...

We should just use the email of our current academic institution, and academic institutions should provide user-controlled forwarding of some type (so people don't need to ask a sys admin if their forwarding address changes).  Simple, effective.

Should we (well, the ones of us that have tenure and power) put pressure on system administrator to change this practice?"

Yes.  Unqualifiedly.  In my opinion, any institution that fails to do that does a massive disservice to its students and non-tenured researchers (i.e., anyone who might leave during their career).  Email forwarding is not hard, nor is it costly.  If someone tells me their institution doesn't forward, I would suspect they have a mediocre administrative infrastructure for research.  Research institutions are built on the successes of their professors and professor's successes are built (in part) on the success of their students and research staff.  If you could improve your school's standing in the research community by one peg by adding email forwarding, wouldn't it look pretty stupid not to do it?
Disconnecting those researchers' emails entirely is a small but non-trivial obstacle that could impact their research careers, which trickles back to the institution (particularly with PhD recipients).  They might miss out on invitations to collaborate, book chapters, and even a heads-up on job opportunities.  To those who say "Well, I always Google anyway," you probably aren't emailing a couple dozen people to contribute to a book (or, for an encyclopedia, think 100+ contributors).  If you did and a couple emails bounced, how much time will you spend trying to hunt down the new emails?
I've been affiliated with an institution that did provide email forwarding, by a mechanism that I thought was pretty flexible.  At the end of your time there, they closed down your email account after a couple months (the storage, that is).  You could request that your emails be forwarded to an alumni address.  This alumni address was controlled by you, in terms of where it forwarded.
So then, you would do the following:

Create an alumni address
Set up your original email at the institution to forward to the alumni account
Set up the alumni address to forward to a stable account (e.g., Gmail)
Emails to either your original or alumni emails would forward to the permanent email

So long as your permanent email doesn't change, you only need to do this process once per institution.  Even if you did change your permanent email, it would take only a small amount of time to re-route your forwarding (one re-route per past institution).


text:
How to improve self-learning as a PhD student?
As a doctoral student, you take some classes, but most of what you do needs material that you must gather from papers, conferences, and other sources. With limited possibilities for communication with authors and such, what's the best way to learn these necessary concepts?
For example, I read a paper (from a big name publication) presenting a novel approach to SVMs with new constraints on the objective function. The description of the optimization was vague, but I needed to use this technique for my own work and my optimization skills are limited at best. I'm sure to a reviewer with the right expertise, the description was fine though.
As a PhD student, one can only take so many courses in so many subjects. Nevertheless, some things (like optimization theory in the above example) are not exactly easily self-taught, and surely not in a few weeks.
So I ask you, what is the best strategy to fill these gaps without devoting entire courses to the subject?
Additionally, how do you do that without just learning things piecemeal? Learning something useful for a hyper-specific case is essentially worthless once circumstances change. How do you balance the need to know both these hyper-specific examples and the more general ideas while doing this gap-filling?

Frequent coaching from experienced people...

"The description of the optimization was vague... but I needed to use this technique for my own work". No, you should never use a technique for your own case if you do not understand 100% what exactly this technique does.

@Alexandros: I would disagree, at least concerning situations like the one I presented here. For example, I understood the results, general concept, and implications. It was in the implementation (i.e. the numerical method to solve the optimization) that I found confusion. Herein lies the problem I am asking about.

During my Ph.D. studies I had to do exactly that: balance my time between learning specific examples and learning where and how to find these examples without wasting too much time. In my case, I did not have that much guidance from my supervisor (he let me be pretty independent) and on top of that my topic was interdisciplinary. Due to the latter, there were gaps in my learning that I had to fill, and taking 20 ultra-specialized courses was not an option because of the time constraint (I had to finish my PhD within 4 years and also publish some papers in that time).

