text:
Would it be rude to ask a famous professor who doesn't know me personally for a recommendation letter if I have published in a high ranking journal?
Would it be rude to email a famous professor asking for a recommendation letter to Dphil, if I had published in a high or moderately high ranking journal in her/his field and just have letters from foreign unknown professors?
The professor does not know me apart from the published paper. Information about whether the professor knows the paper, or knows me due to the paper, might be edited in later. I was thinking to add my grades (the lowest is an A-), curriculum, and send to professors that work in my subject (it is a very small field). But if it is rude doing this, I don't think it could improve my case.

Does the professor know anything about you apart from the published paper?

If you are in a very small field do not assume your professors are unknown.

Do you have any information as to whether the professor does know your paper? If they have (e.g.) cited it, that makes a lot of difference.

Originally the OP said it is a high ranking journal. Now it says  "or moderately high". It is crucial to know if the result/journal is really high ranked.

@Dilworth The very original version (version 1) says "a high or moderately high ranking journal".

Professors outside your school do not have the expertise to write about you as a student; do not send them your grades. But experts in your field do have the expertise to write about you as a researcher.

This question would really be better as, "how can I best approach a famous professor familiar with my work but not known to me personally for a recommendation letter?" rather than the current very bikesheddlike/poll-like question it is.

@enderland: Currently, it is still very unclear whether the famous professor is indeed familiar with the OP's work.

@O.R.Mapper that's a simple detail for the OP to clarify. Right now, this is basically a "yes/no" question, which isn't really a good fit for SE.

@enderland: "that's a simple detail for the OP to clarify" - I fully agree. I, too, am looking forward to that response. "Right now, this is basically a "yes/no" question, which isn't really a good fit for SE." - I disagree, as many valuable questions in here are basically "yes/no" questions ... which come with an implied "and why?".

@O.R.Mapper OP may not know whether the famous professor is familiar with his work. But the only way to find out is to ask. But OP is worried whether asking would be rude, and that's what this question is about.

I wouldn't use the term "rude" but I would say it's (highly) "inappropriate". You're not in a position to ask him for that. There's no basis for the recommendation. However, you could provide the article itself to whoever you want to be recommended to, if you feel that's a strong qualification. Otherwise even if you could get the recommendation it would only be academic "hearsay".

While I don't really like adding answers to questions that have too many already, I also think it's a little hard to cut through the arguing any other way.

It's not rude to ask for a letter of recommendation.  Ever.  (I mean, if you do it rudely, then yes, but the bare fact of asking isn't).  It might be unlikely to succeed, or unrealistic in some cases, but it's not rude.
You should try to ascertain whether this is a normal thing to do in your field.  In my field (mathematics), it borders on inconceivable that an undergrad would carry out and publish truly impressive work without an established researcher in the field supervising them and able to write a detailed letter about it.  Maybe there are some other fields where that can be the case, though I can't say I know what they would be (perhaps some of the other answerers are).  Similarly, JeffE's advice to try to create a dossier of the level that might be appropriate for a faculty position sounds completely preposterous to me, but I suppose it must not be in computer science.
Whenever you ask someone for a letter of recommendation, think about what you are hoping the person will say, and whether they are placed well to say it.  So, I would only consider asking for a person to write a letter based purely on having read my research if I knew they were familiar with it, and could place it in a context that is not obvious to the people reading the letter.  It can be very valuable to have a letter saying essentially "this paper is actually really important.  here is why."  I've read such letters, I've written such letters.  But the paper has to be really important (in the view of the author) for such a letter to work.  I suspect a lot of the argument here is based around whether the answerer really thinks this is an impressive publication or not (which we are all guessing about).

So, if I were you, I would ask some of your professors whether they really think this potential letter writer will be impressed by the publication.  If they think maybe yes, then you can email her/him, and say:
Dear Prof. X,
I'm a student at the University of Y and am applying to graduate schools in country Z (or maybe be more specific) in underwater basket weaving, with a focus on the use of hemp.  Prof. W thought you might be interested in this publication of mine, since it relates to your work on macramae at the bottom of the Mariana Trench.  I was wondering if you thought you could write a strong recommendation for me on the basis of this publication.  Thank you very much for your time.
Sincerely,
Joe Schmoe
Asking someone if they think they are able to write a strong letter for you is good way of leaving them an easy out, and not getting a terrible letter since someone finds it easier to write a terrible letter than to say no (it happens).  I would almost certainly reject such a request since I really wouldn't feel like I could write a strong letter.  But if the publication really is that good, maybe someone will feel like they can.

This is a great answer that also hits two common Academia.SE refrains in one post (Academia varies and talk to your advisor) :)

Yes, very nice answer. The range of (quite passionate!) opinion expressed on this page is a clear indication that your mileage may vary. So, OP needs to find out a) will such a letter help him/her in their particular situation, and b) will the professor be able to write them a strong letter? @BenWebster's suggestions for how to do this are spot on.

Note also the element of "gamble". There clearly (as evidenced here) exist people who would look very favourably on such a letter, and others who would consider it very negatively. So having canvassed opinion, OP needs to decide whether it is worth gambling, or whether they are better off going for a set of "standard" (but hopefully strong) recommendations.

Hmm... I think point #1 is a stretch and likely varies more than what is allowed for by "never, ever." Personally, if someone who knows I had no basis on which to evaluate their work asked me for a letter of recommendation, I'd consider that rude, even if it were someone I knew personally. I would only ask for a recommendation (of any form) from someone who has been closely familiar with my work.

I like very much your letter about hemp on the Mariana Trench!

@reirab What's rude is a personal and cultural judgement, so I can't tell anyone else what to think.  My personal feeling is that graduate admissions or hiring are sufficiently competitive, and sufficiently hard to get good information about that if someone I really can't write a letter for asks, I don't blame them for not knowing; I just tell them that I can't.  My point was more that rude or not rude is the wrong framing for the question; wise or not wise is a much more important question.

completely preposterous -- Do notice that I said aim for a faculty-level application. I'm proposing a change in attitude--act like a researcher, not like a student--more than a requirement for content. I can count the number of prospective grad students I've ever seen that actually looked like faculty candidates on one hand, but that number is definitely not zero, even if I restrict to mathematicians.

The benefit of recommendation letters is that they give insight into abilities that are not reflected in the rest of your application. Your grades and your publication are already in your application. A professor who doesn't know anything else about you has nothing to write that will help you.
To directly answer your question: it comes across more naïve/inexperienced than rude, but either way I do not see how it will help your case.
P.S. This answer assumes that the professor is not already familiar with your work before your email. To be more specific, I'm imagining you sending unsolicited emails to a bunch of the biggest names in your field (selected purely because they are "famous"), who have not previously heard of you or your work (as far as you know), asking them to write a recommendation letter for you entirely on the basis of your having published a paper in a journal.
If the professor is already familiar with your work (e.g. has cited it, or has had an email correspondence with you about it), then I agree with this answer that his/her letter can potentially be helpful. Similarly, I think Ben Webster offers some useful advice about attempting this in a more nuanced - and potentially more effective - way.

Disagree. I think you missed a crucial point of this question: the OP has published a paper in a high ranking venue. Now, if this venue is really a top place, and the OP thinks that the professor knows about the result, which is supposedly a great result, then the fact that the professor doesn't know personally the OP is a huge advantage. This is the best recommendation that one can get: someone that doesn't know him/her but have heard of his/her result, based solely on its scientific merit!

Strongly disagree; see Dilworth's answer.

@JeffE do you still disagree with this answer if the professor in question is not familiar with the work? Dilworth's answer assumes familiarity with the work, so I'm wondering whether you consider that to be a prerequisite or not.

@Dilworth The OP didn't specify that the professor knows the published paper, just that they don't know him/her in any other way. I added that part based on the exchange in the comments: Q: "Does the professor know anything about you apart from the published paper?" A: "No, I was thinking in add my grades (the lowest is an A-), curriculum, and send to professores that work in my subject (it is a very small field). But if it is rude doing this, I don't think it could improve my case. " See the edit history.

I think that treating the admissions committee like ignorant children is far more likely to harm your application than help it.

@iayork: A researcher is not an "ignorant child" just because they don't know a paper from another field. (In fact, looking at the thousands of papers that each field produces year by year, I would not even dare to consider any researcher an "ignorant child" even for not knowing a given paper that seemingly belongs to their field.)

Let me disagree completely with all the other answers here, that I think have missed a crucial point of your question. In short: I believe it is a reasonable plan to ask for the letter.
Here's why:
The OP has published a paper in a high ranking venue. Now, if this venue is really a top place, and the OP thinks that the professor knows about the result, which is supposedly a great result, then the fact that the professor doesn't know personally the OP is a huge advantage. This is the best recommendation that one can get: someone that doesn't know him/her but have heard of his/her result, based solely on its scientific merit!
P.S. do not add your grades. Ask for a reference based solely on the result, and explain your contribution if you're a coauthor.

