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Should I tell a PhD student's supervisor about a lack of understanding and somewhat ethically dubious conduct?
Background to the question:
A PhD student who I worked with during my masters' recently sent me a coauthorship statement for a paper I published whilst I was a member of that group. We started in that group at the same time - he as a PhD, me as a masters' student, and he is now coming to the end of his project. The statement claimed he had a leading role in the project (he didn't) and claimed that he contributed significantly to the manuscript (this is somewhat arguable, but he certainly wrote some of it). I signed the document because I assumed that this was just some formality that he needed to graduate, and I wasn't prepared to cause a fuss over the wording in a document that I didn't view as important. Plus, the form has my former supervisor's signature so he presumably agrees with what was said.
However, now it turns out that he needed this agreement because he wants to write a chapter about my work in his thesis. Furthermore, he is asking me questions about the paper that are extremely basic. I don't want to come across like I am exaggerating, but the questions he is asking me are the sort of questions that are covered in first-year undergraduate chemistry courses - not the sort of thing that should be being asked by a PhD student about to graduate.
Actual Question:
The questions he has asked show such a lack of understanding of the topic that I really do not see how he can possibly put this in his thesis - let alone write a thesis on this topic. However, I am thinking that I should tell his supervisor about the things he's asked me. Given this, what would people advise?

I signed the document — So you also acted unethically.

To be honest, yes. I think I should not have signed it in retrospect. However, there was enough in the document that was technically true - and with my former supervisors signature, that it made me question my memory a bit. The following experience stopped me questioning my recollection.

You wrote:

The statement claimed he had a leading role in the project (he didn't) and claimed that he contributed significantly to the manuscript (this is somewhat arguable, but he certainly wrote some of it). I signed the document because I assumed that this was just some formality that he needed to graduate, and I wasn't prepared to cause a fuss over the wording in a document that I didn't view as important.[...]However, now it turns out that he needed this agreement because he wants to write a chapter about my work in his thesis."

In order to include joint work in your thesis, many graduate programs require a statement to the effect that you are "a first author" on the paper.  So, in fact, that is just what that kind of document is going to be used for.  It's entirely reasonable that the purpose of the document was not clear to you (a master's student).  Maybe your collaborator should have been more explicit about what it was being used for.  Maybe you could have asked.
However, since he is a coauthor on the work, it is also his work, and he is perfectly entitled to represent it in that way.  The fact that he needs to be a first author in order to include in his thesis sounds like "a formality that he needed to graduate" to me.  Your signing this document does not undermine your first authorship on the paper (I assume you are; you don't quite say so) in any way known to me.
One could put a positive spin on the fact that you, a master's student, have done work that has formed a part of someone else's PhD thesis.  That is just about the strongest possible certification that you are doing PhD level work.  Maybe think about how to capitalize on that, e.g. in recommendation letters.  In summary, so far -- no problem.

Furthermore, he is asking me questions about the paper that are extremely basic. I don't want to come across like I am exaggerating, but the questions he is asking me are the sort of questions that are covered in first-year undergraduate chemistry courses - not the sort of thing that should be being asked by a PhD student about to graduate.

Well, that sounds bad rather than good, but without further context it's hard to evaluate.  Presumably this is just a part of his thesis work (you said "a chapter"), so maybe his real expertise is elsewhere?  Maybe his background in his field is really spotty or worse, and somehow he managed to do enough work to get a PhD anyway.  Maybe he's not so bad but you're really great and thereby have higher standards for what a PhD student should know than others.
Yes, it is also possible that he is some kind of fraud or charlatan.  I kind of wonder that you wrote a paper with him and didn't notice until now, but maybe indeed his role on the paper was minimal.  My feeling is that while you can respond to this however you like, you have no "whistle-blowing" responsibility here: you are not one of the several qualified, professional academics who are charged with evaluating the student and his work before he gets his PhD.  It's on them, not you.
My recommendation: stop answering his questions, and instead say "I think you should ask your advisor about this."  He can't lean on you if you don't let him, and you don't need to let him -- as you say, he is about to get his PhD.  If his supervisor is also your supervisor, and you have a good relationship with him, then you might want to bring up the fact that the student has been asking you a lot of basic questions.  If the supervisor doesn't have an issue with that, that's their problem and not yours.  (Even if the PhD student didn't know what an atom was, you still can't do anything directly to stop him from getting his PhD.  The advisor can.)  If you don't have a pre-existing relationship with his supervisor -- I recommend letting it go.