From my experience, a top-down approach is the most effective one. It sounds like you started reading a very specialized paper; try reading something more broad about the subject, ideally a tutorial/video/article/book chapter with emphasis on applications (since you mentioned you need to apply a method to your own work) that will give you a good overview in a shorter amount of time. Then, not only you will gain more insight as to which method is the appropriate one to use in your research and can devote more time to it, but you will also have kept in the back of your head the other ones, in case conditions change and you need to switch methods. Online courses (MOOCs) are a good source of information, as you can adjust them to your time schedule and often are not a semester long but rather a few weeks. I am sure you can find something on what you are looking for on www.edx.org and/or www.coursera.com.
Communicate with people around you. This is crucial. If you are not already in an environment where knowledgeable people are available, put in the effort to find one. Look up people and email them; most of the time professors are passionate about helping out students. I was lucky to have an office one door down from a retired professor, who had time to talk and share his expertise and advice - some insights are difficult to find in books.

Try to get creative with your learning - never is one source enough, try to diversify. It is easy to become overwhelmed by the information, so be organized, take notes, and try to be aware of what you are learning and how it fits in your purpose, with a calm mind. Take breaks when you feel overworked (trust me, this comes from experience).
From the organizational viewpoint, I think sketching out objectives every month or week, and then preparing a summary of what you learned and how it applies to your research (like a progress report) helps a lot in seeing the big picture. You don't want to get carried away too much reading about things you won't use. Of course, that's inevitable, as it is part of research - it is part of navigating in the vast realm of knowledge, sometimes you end up sidestepping.


text:
Is GitHub adequate for purposes of giving a manuscript a timestamp to protect against plagiarism?
I wrote a paper that I want to put on my webpage, but that I don't want to publish anywhere.  I think that I need a timestamp on it, in case someone decides to plagiarize it.  Is GitHub adequate for this?

Did you consider arXiv?

Possible duplicate of http://academia.stackexchange.com/questions/712/how-to-prevent-plagiarism-of-my-papers  http://academia.stackexchange.com/questions/23367/how-can-i-time-stamp-my-data-without-publishing-it  or http://academia.stackexchange.com/questions/435/is-it-advisable-to-put-entire-source-of-my-thesis-up-on-github/442#442

@DmitrySavostyanov - One must be invited to arXiv, and if I want to change the paper later, it is my understanding that I cannot do that with arXiv (I must instead upload a new version, and keep the old one as well.)

If I am not very much mistaken, you can access older versions on ArXiv (see for example this paper). Of course you do not want to constantly revise your paper this way. As for the invitation, if you know other people who have published in your field, there is a high chance that one of them can invite (endorse) you, as you become an endorser quite quickly.

It is not difficult at all to be endorsed on arXiv, if you know people in your field. You're right that arXiv provides full version control with all timestamps - in the same way as public github repo does.

@horsehair Is your aim to be able to edit in case you spot mistakes, or rather - you aim is to have continuous development?

I don't know anyone in my field.  My aim is to have a timestamp that others will believe, in the case that someone claims to have produced my work themselves.  I will only make small changes to the document from now on.

@Dmitry , I would say ArXiv does limited version control.  (For example, you can't remove versions.)  For the basic purpose of providing an independent timestamp, ArXiv and Github suffice.  Legally, a notary is better.

Remember that neither GitHub nor ArXiv can guarantee to still be in business when you need that evidence. If you care enough to want a clear timestamp, getting it notarized is a fairly cheap investment. Especially if someone in your school's staff is a notary (fairly common) and offers discount services to colleagues (also fairly common).

The proposed duplicate does not seem like a duplicate, because it is about data, not a paper.

I don't know anyone in my field. — Then you have a much more serious problem than time-stamping your work!!

@JeffE - I just finished my Master's, and I generally work in a different field.  I know my adviser, but he doesn't use arXiv.  Am I expected to know more people?

Then you do know someone (even if he's not directly in your field)! Have you asked your advisor?

@ChristianClason - Read the comment again please.  He doesn't use arXiv

Yes, but he might know other ways to achieve what you want (certified self-publication) besides arXiv; for example, he could ask your library to publish your paper as a technical report in their digital repository, if such a thing exists.