This is the correct answer. A standard piece of advice in academia, whenever you apply to anything, aim your application at the next level. Applying for tenure? Aim to present a strong case for full professor.  Applying for a job? Aim to present a strong tenure case. Applying for PhD admission? Aim for a strong faculty application. A successful faculty application must have at least one strong letter from a well-known active researcher who is not from the applicant's home department and has not worked with the applicant.  A letter like that for graduate admissions is pure gold.

I write letters for my colleagues because I respect them and want to help them succeed, not because there's something in it for me or my institution.

Usually, yes. We talk in the hallways at conferences. We exchenge the occassional email. We read each other's papers. But I have certainly written strong letters for colleagues I've never met, because I was impressed by their work.

I think this answer makes sense if "the OP thinks that the professor knows about the result", but I don't see any indication of that in the question. Perhaps the OP will come back and clarify.

The indication is in the body of the question: "The professor does not know me apart from the published paper." !

@Roland, certainly writing letters for research colleagues you don't personally know, based on their research only, is realistic.

The OP didn't write that the professor knows the published paper. I added that part based on the exchange in the comments: Q: "Does the professor know anything about you apart from the published paper?" A: "No, I was thinking in add my grades (the lowest is an A-), curriculum, and send to professores that work in my subject (it is a very small field). But if it is rude doing this, I don't think it could improve my case. "

@ff524, sorry, but I don't follow you. So why did you add this sentence? Obviously, if the question changes then the answer changes

@Dilworth Important information from comments is supposed to be edited into the body of the text. I did this the best way I could by quoting the OP's comment directly. If you can think of a better way, please edit the question yourself. Hopefully the OP will come back and edit the question themself to clarify

@ff524, I'm still not following you. Where in the comments did the OP says that the professor knows his paper?

Strongly disagree with this answer.  If I were asked to write a letter of reference for someone I had never met, based on a publication and their grades, I would not do it and would think less of them for asking.  If I were on a committee and received such a letter, I would conclude that if no one the candidate knows personally would give them a positive letter and that their personality must be terrible; it would pretty much destroy their chances.  A positive letter from a personal acquaintance, no matter how obscure, would be ten times better than this impersonal letter.

@iayork, you have to get both personal letters AND such letter from someone who doesn't know you based on your work. From experience, these kind of letters are the best.

Someone asked in a comment: "Does the professor know anything about you apart from the published paper?" And the OP said "No". Hence "The professor does not know me apart from the published paper".

@ff524: I agree the current state of the question insinuates the professor does know the paper. It might be best not to edit that bit of information in until there is some clarity as to whether or not the professor does know the paper. (The alternative would be writing something like "The professor does not know me apart from the paper, but whether I know he knows me due to the paper is unknown as of yet (as I have not yet responded to that inquiry)." ... which would be a bit silly.)

@Dilworth In what context and country are you making this claim (a letter from someone who doesn't know you)? If it is true, then it's critical information that's lacking in the question. The only context I'm aware of where that is true in the US and Canada is for tenure committees and I think it is very unlikely that's what the question is about.

Specifically, the question doesn't specify whether the professor previously knew about the work, or whether the professor will "know" about it as a result of the OP emailing to ask for a letter of recommendation.

I don't think it's helpful to conflate tenure or promotion letters and grad school letters.  For the former you're trying to establish that you have a national or international reputation, and experts who do not know you are perfect choices.  For the latter you're trying to establish potential for success in research, and someone you've interacted with is a better choice.  (That said, given the choice of someone better known who knows you but not as well as someone less established, pick the person who people know.)

@ff524, to my knowledge of English, what you added, and what the OP commented is inconsistent, then. I stand by my claim: had the professor known the result, asking for a letter from the professor is a good way to go.

@NoahSnyder, it's not conflating. It's a bonus. If a grad school letter is even stronger than a tenure letter, it just helps you.

@Dilworth I did the best I could, but if you can think of a better way to phrase it while leaving the ambiguity intact, please edit the question yourself to correct it. Or if you believe the question cannot be answered until the OP comes back and clarifies, flag the question to be put on hold as "unclear what you're asking".

@ff524, okay, I see, thanks. I'll leave the question as it is for now.

@ff524: I have taken the liberty to edit the question so it at least does not imply anything that the OP did not state. Hope you (and the OP) are ok with my edit.

@O.R.Mapper it is indeed awkward, but effective. Thanks :)

@NajibIdrissi, I wouldn't say that a professor that heard your talk in a conference already "knows" your result. You should have prior knowledge that professor has heard and hopefully appreciates your result from independent sources. I.e., that your result is "a known result".

"If your result is a "known result" then surely the committee members would know about it, right?". No! It is known to experts in the specific field. Not to all possible scientists out there!

This may be highly dependent on the field, but in my speciality (life sciences) this answer simply doesn’t apply: referees are often phoned and asked specific, “soft” questions about the applicant. The aim of a reference isn’t to assess the scientific merit of the applicant but rather whether they are a good person to work with — in other words: a referee is there to give an assessment specifically about the non-publicly visible qualities of the applicant; something only an acquaintance can give.

@NajibIdrissi Can I now go see all the famous professors in the audience, ask them for a reference letter -- Yes, of course. -- and expect them to comply -- No, of course not!!!

@NajibIdrissi, you certainly have some chance, though not extremely high. Such a letter is almost guaranteed to be valued by committee members.

Such a letter wouldn't help you.
Since the professor doesn't know you, the best possible outcome would be for them to give very generic praise of you. Chances are the admissions committee will swiftly disregard this letter.
If you look into what makes a good recommendation letter, you will find that it's not so much the prestige of the professor, but how closely they worked with you, and whether they give specific examples of your good qualities. Occasionally you might get situations where a famous professor is so famous, that merely their good word is enough to get you in - but this seems to be the exception rather than the rule. It is also very awkward to write a letter for someone you don't know well.
I would think about finding a more suitable recommender. Granted, if you have not only published, but the publication has attracted correspondence from major researchers, this sounds like it would give you a huge advantage over other applicants - and in principle one could write "I don't know this person but I've read their paper, which is very good - here are all the things this person did right in this paper". It still sounds like a stretch to me. Perhaps talk about the paper a lot in your statement of purpose, and hopefully it comes up during the interview.

A letter from someone who doesn't know you, but does know your research, can write about the specific good qualities of your research. That's far more predicitive of your future success as a researcher than most recommendation letters.

Adding on to @ff524's answer, most professors tend to only write recommendations if they know the candidate for some time or worked/researched with them for a certain minimum period of time. There are also very few institutions who may require LoR's from people whom you are known to for at least X amount of time. Even if not, an LoR which is just a repeat of the résumé may not so serve your purpose.

I disagree somewhat:  When applying for research postdocs (at least in my field) it is not uncommon (in fact encouraged) to get LoRs from professors outside your department.  This will be professors who are familiar with your work but may not necessarily know you personally.  They are writing about the quality of your research and putting it in context for the admissions committee, most of whose members will not likely be familiar with your specific research area.

However, here we are speaking of a PhD applicant rather than a postdoc applicant.  Such LoRs (where the letter writer does not know the applicant personally) are more unusual, but I think this is mostly a function of the fact that often PhD applicants often don't have significant publications.  But I would suggest that if a PhD applicant did have a good publication, then a professor with research interests in the same specific area may be willing to write an LoR, and such a letter would be helpful to the applicant.

I agree with Dilworth and JeffE: letters of recommendation from people who just know you via your reputation "is pure gold" (@JeffE).
A friend of mine is applying for an O-1 visa. Apart from papers and citations, press coverage etc, a crucial part of the application is 7 - 10 letters of recommendation.
Her employer is hiring a lawyer to help her on the process. Here is their suggestion to have a strong application: 3 letters from academic colleagues (including PhD advisor etc), 3 letters from industry, and 2 letters from people who just knows her via reputation (papers etc).
Applying for an O-1 visa is not the same as applying for a PhD (but a lot more difficult IMHO), but I think the way profiles are evaluated is similar. And I believe the lawyer know what they are doing.

On one hand, I wouldn't "ask a famous professor who doesn't know me personally for a recommendation letter." On the other hand, your idea of asking a famous professor in your field to endorse you, based on your work in a high ranking journal, is a very good one.
The "bridge" solution is to get to know the famous professor personally. Since you have published in the same field as him, there must be plenty of people that you know that he also knows. (The editors of the journal for starters.) Find out which of your acquaintances is in this category and ask at least one of them for a personal introduction, or at least a letter/email of introduction. If all else fails, you might manufacture your own introduction by emailing him on his work in your common field, and perhaps asking him to comment on yours.
The likelihood is that you will get a good letter of recommendation. But the tactics in the above paragraph were to "take the temperature." There's a small chance that he disagrees with your approach or (less likely) sees you as a threat. You want to guard against that small chance of getting an unsuitable recommender.

A recommendation is about a person. A review is about a piece of work. Such a professor may review your work, but he is in no position to give a recommendation, since he does not KNOW YOU. I would not give a recommendation to someone I did not know, and in fact, would probably write back telling such a person that his request is not appropriate, exactly for this reason.

A recommendation is about a person. A review is about a piece of work. — And researchers are judged on their work.

