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Writing a recommendation letter for a student I reported for academic dishonesty
A few years ago, I reported a student for academic dishonesty (in a graduate-level mathematics course, they were copying solutions off the internet, nearly verbatim). After acknowledging their wrong-doing with the Academic Integrity office on campus, they were allowed to drop the course.
The next year, the student re-enrolled in my course, and did reasonably well. I had no qualms about the originality of their work this time.
They recently asked me whether I would be willing to write them a recommendation letter for PhD programs in mathematics.
If I write a letter, am I obligated to write about the academic dishonesty incident? It appears to me that the student has already faced the consequences of their actions (they had to drop the course); however, this was a significant part of my interactions with the student and it seems dishonest to not mention it.
(I am aware that I could simply tell the student that I am not comfortable writing a letter, but I am curious to know what one should do in this situation if one did write a letter.)
Some facts: when the incident occured, the student was in their first semester of our masters program. They are also an international student, and this was their first semester in the US.

ETA: Look, I framed the question to be as general as possible so that it can be useful to the community as a whole. Since some commentors are choosing to attack my teaching practices, below are some more specifics, where once again I am trying to not reveal the identity of this student, myself, the course, the university, etc. I am actively trying to do what's best for the student here (note that I clearly state that I think the student has faced consequences for their actions; I am also not using my usual ac.se account to post this), and I don't understand where comments about "shutting down a student's career" are coming from.
I clearly state in my syllabus and on the first day of class that copying solutions off the internet (or any written source) is not allowed. I do this because I encountered this situation as a TA in graduate school. In particular, students are allowed to talk to anyone they like about problems, but I believe that when they just copy a solution, they are not learning. You are welcome to disagree with my policy, but it is my policy and my class, and it was clearly stated in two separate venues.
The copied solutions were virtually indistinguishable from the solutions online. This was not a matter of simply "being inspired". This was not isolated - three out of six solutions were copied, and those were just the ones I spotted. When I noticed this, I asked the student to come talk to me. I told them that I had noticed similarities between their work and solutions I had found online. I told them that I was not accusing them of anything, and they did not have to tell me anything; I reiterated that copying solutions from the internet was not permitted; I invited them to come to my office hours to talk about future problem sets; but that if I noticed such similarities again I would report them to Academic Integrity. They did it again on the next problem set (four out of six solutions).
Although they denied everything once via email, after talking with Academic Integrity (where they owned up to everything), they did find me and apologize. I was cordial to them throughout this event, and continued to be so afterward. We remain on good terms now. I consciously try to ensure that I do not let this incident color my interactions and behavior with them. They made a mistake once but people make mistakes and I am trying hard not to take it personally.
In summary, the incident itself was pretty blatant, the policy was clearly stated, and they had an opportunity to stop such that I would not have reported them if they had. I did not take reporting the student lightly. Nonetheless, I think academic dishonesty is a serious matter and it is our responsibility as faculty members to not turn a blind eye to it.

To clarify, the student was in a graduate-level course, but were they actually a graduate student?

@NateEldredge when the incident occured, the student was in their first semester of the masters program. They are also an international student.

Have you communicated with the AIO? I think it's important to check if the incident was permanently filed with the student's record. They may also give you some policy-based suggestions on this.

Have you asked the student how they'd discuss the academic dishonesty incident in the letter, if they were in your shoes? This will let student know that you haven't forgot about it, and it places some of the burden on the student about how to deal with a problem they created.

I agree with djechlin. If a student comes from a background in which such behavior is not understood as wrong then I would be wary of punishing to harshly. In my PhD, some students had answers to unpublished exams from previous years. Many of the questions were the same as current year exams. Yet, I would not have been happy reporting those students for academic dishonesty. After all, that material is "out there". This is the 21st century. Many students in your class more familiar with strict plagiarism rules could and likely did use online material and just masked the fact.

I think that such detail should be included in a letter of recommendation and of course explained that there were consequences for the student (i.e. already punished). Then it is up to the committee on the receiving end to decide whether they feel comfortable in having him aboard. There is this idea that cheating is common among overseas students. If that is true, I'm sure the committee will know about it and take it into account, and deal with it as they see fit. (Also, if instead of writing a letter one was on the receiving end, would you want to know about it?)

Seems that the student learned the lesson, isn't he ? And that's precisely what students should do. OK, he did wrong and was "punished", what you expect then ? to be marked with a red-hot iron for the rest of his life ? I will write the recommendation and not talk about the previous incident at all.

You have to also account for all the students copying homework that aren't caught. Sometimes this can be the majority of students. I wouldn't mention it unless it was a big project, an exam, or a bachelor/masters paper. You should ask yourself the question how honest your co-students where when you studied, or how the general climate is these days. Maybe they were caught because they're honest? If you never cheat you are quite bad at it, while some people have mastered the art and are never caught, but never do any work either and just learn for exams, slip by and forget everything immediatly.

Why do you feel so strongly about "copying solutions off the internet"? What about copying solutions off a book, off a fellow student? I guess everyone does research on the internet if they can not solve a problem, do you consider that unethical? Where do you draw the line between drawing inspiration and "copying a solution"? Did the student claim at any time that it was their original work or did they just hand in some exercises they found on the internet?

@Marcel the questions were exercises from the standard textbook in the subject (you should think Hatcher, or Lang, or Atiyah-Macdonald). These are questions that all graduate students should solve. I find it strange to be attacked for assigning such questions.

You know what they say, what is called collaboration in the workplace is called cheating in school.

@Marcel the premise that any time a student cheats the lectures or exercises are to blame is ridiculous.

I don't think I'd care if they copied solutions off the internet or anywhere else. I'd just re-structure my class so that test grades have a higher weight - if you're not practicing you're not learning and you won't get a good grade.

In grad school I was assigned to teach an independent study course where plagiarism was a frequent problem.  It was a course in technical writing in applied math.  The following semester, I scheduled a mandatory orientation session at the start of the semester, in which I showed the students examples of correct citation of someone else's work, and examples of incorrect use of someone else's work.  I made sure they understood what is plagiarism and what isn't. No plagiarism occurred that semester. I have to say, the department was very supportive of this approach.

Well, you just gave a short version of what happened the next year. From the sentence "the student re-enrolled in my course, and did reasonably well.", however, I think that he changed his approach, at least with your course. It is impossible to judge a person just by a small period, and much less by a few words on an online forum. Personally I'd just evaluate its most recent "performance" if you feel that he changed his approach. Maybe speaking to other teachers you can get a better idea on the student. And in the end,if you don't feel comfortable just be honest to him and tell what you think

@Anonymous_professor remember. This is the internet. While I am not at all being accusatory keep in mind that people who complain might've had bad experiences... or worse: chested themselves. I'm being completely neutral here. Just saying to take advice of that nature with a large grain of salt. However, if 90% of the class were reported for cheating... then I would start to wonder if someone wasn't making stuff up.

TL; DR: The student probably wants you to write a letter to mitigate the harm of the incident because they already expect admissions committees to know about it. In that case, mention it briefly and move on to your standard letter.

There are only three reasons I can think of why a student would ask you to write a letter in this situation. How you respond depends on the reason.

Despite, or perhaps because, of the incident you have become a mentor to the student and genuinely know the student very well. The student knows that they have regained your trust and confidence, and that you're in a good position to give them a solid recommendation.

A. If this is the case, and you truly do now trust the student and want to offer a strong recommendation, you can mention that the two of you got off to a rocky start,  and allude to the issue without going into detail (you don't need to use the words "misconduct" or "cheating"). You could say that the student worked hard to regain your confidence, and that you are now happy to strongly recommend etc.
B. If this is only sort of true, and you don't think very highly of this student and/or have reason to think they might cheat again given the right circumstances, you should decline to write the letter.

It doesn't sound like your situation falls into the first category, however, which brings us to the second possibility.

The student knows that this incident will appear on their record, and that their prospective programs will see it. They believe they have at least somewhat redeemed themselves in your eyes, and are hoping that a generally positive letter from you will mitigate the harm of the incident. I suspect that this is what's actually going on. If so, you should confirm this. Ask the student specifically whether the incident will already be known to admissions committees.

A. If the answer is yes, write whatever letter you would have written absent the misconduct but with an additional paragraph noting that you were involved in the incident and believe that the student has faced sufficient consequences, and that your letter focuses on their performance in the subsequent class. If you have reason to think the student has learned from the incident and it's not likely to be repeated, include that in the paragraph acknowledging the misconduct, but don't dwell on it.
B. If the answer is no, the misconduct is sealed or otherwise unlikely to become know to prospective programs, we come to the third possibility.