Why do you want to 'put the paper on your webpage', but not 'publish'? If you believe there is a chance of plagiarism, then your paper should be interesting enough to send to a journal, shouldn't it?

Let's be scientists (It was fun to try out):
below is a small repository, where I first tried 'lol' to have a timestamp in the future ... doesn't work; but at least in 'history' I could backdate (bit unlikely that I authored s.th. in git 1980 ;-).
But at least the day that I pushed is set by github.com. In total, though, I wouldn't trust this scheme. ``I forgot to push but look at the authored date, I totally solved it years ago''.
Jul 15, 2014
history
2b5d4208aa Browse code
choener authored on Jan 1, 1980
lol
fc2a68a571 Browse code
choener authored just now
https://github.com/choener/lol/commits/master

For plagiarism protection git timestamps may be useless, but exposing code publicly (public awareness, possible forks, Wayback Machine) GitHub may serve its role (vide there was a post that the best way to protect against plagiarism is to sent a draft to many scientists).

Absolutely! I only considered the technical 'timestamp' aspect. I prefer to have all my libraries on github and all my preprints on my webpage + preprint servers. (And the community is small enough that it doesn't matter for me)


text:
Should one put their Master's thesis online?
I think of a thesis as sort of an immature document, by definition.  It delineates the university era from the professional era, and is bound to lack some practical elements.  Should a student refrain from publishing his or her thesis on the Internet, for this or any other reason?

I will say when it comes time to implement something (in computational fields) there is usually way more useful information in the thesis than in any journal papers by the same authors. There's a lot more room to explain and detail how something actually works. I'll seek out a thesis or lecture notes once I find something interesting in a journal paper.

I don't know how people think about these things, but I can tell you how I think: If I don't see it, then it's as bad as it gets, beyond imagination; if I see it, then it may not be so bad.

It delineates the university era from the professional era — False.  If the thesis isn't professional, it isn't finished.

Every document is, in the way you define it, immature. With everything you write your writing improves. Your papers will not be better because you have a degree. They will be better, because you learned something (i.e. made mistakes) before.
However, there might be reasons not to publish your thesis, but it is not so different from normal working papers. Maybe your thesis is just bad, you did not get any meaningful results, you have made significant mistakes, etc.
So if your university allows, publish it online if you want to (or if you think it may be worth reading / you can not think of a good reason not to); everyone knows, it is only a master's thesis and will read it in a different way than they would read a published paper (or not at all).

University allows?  I've graduated.  Do I not have rights to put my thesis online?

Not necessarily. Most universities allow publication but that really depends on the university.

I would love to know examples of universities that do not allow this: I will gladly direct students elsewhere.

@PeteL.Clark I hope there are not many universities like this. I have never seen any. However, it is very common that they require certain information to be included if you "publish" you thesis and as soon as there is money to be made it is a different story.

I'm glad to hear it.  "As soon as there is money to be made..."  When I joined my university I signed some forms that could be very problematic "as soon as there is money to be made", but that doesn't keep me up at night for one second.

@horsehair : If it is standard practice of a university that the student includes a copyright notice claiming copyright ownership by the student, then how could there be a question of whether the university allows it?

Like you say, a thesis is not necessarily as thoroughly peer reviewed as a journal article. In my opinion, that doesn't mean the thesis should not be publicly available, just that a reader should keep in mind that the document is a thesis when reading it and (potentially) citing it. The onus then falls on the reader of a thesis, not on the writer.
In the end, the decision of whether to make your thesis public is more about your university's policy. At the University of Waterloo, for example, all accepted theses are publicly available by default through the same web portal. Other university's have IP policies that may not allow you to publish your thesis (though these policies are rarely enforced).
When the policy is ambiguous or left up to you, I would strongly recommend making it publicly available.

It's surprising to me that any university would forbid students to publish or post their theses online. Do you know of a specific institution with such a policy?

I believe it is the norm that work done towards a degree is technically (at least partially) owned by the university. Of course, very rarely will a university ever exercise those rights unless the researcher starts a for-profit company based on that research.