Thanks for the great response and good advice. I hadn't actually considered that I don't have any responsibility in this situation - sometimes it's hard for me to realise that when people are pressuring me, unfortunately. I will write something out telling him that I don't feel comfortable with his questions. Thanks for the advice :)


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How do they add you to their blacklist?
I have heard if you send papers to a journal/conferences there are some conditions that might be dangerous for you academic progress! I researched about it but I wasn't able to find a good definition to be aware. My main question is how they add an author to black list and how is the procedure? moreover, what is the reaction to original researches which might be weak or bad written? I know they will reject but is this the end or they will mention your prior effort in future?
My research field: Computer Science
Thanks in advance.

Your question is somewhat unclear, but it seems you are worried about being blacklisted for submitting a weak/bad paper. Blacklisting is generally reserved for academic misconduct (concurrent submission, plagiarism, falsifying results, etc.). So, as long as you are submitting in good faith and follow academic norms, you should be fine.

@Thomas, thanks. You've realized my concern correctly.

The use of black lists to prevent low quality submissions in academia is pretty rare. I have never heard of a journal or conference having a formal black list procedure. The first I ever heard of a formal black list system was the one implemented by EPSRC in 2010. There was a discussion of the system published in Nature soon after it was implemented. Basically, the system works as follows, if a PI had 3 proposals that were either not scored or scored in the bottom 50% in the last 2 years, they are only allowed to submit one application as a PI for a 12 month period. Grants submitted where you are a CI do not count against you and even when black listed you can be listed on an unlimited number of applications as a CI.
The fact that formal black lists are not frequently used, does not mean that submitting low quality work does not hurt your reputation. It is quite likely that if reviewers frequently see low quality work from a researcher that they will have a negative bias towards future work from that person/group. The opposite holds for individuals who consistently produce high quality work and sometimes get the benefit of the doubt. In fact, I think these biases are one of the reasons for a double blind review system.

If you do something egregiously bad, or are extremely abusive towards the journal, then they might blacklist you. But you need to do something exceptional. Simply submitting bad papers won't get you blacklisted (since desk rejection doesn't usually take long), and neither does submitting poorly written papers (which are even easier to handle since they just send you a "unable to understand your paper" email, which they might even have a standard version of). It's usually to the journal's advantage to receive potentially-publishable papers, after all.
Here's a real life example of a journal banning someone from submitting. The person in question is Jaime A. Teixeira da Silva, a plant scientist who has received 21974 citations as of time of writing. Scientia Horticulturae cited personal attacks and threats for their decision. One of the emails sent to the journal's editors and cc'ed to other scientists was:

I will expose your fraud to every scientist I know, and make my case public from now on that corruption and fraud, lack of professionalism and libel are the four corner-stones for the publishing frame-work by Elsevier and this journal, Scientia Horticulturae.

da Silva also wrote this:

Moreover, if I do not see a resignation [by either of the journal's two editors-in-chief] in 72 hours, I will immediately post this libelous case of editorial bias and witch-hunting on Retraction Watch and other blogs.
MOREOVER, IF I DO NOT RECEIVE A CONFIRMATION, WITH PROOF, OF STANDARD AND UNIFORM INQUIRY TO ALL AUTHORS, AS WELL AS A RESPONSE TO THE NEXT 8 QUESTIONS, I WILL CONTACT ALL SCIENTIA HORTICULTURAE AUTHORS AND ALSO THE INSTITUTES TO WHICH ALL SCIENTIA HORTICULTURAE EDITORS BELONG.

As for the procedure itself, I imagine the publisher would add a note to your profile in their editorial management system that you are blacklisted and all your submissions are to be rejected without review.

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Is it possible to contribute a native speaker for editing the paper and add him/her as authors? Is there anyone?
I'm working on SIMDization and Optimization. I usually do some great jobs. But writing a good article needs a good knowledge of writing skill. I've implemented many programs. I can write and organize the paper. But editing the article take a lot of time for me, because of some silly grammatical mistakes. I just thought it might be possible to contribute someone who knows English well and add him/her name as the second author. Is It a good Idea? If yes how can I find someone? Preferred from Toronto Ontario.

So ... you want someone you don't know and is not at all familiar with your work to proofread and edit your paper for free ... respectively for appearing as an author? First, this person won't fit the definition of authorship. Second, if it's not one of your close colleagues where you already implemented a give and take, you should/have to pay for the proofreading.

I meant to find someone who is interested in researching especially my field as a coworker. Not only edit the paper for free and add the name.

This may vary in some ways by field, but it is generally not considered sufficient for an individual to be included as an author on a paper if that person's sole contribution to the paper is proofreading and editing. Readers, reviewers, and journal editors expect that each author has made a significant technical contribution to the material presented in the paper. If there isn't a monetary payment involved, credit to someone for editing a paper usually takes the form of written thanks.