The student is extremely naive, and doesn't realize the potential harm you could do to their admissions chances by writing about the misconduct.

A. In this case, absent any particularly strong admiration for the student, I would decline to write the letter. At the very least, you need to strongly caution the student about how bad a letter from you could be for them.
B. If you really still want to write the letter and your student still wants you to write it after being warned: You could take either approach above, depending on what feels more comfortable to you—either allude to the issue in the most general terms, or mention it but state specifically that it is not the focus of your letter. You should definitely warn your student about this beforehand, though, and perhaps allow them to see the letter before you send it.

As of my observation, many undergraduate programs in third world nation fail to warn their students about the negative impact of plagiarism. So they come to the grad school without realizing that plagiarism is never tolerated. The faculty should make sure that these rules (expectations regarding paraphrasing, referencing, and citing) are well communicated for the sake of these students.
I believe that it can be the scenario #3 you mentioned. The student seems to be underestimating her/his academic misconduct.

@PradeebanKathiravelu Yes, it certainly could be that; that's why it would be very important to verify the student's thought processes. It's also possible that it's something between 2 and 3—the student thinks the incident is obvious in their record, but it actually isn't—or between 1 and 3—the student thinks they've impressed the professor more than they have and that the incident had/will have less impact than it actually did/will have.

This is a really good answer. Any answer which doesn't take into account this highly disparate sets of circumstances will not give useful advice.

The best option is:  Don't write the letter.  In a case like this, I would outright refuse to provide a recommendation.
However, if you are not comfortable with a non-negotiable refusal, you might want to simply tell the student that you cannot provide a positive letter for them.  If the student insists, then you should write an honest letter that gives a balanced evaluation of their ability and personal traits.  The fact that you caught the student cheating is a critically important piece of information in this regard, and it needs to be included. The cheating will almost certainly be the most salient feature to anyone who reads the letter, which will make the net effect of the letter, regardless of whatever else you say in it, strongly negative.  And if the student insists on you writing the letter in this situation, that is basically what they deserve.

Yes and a critical issue is that they were a graduate student.  If it had been a freshman cheating, you could chalk it up to immaturity and a lack of understanding of the gravity of what they were doing.  As @Buzz said, you shouldn't write the letter.  They may have learned, but at that point they should have known.  Integrity is a big deal in academia and any entering graduate student should have known better.

@user25459:  Yes, that's another important point.

@user25459 note that the student is from overseas, so it's quite possible they are from a country where academic integrity is less valued and emphasized than (say) the US or Western Europe, which I think would completely invalidate your point.

@DanRomik - I've heard versions of "overseas students don't know about cheating" for the last twenty years and I call bullshit on it. 1) They should know; 2) They should know it has consequences; and 3) There should be real consequences.

@RoboKaren well, from my personal experience serving for two years on my university's Campus Judicial Bkard, during which time I participated in many academic misconduct hearings, I can attest that there was a suspiciously high percentage of overseas students (from certain particular countries). Moreover, those students were also the ones who made some of the most absurd and laughable arguments in their own defense. This is anecdotal of course, but It is consistent with observations by many other people. Why deny that this is a real phenomenon? I do agree with your assertion number 3 though.

I don't deny that it's a phenomenon but I think it's a handy excuse both for the perpetrators and those who want to defend the perpetrators. I think the only way we can solve this is by disallowing this as an excuse and making sure that there are consequences.

By the way I don't mean to suggest that overseas students should be treated with any more lenience than other students. Simply, it should be acknowledged that there are cultural differences at play, and this fact was relevant in the context of the comment made by @user25459. So yes, I completely agree with you it's not an excuse.

@Magicsowon once again, I am not advocating for any leniency based on geographical origins. I was simply making a point about user24549's point being potentially invalid. The student should face consequences for cheating, and by all accounts has in fact done so. It doesn't mean the consequences should be career-killing ones.

I don't excuse it on cultural grounds, but I can't claim some kind of superiority for Western culture.  In 2004, I found online five copies of a pretty good essay on philosophies of education.  All five were on professor's websites with NO attribution, giving the impression that it had been written by the professor running the website.

"cheating will almost certainly be the most salient feature to anyone who reads the letter" is a pretty broad (imo wrong) statement. Letters of Rec aren't going to be read until at least one or two good cuts of the application pool based on things like program of origin and GPA/tests. At that point my feeling is most admissions committees are looking for reasons to include people in the program rather than exclude. Nobody has a perfect academic record- cheating is certainly a serious offense but does not make someone a pariah.

@Magicsowon By “overseas”, do you mean the US or Europe? I’m asking because it depends on where you currently are. And surely you’re not implying that “Western” scientific culture is somehow inherently more honest than the rest …?

@Magicsowon I studied at a US university, and there it was considered cheating if I spotted someone else (next to me or halfway accross the room) cheat and NOT report it. I actually got in trouble because a TA overheard a conversation I had with a friend about it, and I did not want to denounce the culprit (I simply acted as if I did not remember who it was). Where I come from, this is NOT cheating.

Eh..."You break the law, its there for people to see, why should you get the same as an honest man like me..."

@solalito That is pretty extreme. Im also in the US and while I didnt get in trouble the professor was a little irritated when I mentioned the person sitting two or three rows away was disruptively cheating to the point that it was impossible to ignore, and while they didnt get mad they did seem kind of taken surprised. Perhaps they already noticed, but it gave the impression you dont have to actively watch for/report it. Are you sure the TA wasnt being rude? Sure he/she didnt lie cause you made them mad? TAs are usually just fellow students. They couldve just had something against you.

Granted, in the same respect, actively watching for someone cheating is not the same as just ignoring it. Still though. That seems weird that you would be punished. The TA seems weird for even assuming you know who cheated and didnt just notice it...

@TheGreatDuck The TA may have just been in-experienced and a bit over-zealous in his attempts to stop cheating rather than rude. As - at least it seemed so to me - so much of your work as a TA has become making sure source code and other work isn't plagiarized, especially when student submissions use your own code from Github account or an answer on SO, that you may overreact when confronting it. I'm pretty sure during my early graduate years I snapped at an undergrad or two not due to anger at them but just because I was sick of cheating in general and in-experienced.

@JGreenwell oops. I thought you meant SI.

@RoboKaren: "@DanRomik - I've heard versions of 'overseas students don't know about cheating' for the last twenty years and I call bullshit on it." - I definitely see certain limits when it comes to e.g. handing in someone else's text when one's personal writing skills are supposed to be tested (because that clearly undermines the purpose), but certain views and assumptions can indeed differ by culture - even within the so-called Western world: On this site, I learned about the idea that sometimes, looking at previous exam questions is apperently considered cheating in the U.S. and ...

... students should rather ask the instructor for permission first. From my German perspective, that sounds quite incredible as students here are normally expected to actively collect any information they can get about previous exams as a part of their normal preparation that goes without saying.

To what extent has the student regained your trust since the incident?
As other answers say, the incident is too significant to ignore.  However, what you write in the letter should be not just “X happened”, but “X happened, and here’s how it affects my judgement of the student now.”
Most probably, your trust in their future honesty is still shaken, in which case (if you’re honest about this) your letter will carry a significant negative impact, to the extent that you should probably decline the request.
However, there could be mitigating circumstances that make you genuinely confident that the student will not re-offend.  For instance — since you mention they were a newly-arrived international student — perhaps their home country had a different culture around expectations for homework, but you feel confident that they have now absorbed US academic norms.  In that case you can say so in the letter:

I would be remiss not to mention that [incident occurred].  However, I feel this should not be held against X’s future prospects, since [mitigating circumstances, and why you feel they’ve regained your trust].

I would expect, for most readers, this would still have some negative effect on their assessment of the student — but much less than if they learned of the incident some other way (e.g. mentioned on the student’s academic transcript) without an explanation of the mitigating factors.  So overall, submitting this letter would be a positive thing (provided that the rest of it is enthusiastic).
Disclaimer: I have only a little experience of admissions/hiring; I hope more experienced users can confirm (or differ with) my expectation of how such a letter will be received.

In the same situation, I would be wondering whether the student has learned that the behavior was inappropriate, or whether he has merely learned that you don't get away with it in a university in this country.

@immibis I think GregMartin just means that the sentence should have "or whether they have merely learned", i.e. agrees with you and thinks gender shouldn't be there.  I think you may have mis-read the intent of the comment.  Unless I have!

@MichaelDurrant There may be a (completely inconsequential) bias towards using the pronoun "he", but since the student's gender makes no impact whatsoever, I wouldn't imply that the answer is biased because of it.