Hmm.  The universities where I've studied have IP policies that specifically disclaim any copyright interest in scholarly works created by students (and even faculty).  If a thesis contains ideas that are worth money, they might in some cases want a cut of the profits, but the document itself belongs to the creator who can publish it as they like.  I kind of figured that was standard but perhaps not.

@tbekolay: Do you know of any specific university that neither publishes their theses online themselves nor allows students to do so?  I would find such a policy peculiar and perhaps worrisome: it seems to evince a lack of confidence in their product.

Unless there is a compelling reason not to, yes, you should put your thesis online.
A thesis is supposed to represent your first foray into academic research.  The whole point of academic research is to make a contribution to the body of human knowledge, and share it with the academic community.  As such, I would encourage you to make it as convenient as possible for the community to read your thesis, and posting it online is a good way to achieve that.
If your discipline uses arXiv or a similar preprint or document server, I would encourage you to post it there as well; that way it will remain accessible even if your web site moves.
I would not worry about your thesis containing "immature" work.  It's a thesis; everyone knows that it's your first research product, and nobody is going to judge you harshly in 20 years because your thesis wasn't a work of staggering genius.  But on the other hand, they very well might still find it useful.  You spent a lot of time writing that thing; don't you want it to be able to do some good?
Also, there's a good chance that your thesis is already publicly accessible (via interlibrary loan from your university, or a commercial thesis database, or something similar).  If so, then posting it just saves (possibly a lot of) time and effort for those who want to read it.
Here is a non-exhaustive list of compelling reasons why you might not want to post the thesis.

Your university's intellectual property policies forbid it.  (If so, shame on the university.  This seems unlikely to me, but some other answers think it's plausible, so I suppose you should check.)
You have submitted parts of your thesis as a paper to a journal / conference / similar outlet, or plan to do so, and the journal's copyright agreement forbids you to post the thesis.  (If so, shame on the journal.)
Your thesis contains collaborative work (such as jointly authored papers), and your coauthors object to you posting the thesis.  (If so, shame on your coauthors.)
You have published your thesis as a book, or plan to do so.  In that case, posting it might hurt sales of the book, and might also be forbidden by your agreement with your publisher.
Your thesis contains ideas of commercial value which are not yet patented, or un-patentable ideas that you plan to exploit commercially.  (But as noted above, your thesis may be available to the public already, albeit less conveniently.)
Your thesis contains a serious error that invalidates its results.  (But you might still want to post it along with an addendum that explains the error; there may be parts of the thesis that people would still find useful.)

My school, while doing a Master of Advanced Studies (MAS),  required a thesis to be publicly available. It only grants exclution to this for commercial reasons, when the thesis is sponsored by a company. However, still, the abstract will be published.
The school provides a search for all Thesis papers, for example here (search is german, but papers are sometimes english):
http://www.ti.bfh.ch/de/master/msc_engineering/studierende/master_thesis.html
I like the idea of publishing my thesis, it's a work I am somewhat proud of. I even have a download link on my personal homepage.

If your thesis contains classified material, you obviously cannot put it online. otherwise do it.
You will get feedback and you will get pointed out about good or bad things. This is a standard scientific process and as well a good opportunity for you to optimize your neural network (aka "learning").
If it turns out that your thesis is overly bad, you can still take it offline later. And if someone later still has a copy and asks you why your thesis was so bad, then accept and explain that you know that and learned from it. There is no shame in improving.


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What is the difference between open access and open archive?
In Elsevier ScienceDirect search, there are two types of access type filters; Open Access articles and Open Archive articles. What is the difference between these two? Is there a notable difference between the terms themselves?

As Elsevier uses these terms, "open access" means an article is free to access as soon as it is published. "Open archive" means an article is published in a journal that makes articles available for free after some embargo period (not immediately when it is published).
More on Open Archive:

Elsevier enables subscribers and the general public to have free access to archived material in 98 Elsevier journals... Articles featured in the archives are free for everyone to read and download and are made available after an embargo period.