Since you find yourself unable to spend money on editing services by publishers (in chemistry I know only about them by ACS or Wiley) or local proof readers (like this example in Toronto lists 33 names/contacts) maybe there are programmers you know (because their work inspired you, or/and will be cited by you) you may reach out.
Or --- relating in analogy to R, Python, Emacs --- contacting a local usergroup (like this about C++) of a programming language / software you use is an alternative; in contrast to an English student at the university they already know the technical terms of your field, and you could pay them not only by money.

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If a professor analyzed my work, does the university own my idea?
If I had completed work on a certain idea, and would like to have it analyzed from an expert in the field. And shared it with a few professors, to get their opinions on my work... would that mean the university has contributed to my work? And somewhat has rights to the idea? Knowing that I never used the university's resources or facilities during the development of this concept.
I wont publish anything, just need an opinion on my work, if it has errors and overall worth pursuing.

If you want an opinion from someone who is an academic, not an attorney: if we are talking about, say, a paper that you circulate to faculty members for comments, then it seems extremely unlikely that the university would have any legal claim to your ideas.  (I have worked as a professor at my university for years, and I am not aware of any meaningful sense in which my university owns any of my ideas.)  If you want an opinion from an attorney: ask an attorney!

Do you intend to capitalize on your work in any way? How you share your work may affect the process to obtain to patents or inventions. Who actually has a stake in your work would matter as well (e.g. you used an ATCC cell line under a material transfer agreement to do your work, they still own the cell line and you would need to license their cell line to commercialize your work, for example.). You institution should have an intellectual property lawyer for these matters. Things to consider are non-disclosure agreements and MTA's of your own. IANAL.

This is a good question for the legal department at your university. At the university where I teach, there is a standard software license agreement form that I sign with students to basically ensure that software is owned by everyone at the end of the class. But your university will likely have its own rules and policies. If you have your own attorney, you can work with the university to modify such agreements.

I don't want to downvote your answer, but if you're really concerned about your intellectual property then you MUST retain your own lawyer. Your university's lawyers are paid to argue that they own anything and everything they can lay claim to. Your lawyer is paid to defend you. Simply asking your university's legal department is a bad course of action.

I agree. Retaining your own lawyer is the best course of action. But some schools do offer legal services to students. I meant to suggest that as a starting point, especially since most students can't afford lawyer fees. No doubt hiring your own layer is the best option.

As others have said, ask a lawyer.
One general point worth making- undergraduate students and graduate students are very different in this regard. My university explicitly disclaims any interest in work stemming from undergraduate coursework. Graduate students are the exact opposite- work conducted at the university in the course of graduate studies is explicitly owned by the university. My understanding is that this is a fairly common situation, but not always.
With respect to your specific question, it sounds like you want to know how little has to happen before the university has a claim over your work. A university probably has a claim to any work that is related to your university work, or any work that was accomplished with university resources or any of the university's proprietary information. You're potentially putting yourself in legal jeopardy if you're using any university resources, even something as ubiquitous as a university-owned computer, a university-provided internet connection, or the the office you sit in.
One really good reason to consult a lawyer is because state laws vary on this issue. For example, California has relatively strong protections for employee-generated intellectual property. Other states do not.
A good rule of thumb, especially in your position, is to document the current state of your work before you bring it into the university context so there is no question as to what you exclusively own. Then, as you work on your side-projects while at the university it is also important to document how your work was not performed on university time or with university resources. Note that if your side-project is related to the scope or content of your employment with the university then it will be extremely hard to argue that the university has no interest there.
If you are a graduate student or employee of the university then there is certainly a contract somewhere that spells out the university's rights and your obligations. If you are an undergraduate student then there is probably a policy that covers the same.
But again, ask a lawyer.


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Referring to article names in text
I've found lots of documentation on in-text bracketed citations and referencing list styles, but very little on the following.
When referring to names of articles in text, should the article name be surrounded by quotation marks?
For example:

In 1990, John Smith presented his work: "A question on quotation marks".

Or, alternatively:

In 1990, John Smith presented his work: A question on quotation marks.

In my case, the required referencing style is ACM format, if needed.

After research your question, it appears from multiple universities that the proper way to reference a source in text with ACM format is:

So we see that Smith [1990] ...