I disagree, and so does research into the matter, e.g., http://www.apaonline.org/?page=nonsexist and https://web.stanford.edu/class/linguist156/Gastil_1990.pdf

@Kat: as you say, there's a long tradition of using “he” as a generic pronoun. However, as Gerg’s links show, that usage isn't unconnected from the sexist biases we all unconsciously hold. (For one thing, I've heard people invoke that to defend their use of “he” for a generic mathematician, but then as soon as they have cause to talk about a generic secretary, suddenly they use “she” .)  So I wouldn't take anyone's use of “he” to indicate a deliberate gender assumption — but it is nonetheless a small piece of sexism that I think is worth trying to avoid.

Gender pronouns aside, the takeaway from PLL's answer is that the professor has 3 gambles to choose from: (A) Include the incident in the letter, but justify the student's progress and hope that the reviewers are equally forgiving; (B) Write the letter without the incident, and risk that the reviewers won't discover this information without the context of the student's improvement; or (C) Don't write the letter, and leave the student's fate to factors outside of the professor's control.  My first choice would be C, second choice would be A.

I don't understand where this idea of "cheating is their culture" is coming from. Academic dishonesty is academic dishonesty. People get kicked out of school for it all over the world. The student's honesty or lack thereof should be judged on its own merits, and based on their individual interactions with the professor, not on some patronizing assessment of substandard ethics overseas.

@AsadSaeeduddin: going on my own first-hand experience in N America and Europe, the following all definitely vary widely between institutions and countries/regions: (a) the prevalence of cheating; (b) the severity of penalties for cheating; (c) the perceived moral severity of cheating; (d) the relative severity of cheating on homework vs. on exams; (e) the threshold of what counts as cheating.  So, when people with first-hand experience have told me that these vary even more in other parts of the world, I’ve found that very plausible.  Comments on other answers include some specific examples.

I do not think that you have to mention the incident and that you may well choose to not include it. What you do should mostly depend on what you think of the student now as the recommendation letter is used to estimate how the student will perform in the future and not to assess how they had performed in all previous life.
If you have reason to believe that the student learned their lesson from the incident and you think that you can recommend them, then I see two options:

You start from the assumption that the incident should not be something that should haunt the student forever and you just do not mention it. This is in line with your saying that "the student has already faced the consequences of their actions". Also, it's based on the view that the student should not be penalized twice for the exact same event. Also, copying solutions from the web verbatim does not appear to me as something which is so genuinely dishonest that the student should carry the weight of that incident forever.
You include the incident in the letter but add that the student has performed well in the class and no other dishonesty has appeared so far.

If an incident of failed integrity is known, and the choice is made to not include it in the letter, does that not equate to failed ethical integrity on the part of the letter writer?

@NZKshatriya: Only if you believe the letter writer has an ethical obligation to include it.  Dirk apparently thinks they do not.

Maybe the "if you have reason to believe..." part should be emphasized more.

@NZKshatriya good question. You pose it as a rhetorical question but the answer seems far from obvious to me. For example, I stole a candy from a store when I was a kid. Does that mean that every person writing me an LOR in the future after reading this comment should be required to mention this "incident of failed integrity" or be tainted by a similar failed integrity themselves?

@DanRomik Well, as far as academic integrity goes, everyone's view on how far back to track transgressions is different.   Stealing candy, and cheating in a class, at least to me....seems a bit odd of a comparison.

@NZKshatriya exactly, your last comment reinforces my point: if as you say "everyone's view on how far back to track transgressions is different", then a choice not to mention a cheating incident from a few years ago is entirely reasonable. Hence your sweeping statement (expressed as a rhetorical question) about failed integrity being automatically transmittable through an LOR-writing relationship is overly general and simplistic.

I found myself in this very same situation several years ago and informed the student I would not be able to write a letter without mentioning the incident that brought them before the AIO. The student insisted, and so I wrote an honest letter of recommendation, which included an account of the incident. The student wasn't accepted into the program they had applied to do their PhD (she was eventually accepted into another program that I had not written a letter for), and a year later, a professor from the first program who received the letter complained to one of my colleagues; claiming I should have recused myself despite my having stated in the letter that the student had insisted I write one. I would have thought the program the student applied to would appreciate an honest review, but that isn't always the case. Lesson learned - don't write a letter of recommendation unless you have nothing but good things to say about the student.

I disagree with the complaining prof but appreciate the first-hand insight; +1

"The student wasn't accepted into the program they had applied to do their PhD (she was eventually accepted into another program that I had not written a letter for), and a year later, a professor from the first program who received the letter complained to one of my colleagues; claiming I should have recused myself despite my having stated in the letter that the student had insisted I write one." You got a complaint about a letter in which you were honest in your reporting of relevant information?  That sucks.

@PeteL.Clark What injury was done to the complaining professor, I wonder?

"I would have thought the program the student applied to would appreciate an honest review" - it sounds like you essentially dis-recommended the student with your honest review, which is why that Professor complained.

Yes, no doubt my letter was instrumental in the decision to reject her. What I failed to mention in my first post was that I only spoke of the one incident because it was the only one that resulted in a sanction.

+1 as this answer gives direct indication of how readers of such a letter reacted.

@MatthewLeingang The complaining professor was disappointed to waste time on an not recommended student. Without this honest review (which is not the same as a recommendation letter), the student would not have applied, or it would have applied using a real recommendation letter. In the first case, no time is wasted, in the second case, the committee would have had the chance to know what recommends this student, which they couldn't find out from the honest review.

First of all, from an ethical point of view I don't think you have an obligation to report the incident. Mentioning it would likely destroy the student's chances of getting into a good PhD program, so if your philosophical view about crime and punishment is that a single incident of cheating does not prove that someone is irredeemably morally corrupt, and specifically think that there's a fair chance that this particular student learned their lesson and will not repeat the offense, it's reasonable not to mention it.
Second, I can suggest the following course of action that would make it possible for you to get to a more comfortable place about the decision to write a letter for the student. Invite the student for a chat, and explain to them that you think they're a good student with potential to succeed in a graduate program, but that you have a dilemma about whether to write the letter because of the cheating incident. Ask them to tell you their view about the incident - why they did it, how they feel about it now etc. I think the student's answer is likely to be quite revealing and either make you more sympathetic to their situation and more comfortable writing the letter, or make you realize that they probably didn't learn their lesson and that you should not write the letter after all. In any case it will allow you to reach a more informed decision that you are more at peace with.

Not that I disagree with you, but your first paragraph seems to indicate there is a problem with ideal reality somewhere.  If the incident should disqualify the student from good PhD programs, then not mentioning it is somehow dishonest.  If it shouldn't, then mentioning it shouldn't destroy the student's chances.

@Kimball you are spot on, indeed there is a very real "problem with ideal reality": in an ideal world, mentioning an incident of cheating shouldn't necessarily destroy a student's chance of getting into a PhD program, but in the real world it almost certainly will. This is precisely why there is an ethical dilemma here, since it puts two values (the professor's wish to make the LOR as honest as possible on the one hand, and their wish to do the thing that results in the most just outcome on the other hand) in direct conflict with each other.

@Kimball: I don't know enough about letters of recommendation for academic programs (we basically don't have them in my country) but over here letters of recommendation written by employers are highly codified in their phrases and only give positive sides (the analogue for the present question would maybe a phrase missing that states OP has always known the student to be acting strictly honestly). Likewise, I suspect that how things should be ideally is less of a concern than adhering to (unwritten) rules of whether and how to state what in this situation.

@cbeleites A lot of academics write letters in a similar way, but your suggested analogue doesn't make sense here because professors wouldn't normally write something like "this person has never cheated" as it's taken for granted.  Another issue that the community is small, and if your letters are not honest people will realize this and start ignoring them.

@Kimball: another difference is that the employer cannot refuse to write such a letter, while the academic can. And I suspect (also from reading the other answers and comments) that this is the answer to the question.

Interesting question!
Seeing as you are even entertaining the possibility of writing a letter, you might want to check it up with the student, to inquire about his/her point of view in coming to ask you (despite your troublesome history) for a recommendation letter. It should be as clear to him/her that you would be at least partially split on the matter.
Maybe the student considers facing the consequences of a wrong-doing and mending the bridges to be an important lesson, maybe that's the theme the student is going for... I don't know, I am purely speculating here. It's equally possible that the student thinks that what's done is done and now forgotten. Obviously the two alternative scenarios do not warrant the same type of response.
But by engaging in a dialogue, you might gain insight as to how the student in question thinks, and thereby make a more informed decision.

However, I think that while the student's view is important information in judging whether they learned their lesson or not, it is even more important for the letter to adhere to the (probably unwritten) rules for letters of recommendation. Otherwise the message read may differ a lot from the intended message of the writer.