What's with the embargo period for open archive? Why the delay? How are those articles different from open access articles by nature?

@ÉbeIsaac The difference is that the authors of those articles did not choose to publish them in an open access journal, or as open access articles in a hybrid OA journal. That's all.

Does this mean open archive facility is an added advantage to general authors who didn't pay for the open access in Elsevier? If that is so, what should an author satisfy to attain this added privilege?

@ÉbeIsaac Yes, and publish in a journal that's an Open Archive journal. (Follow the link to learn more)

It appears that many  (or maybe all) of the 98 journals on that list simply "open archive" all of their articles after the embargo period. The author doesn't have to do or pay anything.

So I see. There is a completely separate list of journal titles in Elsevier that becomes OA-like access after a certain period called the embargo period. This is totally different from other Elsevier titles like Pattern Recognition Letters, right? May I know what is the rationale behind grouping journals in these two groups? (PS: Thanks for the link @ff524)

@ÉbeIsaac: as far as I know, the open archive was installed by Elsevier in response to the "Cost of knowledge" pledge of about 15k scientists not to get involved with Elsevier anymore.

That's amazing, why hasn't anyone done the same for IEEE?


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Is it advisable to cite a lot of commecial product web references in a survey paper?
I'm currently writing a survey on a specific topic in biomechanics. In one of the sections, a tabulation of tools with columns name, type, description, and study is included.
The plan was to cite the home page of the commercial product next to the tool name and cite the relevant literature that use them in the study section. This would mean 20+ product home pages in the in the reference section out of around 200 references. My intention was to allow the reader to refer the product page for more detail regarding the tool concerned.
From a reviewer's standpoint, is it a good idea to cite so many commercial product links in an academic article?

After a deeper thought, I've come to a conclusion not to cite commercial product pages as it would turn part of my academic paper into an online shopping catalogue.
The following are the alternatives adopted:

Include the name of the company along with product name
Cite patents of the products
Cite product-specific publications


text:
What is the benefit of 'voluntary page charges'?
There are quite a few journals which ask for voluntary page charges. Some may do for the whole journal and most for the first couple of pages.
Take IEEE Transactions on Forensics and Security for example.

Voluntary Page Charges. Upon acceptance of a manuscript for
  publication, the author(s) or his/her/their company or institution
  will be asked to pay a charge of $110 per page to cover part of the
  cost of publication of the first ten pages that comprise the standard
  length (two pages, in the case of Correspondences).
Mandatory Page Charges. The author(s) or his/her/their company or
  institution will be billed $220 per each page in excess of the first
  ten published pages for regular papers. [...]

Surely $110/page is not a charitable amount for an average author. What is the benefit the author/institution receive for agreeing to pay these voluntary charges?

I think the idea would be that one's institution would foot the bill through some sort of policy to fund open and semi-open publications rather than a belief authors themselves will randomly foot the bill. But I can't read the minds of the people who thought up this idea.

Neither I nor my institution have ever paid voluntary page charges.

@JeffE Yes; I don't know of anyone who will. Yet voluntary charges exist nonetheless.

All publication funds I know only cover charges that are necessary for the publication. This excludes voluntary page charges.