Keep in mind that the "famous professor" is bound to be very busy.  There's no exception to that rule.  If you're Ramanujan writing to Hardy, or Bose writing to Einstein, then you're making it worth his while.  Otherwise, what's in it for the Prof?  Warm fuzzy feelings?  Notice that the OP is not suggesting, for example, a collaboration.  That might be worth something to the professor.  And it could be the basis of a strong letter of recommendation later.

No
If I was part of the admissions board, and received a letter of recommendation saying essentially "I don't know them personally, but this paper they wrote is great", this is what I would be thinking:

You are applying to a place where you believe no-one is capable of evaluating your paper on its own merits, so you need to get someone else to look at it and explain its quality to them. In that case, why are you even applying? It's clear that there is nothing you can learn from them. After all, if they are not even competent enough to evaluate your previous paper, how are they going to be able to evaluate any future work?

I wouldn't dismiss you out of hand for it, but it would definitely count strongly against you - someone who thinks they already know more than the professor is not someone I would want to be teaching, and is almost certainly going to be causing problems throughout their course - potentially even legal trouble, if they start making accusations of discrimination when the professors give them anything less than full marks.
If you think your paper is very good, and should be considered, then include it with your application. Otherwise the best case you could hope for is being damned by faint praise; the worst is something like I describe above.

This argument doesn't make much sense to me. It is certainly plausible that there are faculty in the department who are in the same subfield as the OP and would be able to evaluate the work, but happen to not be on the admissions committee. "The paper they wrote is great" is not helpful, but "The paper has revolutionized subfield X" certainly is, and it's plausible that the admissions committee wouldn't know that if they're not in subfield X.

I would expect that the faculty doing the evaluation would be (or would be able to consult with) the faculty involved with that specific programme. Otherwise, how could they properly evaluate the applicant? Unless their academic ability is not being evaluated, in which case I would expect the recommendation to not count for anything.

Well, a letter about the impact of the research might get them to consult with faculty not on the committee :) Given the large number of applicants to prestigious programs and the ease with which applications that are not obviously outstanding can be filtered out, it can be helpful to have something in the application to suggest to the committee that they do that.

@ff524 But why would you need to refer to a third party? Surely the reviewing committee is capable of recognizing the name of prestigious journals in their field. OP can just include in their CV "I had an article published in Nature" (or wherever), and that should be enough to get their attention. I the paper they wrote really is a big deal, then the faculty should be able to recognize that for themselves, otherwise why would you want to learn from them?

Some papers and journals are widely known throughout the broad field they are in. Some are very well known and highly regarded in their specific subfield, but not nearly as much outside of that.

The point to a letter of recommendation is that it is a recommendation.  If they don't know you, then what is their basis for recommending you?  If they're straightforward and honest, they can't.  Therefore, the request is basically asking someone to lie.  Yes, that is rude.
Hence, I favor the first sentence of Ébe Isaac's answer.

You might want to quote or paraphrase the current first sentence of Ébe Isaac's answer, in case it is ever modified or removed.

@JW : A sensible idea.  The reason I'm declining to make the change is that I'm intentionally pointing people to Ébe Isaac's, where they are more likely to check out his entire answer and give him the up-vote he deserves.  It's not my goal to steal his thunder by copying the info.  His original sentence should remain in history if his answer is edited.  So, until I notice it changed, I'll be nice to Ébe and keep sending people that-a-way.  All that said, though, you are right, and I do appreciate your kindness by pointing out the idea.

Certainly couldn't recommend someone for admission to a PhD program based on the quality of their published research, even if you didn't know them personally?  On the other hand, I might know a lot of professors personally, but most of them may have no idea about my research work.

If they don't know you, then what is their basis for recommending you? -- Your work.


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How long can a pure math(Algebraic Number theory) PhD holder can work as a Post Doc/research associate in their career?
This is rather a curious question based on future career after PhD, looking at the crisis in academic/teaching job market.
If one completes PhD with pure mathematics (Algebraic Number Theory) with few good(not excellent) publications and to some extent good background (not excellent). Assume they are not ga enius but they are hard working. Assume they are searching for a permanent job in college/university teaching but is suffering while there are options to work as post-doc/research associates for them.
The question:
Exclude the possibility of getting a permanent teaching job. Can one prefer to work as a post-doctoral/research associate throughout ones whole (at least upto 40 years) career including several institutions and in any country ?
or, simply
How long can a researcher remain as a post-doctoral/research associate in several institutions and several countries, in algebraic number theory, in their career ?

If you are more than 6 years past your degree, I can’t hire you as a postdoc. But that is just one institution. Perhaps you should look to research labs or industry rather than academia.

I think that the differences between different countries or even institutions are really large in this context. Do you want to specify a locale?

@Christian, I didn't get you. But I meant I am ready to work any country not just my home country. For example, after working 1/2 years in some institution, I can go to any country for new appointment as post-doc/research associate. My question is-how long can one continue such process ? For example, the comment of Jon Custer says, he won't take anyone if one got PhD 6 years ago.

@JonCuster, thanks for your nice comment

@MAS I know of institutions which do not have such requirements but might not be able to give you a temporary contract more than once. Some countries like Germany have an overall time limit for temporary positions. So, I do not think that it is possible to give a reasonable answer which goes beyond "it depends".

@Christian, thanks for your comment

@DanRomik, I think astronomy and pure mathematics has a difference in the sense that one can work on astromy in many physics/engineering laboratory. In pure mathematics there is less possibility in that way

but is suffering --- Depending on what this means (financial suffering? current department/university politics suffering? current academic bullying suffering? current living location too hot, too cold, too dangerous, etc.?), being more specific might help with replies being more relevant to your personal situation.

@DanRomik, yes thanks

@DaveLRenfro, I think it is clear and obvious because i have used the term "job crisis in market"

@MAS I'm not sure that there is really a "crisis" in the academic job market; "crisis" implies something restricted to some moment in time. Rather, there are simply fewer long-term academic jobs than there are people trained with a PhD. This isn't particularly new, and is certainly not new since the time you started your PhD.

@MAS " For example, the comment of Jon Custer says, he won't take anyone if one got PhD 6 years ago" You are misinterpreting the "can't". The institution will not allow him to hire anyone 6 years past his PhD. Each instiutions will have different rules.

@MAS "one can work on astronomy in many physics/engineering laboratory" Absolutely not, there are way less astronomy position than pure mathematics, and physics/engineering laboratories are hiring (sometimes) physics and engineers. But they also have to spend a lot of money on machineries/tools/computers. Actually, you are more likely to work in those labs, rather than an astronom (keep in mind, you still have very low chances, but relatively higher than an astronom)

@BryanKrause, sorry, but I don't agree at all. How can someone who is established understand the difficulties faced by early career stragglers ?   In my country we say "unemployment crisis" when the vacancies comes out is very less with respect to number of applicants every time. Due to Pandemic, the situation has come to at more  severe situation. New recruitment advertisement  has been very less

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text:
Is it illegal to use resources in a university lab to prove a concept could work (to ultimately use to create a startup)?
While I understand this is not a legal help site and it may differ from university to university, I am curious if anyone has any thoughts on this.
I am in an undergraduate programme in a life sciences-related field. My friend and I have an idea for a genetically modified organism product that we would like to bring to market.
We plan to make the full product elsewhere, but we need a proof of concept which we could easily create in the lab we both work in, just using leftover chemicals/DNA that would be disposed of if not for us using it. We simply want to create one organism to prove it could work, so we can then get evidence and support to complete the project elsewhere.
However would there be legal ramifications for just making the proof of concept in this lab?

Are you fine with the university claiming intellectual property rights?

And if you're going to ask about the law, you'll have to name a jurisdiction.

Universities usually claim patent rights on things created there. There is also the issue of safety, not just of law.

This would be in Illinois. The product would not be patentable, as due to the nature of source DNA the patent would belong to an outside lab however we would have permission for its use.

What Buffy is saying is that if you create a GMO with university resources, likely the university could claim to own the GMO.

You probably need approval from higher up in the university to try anything using DNA.

If I understand the legal terms correctly I believe in this case the GMO would automatically be owned by the outside lab that had produced the plasmid.

Ask the person in charge of the lab.

I have done a bit of pro bono work for a friend's startup, and when they were getting acquired, as a part of the due diligence they had to circle anyone who had contributed in any way, and have them sign an agreement where they give away or sell their contribution.

Illegal... It's unlikely (except perhaps if you could be accused of stealing the chemicals)... Against university policy and quite likely to get you sacked... Absolutely. You probably also would have a hard time asserting you actually owned the resulting IP.
Long and short of it, don't do this without at least asking.

All the comments about IRBs and patent claims and so on are, in my opinion, irrelevant.  The issue is  very simple: The lab and the equipment in it belong to the University. Doing anything in the lab without asking the University's permission is potentially tortious. And this is a good rule to follow in general: don't use other people's stuff without asking them first.

That's not how patents work, it doesn't matter who owns (/discovered/...?) the dna. Only relevant question is who invented the product and possibly who that inventor(s) needs to assign the patent to for contractual reasons.