"If you can't say something good about someone, say nothing at all." This is a letter that you obviously don't want to write. Tell the student that you are simply unable to write a letter that would be acceptable to both of you. Then simply move on.

While I entirely agree with your opinion, your answer does not answer the question. @Anonymous_professor asks if it would be unethical to not include the incident in a recommendation letter, once he decided to write a recommendation letter. So, the letter is happening for sure, not writing it is not an option at this point.

I do not think it's appropriate for anyone to suffer the consequence of a single misconduct twice. Hence, I would rather you decline the student's request to write the letter or pen down something good about him if you do decide to oblige him.

I have to admit that I agree with everyone but Buzz and Inde.
The AnonProf should

Talk to the student. (I would have done this the moment he/she approached for a recommendation.)
Warn the student that the recommendation might include this incident (including any positive outcomes), but maybe not.
AnonProf needs to search his/her own soul about "crime and punishment" or "infraction and redemption" and how he/she feels about the student's rehabilitation,
and, independently of the incident, AnonProf needs to search his/her own head about this student's performance in mathematics.
Then AnonProf needs to decide whether or not the cosmos would be better off writing the letter or not.  That is not synonymous with whether or not the student would be better off or if the academe or the mathematics profession would be better of, but may be very closely related to that.

I'd like to add that AnonProf (even more than they already do with this question) need to find out the local (country specific) "code" or "etiquette" for letters of recommendation in such awkward situations. Which I guess may very well turn out to be "refuse to write one".

I like this answer. Personally I'd have put point #4 as point #1. Can AnonProf say that he is now convinced that the student is a gifted mathematician, or not? In other words, has he interacted with the student in an environment such as tutorials where cheating was quite impossible, and found the student's mathematical abilities on a par with, or even superior to, his own?

An in-between option
Write the letter as you normally would, and mention that you had a disciplinary incident with the student, without details. This would most likely give them the possibility to explain themselves to the addressee of the letter, and if the latter chooses to contact you for details, you would naturally explain what happened from your point of view.
You could say for example, "The student took my course X and dropped out due to a disciplinary incident, then in the next year took it again and I saw them to be this and that"

I would consider showing the student a draft of the letter and seeing if the student wanted me to submit it.
I generally assume that even if a student waives the right to see the letter, there is still the possibility that he or she will see it anyway.

Only write the LoR if you are confident that the student learned from the incident and if you are fine letting it go. If you are not able to write the letter without mentioning the incident, then avoid writing it altogether.
Including it in the letter could jeopardize two things: your integrity as an educator and the student's future hireability. If the institution and the student and yourself have all come to an accord, no need to hang the student out to dry by opening him to questions by a future employer. Additionally, if this student goes on to perform poorly or in some way cast a poor reputation on whatever company hires him, then future students from your institution may be viewed from a deficit. Lastly, a letter of recommendation from you would be suspect to further scrutiny.
Commit to abstaining or supporting the student. That's a call only you can make given what you know about him/her.

cast a poor reputation on whatever company hires him? A kind reminder, the OP's student is asking the OP to write them a recommendation letter for PhD programs in mathematics

Ahh, I seem to have overlooked that, my apologies. Regardless of what institution/entity is applying to, I feel the same principles of reputation still apply in some manner.

It is not unethical, if you do not mention the incident. Of course, this is under the obvious assumption that you truly recommend the student for the PhD position, since you decided to write a recommendation letter.
Moreover, I consider it unethical to include negative comments in a recommendation letter. My reasoning for this is that a recommendation letter is just that, a recommendation letter. If one's not recommending in a recommendation letter, one is not writing a recommendation letter, but just a letter, and one is failing to uphold the agreement that it made with the student to recommend him through a recommendation letter.
A recommendation letter should only include why you recommend someone, the fact that you recommend that person is already clear from the existence of the recommendation letter.
A recommendation letter is NOT:

a summary report on previous activity of the student
a letter in which one gossips random unrequested facts about a student

The moment one includes not recommending comments in a recommendation letter, you start being deceptive (by definition):

towards the person that you are recommending, by giving false hopes
towards the committee to which the letter is addressed, by recommending (hence the existing of the letter) someone you do not believe it should be recommended, since you include damaging aspects

Breaking an agreement and being deceptive is not ethical.
In conclusion, not only that not including the damaging story would be ethical, but the reverse, i.e. including the damaging story, is definitively unethical.


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What should I do to maximize my chance at grad school (mathematics)?
I'm a second year student who has had a terrible semester. I don't live in a great place this year and I became really unhappy because of it. I'm also involved with too many extra curricular activities and took an extra course (biochemistry) that all together brought my GPA (and motivation) down incredibly.
I'm positive next semester will go much better, I've taken a step back and analyzed my situation and what I need to do to bring my GPA back up (I might take some summer courses too). Lucky for me, the course I'm doing terribly in isn't a math course that contributes to my major, and the other two courses I anticipate I'll end with a B/B+.
If anyone has any advice on what else I can do to make my applicant profile look better for grad school, I'd really appreciate it. I'm planning on asking professors to see if they'd be willing to take me in for research, hopefully my stellar math grades will make up for the crap ones I've got this semester.
Otherwise, I'm hoping to take the Putnam and GRE of course, but if anyone has a similar experience, I'd really appreciate hearing about it.
Thanks!

Possible duplicate of http://academia.stackexchange.com/questions/38237/how-does-the-admissions-process-work-for-ph-d-programs-in-the-us-particularly

Perhaps you could narrow your choice of extracurricular activities and choose classes and professors that get you really excited about learning.

Grad school decisions shouldn't be taken lightly, & should likely not be determined while 'down' about academia & an overbooked schedule (b/c that is essentially grad school). GRE's get your foot in the door of programs w/ min score requirements, but do little else (though you better do well on the math portion!!). GPA isn't even necessarily the most important factor -- think about it, even w/ straights A's/B's, you look like every other candidate that is applying. Focus on getting teaching, research, or other experience PRONTO. EXPERIENCE outweighs academics and makes you stand out. Period.

Also, try your hardest to retain your dedication to and interest in participating in extra curricular activities while in grad school. The work-life balance issue is a HUGE issue for many graduate students (and academics in general). Extra curriculars are a good way to reduce stress and mix up your line of thinking every once in a while. Just make sure you work on your time management ;)

If you are a second year student in the US looking to go to a PhD program in math, here is a list of some "standard" things to do:

Take as much math as you can, and excel at it. You should aim to not only have As, but high As, in many upper level classes.
Cultivate relationships with professors for letters of recommendation. This could involve research, but it could also involve class interaction, or attending appropriate seminars, or other ways of interacting with your professors.
Take the subject math GRE seriously, and study well for it.
Consider applying to REUs for the summer after you junior year. At more selective schools, many of the U.S. applicants will have gone to REUs. At the same time, the value of REUs is highly debated, with some favoring them and others suggesting that other kinds of preparation could be equally valuable, if not more valuable, in their opinion. In any case, you would apply to REUs in the fall or early winter of your junior year. Similarly, you could consider semester-long programs like the Budapest Semesters in Mathematics, the Penn State MASS program, or similar.
Begin researching graduate programs early; you will apply in the fall of your senior year, and the deadlines always seem to approach too fast.
If there are extracurricular activities you enjoy, continue to participate in them, but avoid getting too busy.

Other than the standard things, do what you enjoy. If you want to go to a PhD program in math you need a very strong track record in math. But that does not mean you need to be one-dimensional. Many of my friends at graduate school had other hobbies that they took very seriously.

"At more selective schools, the majority of applicants will have gone to REUs." I wonder if this is really true.  In my department, a substantial minority of applicants have done REUs.  At a really top department like Harvard, I would expect the vast majority of the applications to come from outside the US.  Also, although I went to an REU, got a lot out of it, and recommend it to others, I'm not sure I recommend it purely as a strategy to improve one's graduate admissions chances.  Most of what it conveys is that your coursework and grades were good enough to get you in.

That is very helpful feedback - I have never been on the admissions committee for a top-25 school, so I am basing it just on what I have heard talking to colleagues at such programs. I did mean to say U.S. applicants; I  agree of course that international applicants are not likely to have done an REU.

One particular hidden benefit of REUs (at least claimed) is that someone at a well known REU can write a letter comparing the applicant to the others who have attended the REU. If the student is at a small or less well known undergraduate school, it may be hard for the PhD program to know how to interpret letters of recommendation from faculty at that school. So the REU might, in some cases, serve a sort of external benchmark. Students at top undergrad programs often already have research opportunities at their home institution matching or exceeding most REUS.