The benefits of "voluntary" page charges are much the same as for "mandatory" page charges - you are paying them in order to support publication of the paper. The only difference is that, technically, you don't have to, and you can avoid it if you wish.
Why do we have such a weird situation?
There is a long and complicated history here; what follows is mostly a precis of this paper, which is an interesting read.
This particular journal seems to be using an unusual holdover from an old-fashioned way of handling page charges.
Page charges date back to the 1930s. (You may want to remember this the next time you see someone saying that paying publishers is a shocking modern development.) The majority of journal subscribers at this time were individual members of scholarly societies, rather than libraries, and so there was a fairly low limit to how much you could reasonably charge for a subscription.
However, particularly in physics, the amount of stuff people wanted to publish was growing dramatically - Physical Review doubled in size during the 1920s, and even then still had a growing backlog. Printing and mailing larger issues more often obviously costs more, but subscribers would balk at rapid subscription increases, and the societies were already (mostly) losing money publishing the journals to begin with. The solution by the American Physical Society (followed by many others) was to shift part of the cost onto the authors, allowing the cost charged to subscribers to stay the same even if they now got more pages in their journals, or if the amount of papers dramatically fluctuated in a given year.
But not everyone had the money to pay the charges. For the first couple of years, a generous benefactor paid for everyone who couldn't; after that, unpaid charges mounted up. Some institutions and funders were asked for donations to help cover the gaps, but, critically, authors were not penalised for failure to pay, nor were they chased for the money. The sense that these were "optional" charges became quite well entrenched, and while most authors paid, many avoided doing so without complaints. The US government gave tacit support to the emerging model in the fifties, when it was decided that federal agencies could pay page charges as long as they were the same assessed on non-federal authors, and they were voluntary. (You have to love the logic of "we'll pay if voluntary, but not if mandatory")
By the 1970s, page charges were well established in the scholarly landscape, and almost 40% of US-published articles were in page-charge journals - higher than 80% in some fields. (It was much lower outside the US.)
In the 1970s, the US Postal Service got involved. They took the position that a page charge was essentially a fee to distribute advertising about your research, which would mean that the journals got hit by much higher postage charges than if they were simply distributing public-good information. The IRS made a similar argument about payments being commercial and threatened to increase taxation. The negotiated solution was to very clearly emphasise that page charges were a voluntary contribution, rather than a mandatory one, neatly evading some of the legal issues.
Page charges mostly died out after this. American society journals were always the major users of page charges, but during the 1980s, most of them were absorbed by commercial publishers (who almost without exception stopped levying page charges). Many of the remainder, presumably, found that they could shift away from page charges by taking advantage of the very dramatic increases in subscription charges during the 1980s and 1990s (the famous "serials crisis").
But you'll still find a few today - eg PNAS, or the AGU titles. Most of these now structure page charges as mandatory - I suppose the complex financial issues from the 1970s have now been solved in other ways, or else the fact that you can ask for a fee waiver means they still technically qualify as "voluntary". Not quite sure how this circle got squared... but, regardless, that's where we originally got the "voluntary" text.

Though it is a little long, I'd say it's much needed for this question. Thank you.


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What can I do with my paper that is out of a work which contains no improvement of the methodology?
I've started a research, and after replicating methods of other researchers (running experiments on my data), I've realised that I cannot add anything new to the field. The work contains no improvement of the methodology, I just used the established methods to analyse my data and I ended up in having some results. Consequently, I cannot publish a paper out of it (which I am almost done writing).
Nevertheless, the obtained results are new (applied to a specific problem), so they could be of interest. Furthermore, I don't want that my time and the possibly valuable results end up in the trash bin.
What can I do with it? Is arXiv suited for this?

What is your field? Why do you think you have to improve the methodology in every paper? That seems fundamentally unsustainable. In many disciplines researchers will use a de facto standard methodology, because it makes their results comparable to the results of others.

There are TONS of papers here people dont improve a methodology but shows great achievements using a methodology or a combination of methodologies. Of course, this is field dependant: wont happen in maths, but very likely will happen in chemical engineering. (random examples, no specific feeling against either of them)

You say that your work on methods is uninteresting, but that you believe the results to be valuable.  That's great!  You should write a paper about the results!
Sometimes people feel like the amount of manuscript text they produce for each aspect of their work should be proportional to the time and energy put into that aspect, e.g., if you spent 3/4 of your time working on the methods, then your text should be approximately 3/4 about the methods.  That is incorrect.  The amount of space something takes up in the text should be proportional to how interesting it is to the reader.  Sometimes you have to put in a lot of work on something that is very simple to explain, and that's OK.  Focus on the bits that will be interesting to the reader, and instead tell your friends the stories of how long and hard you worked on the "uninteresting" bits to get there.

What to do with results that ended up primarily or entirely as replication studies depends a bit on the culture of the field.