I would offer a more general guideline: if you are using someone else's resources in any capacity whatsoever, it is only prudent to negotiate in advance what happens to the products of your work.
This applies not only to startups, but also to publishing results of your previous work without giving any measurable return on investment (affiliations, co-authorships) to the lab you performed it in.
It is exceedingly rare for the work to be blocked altogether, because then no one wins, everyone loses. The crucial detail here is both sides explicitly agreeing that the deal is fair. It need not be purely monetary, either, but IP has value.
Look at it from a managerial perspective: you take in taxpayer dollars and produce something of value to the taxpayers. Overseeing agencies like to see funding statements on all the things the lab has produced, and they are often fairly specific. As a manager, I get a pat on the back for the lab being efficient, and am generally interested in you doing cool things with the equipment which taxpayers could perceive as a good use of their money. If you do not provide me with grounds to say "hey taxpayers, we did this, is this not great?", then for all I care, you just took the money and ran off. Not great. There is another caveat, too - like BillOnne points out, if something unethical or substandard happens on my watch, I am liable for that and very much not happy about it!
All in all, you should do everything completely above the table, and it may mean jumping through more hoops than otherwise. But these hoops are in place for a good reason.
Indeed, you face a risk of investors clawing back a lot of your hard-earned money, but "either you get a little, or no one gets anything" is not too bad of a negotiating position. There are, indeed, businesses which became successful because of appropriating something valuable at the start, but doing so sneakily is certainly not the way to go.

I agree strongly with this answer, not least because this may vary widely according to circumstances:  What country, what research outputs, what discipline, what lab in a given university, maybe even what piece of equipment depending on how the equipment was funded.  (I am sure I am not the only person who has overheard enterprising young undergrads and grad students suggesting bitcoin mining operations thinly disguised as 'research projects' using federally funded equipment....)

Apart from the legality of who owns the product, and the issue of using the resources and equipment without permission, there are other considerations.
You would be doing biological research. You give very little detail other than potentially a novel GMO is involved.
Usually such things have at least a minimal review for ethics and safety before they start. Possibly it would be fairly trivial, depending on what actions you were considering. But there are MANY bilogical processes that the university would be maximally upset to find out you had done without the review in advance.  And in the most extreme cases, they could be induced to come after you with legal consequences.

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

You would need to negotiate an intellectual property agreement with the university's technology transfer office (and other interested parties).  Regardless of legal necessity, if you want investors to put money into your business, you should have that agreement available for the investor to examine.

The technology transfer office is not there to get money from you right now.  They want your business succeed, which makes them look good and maybe gets them a much more substantial amount of money in the distant future.  They probably know who would like to invest in your business.

State universities in the US have a mandate to support and foster the local economy by developing research and technologies that can be economically exploited. If you have a good idea, the university might be quite open to it.
However, you need to go through the proper channels in order to use university resources. First step would be to talk to the supervisor of the laboratory, who would also be more familiar about the procedures that need to be followed. You might also want to write up your idea beforehand in as much detail as you can muster and have someone else sign each page, as it is not unheard of for discussion about priorities etc. to ensue later.

This is not a legal help site, and the only correct answer is to find a competent IP lawyer in your jurisdiction to review your contract with your university. It is very possible that using university resources to create new IP would result in you losing some or all of your IP rights, so this is not something you want to  take lightly if you ever hoped to start a business or sell your idea. Even just having doubts about the legal ownership of your IP could be enough to make it effectively worthless.

This is not a direct answer to your question, but apropos this topic, you might be interested to note that Noam Chomsky has written a lot about how various industries have used the university system as a source of tax-funded research whose products they then privatise for their own firms (for a gentle introduction, see one of his talks on this topic).  This is particularly common in military research but it also occurs in technological fields across many industries.  So, the cynic in me says: the legality of this practice depends on your ability to use the political system to do it at scale.

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My Korean professor and Korean lab members threaten me to give my research to them. Please advise me
I obtained my research degree under rather abusive circumstances from a Korean university. My research work involved a data set from a company. During my studies, I presented my work at a conference as the main author. I won the best paper award. Under pressure, I handed over the tools I developed and the data set to another student in the group.
I have now been invited to submit an article to a special issue dedicated to this conference. My (former) professor is threatening me to name that other student as first author, otherwise they will submit the article without me.
What should I do?

Is this a PhD thesis you are talking about? I am unfamiliar with Korean academia, but from what it sounds like - if you already received your degree from the university - it might be the best to leave this xenophobic mess behind you and move on.

Although this situation may have to do with the specific country, I wonder whether it's appropriate to focus that much on nationality and (potentially) xenophobia. Even if we suspect that it has something to do with Korean university culture, couldn't the same thing happen to a Korean student/assistant as well? And could useful answers not be given by people experienced with similar situations in other countries?

I read a lot of abuse in this question, but not a specific question anyone can answer. You apparently got your degree, so at least you have that. For the interpersonal conflicts, my suggestion is to talk to the department head or a grievance office in the university. I would suggest to think about what specifically you want to have addressed, because that is not clear to me from the post.

@FarahJabeen I've rewritten your question, focusing on those details that seem relevant to the publication dispute to me. You can roll back my edit if you disagree.

@ChristianHennig I mostly agree with you, but I've left information that this happened in Korea in regardless when editing. There might be some useful culture-dependent advice in how to navigate the social dynamics of this.

While overall it seems prudent to minimize any future inactions with these people, getting this paper might be worth it to engage a little bit longer. You have your degree, and thereby the power of your former professor over you is significantly diminished.
For this publication, there are two independent things to do before interaction with them further.
One, make sure that you have all the relevant document of your work on the project in safe spot. You don't want to find that your draft on the university's SVN is suddenly gone without a trace, something like that. With the conference presentation already out there, you are in a very good spot anyway.
Two, make a rough tally of what work still needs to be done for the article, and who could do that. If there is a lot more work to do, then letting the other student do it in exchange for first authorship might be a better course of action than fighting for it and doing it yourself. In the rest of my answer, I assume that her earning it isn't a feasible option.
Having done those two things, you calmly point out to the professor and other student that you have ample evidence of your crucial contributions to the project, and that any attempt of them to submit the paper without you will end up with you pointing this out to the relevant editors, which will then look very, very bad for them. Instead, provide a simple plan involving limited interaction for how this paper is going to come to be, if at all.
One important question is whether the professor and/or the other student themselves can make a decent claim to authorship rights. The answer is probably yes for at least the professor, and that means that just as they cannot publish without your approval, you can't publish without them either. Do consider whether you are prepared to walk away without the paper happening.


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Open Access Crowd Based Publications (StackExchange like)
I am a PhD student in computer science and sometime in the (more or less) near future I have to publish my results. Yet, I am rather sceptic about the current state of publishing, aka peer-reviewed journals, especially when they are not open access. I have published before on Elsevier and honestly I am not sure whether I should do this again. I have political concerns as well as concerns about the quality of the peer-review process.
I wonder what "new ways" are out there for publications?
I am a big fan of StackExchange (especially StackOverflow :-) ), so I am asking if there exists a very similar forum for scientific publications?
Accordingly, a publication happens in form of forum post like this one. Instead of anonymous peer-review, every member of the forum can comment and rate the publication. Is there something like this out there? Thanks a lot!
Edit: Great that someone had the idea a year ago :-) (Towards a Stackexchange-like comment/reputation system for research papers)
Have been there any attempts to create such a system since then?

If you haven't already, you should check out Peerage of Science for an alternative way to do peer review. Still made pre-publication, but meant to be open, journal independent, and with reviews of reviews. This is not dealing with "crowd-based" publishing though.

The usual way to deal with outdated questions and answers is to post a bounty on the outdated question and not create a new question. Obviously you don't have enough rep to post a bounty, but if you leave a comment on the original question, I would be happy to post the bounty on your behalf.

Ok, thanks. Yet, I am also required to have 50 reputation for comments on the original question. So, I cannot even request a bounty from someone else there :-D

Instead of anonymous peer-review, every member of the forum can comment and rate the publication. Is there something like this out there?

Yes.  The forum is called "the academic community," the comments are called "what they say about your paper in their paper," and the ratings are called "citations."  They are not anonymous.  Actually, citations alone are misleading, since they can be negative as well as positive.  The real way to determine if your idea is good is to see if people use it to build new, interesting ideas / explanations / products / companies / whatever.  (I think they call that "impact?")
In other words: publishing is the easy part (these days).  Getting people to say good things about your research is the real challenge.
I do think you are wise to think about publishing in open-access journals—and not for some self-righteous political/philosophical reason.  The real reason for making your paper freely available is: more people will read it!  Plenty of interesting people in the world live behind the Great Paywall of Academia.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


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Referencing: Which one is more ideal? (cite as from cited or direct cite)?
Well, while carrying out a review of literature for drafting a proposal I found like these in some of previous works (reports).

Some benefits of the “certain thing” on xyz are  abc( person1, date) , cde( person2, date), fgh( person3, date) , ijk( person4, date)

and

Some of the more researches in the field include ( person1, date;   person2, date;  person3, date;   person4, date).