Well, first of all, I've only done admissions work at my current institution, which I'm sorry to say is not in the top 25.  (Multiply by 2.)  When it comes to REU recommendations: to me at least, the letters always read the same way.  The student picked up everything immediately, it went amazingly well, and (not always, but increasingly frequently) it led to a paper.  I agree that it would be possible to write an REU letter of the sort you mention, and that would be more helpful.  Maybe these letters are being written, and I just haven't seen them.

Thanks - I genuinely think that your perspective is very helpful. Very few people have experience with more than a handful of PhD programs (I certainly don't), and the variation between programs is extremely large, so having several people comment on the same question helps enormously. My hope was that my answer would cover the "basics" and then others may be able to add additional points based on their experience.

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Using industry productivity tools and techniques for managing student projects
I'm heading a group of engineering students (from different fields) which need to build a robot (which performs tasks autonomously) as part of their courses.
There are 10 students in this group and they are divided in three or four subgroups which work on different engineering aspects. As the time frame is pretty short (2.5 months) and the students have a lot of other things to tend to, I wanted to optimize their work a bit by using some tools for project management and communication.
As I have recently been around a lot of IT people, I got to know about some of the methods and tools they use in the organization of small to medium-ish  sized(startup) companies. So my question boils down to:
Is it advisable to manage short term - medium/high workload student projects using productivity and management tools(e.g. Slack?) and techniques, or could this actually be of little use to the project(especially if the supervisor has no experience using them)?

There is a reason why use such tools are used by the industry, and it is to let everyone know when one has to do what. So I think it is a very good idea.

I suggest Trello or equivalents to my students for their project's task management. They then choose if they want to use it and how. For communication, I'm not fond of adding yet another medium when they already have many sources of input (internal messaging, pro/perso email, diff. IM systems, ...)

Yes, but don't overdo it.
Using one or two services such as Slack (the one I have the most personal experience with) can be really helpful in the sense that it can facilitate and organize communication. It's easy to share files, and to collaborate and make progress even when everyone can't be in the same place at the same time (an issue with busy students). It's also good to have some kind of central communication system, where any and all meeting times and information are announced, such as goals, deadlines, progress reports, etc.
However, for it to work, everyone has to be fully aware of 1) what service(s) the team is using 2) how to sign up for and access the service (Does it have an app? Does it send alerts? Emails?) and 3) what is expected from them in terms of the service (How often are team members expected to check it? What are they supposed to report on?). Make sure that if you decide to use some service, that you have a meeting where every member of the team gets together, signs up for the service, configures anything necessary, and discusses expectations. If everyone isn't on the same page, then you're not really going to see any benefit from using it.
Also, limit yourself when choosing your tools. There's a lot of cool team management software, and organization tools out there, but for a 2.5 month project, you probably only need one or two that are most essential to the tasks at hand. Make sure that you have some tool for communication, because effective communication between busy team members is what will ultimately keep the project on track.
If you use a tool for a week and find that it's either hindering productivity or not increasing it, then either choose a different one to replace it or just scrap it totally. Don't persist in using something that isn't helping.

I think this is potentially a good idea for two main reasons: (1) the tools are likely to be helpful for project management in their own right (which is why they are used in industry); and (2) in addition to learning engineering, the students get some practice using project management systems they will encounter in subsequent professional work.
As with any new tool, there is an initial time-cost to learning to use it; in the case of programs like Slack, etc., you will need to allocate some time to help your team get set up with these programs and learn the basics of how to use them.  If you are serious about this then I recommend allocating some of the course time and marks to successful learning and use of these project management tools (e.g., have a 5% mark allocated to project management, which is assessed on the basis of demonstrating competence in using this system).  Also, as in any industrial/professional setting, you should ensure that your use of project management tools is suitable for the project and commensurate with the complexity of the project --- i.e., use these tools in a way that makes project management less complicated, not more complicated.  (For the purpose of looking at trade-offs here, you can reasonably ignore the initial time-investment to learn the tools; pretend that you are all working inside an industrial firm where this set of tools is used for all projects, so that learning them is mandatory.)
Like any potentially good idea for innovative teaching, there is no guarantee it will work out.  It might turn out that the time needed to learn these tools is excessive, and cuts too much into time spent on substantive engineering work.  It might be too hard to assess the competence of individual team members in using the project management tools, and it might be hard to diagnose the causes when problems arise.  Still, it is a good enough idea to be worth trying out --- if it is successful then it is something you could potentially build into all future student projects for these courses.

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How to write practice exams as a student as a way to study
I'm an upper-division physics student. I have finals coming up next week and I want to take the advice of one of my professors from several years ago: write your own exams for practice and give them to peers. It'll help the test writer to review topics and your peers to have practice questions. However, my finals are all upper-division physics exams. Quantum mechanics, electricity and magnetism, and statistical thermodynamics. Homework and exams are generally pretty difficult, and I'm not sure how I can write an exam that will be on the same level that we can expect on the final.
Does anyone have any suggestions on how to make up questions to create a practice exam for study purposes?

Look at exams from previous years? Make sure to cover a bit from every part of the course.

Unfortunately we don't have access to those exams. Only one professor consistently teaches the class (QM), I wouldn't be able to get exams from previous years because students who have taken the other two classes are no longer at my university.

This won't help you now but maybe you could start helping future students. At our university we create memory logs of the exam, right after the exam sit down and write down everything you remember. Maybe talk to friends and split who should remember questions x to y. After the results are published we can take a look at our exams again. Memorize the parts you didn't before. Store these logs in a Facebook group for your studies, shared Dropbox, forums etc. Over the years we accumulated quite and extensive repo of old exam questions for most subjects.

For upper-level physics in particular, I would consider using book problems, as it's hard to develop questions that are easy enough to solve in ~15 mins but hard enough not to be trivial or memorization.

If you're using a good textbook, then you have likely done quite a few of the problems already for homework / in class, though it's still a good exercise to redo them on the board (make some substitutions where possible) under time pressure and without notes
There are also other good books you can likely find in your library: Griffiths or Purcell for E&M Griffiths or maybe Shankar/Sakurai for Quantum; (not sure about Thermo, I've never found a good thermo book). These will have good problems -- finding answers might be tough, but you can likely figure them out as a group if you choose ones at the right level

This could be in addition to some simple but useful concept questions that you could probably come up with on your own (e.g., what are the implications of the fact that electricity admits a scalar potential while magnetism requires a vector potential?)

+1, it's just not realistic to create your own exam questions unless you are very familiar with the material already. Check out past year papers, questions from books, etc. Don't try to set your own.

One way to do it is to make a kind of game out of it. Instead of trying to write a complete exam, just come up with one question. Give it to your peers and expect an answer in a few minutes. The first to give a correct answer asks the next question. Each person will need at least a couple of questions to get started, but not a complete exam. Questions asked will, hopefully, help people think of additional questions.
It would be good to do this face to face, but it could be done online if in real time - everyone simultaneously at their computer.
If no one answers in the allotted time, the asker gives the answer and another question is asked, either by the same person or another.
You might be able to use an online forum such as the physics section here to prime for questions. But searching for answers online sort of defeats the purpose of the exercise.

Start by making quizzes rather than exams. Try to come up with True/False and multiple choice questions. Add other types in as well if you want. The point is that you can't make a good question about something if you don't understand it.
I wouldn't bother with sharing it with peers. The important thing is to go over a section and ask, why did the professor bother talking about that section. What was its purpose. If you had to test someone on it, what is the core principle that needs to be tested?
The best thing I have ever received feedback on from students was when rather than giving them a quiz, I made them make and answer their own quiz. It forced them to think about the material. That is all your previous professor was getting at. In my opinion, sharing it with peers is neither here or there. You can do it if you want, the benefit would be to see the mixture of questions you all come up with. But you should also be capable of doing that on your own at this point. Figuring out what is important is the main take away from education.

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How to avoid theft of potentially patentable IP when trying to obtain a Ph.D?
When I was fresh out of college, I worked with someone who had their Ph.D who I'll call X.  They told me that they had lunch with a person from Facebook who had told them about a Novel Algorithm Facebook had created.  X decided to do a patent search on this algorithm, and it did not exist. Therefore, X decided to patent it himself as a System and Method.
My researched solution to a problem could potentially be worth millions of dollars.  I don't mean to sound braggadocious or grandiose, but I have experience in the industry, and I'm aware of how potentially valuable it could be.  I was thinking about doing a Ph.D on it. How do I prevent professors such as X from patenting my solution, or presenting it as their own idea in a publication? Since my solution could potentially be worth so much money, should I just patent it myself? The only caveat is that it is super expensive to do that.  Should I apply for a grant on grant.gov?  Should I write a manuscript in arXiv.org?  Should I try to write a business plan and try to get funding?