A preprint server such as arXiv or PeerJ should always be a suitable place to report on replication studies. Of course, for CV and visibility reasons, a reviewed publication would be preferable in most cases.
Some journals, specifically PeerJ and PLOS ONE, have a reviewing policy of judging papers solely on technical correctness, but not on novelty. That is, a paper that is sound but "only" replicates results that were previously already known is perfectly acceptable in these journals. The reasoning is that replication studies actually often provide significant value to the community, as independent replications can increase the trustworthiness of results.
Some more traditional journals are also (more or less) happy to accept replication studies, but the extent and conditions vary by journal, and, more importantly, by field. In medicine, for instance, replication studies are extremely common, and practically all journals accept them as far as I know. In applied computer science, replications are (unfortunately) almost impossible to publish outside of PeerJ Computer Science.
Even journals that per se do not allow for replication studies sometimes have special issues dedicated to them. Of course you need to get lucky to find a suitable special issue with a topic and timeline that suits you.

If the method you used to obtain the results -- albeit established -- are not traditional, then by all means you may publish them. Make sure you include relevant literature review to prove you've done the necessary ground work in the manuscript.
Any fact that you believe might benefit the community of your research may well be deserved to be submitted for publication. To what extent it deserves to be published depends on the reviewers.

Publish the results of the experiments in a conference or journal. If it won't get accepted to your original target because of the lack of methodological innovation, look around for another.
From the outside (and with very little actual detail), it sounds like a somewhat interesting observation that you tried all of the typical methodologies in your area and found now (current) way to improve them. I think you would have to structure your evaluation of those methods (i.e. what were the criteria that helped you judge that they did everything you needed?), but you could contribute to your community by identifying that. If it's wrong, the peer review you will receive will guide where to target future work.


text:
Importance of order of authors in published paper when applying for PhD positions
In some subfields of Computer Science, usually the order of authors in papers indicate the importance of contributions of authors to a paper. I am currently contemplating the possibility of pursuing a PhD degree. Accordingly, my question is, when applying for PhD positions, do admission committees consider (and if so, how do they evaluate) the order of authors in papers that I have published. Is the number of papers in which I have been the first author an important factor for admission committees?

Usually in some subfields of computer science... In particular, in my subfield of computer science, authors are always ordered alphabetically.

@JeffE you are right and I edited my question. In Soft Computing and Machine Learning, authors are not ordered alphabetically.

It depends. Authorship order doesn't always indicate who did the most work or the most important work on a paper in many fields. Some fields are alphabetical. Some fields have the lab leader or the person who won the gran last. Hopefully the admission committee understands the norms of their own field and the field you are coming from (if they are different) to be able to make a good evaluation.
I've never served on a PhD admissions committee, but I understand that they generally will try to determine your contribution to your publications when evaluating your application.

In addition to a list of publications you will of course be submitting a resume where you can specifically add your contributions in some or all papers you have published.

@kabZX, I would probably skip such self-serving statements when looking at a PhDed person's CV unless I was worried about their contribution. I've hired ~20 people into researchy positions over the last dozen years, and while I've skimmed their paper titles, I've never studied the author order carefully.

Primary authorship is best. However, any authorship when applying to a PhD is good.
(Depending on the field and subfield, being listed first indicates being the primary author).

Can you please elaborate a little more? Is it possible for you to share some of your personal experiences or provide some references?

authors: Александр Кобяков


text:
Should I take class time to explain software?
I'm teaching a course that introduces linguistic field methods. We have fewer lectures than a typical 3-credit course, but the students have ‘lab’ sessions eliciting data from speakers, and they're expected to work a lot on their own.
Analyzing the data requires the use of specific linguistics software. The software doesn't teach concepts; it's just helpful for analysis. In the past, some instructors have taken lecture time to introduce this software, but that has always rubbed me the wrong way:

I found such demonstrations tedious to watch as a student, and tedious to teach as an instructor.
Most students seem to be able to figure it out on their own; for the others, there are succinct instructional videos, and there are office hours.
Teaching students how to use software just doesn't feel like university education to me. I would much prefer to talk about bigger picture issues—e.g., database technology or data portability in general, rather than how to use one particular piece of software.