Now If I have to include and cite those in my report, which one is better idea? Also, please notice the nature of contents being cited(benefits and previous works).
Option 1: Cite as “as cited in report X” which I read and have only one reference of that report
(pros: less references)
Option 2: Go to each report, study and include each one(cited) as separate citation in my report
(pros: may be, will look more detail investigations. But is it required in cases like this one?)
Which one should be more ideal?
So, what should I do? Any suggestions?

Please note that you are probably mixing two issues here. One question (the one you seem to be asking) is: Should the content of referenced works be briefly alluded to (if only by a single keyword)? The other question (that you are not asking, but that could be asked, given that your two samples choose different paths) is: Should references be used as annotations that could be deleted without syntactically breaking the sentence (1st sample), or should references be used like words (2nd sample)? (If I recall correctly, the 2nd question has been dealt with before here on Academia SE, and ...

... in order to ask the first question without touching upon the 2nd one, I suggest swapping your 2nd sample with something like "There has been more related research in the field (person1, date; person2, date; person3, date; person4, date).")

Option 1 is lazy and does not give credit where credit is due. I'm not sure what the proposal is for but it irks me when people constantly cite reviews instead of the original sources. You should choose option 2 not because it makes you 'look good' but because those studies should be acknowledged.

@user49483: Apparently, I am interpreting the question completely differently from you, as it seems to me that in both options, the very same (amount of) credit is given for each of the four cited works. The only difference is that in option 1, the content of each publication is briefly addressed, whereas in option 2, there is just a superficial remark that the four works are somehow related, and they are listed without any further comment (so readers will have to go to each report to find out what it is about). OP, could you please clarify your question?

@O.R.Mapper I was interpreting the quoted bits as examples of reports/reviews that contain information the OP needs to acknowledge in the proposal rather than examples of how to cite multiple works. OP then seems to be asking whether to cite a review not the original sources (option 1) or cite the original sources (option 2). But it is confusing and I might be wrong.

Exactly as mentioned by Mapper,I think it’s just making things concise than not crediting.We point to X which points at a,b,c,d. Moreover, citing the cited work includes “as cited in” which tells the report is not original author or report has just cited(from somebody else, which will be listed in his ref).Suppose literally there is a line; The benefits of computer are speed (ref 1), accuracy (ref 2), storage (ref 3). If I simply want to tell,some benefits of computer are speed, accuracy, storage, [report x] and put 1 in reference with keyword “as cited in..” than 4 refs then is it really bad?

Same with Previous works, I am not discussing what has been discussed in each of the previous works but just mentioning as information that x, y, z, a, b, c were researches on this topic as well. Again, it will be cited as content cited somewhere(as cited in...). If I were interpreting then it would have made sense to include each as principal references. Only problem I see in it is it will show as if you are bit lazy(but my question is is it required in case of previous studies,benefits) Even there are many tutorials on it http://www.noodletools.com/helpdesk/kb/index.php?action=article&id=152

Sorry.My comments were so packed that even i could not talk for your replies.Thank you for the replies.

The value of a review is the way in which it gathers and synthesizes prior work to form a more complete picture of the field.  How you should cite things you learned about through the review depends on whether they are being used as examples of that broader picture or unique elements.
If the work is an example of the broader picture, which it sounds like it is from what you have written, then you need to credit both the review and the individual examples, e.g.:

Other research in this area is thoroughly reviewed in [REVIEW], of which the most relevant to this discussion are [X], [Y], and [Z], because of reasons.

On the other hand, if you really just want to talk about paper X, and the only value of the review to the discussion is that it's where you first stumbled across X, then you only need to cite paper X.
In both cases, however, you need to actually make yourself familiar with the work that you cite, not just take somebody else's word for it, since the review may well have misinterpreted the work or presented a slanted picture since the author had an axe to grind on the subject.

Yes, got it. Thanks. Makes lot of sense. As an analysis of previous works, I read more than 15 reports in detail and included 10 of them in the proposal analyzing & presenting their findings and limitations (paragraph for each). But there are some more researches listing in a report, which I was trying to include as “In addition as mentioned in report x following researches …….[10 researches]  are also carried out in topic”. But, may be better idea will be to study (check) each one and put very relevant ones only and put a direct reference. Thank you.

Like user49483 said in the comment, citing a review is considered very bad form. Basically, it is your job to read a lot (reading widely) and cite what is appropriate.
As one who marks papers, I definitely reduce students' scores for citing indirectly like this (and I see it all the time).
When you cite indirectly, you are saying "I know this is important because I am citing it but I did not read this important piece." JeffE said in a comment (which I cannot find) that not citing the original is actually you saying that you could NOT FIND it because if you CAN find it you MUST read and cite it (or something to that effect).
One of the many reasons to read and cite the original is because the third party (reviewer) might be reporting on the original work incorrectly. I saw this one time when someone said a famous author in my field had said something which did not sound like that author at all. So, I re-read the writing which was referenced and it was simply being mis-reported. If a reviewer mis-reports and you cite the review then you are showing that you do not have the proper understanding (and your grade should reflect that lack of understanding).
Is it more work to cite properly? Of course it is. Doing anything properly takes more time but we do it because it is the proper way and taking shortcuts simply leads to poor results in any field or study or work.

Thank you very much. Yes, it makes sense. But I was just curious to know on those specific cases such as literally just listing previous works or benefits. So if report x says: (report1,date), (r2,date1), (r3,date1), (r4,date1)  were some researches on in topic then if I have to mention same thing as info in my report then I can say: some of the researches on this were (report1,date), (r2,date1), (r3,date1), (r4,date1) and list 4 original refs in my report?(legally put or forget about where I found it as it's not his work). Will it be plagiarism or not? I am really confused and curious.

@user2700108 I don't really understand your question clearly so my answer might be off. Normally, I would expect someone to write about what those authors did. Just to say they "researched on this topic" is not very useful. If you did not read the original work, you should not cite the original work. If you want to read the review and cite the original, that is not the right way, an indirect citation is better than an inaccurate citation (the citation says you actually read the piece you are citing). If my answer does not fit your question, please clarify the question.

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How to cite a paper whose place and status of publication is questionable or unknown
I want to cite the following paper:

Cem Kaner & Walter P. Bond, “Software engineering metrics: What do they measure and how do we know?” 10th International Software Metrics Symposium (Metrics 2004), Chicago, IL, September 14-16, 2004.

Most of my citations of papers in proceedings contain page numbers.
The PDF file does contain page numbers from 1 to 12. However, I cannot find any contribution from the author in the table of contents for the proceedings. Other citations cite the paper without page numbers.
What should my citation look like? And in case I encounter something like this in the future: what explains the apparent mismatch between the author's website and official proceedings?

I have changed the title to address the actual issue. The previous title, Finding page numbers for citation, made me expect quite a different question. Only after reading the question text, it became clear that the question is not actually asking about the page numbers as such, but the lack of reliable page numbers are only a symptom for the underlying problem at hand, that a paper does not appear to have been published in the venue that it claims to be from.

I have double checked in IEEE Xplore. The paper does not appear in the table of contents, the authors do not appear in the author list. Additionnaly, I cannot trace it in ISI Web of Science (which mentioned other conference papers by C. Kaner in 2004).
There are three options (in general):

A mistake in the proceedings for a regularly accepted paper,
The paper is more a tutorial, a keynote, a late breaking paper that has not been through the standard review process,
A paper that was not published in the conference, and which was put online carelessly in the conference paper shape.

As I am really unsure, and know that papers sometimes cite papers they have not read (and papers that do not exist), I would cite it only as an online document, or a preprint, with the url, without page number, and a potential note like "(often refered to as published in Metrics 2004)".
Most of all, I would suggest you not to cite it, unless it is really useful for your work. Or cite a paper really "published " by the authors instead (good luck with that).
EDIT: after a long search, I have found using the Wayback Machine that this paper could have been part of Metrics 2004 Late Breaking Papers:

The purpose of the late breaking papers session is to give authors the
  opportunity to present work from on-going projects, new ideas and
  papers not complete at the time of the original call for papers. Each
  paper has been peer reviewed by at least 2 independent experts.
The late breaking papers sessions allow authors to make a short
  presentation of their work in the main programme. Printed copies of
  the extended abstracts are circulated in delegate packs and, due to
  the timescale, the full papers will be published electronically on the
  conference web site.

Finally, I observe that with some online journal, it gets more difficult to have standard page numbers. Sometimes each paper gets a number. As much as I like citing papers correctly, may be page numbers are becoming  useful when the work only exists in paper-like form: a DOI is an interesting alternative.

If it is as you describe, this was meant to be an informal session, showing preliminary results, not (yet) ready for publication. No wonder it wasn't included in the proceedings. So there should be a definitive version by the same authors elsewhere, or they just gave up because they found a fatal flaw (or just got bored, lost funding, ...). Take with a healthy dose of salt, and if citing it, mark it as an informal document.

@vonbrand Indeed, as far as I could check, none of the late breaking papers are in the ToC.