What is a patent troll?

I think the usage here isn't the standard one. Patent trolls normally buy up existing patents and then sue people for infringement on shaky (or not shaky) grounds. I think the intention here is to imply someone stealing the idea and patenting it themselves.

If you did a PhD on the topic, in many institutions that would give them a claim on whatever you produce (sometimes giving you only minority royalties even if sold), whether you try to patent it or have them patent it. Policy/agreements vary by institution. Ultimately the strategy you should take for monetizing or defending intellectual property will be beyond the scope of this stack, as it requires a deep familiarity with your local laws, market for IP in that industry, etc. Many Universities have IP development/grant programs, so you might consider checking what they offer. YMMV

If you publish it on arXiv or disclose it in a business plan, you're just making your idea public. That's fine if your goal is to be famously recognized as the inventor, but not if you want to be the first to commercialize it. It might depend on the jurisdiction but usually a patent can only be granted for an idea which hasn't been published before (but IANAL).

"Theft of intellectual property" would be a more accurate label, not "trolling", etc.

The story told sound completely implausible to me. If Facebook is far enough along development of something patentable that a description over lunch would allow someone to scoop it, then they would have already patented it.

If X is patenting something that someone from Facebook told them at lunch has been invented at Facebook, then either 1. the blabbermouth, 2. the person that failed to patent it (if so) or 3. prof X are in for a very big surprise, possibly all three. I am surprised that such information about a vulnerable invention would go out without an NDA. OP may want to inform themselves about the IP policy of their academic institution. It is probably not as powerful as FB, but will still be interested in IP not getting violated.

In the US, provisional patents last a year and are secret. Pending patents can take years after that to become searchable. The friend really had no idea if facebook submitted a patent on the idea already or not.

What's stopping you contacting patent lawyers and patenting your idea before doing the PhD?

Are your fears of getting it stolen rational? Have you asked yourself whether the invention is truly "worth millions of dollars" for the inventor (that is, not only market turnaround or the most common scenario, a big player keeping the benefits)? Are you aware that people tend to dismiss new ideas, and that probably you'll need to shovel any new idea down their throats?

@Quora Feans Yes, it is rational.  Any technology that can stop malware propagation is potentially worth a lot of money.

@GaryDrocella: inventors tend to overestimate the earning potential of their ideas, and to overestimate the share of earnings they will keep.

@Quora Feans I am aware that I could be overestimating it, but I could also be underestimating it.

@BryanKrause, sadly, that is one way that patents can work. Since 2011, substantially all countries implement a "First to file" system for awarding patents (that being the year the U.S. converted to that approach).  What the OP describes may not be ethical, but that does not impact the potential validity of the patent.

Do you even need to make the PoC first? I'm not a patent lawyer, but I am listed as the inventor of a patent (only a software patent - not a real one!), and I spoke to the patent lawyers who were drawing up the application on a couple of occasions: I sent them a written explanation of the algorithm and then talked them through it on a phone call. They did everything else. (In my case I was never going to be listed as patent holder, I don't agree with software patents anyway, and I don't think that it was ever granted in the end because it was something silly)

@Aaron F I read somewhere on the internet that you need to build a prototype first, but I am not sure of its validity.

@JohnBollinger Seems you are right, comment removed. They would still be potentially able to challenge the validity but it seems to be an uphill battle in particular if the conversation is not documented.

Let me describe fairly typical practice at reputable US universities. When someone has a patentable idea, the university itself will take over the patent process, paying lawyers and fees. The university will probably be the patent holder of record, but will make arrangements with the actual creator(s) to share any income that results from exploiting the patent.
This can be good or bad, I suppose, but the good part is that the university covers the cost and also provides backup if anyone challenges the patent at any point. This can be very difficult for an individual to do on their own. The bad part is that the patent is probably in the university's name, though that may vary.  Another point is that the university may take it upon itself to find ways to monetize the patent if it is awarded. Again, this can be a large expense for an individual.
But one protection for you, a student with an idea, is that if the university is, indeed, reputable, it won't try to steal your idea or let a faculty member steal it.
But faculty at the (reputable) institutions that do a lot of patentable research normally require this (or a similar) process as part of the contract with the faculty member. Such agreements might also be necessary for a student to participate in such work. And there is usually an office, full of lawyers, dedicated to shepherding such work. So a further expectation is that the university is not only reputable, but also large enough to support that office.
And the sharing arrangement may be standardized or, possibly, negotiated, so long as costs can be expected to be covered.
The situation and the rules will also probably vary by a lot in other countries.

For completeness, I'll note that large companies doing important research also tend to have (and require) some similar arrangements with their own researchers.

The University of Cambridge is not a US university (but I would argue it is reputable).  They too have systems in place to protect IP developed during research, and a mechanism to develop it.

@MartinBonner, ha ha ha. Yes, I would agree that Cambridge is (a) not US and (b) reputable. I've been led to believe that UK has many reputable universities, actually. ;-)

Well yes, but I only have direct knowledge of one.

Hi Dr. Buffy, would a top 10 school be considered reputable?

About doing a PhD, before thinking about academics stealing your idea you might want to think about how you are going to publish papers (usually a requirement during the PhD) if you want to keep your idea secret. As far as I know you won't be able to publish anything before the patent is filed (*), and that could take a few years. It doesn't mean that it's impossible but it might be tricky.
The alternative to the academic route described in Buffy's answer is to create your own start-up first, then develop and patent your idea under the name of your company. This might take a few years and will cost a lot of money indeed. If you can make sure that your idea is viable and really worth millions of dollars, then it's still a sound investment.
The first step would be to consult with a good specialized lawyer who will advise you on how to proceed (for instance inform you about NDAs, you will probably need these). Again, it's worth the expense in order to avoid making mistakes which could easily ruin your business.
(*) [edit] I initially thought you can't publish until the patent is granted, but I'm told in the comments it's actually only until the patent is filed... That's a good illustration of why you need a lawyer ;)

I guess that details are more complicated, but my IANAL understanding is that you can publish anything you want once the patent application is FILED.

@HonzaBrabec Thank you, you're probably right. I edited my answer and added one more reason to ask a lawyer for advice!

What you describe is closer to "scooping" than "patent trolling". But actually it's just theft.
If you truly believe your invention is valuable, then you can patent it yourself. You would need to find a reputable patent lawyer. And you can expect to pay thousands of dollars in fees. (Beware of disreputable patent lawyers.) Plus you will likely need the help of lawyers again to actually collect any money from your patent, as you must sue those who infringe on your patent, or at least threaten to do so.
If you just want credit for your invention, write a paper about it and stick it on arxiv or a similar repository. The arxiv timestamp clearly establishes precedence. That means no one else can subsequently patent the invention -- your work becomes prior art that invalidates any subsequent patent. Sharing your invention like this does not immediately prevent you from patenting it. However, there are time limits. I believe you need to submit a patent within one year of making it public.
Note that your employer may claim ownership of any intellectual property that you create. For example, most universities do this. On the positive side, this means they may pay for the patent. On the negative side, they may claim some or all of the money you get from it.

Keep in mind that doing this instantly makes it prior art in Europe. There's no delay.

Edit: Sorry, misread question. Salvaging what I can of it.
It's best not to get too carried away with the commercial potential of new ideas. It's one thing to come up with something, but something else entirely to connect that to a customer who will pay more than it cost you to develop it. And then there's the possibility that Facebook and others already know about it and are treating it as a Trade Secret. In the latter case your patent may not be worth much at all and could potentially be overturned in court.
I'd suggest thinking carefully about what your business plan would be, who your potential customers are, and how your product would be used by them. Would they license your IP? Would you work as a consultant to implement it on their systems? If the idea is just to "make millions" simply positioning yourself as a gifted developer who independently discovered X could be enough to get your foot in the door of some very high-paying firms. Or to put it another way, you may be worth a good deal more than your patent.
For Universities, policies will vary from place to place so you should consider consulting them directly. In Australia students generally are not required to give up their IP, but can voluntarily do so in return for some royalties and the University footing the bill for patent applications and legal protection of said patent. You'll need to assess for yourself whether the trade-off is worthwhile.
And finally, if you're worried about being scooped by Prof X then I'd strongly advise #1 not telling him and #2 documenting the development of your idea in a way that would be independently verifiable in court if necessary.

"if you're worried about being scooped by Prof X" If Professor X wants to scoop you, you're screwed; he's psychic.