Computer work has always been easy for me, and I recognize that I may underestimate how difficult it is to learn new software. I wonder if anyone has a sense of how much computer competence we can expect of the ‘average’ student.
I am also curious whether my intuition about the content of university education is appropriate. This is a practicum, after all.

If you think it's tedious for some students, then you can e.g. give the demo at the end of the lecture session and tell students they can leave early if they believe they can figure it out on their own.

Yes, that's possible. I try to take the time budget seriously, so on the one hand I don't want to ‘waste’ my lecture time (so that I can't cover other topics). On the other hand, I don't want to schedule extra lecture sessions that then become implicitly obligatory. Maybe an optional session would be the way to go, though.

I have found that incoming undergraduates in the past 3 or so years have almost zero computing skills other than word processing and using simple GUI applications.  They typically don't know how to reference a path to a file or even that files reside in a directory structure.  Graduate students are a little better, but it varies wildly based on experience.  @ff524's demo idea seems good.  You may poll and see if there is interest to hold an optional, one-off using software demo class period in addition to the usual lecture.

Proto-answer: I don't think it's required that you teach the software in class. If in your professional opinion most students can pick it up outside, and you have better things to discuss (and I think you make a compelling case for big-picture concepts), then it's completely reasonable to not spend time in class on it.

"Modern Approach": I would suggest creating a video demonstrating how to use the software. Free software like CamStudio makes this easy to do. There might even be a video already online.
The video would allow students that need the assistance to view the video outside of class or follow along in class. This puts the freedom in the students hands and would also free up your time to focus on the subject matter. This could save time for future classes as you integrate it into your class structure.

Additionally, the creators of the software in question may have prepared orientation/basic training material. One (commercial) example is MATLAB whose free "On Ramp" course is actually quite well designed.

I would strongly disagree but there is a time and place for everything. It would be even nicer to have both video and text which students could choose from. Stating that videos are inefficient is simply not valid and is personal opinion.

Stating that the case against videos is "simply not valid" is itself personal opinion.

The statement itself may be but its at least factual. Read up on the subject. Like it or not its also the shift. Open course ware from places like MIT and Stanford has been greatly beneficial to students learning.
http://jolt.merlot.org/vol5no3/rose_0909.htm
https://onlinelearninginsights.wordpress.com/2012/07/13/are-video-lectures-effective-in-online-courses/

Software is a tool for academic practise and research. It implements algorithms and principles that are the foundation of what we do. Whilst the minutiae of any individual software package is usually not relevant for university education, the practical implementation of the underlying principles is.
In this context I'd strongly recommend this paper by Jacobs et al., with this associated blog post and this set of slides.
Done properly, teaching the software can be a very useful way of embedding core skills in a practical fashion. Done badly, it's very easy for students to disengage and copy each other.

I think it depends on the software in question.  Some software has ample resources to learn how to use it. OneNote, EG, can be easily researched and learned via video, text and online lessons and can be incorporated on any device.  I simply presume that the notebooks and course information I distribute in OneNote will be consumed. In the 5 years I've used it as my primary distribution solution, I have had exactly 1 student that needed handholding on the use of the system. Telling a student to use Revolution R Open (now Microsoft R Open - statistical analysis software) and presuming they will just figure it out is an unreasonable demand. The idea that a student has infinite time to learn my selected tools strikes me as disrespectful of their investment in my field.
If I thought that the specialized software was something all students would have used in the past, I would still record a video or provide notes for how to use the software in my labs (in general) so that a neophyte would not have to take too much of their time to learn my selected tool.  I would not at all rely on the supplied documentation, particularly in specialized or complex software.  A rule of thumb is that the likelihood of documentation being useful to the average human is inversely proportional to the factors of the complexity of the software, multiplied by the specialization of said software, (and often multiplied by the price of the software).  As an example review the Linux/Unix man page for awk.