First off, the function of bibliographies is to make whoever reads your work can get hold of the referenced material, be it to check you didn't misrepresent anything, to drill down on some particular point, or something else. With this in mind, you owe it your readers (and yourself, later on building on the previous work) to make this as easy as possible. I.e., give as complete and detailed references as possible.
There are several possibilities. If this work was just presented, but not published in any proceedings, there just might be no "page numbers" at all. Some conferences just publish the papers as separate files e.g. on their webpage, again no page numbers. I've also seen (sloppily done) proceedings in which each paper had their pages numbered from 1.
I'd make an effort to get hold of a copy of the final version (as published) and check that one. How much effort really depends on how important it is to you. I have several BibTeX databases collecting what I've cited and used, and even documents I've checked but never used. From time to time I go over them and try to fill in missing details, check if the URLs I keep for my own use in there are still valid, and so on.

"I've also seen (sloppily done) proceedings in which each paper had their pages numbered from 1." - this may be a matter or preference. I would see this kind of "semantic page numbering" (somewhat meaningful page number in document, rather than an essentially arbitrary (with respect to the paper) page number in a collection of documents) as "intuitively done" or "straightforwardly done". With that said, I cannot remember I have ever used the page number from a reference when digging up a referenced document.

@O.R.Mapper, I have had to request documents by interlibrary loan, and giving exact page numbers was critical to get (copies of) the pages needed.


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Is checking the format of a paper an expected part of the reviewing process?
I have some papers to review and I am wondering whether I should do an in-depth inspection over the whole paper format? I see nothing major but there might be some tiny format errors here and there..

Does the organizing committee expect reviewers to check submissions
  against the conference format?

I would say the responsibility of the reviewer is to judge the content of the paper. So, checking if the format of the journal/conference has been followed is not part of this job. Very large and obvious deviations can be pointed out, but for example spotting that the font of the caption is in size 11 and not 10 is not part of a reviewers task.

In general I agree with the other two answer but somehow in every paper that I have ever received a review for there has been some sort of comment on something formatting related from at least one of the reviewers. These have ranged from suggestions for changing the fonts of the formula or captions to spotting that font for footnotes should be 9 instead of 10 for that journal etc.
I think there is some sort of a code that if you find something you don't neglect it and ask for correction but in general that's not your job and you don't actively seek them you just "catch" them.

Reviewers check content. Copy editors, prior to publishing, check format and adherence to publication style guides.
Your Milage May Vary based on the expectations of your committee.  If you have a question about what you are supposed to be checking don't be afraid to ask.

As grauwulf comments, your job is to focus on the content. However, when poor formatting clearly affects your ability to understand the scientific formatting, it should be commented upon. For instance, when somebody writes "x^2", but really means "x (Ref. 2)", that's a problem that should be commented on (because a copy editor might not catch that!). Similarly, if the way a graph is formatted makes it difficult to interpret (labels or legends too small to read, or are garishly presented), then it behooves the reviewer to mention it.


text:
Creating an central multi-purpose dictionary / database
I am trying to organize my workflow and make it more effective.
As non-native English-speaker studying in a foreign country I often need to look-up domain-specific translations (in 3 languages). As there are no specific dictionaries I am using textfiles containing translations I have collected over the time.
This is quite uncomfortable.
Often these words are related to some kind of mathematical definition which has to be stated as a theorem for proofs. Right now I usually copy these from my old publications.
It would be great to have some kind of central dictionary or knowledge-base where I could organize all this (Translations and Definitions).

Anyone who can recommend a program for this?
How do you organize definitions and domain-specific translations?

The question was intended to be more about managing knowledge than actual coding, the technical things were used to illustrate the intention, I changed the Question. Hope its more on-topic now.

thanks for editing into something more appropriate for the site (and welcome to Academia Stack Exchange!)

I would try http://termbases.eu/ a site that was mentioned under Software: Lexicons in Linguist List.
Broadly, what you have described is a lightweight variety of a dictionary writing system, software for developing a lexicon.
If you were translating digital documents, I would recommend translation memory software. Collecting and managing your multilingual context-specific translations is part of what translation memory software does.
Another possibility, if you happen to be comfortable setting up a wiki, is to create a wiki in the manner of Wiktionary.

The first website you introduced seems not to be free and has limitations over the free version. Do you know some open-source/free softwares or website services too?


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The exam time was less than the students expected
Some time ago, a course I visited had final exams, and the time announced to the students in advance (several weeks earlier via email by the instructor) was 3 hours. Rather shortly after the students began to write (about 20 minutes), it was announced as a clarification that the room was booked for 3 hours, while the test itself would only take 2 hours.
I did not take part in this exam (I took the second one, which had similar conditions), but I'm sure the students were quite surprised. The exam itself was of average difficulty, had it been 3 hours, but very tough in only 2. This was reflected in the results: 90% failed, instead of the usual 30-50%, and the best grade was only a "B-".
I'm interested if this sort of thing is less unusual than I would think, or if there is a protocol how to deal with it as a student?

If the instructor planed the exam for 2 hours, then an extra hour would had not helped: a 3 hour exam would had have more questions and the time average per question wuld had been the same...

So, was the problem only that the time during the exam was announced wrongly, but corrected quickly afterwards? Why would this be something that a student needs to "deal" with? Even if the announcer have said it correctly at the beginning, the exam would still have been difficult.

I was once in an exam we were told would be two hours, only to find that it actually lasted three hours. As @NickS suggests, the exam wasn't easier as there were just more questions than we expected.

Also, can you clarify what you mean by "It was announced to the students in advance"? Was this on the course outline? Announced by the instructor in class? Or was this done by somebody else than the instructor (i.e. exam times post around campus,...).

(I have edited in some clarifications)

Thank you all for your responses. I am not certain what time frame the instructor actually planned for. The exam's high difficulty and stark un-clarity before it made it seem as if he did not know it was going to be written in only 2 hours himself. In case it was intentional, though, I think you are completely right, and it was simply an unusually tough exam.

To avoid this, in all the exams I have taken, the time of ending was written in big letters on the blackboard before starting.

I would hope this is unusual because it's not very nice to the students.  Students deserve to know in advance how much time will be given for the exam. And in my experience, they usually do know this quite far in advance.
It doesn't make sense to me that the figure mentioned in
the instructor's e-mail would refer to how long the room was booked (which is not something that the students would care about) rather than how much time would be given for the exam.
Another thing that doesn't make sense to me is why, when the instructor realized that the students thought they would have three hours for the exam, he didn't just keep quiet and let them have the three hours.
However, I don't know what you mean by a "protocol how to deal with it." You could certainly let the instructor know that you are unhappy about this aspect of the exam.  But is there something that you think the instructor should do at this point to improve the situation?
Also, what does it mean to say that 90% of the students failed the exam?  It's not necessarily a bad thing if 90% of the students got a numerical score below 60% on the exam, but it would be a very bad thing if 90% of the students got an 'F' grade in the course.

Those things made no sense to me as well. I'm not sure what additional actions could be taken, it certainly depends on if the exam was originally planned for 2 or for 3 hours.
The 90% referred to the percentage of 'F' grades. Usually, only about 30-50% of the students get an 'F' in this course.

@mafu That's a lot of 'F' grades, so the administration might see it as a problem even without knowing about the confusion regarding the allowed time. But in any case, probably the most it would do is to strongly suggest that the instructor not give so many 'F' grades in the future.

First, I think this is unusual, but I doubt that there is serious data about how common things like this are.
But the more important question seems to be: Can/Should I take action? What action?
This clearly depends: First, there may be a policy how the conditions of final exams have to be announced. At my university many "moduls" (i.e. courses) have a description where it is written "final exams according to the instructors announcements" and there is a general rule that this announcement has to happen in the first week of the course. Also there are general rule that say how long written exams can be. So if the announcement or the time constraints do not fit the actual conditions there could be room for an action to be taken.
What would happen if you (or a group of students) would file a complain to, e.g., the dean of student affairs (or somebody similar). I expect that the dean would talk to the instructor and asked what has happened. The instructor may answer respond that it was obvious that the exams time had to be shorter than the announced 3 hours and that he planned the exam for two hours. The dean may still be suspicious because of a high fail rate but this may also have other reasons. So in short: The instructor may get into mild to mediocre trouble but anything beyond that is unlikely. In an extreme case there could be a chance to rewrite the exam…


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Meaning of et al. when referring to multiple papers with the same first author
I am citing some papers with the same first author but different co-authors.
For example, [1] is a paper by X, Y and Z, and [2] is a paper by X, A and B. Would X et al. [1,2] be appropriate here? because essentially et al. in [1] refers to people other than those referred to by et al. in [2].
There is a similar question about Harvard references. But I am interested in cases where only the reference number is shown in text.
Update in my field in computer science, it's common to refer to the first author and use et al. When there are multiple ones. Usually the first author is regarded as the one who did the majority of the work.

I understand this "X and others" to mean one specific set of (unnamed) people, unless they are the same bunch I'd write them separately. Just like when I was citing two papers by Chen together, but they were different Chens.
Perhaps use "X, Y et al. [203] and X, Z et al. [205]"?

In my experience with engineering, I usually see X and coworkers [1,2] in these situations. I have no knowledge if it is grammatically incorrect to use et alia ("and others") to refer to multiple papers with different authors, but I haven't ever noticed it being used that way. Also, you may come across the convention that it is not necessarily the first author used with X and coworkers, for instance, if the works all come from the lab of a well known researcher, one might prefer Smith and coworkers [1-3], where Smith is the PI of the lab.
See also this answer from Strongbad to a related question.