We weren't working at Facebook at the time, and this all occurred sometime in 2013. I don't think that Facebook would have any idea about my invention.  It's kind of outside of their scope.  I do fear that some of the big dogs such as McAfee would come after me, though.  I haven't worked there, but my invention could seriously undermine the necessity of their product.

Your solution would need to be implemented, no? Sounds like plenty of work for McAfee and their peers. I'd imagine large companies like that would rather buy you out and make you sign an NDA rather than try and steal your technology. Sure, they could steal it, but a couple of million is probably money well spent if it stops you sharing the product with their competitors.
In any case, I think you're underestimating how much work it would be for every individual and company on earth to implement your technology. You're better off getting 1% of $1,000,000,000 than 100% of $0.

Its important to note what a university's position on IP is. At my university, all students sign the university's PI policy. That policy states that students cannot be named as inventors on patents that arise out of university supported research, only their supervisors can. By doing a PhD on your idea, you might be guaranteeing that you cannot patent the idea.


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Publication ownership for students
I have few questions related to the owner and independent of PhD students research. In my case for instance my committee members including my advisor are too busy to read deeply or know the details of my work. One of them however showed some interest in one portion of it 20% or less. I drafted a manuscript and send it to them and non of them responded. I spoke with my supervisor in person to remind him and send it again and the same no response.
As this might be a narrative story, below are some general questions:

Do advisory committee given a different treatment when it comes to the contribution? Are students expected to list them as authors?
How are contribution and authorship communicated, what is the norm and when draft is sent or circulated through email (between members) should the student add their names as authors, leave it blank, so whoever want to contribute will add his own name?
Should the PI providing the data or equipment be listed on the students work even if he doesn't light or contribute to the drafting them a script?

What field are you in?  The conventions are highly field-dependent.

The filed is public health, and please note that the PI providing some of recourses but he is not paying me anything as salary or tuition etc

Generally asking multiple questions in a single question are discouraged on Stack Exchange sites, since asking questions in bulk reduces their exposure as individual questions.
@jakebeal is correct, authorship and the ordering thereof, is extremely field-dependent. A tag search on Academia.SE should give you an idea about how different things are in different fields.
Here are some general answers that might hopefully be of some use:

Do advisory committee given a different treatment when it comes to the contribution? Are students expected to list them as authors?

Co-authors are people who have contributed to the work at hand. How that's defined is quite up to the field and sometimes even specific groups. I know for instance that in maths and physics, even having a lengthy conversation over a cup of coffee or two might be rewarded with a co-authorship. It is somewhat more strict closer you get to biology and medicine. But there is no written rule as far as I know..

How are contribution and authorship communicated, what is the norm and when draft is sent or circulated through email (between members)
  should the student add their names as authors, leave it blank, so
  whoever want to contribute will add his own name?

In my experience, it's usually (and hopefully) decided in advance and revised prior to submission or after reviews, in case any extra work is required. I have never heard of "sign up if you wanna be a part of this article" approach before.

Should the PI providing the data or equipment be listed on the students work even if he doesn't light or contribute to the drafting
  them a script?

There's a long, and I mean long path between drafting a manuscript and getting it published. The PI will most likely be involved in those steps in between, if not in the beginning.
You also need to see that the role a PI assumes might vary from person to person, some are hands-on and some adopt a more sink-or-swim approach. Some will micromanage details, and some will leave it up to you to figure things out along the way. My point is, if your PI hasn't been contributing much so far, there might be more than one plausible explanation for it, don't be quick to judge.
And finally to answer the question, I cannot imagine a world where you can exclude the PI who's providing your salary, and the resource you've used from a publication that you have produced, unless the person specifically tells you to do so.

People who follow the criteria of the Vancouver Protocol (PDF) (also distilled here) can easily imagine a world where PIs are excluded because they are not involved. I tend to be a bit more generous, but there are hundreds of journals that have agreed to this protocol.


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Is there a potential for bias when a researcher chooses a topic they personally find interesting?
When choosing a research topic, many researchers (in the field of psychology, in my case) often choose to study a topic they find interesting or have experience in. Does this introduce more potential for bias in their work?
I have done this myself. I am doing research into an area that I also work in, and enjoy as a hobby. I see that this has the benefit of existing knowledge in that area, and more motivation to continue researching the topic. But to what degree is it problematic that the researcher is personally involved in their field of interest? Is there a conflict of interest when someone struggling with addiction does academic research into addiction? Does the methodology affect this? Does a qualitative researcher have less personal bias than a qualitative researcher interpreting their findings?

Think at the potential bias you would introduce in a topic that you find boring ;-)

Not sure I understand the question. Do you mean that the results of such a study could be wrong (biased)? If so, why?

Please ask only one question per post.

@massimoOrtolano haha that's a good point! But I feel a researcher can remain relatively neutral towards a field. Many people have jobs they don't love, but they still perform them effectively.

@lighthousekeeper potentially. A researcher's personal experience with a topic may bias their results with their subjective opinion on the topic. A researcher may go into a topic assuming a result from the start, for example.

@AnonymousPhysicist my bad, I will do so in future.

@RossKeenan Then it depends on the type of methodology. For example, in a questionnaire, one might formulate leading questions and this definitely is an issue. Normally, there are for each methodology catalogs of "threats to validity" available that help to mitigate these issues.

Is one of the "qualitative"s in the last sentence suppose to be "quantitative"?

Yes, but in an area that one has no interest in, one could be biased by making assumptions or having a lack of understanding. One needs to test the internal validity, external validity, and reliability of the measurement instrument. One also needs to setup the analysis plan at the beginning to avoid trying different analyses until you get the result you expect.

@AnonymousPhysicist, please don't be so picky about "one question per post". Separating them here would be less than useful, and they are all aspects of the same thing.

@Buffy I see at least three completely orthogonal questions.

The short answer is, well, yes. But what alternative would you propose? Forcing researchers to work on topics they aren’t passionate about seems like a bad idea. Academia has few financial incentives as compared to industry. The only reason many stay is because of the freedom it affords them. Take away that, and there’s not much keeping people in it.
Keeping researchers’ biases in check is what peer review is for. Even if you happen to work on a topic you aren’t super passionate about (say, you got moderately involved in a project due to a very specific skill you bring in), you still have an incentive to publish the results, which should be kept in check regardless of personal interest.

I think the actual "yes" demands some more explanation, as some types of methodologies are certainly more prone to such bias than others.

I agree. There is potential for bias either way. But being forced to work on a topic you don’t enjoy seems unreasonable.

There shouldn't be any bias issue in selecting interesting questions. But there certainly is if you choose to search out support for what you think a priori is the correct answer.
Questions, themselves, have no bias. But it is the evidence that answers the question. If any other "techniques" come in to play than honest search for truth then there is a problem.
I found that first time researchers need to be taught this lesson. I also had to assure them that  if the evidence leads to rejecting the main hypothesis that they have succeeded, not failed, since they have new evidence of what may be true.
But selecting a question or an area of study because you have some deep connection to that idea is not, in itself, any cause for alarm. In fact it can (and should) result in dedication to the task of finding truth.
Suppose someone with a medical issue of some kind decides to research that. It does them no good to fake research or bias it in the direction of anything but the truth.
Companies, on the other hand, often have a financial interest in promoting not-truth. Overstating the benefits of a particular vaccine is a particular danger at the moment. Likewise the "research" done and published and promoted by tobacco companies was/is not a search for truth, but for financial advantage, since the costs fall elsewhere.

"Questions, themselves, have no bias."  Classic counter example:  "Do you still beat your wife?"

Scientific racists (not real scientists) are skilled in asking biased questions.

Sorry, @AnonymousPhysicist, but that is an idiotic comment that has no relevance to the question or answer. Sorry that I've pissed you off again.

You have never pissed me off.  I just get slightly disappointed at worst.  I picked that example because it is well known, I agree it's not the most relevant.

This is a really good point. Someone with genuine interest in a field is less likely to make false conclusions, as the findings directly affect them!

Bias is defined as any tendency which prevents unprejudiced consideration of a question. In research, bias occurs when “systematic error [is] introduced into sampling or testing by selecting or encouraging one outcome or answer over others” .
https://bit.ly/3q4Ijzf
Selecting or encouraging one outcome or answer is scientific misconduct.
As far someone doesn't do that, they can get their otherwise biased data or give their biased interpretation of them, of course. In the best case they change mind soon or later, for what their individual opinion matters. Or the rest of the world find out they were the biased ones.
To me, a not interested individual under the pressure of the environment is perhaps more prone to actively falsify data or be "victim" of biases than a genuine enthusiast.
Of course, this refer to genuine scientific interest.
If the financial asset of a researcher, to take an extreme example, is sensitive to a result, I suspect that bias and even fraud becomes much probable.

@Libor not interested in starting a discussion on the meaning of biased data. Link is not accessible to me. I will edit my answer to avoid misunderstanding.

Then ask OP in which way it intends interest as a source of bias @Libor

@Libor already you recognise that words might have different meaning. You were biased as for you statistical bias is the only one. IMy answer is about bias in research, and especially for the bias which might be introduced by the researcher. Other type of biases should not depend on the emotion or the happiness found in conducting a research.


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I get overwhelmed while self studying courses. What can I do when I can't sit in classes anymore?
I am learning a new numerical modeling technique (molecular dynamics) that requires learning graduate level maths and physics concepts. I am learning from youTube videos and books. However, I am getting all overwhelmed and am retaining nothing.
I am feeling disappointed because I am not able to grasp the subject that is very important for my postdoc success. My entire postdoc contract is based on the assumption that I can learn this in 6 months and produce results in the next 6 months.
I cannot sit through classes as postdocs are not allowed to do so in my university. I have access to online materials only.
I am feeling super stressed out and overwhelmed. Any advice?

Reading and watching videos is not a substitute for learning. Treat the material like you would if you were in a class. Find exercises that you can do to assure that you have "mastered" the material. Take notes. Make checkpoints at which you can assess your progress. You learn from reinforcement and feedback. The latter is hard in online learning. Find someone who can give you some feedback and answer questions. Find a working group if possible and learn it as a group, reinforcing one another.
I wonder, also, whether you can informally sit in on a course while not taking it. A friendly professor might permit it and even let you take exams informally. I've done this as a professor, actually, when wanting to learn the basics of a new field.

As Buffy said, reading books and watching videos, although you will learn a bit, is not a good way of learning. There are many different substitutes that will actually help you. When watching videos (as you have been doing), just sitting and watching won't help you. You need a way to retain that information. That could be taking notes, typing on a google doc, making bullet points, etc. You should also always have goals in mind. If you have goals, you have something to push too. I have found that making goals are very helpful when learning something overwhelming. Taking it one step at a time.
If you have a friend that is good at this topic, ask him/her for questions. Don't be afraid to ask! I have found that asking family and friends for help really helps you out.
Some other things that could help you not get overwhelmed are:

Breathe and take frequent brain breaks. If your brain is constantly working, you will get tired and start seeing blurrily.
Take a walk, being outside with nature is scientifically proven to calm you down.
Get better sleep, being overwhelmed does not mean you have to stay up all night trying to understand a topic. Your body needs sleep!
Focus, don't get distracted by funny cats during your youtube video lessons. Always stay on topic.

Hope this helps :)


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Strategy as a PhD student for earning good letters of recommendation in 1-3 years
I'm a PhD student in a 3-4 year program (UK), nearing the end of my first year.
I want to stay in academia, so I want to have good LORs. I was wondering how to earn good LORs that I may need in 1.5years (at the earliest) for postdoc applications, from someone other than my supervisor (obviously they should write one).
I dont have a secondary/co supervisor, so that is not an option. Indeed, there aren't really any professors in my department working in my subfield.

I suppose I'd need to develop a professional relationship with a Professor at another department. How do I go around doing this? My work is theoretical so collaborations don't seem standard (at least my supervisor hasn't suggested this).
Is there added value in the letter coming from a PI at a different university?
My subfield is interdisciplinary, should I aim to get a LOR from someone with background in the field opposite to mine?

I'm having difficulties to follow the sentence "My work is theoretical so collaborations don't seem standard". Why would theoretical work contradict collaborations? (For instance, I am in pure mathematics, and one could argue that it doesn't get much more theoretical than that; but still most people here collaborate all the time with various different people.)

And interdisciplinary - seems natural to have collaborators in the other disciplines? Good letters of recommendation come out of doing good work with other people. Worry about that first, the LORs will come naturally.

why not concentrate first and foremost on doing good work?  THAT will get you noticed by others…

@JonCuster, JochenGlueck I agree with both of you - I'd like to collaborate, but my supervisor isn't very keen on me reaching out to people to collaborate, since I'm only a first year PhD student...

@ZeroTheHero I agree with that, but I doubt that someone having read my papers and liked, maybe even cited them, would be sufficient reason to request a LOR, let alone result in a strong one. Maybe I'm wrong though and this is standard

@mmm you’re overthinking it.  Do good work and then worry about LoR.

First and foremost, you should concentrate on doing good work, and let positive judgment from others flow from the quality of your professionalism and your work output.  Also, when you are a PhD student, you should be careful about engaging in "impression management" since it can detract from your candour in identifying your own areas for development and seeking help to improve your work (and actually that's also true for people in higher positions too).
With those two caveats in place, one thing you can do here is to take actions to form a broader network of people who know about you and your work.  There are a number of actions you could take to do this, such as:

Reconsidering opportunities for collaboration or multidisciplinary engagement in your research (e.g., publishing a joint paper with an academic, etc.);
Seeking opportunities for joint research work with academics at your university or another university;
Regulary attending appropriate talk/seminar series at your university and giving occasional talks yourself to let people know about your research
Asking to attend research committees that arrange research activities in your faculty (even just as an observer, since you are only a student);
Undertaking teaching/tutorial work for one or more academics in your faculty; or
Starting up a PhD student discussion group on a broad academic topic of interest to you and others, and asking an academic with knowledge in that field to be the patron of the group (attending meetings, giving advice and opinions, etc.).

All of these are things you could consider doing that could potentially expand the network of academics who are familiar with you and your work.  Bear in mind that any activity you do has an opportunity/time cost, but consider the above as things that could enhance your PhD program and your broader academic network.

Thanks for the suggestions. I'm unsure about what you mean by 4. I've done 3, 5 and 6, but I'm unsure these are enough reasons to warrant a good LOR (eg I doubt someone can write me a good LOR based on how well I taught their students). Even if I used that to get me noticed, my subfield is very disconnected from the rest of the department (as an example, think being the only bioinformatician, from a CS background, in a biology department), so the LOR's from other PIs would be useless. I wish I could collaborate, but my supervisor isn't very supportive of that

I think this is a good answer. Doing 3 and 5 is a great thing, particularly in the other part of your interdisciplinary sub field. You could also organize conference panels on your topic and use these as a jumping off point for conference meetings with people in your field.

That seems pretty hostile to the student to me.  If a PhD student wants to work in academia, it doesn't seem unreasonable to me that they might ask to observe some of these kinds of proceedings where academics arrange their research agenda.  As to "abiding his presence", shit man, if an academic can't abide the presence of a PhD student, academia is probably the wrong profession.  Anyway, thanks for your perspective.


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How can I ask to not be assigned a seat near a particular person during exams?
I'm going to write my exams next month, but since COVID-19 we have special rules on how exams should be carried out and one of them is that every student is assigned a place to sit in the examination hall in advance. I won't go into details, but there is one person next to whom I don't want to be sitting. My reason to not sit near him has nothing to do with the pandemic. And since our class is pretty small, it's very likely to get a place somewhere near him.
That's why I'm planning to write an email on Monday to the unit in my university, which is responsible for the organization of the exams (if necessary to my professors as well), explaining them that it doesn't matter to me where I'm going to sit, but I just want a seating place which is not directly next to him.
Do you think that's a good idea and is there anything else that you could maybe recommend me to do?

Just don't tell anybody in case your wish is granted. If next time five people want special seating arrangements ...

Please do not vandalize your own question. Please see here for an explanation, and some other options.

Yes, I think you can ask. You don't need to give a reason if things are handled justly. "Personal reasons" should be enough. If the person has harassed you in the past or is known to you to cheat you have adequate reason.
And, it might be important to do so if you think that it would affect your performance.
You will need to decide whether to give a reason if asked. But be honest without revealing more than necessary. You might not achieve your objective, of course. Be ready for that.

Thank you, I'm actually planning to write my email and ask without giving the name of the person first, maybe just saying it's due to personal reasons. And then, depending on what kind of an answer I get, to give them the name as well. Maybe this should be the better way to go?

Sounds pretty good, actually.

@rey227 not mentioning the name only creates additional work for them (more e-mail to read and write, on top of their likely heavy load), and makes it less likely they'll do it. If you're asking for a favor, make it as easy as possible for the person you're asking.

@dbkk Then perhaps OP should tell them what she told us: "I don't wish to identify the person unless my request is approved."

I agree with @dbkk that OP should give the name in the first request. See from the perspective of the admin clerk: if there's no name, they have to reply back, wait for a respond, put off arranging the seating until after the response. Much easier to just say no if they have discretion.