Remember that no matter what you write in the text, the really important thing is the bibliographic item. I would personally tend to avoid using X et al. [1,2] if [1] and [2] do not have the same list of authors. If I came to this point in writing, I would try to reword the sentence.
On the other hand, I would use sensible judgement. If it's clear that the articles come from the same group of investigators, just with one name missing or so, you are probably fine keeping the two things together.
Some other "out-of-the-box" options include:

Using [XYZ12] citation style; then it's clear that X et al. [XYZ12, XAB13] do not have the same list of authors.
Avoid putting people's names in front of the citations (not preferable in general I think)
Use more than one name before et al.

It is customary to use "et al." in a context in which it refers to one source only. If one author is not enough, one should add names until the reference becomes clearly identifiable.
If the authors are A, B, C, D, E and A, B, X, Y, Z, you could put
A, B, C et al., but "et al." is not used to refer to several papers.

If you need to mention X, et al. (et alii) would not  be appropriate, these are not the same "others". And it should generally be used for three or more authors.
"In several works X coauthored [1,2], we see that" or "In [1,2] X and his coauthors say..."
But why would you need to mention X? You can use "From [1,2], we know that..."

Note that in some fields, your last form would be considered grammatically incorrect (due to historical reasons where references were originally footnotes, which cannot be part of grammatical constructs).

In some fields, indeed.


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Responsibilities of instructors to students when teaching controversial subjects
When teaching a course on a topic that might be controversial, what are the responsibilities of instructors to facilitate an open learning environment?  If the instructor has a strongly held opinion, is it appropriate for the instructor to structure the course and the readings around this opinion?  Does the instructor have a responsibility to structure the course in a way that is agnostic about the topic?  When selecting the readings and the lecture schedule, does the instructor have a responsibility to give equal time to opposing viewpoints, if those opposing viewpoints plausibly have equal intellectual merit?
I'm familiar with the notion of academic freedom for instructors, where instructors should be protected from external influence (from outside the academy: e.g., from politicians) in their ability to shape their courses and express their findings and opinions.  Is there a corresponding responsibility to protect the academic freedom of students, by structuring courses so that they do not make students feel uncomfortable expressing views that disagree with the instructor's?
Are there any guiding principles or resources for how these issues should be navigated?  What are the social norms within academia?  Are there any lines that, if crossed, might lead to disapproval from a significant fraction of fellow academics?  I'm mostly familiar with engineering/science/mathematics courses where this sort of issue rarely comes up, so this is new to me.

@BenCrowell, that link doesn't answer my question.  That question talks about what privileges are owed to instructors (and what is the impact on a professor of taking controversial opinions).  I am asking about what instructors owe to students, and what the social norms are in academia.  It's a different question.  (FYI, I'm not asking about the guiding principles of academic freedom; I already know them very well.  Rather, I'm asking about the guiding principles of teaching a course on controversial subjects, in a way that respects our students.)

@BenCrowell, by the way, thank you for the comment that the question seems scattered and unfocused.  Do you have any suggestions how to make it more focused and less scattered?  I'd welcome any ideas or suggestions!

@D.W. a motivating case might help make the question clearer. I would imagine in philosophy courses this could come up as the difference between materialism and a variety of Platonic idealism. Or economics courses where there are several current and intellectually reasonable "schools" as it were.

If the students are being assessed by you, some (most?) will start to tell you what you want to hear in order to get the highest grade. This is rarely what we as educators want in our students. We want to build within them critical thinking skills.
Controversial issues are common in some fields. For example, one of the subjects I teach is Business Ethics and I have clear beliefs and values in this area. Is it OK for me to focus on the arguments in favor of my view and discount competing arguments? No, it is not.
Can I tell my students my opinion? Opinions differ on this but I believe it is OK, as long as it is done very carefully with LOTS of evidence that my opinion is wrong. Again, students must be taught to think for themselves, including how to critically evaluate what they consider right and wrong. If I just make my points then it is not education, it is indoctrination and that is not what higher ed is about.
As far as social norms, I would say that if you are trying to get your students to 'believe' anything, then you are doing it wrong. If you are trying to get them to think critically, then you are doing it right. If the students feel they must agree with what you say, you are doing something wrong. If they feel like they are getting balanced information and a class ends up with many different opinions, then you are doing something right. If everyone is thinking the same, then nobody is thinking...and that's not good for anyone.

I am confused by I believe it is OK, as long as it is done very carefully with LOTS of evidence that my opinion is wrong. Also, should the first want in will start to tell you want you want to hear in order to get the highest grade. be 'what'? I like your answer, but I hesitate to upvote.

@scaaahu My point is that it is being 'untrue' to the spirit of seeking the truth if we are unwilling to state what we consider true (when many truths are possible). However, it is a slippery slope and it is very easy for a teacher to become a preacher of his 'one true way' as opposed to opening the eyes of the students (should be our goal). So, if we, as educators, share what we believe, we should only do so if we we also give plenty of counter-evidence showing clearly that, while we do have our views, we also see the value in other views. Also, thanks for catching the typo- I've fixed it.

Although I cannot say how the principles of, or basis for, university education are formulated everywhere, one guiding principle in the system I work is that courses/teaching should be founded on science. In the term science lies objectivity, that is to show both pros and cons for a specific idea. this does not preclude one from having personal opinions we all have. One example:
In my university a scientist, known for controversy, decided to run a course on divining rods under the pretext they were serious and work. Now, one can have an opinion about this but when trying to look for a scientific background, the best one can say is absence of evidence is not evidence of absence. The university clamped down very hard on this because it broke the founding principles of university education due to a lack of critical discussion.
So, a person's opinion should not taint the material so as to skew the picture based on unscientific principles. If one runs a course that uses sound scientific principles to criticize a view point, the exercise to evaluate the criticism may be sound in itself. The issue therefore lies in openness about any "one-sidedness" of the course. The role of a university teacher/teacher, is after all to provide objective critical view of materials.
One way to look at this is to compare with research. If we try to push a view uncritically, our peers are likely to suggest rejection of that article. To not approach teaching with the same serious rigour is, I would argue, unprofessional. The problem maybe lies in that there is no peer review of course materials.

I am unsure whether the supposed objectivity, the term "science" carries, is a sufficient guideline for controversial issues. If you look at debates about e.g. alternative medicine, people express different opinions about the content of "objectivity", "evidence" and "criticism". A recent popular case in Europe was prof. Walach who advocates a so-called "weak quantum theory" to defend homeopathy. Maybe, you could specify more precise what objectivity means in science?

The continuation of the second sentence is fairly clear to me. If you advocate something, you are not weighing pros and cons and providing the information without bias.

Although I agree with you (especially in the given examples), I don't think that this argumentation is sufficient because pseudoscience actually claims that the "orthodoxy" in science is biased in their basic concepts. Therefore, I think it would be good to make very clear and transparent what concepts like objectivity and evidence mean in science. I know that this is tedious and it might seem too obvious to scientists.


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Changing Interests After Getting Accepted for PhD
I have brought some trouble onto myself I know, but what can be done by someone in my situation.
I applied and got accepted for a PhD program in Computer Science.  I automatically assumed that I wanted to continue the work I did on my Master's thesis and I identified a professor who would be willing to work with me on that subject.  When I got there, I reviewed the literature (there had been a few years of gap since defending my thesis) and decided I really did not like the direction the field was going in.  I had been developing a new interest anyway, so I changed sub-disciplines.  Now, no one will commit to be my advisor, at best maybe co-advisor with some outside expert.  Part of the reason is because my school lacks experts in that area.  I personally (on a friend basis) know some Computer Science professors, but none are experts in my field.  What can I do?  No advisor = No PhD, I know that much anyway.

Changing a subject during the PHD course is legitimate, and not very rare. However, finding an advisor is a must. I think in that case you'll have no choice but trying to convince professors to be your advisors.
A possible way is to find an expert from a different university, that will be your co-advisor. That way you'll just need to find another faculty in your university that is not-too-far from your interests. You might find someone that will tentativly be your advisor, and once you show some progress will agree to take you under..
But maybe the big question is,
why not moving to the place where the "experts" are?

Alternatively: Why choose a research area with no local experts?  Are you really completely uninterested in everything your department's faculty does?

@JeffE Does it really make sense to work in academia mainly on a topic one is not interested in?

@PiotrMigdal: Nope.  On the other hand, does it really make sense to work in academia if you're only interested in one narrow topic?

@JeffE I would say I have a passion in what I am doing now, I just did not go down an a la carte menu saying I would like this and that.  But, yes, I am not very interested in what the faculty does and they are not very interested in what I do.  Like I find robotics cool, but cool does not make a PhD thesis.

@RanG. Yes, jumping ship would be great, but I would lose what I have done so far and because I would assume I would have to establish some rapport first and perhaps even have a commitment before I jump ship from someone who would be my advisor.  It just seems difficult to get my foot in the door and convincing someone outside my University that doesn't know who on earth I am that I am someone worth working with and in the event of another University that in addition to the students properly admitted that I am worth the time.

I do not think changing topics on a PhD research is totally unheard off. In fact, as Ran mentioned, it's probably more common than one would think.
Now, the advisor is indeed an issue. The problem is that it looks bad on professors if they do not understand what are you doing, and if the field is unrelated to them that might happen. Did you try looking for an advisor in other area, where what you want to do is applied?
Perhaps a nice way to approach the issue is to do a more formal research plan and a good application in mind, that might attract some advisor or at least give a strong case to an outside expert.
In these days distance should not be an issue for a CS research.

The applied aspect is a great suggestion and could have worked for me, but in the overlap majors my University also is not so strong.  I also like your suggestion about trying to get that outside expert.  I am trying to do my own research and pin down exactly what I would propose for my thesis work.  Maybe even get published on my own if I can.  It feels like such an uphill battle without the support of an advisor, but hopefully I get that advisor.

To get an outside expert just google the name of people related to the topic. Try seeing who are the top of their field, and look for recent graduates that just got posts, they are also in dire need of people to supervise to pump their resumes


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Simplest way to jointly write a manuscript?
As with many papers in the sciences, there are multiple authors who aren't physically close to each other. I was curious about the most efficient and simplest way to technically share the writing. On the more complicated side would be LaTeX and subsequently using subversion to merge all of the changes. Then there is google docs. Finally, there is the traditional write out edits on word and email the document with comments back and forth.
What works?

You forgot one traditional approach: "I am releasing the token for Section 2; updated latex source is attached to this email.  I now claim the token for Sections 3 and 4."

I should add, my advisor is not technically proficient. Hence the emphasis on simplest

Look here: Simultaneous collaborative editing of a LaTeX file - tex.SE.

I use a SubVersioN repository service, many of them are available online for free (see e.g. http://xp-dev.com/).

You need to put one of the authors in charge. Otherwise the one who is not technically proficient would be the bottleneck.

If you literally mean the simplest way (even slightly more so than JeffE's excellent comment), then you can't get any simpler than the naive approach: pass a single file back and forth by e-mail, with the recipient having total control until they e-mail it back.  This is the only approach I know of that requires no technical proficiency or special software at all (beyond what is needed to write a single-authored paper), and that avoids any complications regarding multiple files, copying and pasting, or who exactly has permission to do what.  This may be overkill, but sometimes it helps.

@AnonymousMathematician - Having the technically incompetent one edit and the competent one do the merging can work just fine.

@eykanal: Good point, although you still need to have made some arrangement for how to avoid (or handle) conflicting edits to the same section.

@JeffE I look forward to the day when manual token passing is viewed as an antique relic akin to etching on stones :)

@Suresh Aawwww.

If your collaborator is not technically inclined, then there are a few possibilities:

Google Docs
It is very simple, robust and real-time (no need of thinking 'which version is the most recent'). I created a lot of documents with it (though only 1 scientific article). A good idea is to use different colours so that it is clear who wrote what. One drawback is that it may be not as simple for equations and than you will need to copy things from there to LateX manually.
Annotating PDF files with Adobe Reader or sth equivalent
Also simple and robust. However, as it is not real-time you need to keep track of which version is current and it is not possible to make changes in the same time. Here you are the only person responsible for changes in LaTeX file.
Annotating or changing with OpenOffice, MS Word or another office package...
Another variant which allows you collaborator to make direct changes, at cost of some robustness.

As a practical remark for the two last: always keep track of the version, e.g. draft_20120424_prof.pdf, where you add both date of the last edit (not final5!) and name of the last editor. When exchanging things by e-mail it is easy to loose track which version is the most recent and in fact lost changes (often not knowing about that.)
Other possibilities, requiring some technical knowledge:

writeLaTeX or sth similar (ShareLaTeX, ScribTeX, LaTeX Lab - the one using GoogleDocs, ...)
Tools for editing  documents collaboratively (in real-time) and compile it within one's browser (so no need to install anything). Though some knowledge of LaTeX is required (at least to know how not to spoil a file).
ScribTeX(the only one I used) gives version control and you can see which lines were changed (as in version control system), so not need of guessing what might have been changed.
EDIT: ScribTeX is being replaced by ShareLaTeX.
writeLaTeX has live preview and may be the most suitable for beginners.
Git or another version-control system, e.g. at GitHub
However, it may require technical skills beyond edition of LaTeX. While it is not hard to use it, I never did I am using it for writing papers and I would never try to use it with someone with low computer literacy.

When it comes to Dropbox - it is a good stuff for sharing files for a project but NOT for making changes in files. First, you never know when the changes happen. Second, you don't know where the changes happen.
There is also an article on it: Research tips - Online collaborative writing.
See also a few questions:

Simultaneous collaborative editing of a LaTeX file - tex.SE
Tools for collaborative paper-writing - MathOverflow
Compiling documents online - tex.SE

+1 nice array of possibilities, and warning about Dropbox! LaTeX + Git is still my favourite.

As the third suggested question points out, the LaTeX Lab is a good solution. However, it lacks some functionality. But it would get you started. I prefer that option.

@adn: Added LaTeX Lab, thanks. Actually, I have tried it before, but the  "revision history" was not working (and still it does not work).

If you're working with Word documents, Word 2007 included a very nifty merge changes feature. This online help document from microsoft.com details how it works, but doesn't really do the feature justice. See the following screenshot for an idea:

Briefly, you can click on "compare" (in ribbon, third from right), and it lets you choose two source documents. From there, it opens the very nice interface shown above, with the two source docs on the right, the merged doc in the middle, and the changes on the left (or bottom, you can hide it if you don't wan t it). You use it like any other "track changes"; just go through, change by change, using the "previous", "next", "accept", and "reject" buttons om the Changes section of the ribbon. When you're done just save the combined document, and you've got your merged doc.
I've used this a number of times, and it's a very useful feature. By far the best aspect of this is that it can be used with the technically incompetent. Just tell them, "take the document, make changes, I'll deal with it"; I've used this with my technologically challenged boss a number of times, and it's been a lifesaver. Given your situation, this may be your best bet.

Horrible. Writing a paper in Word.

@DaveClarke - When life gives you lemons...

shrug If you need to use it, here it is. I've never written an academic paper in Word, and I never will, but for those who do, here you go. I'm not recommending it; I'm just informing of a feature.

unfortunately, many ecology journals will only accept Word files.  I have taken to writing my manuscripts in html just so that word will open them - it is embarrassing for my field.

We do token passing and some kind of method to exchange the files. I think this method was covered in the comments but let me elaborate it here. I'll use Word as an example, since chances are if you're doing manual token passing, it's because you haven't been able to convince anyone in your team to switch to LaTeX, and people who don't want to switch to LaTeX are probably the type who don't want to deal with version control.
The "shared folder" is the mechanism  you use for sharing files. It could be a Dropbox folder, email, WebDAV, a remote directory on an SSH-accessible server, etc.

Locking: Person who starts with the file renames it so that their name is on the end. They send an email to the group saying, "I am locking Section 1." List the locks in the email.
Unlocking: This is a multi-step process.

a. If no one else unlocked a section before you unlocked, then you can rename the file to the current date and time, then put it in the shared folder.
b. If another collaborator unlocked a section before you unlocked, then you must take the latest version off of the shared folder, copy the section you were working on, and paste it into the latest version you just downloaded. Rename the just-edited file to the current date and time, then put it in the shared folder.
The reason you do it this way and not the other way (copying and pasting everyone else's sections into your document) is because doing so means you have to keep track of what everyone else did, whereas this way you only need to keep track of what you did.
That's basically it. The biggest problem is when someone's not paying attention and doesn't merge properly, or when two people try to lock something at the same time (since Email has a delay) but usually you'll have to have someone who knows the process keep an eye out for it.


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Organizing my reading list in Mendeley
I keep publications from the literature in Mendeley for later reading on my iPad. There are many publications, so I need some sort of way of prioritizing the ones I need to read first versus the ones I might read someday. Right now, I use folders with varying priority levels. The biggest problem is that I cannot move articles to different folders on the iPad, so I have to do this prioritization while I'm at my computer (where I usually have more important things to do). Also, I feel like I spend most of my time assigning priorities to articles rather than reading them, which is not ideal.
Do you have better suggestions on how to prioritize and organize the publications I want to read using Mendeley?

Can you use tags instead of folders? I think you and add and remove tags using the iOS client, but don't have one handy to check.

My other question would be what you're trying to accomplish with prioritization. Maybe instead of pre-sorting them you could just search for a keyword or author or tag to pull up the ones you want on-demand?

You can add and remove tags but I don't think you can search by tag. I'm not looking for specific papers, I need a list of papers I should read now, soon, or someday.

Yes, you can search by tag (in the desktop version only, though. Not online, afaik). If, for example, you want to find the papers tagged with the word andrea, you just type tag:andrea in the search box.

One option would be to create a tags P1, P2, P3, P4 ... and assign "rating" to articles how much priority they have. Tags could be updated as priority changes.
(similar system could be used with Delicious.com tags to websites)
Tags are more flexible then folders. Mainly - Multiple membership in more than one tags