Therefore you should not need to reference the actual article name.
https://biblioteca.info.unlp.edu.ar/uploads/docs/guia_acm1.pdf
https://www.cs.ucy.ac.cy/~chryssis/specs/ACM-refguide.pdf
https://www.library.unh.edu/research-support/citation-styles/acm-style


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How do you prepare to attend a conference where you may have trouble following the talks?
I am fairly new to academic conferences. I am registered to attend (not present at) a mathematics conference (graph theory, to be specific) in about a week and a half; I recently received the agenda and, based on the topic, some of the talks seem a little "advanced" for me. I have a decent general understanding of the topic (I have an undergraduate math degree and a master's degree in computer science), but am still unfamiliar with some of the advanced topics.
What do I do in cases like this? How can one do self-study to prepare for conferences like this to make sure that you'll understand the topics?
Also, how much of the talks "should" one expect to be able to comprehend? How much is "normal" for individuals at various "levels" in the field (e.g. undergraduate students, graduate students, working mathematicians)?
I do realize that, given the short time frame, there'll probably be a limit to how much I can do to prepare for this particular conference. However, I would like to be better prepared for future conferences in this area.

There's a saying about PhDs in mathematics: For most dissertations, there is only one person who understands it and only one person who cares about it, and they are not the same person.

There is a saying that typically, one third of math talks is understandable to any mathematician, one third is understandable to the handful of people who work in the specific subfield, and for the last third... if the presenter doesn't understand that part himself, no problem. And: if the three parts are of unequal size, no problem either.

@StephanKolassa I think having the beginning understandable by any mathematician is a goal for general audience research talks like colloquiua and job talks, but not for specialized conference/seminar talks.  That said, even for general audience talks, I'm not convinced this goal is achieved the majority of the time.

I don’t! Have fun at the conference

You might have already heard this. There's a famous quote from Von Neumann: "Young man, in mathematics you don't understand things. You just get used to them".
I guess by this quote Von Neumann has helped countlessly many PhD students in mathematics (and neighboring areas) not to quit their studies.
So, I'd recommend writing that quote as a reminder in every place you could possibly think of (as long as it wouldn't count as vandalism and is legal of course!)

Isn't the point of attending a conference to improve your knowledge? Isn't that the same as catching up on things you don't (fully) understand?
Then again, how much chance is there anyone could attend every talk? Why not just go to those talks that interest you?

I read some interesting advice here (also see the "More general advice on going to talks" linked at the top of that page).

Nobody can know everything. Even just in mathematics the last time it was possible to literally know it all was early in the 20th century. Things have advanced too fast and too far for such things now.
A conference might be expected to present the latest ideas in a sub field. If that is your specialty you would be expected to follow "generally" but would probably require additional study afterwards if the subject of a talk was important to your work. But a "general understanding" and a few notes about how and where to follow up is probably enough for most people.
I doubt that your education, as you describe it, puts you at the research edge in graph theory. If you are doing research in that, then a quick literature survey of closely relevant topics would be good preparation, but I'd guess that few  people do that. If the proceedings are available in advance, skimming the papers will give you an idea of where the holes are in your understanding.
But at the conference take a few notes, especially on topics that are not known to you, as a guide for further study. If you attend (physically or virtually) with colleagues, start a conversation over coffee/tea/whatever to ask others for their insights.
On the other hand, if one of the speakers is your dissertation advisor, you'd probably be expected to understand most of it. Or at least grasp the general trend of thought.
Math is pretty esoteric at the edges.

Another kind of "preparation", however, is to prepare to meet new people and share a few ideas. Harder now with thing mostly virtual, but a great way to build contacts.

You are correct that I'm not quite at the research edge in graph theory at this point - my knowledge does have some rather gaping holes in it (which I'm trying to close as quickly as possible).

@EJoshuaS-ReinstateMonica In my experience, the more gaping holes you close in your knowledge, the more you find. Which doesn't mean that you shouldn't fix the ones you know about! Just be chill about it, and accept you won't ever understand everything, or even most of the stuff...

Even in the early 20th century it was not possible to "know all of mathematics".  The collected works of Euler alone (18th century) fill over 80 volumes.

@BlueRaja-DannyPflughoeft, well, you couldn't probably have "memorized" them, but that isn't the same. But see: https://en.wikipedia.org/wiki/Henri_Poincaré

@BlueRaja-DannyPflughoeft: That's a little misleading, because Euler wrote a crazy proportion of the math papers in the 18th century.  Yes he has a lot of papers, but if you understand those papers then you're most of the way to understanding 18th century math.  Saying "Euler alone" makes it sound like that's a small proportion of all the papers.

That part about "one of the speakers is your dissertation advisor, you'd probably be expected to understand most of it" came as a huge disappointment to me at least. I barely understand my advisor when he talks about a paper we co-author(ed), yet alone his other works.

@nara, certainly some people work more closely with their advisor than others.

On top of this, trying to follow the fine details of every talk in a conference is too much to take in even where it's possible.  The art perhaps lies in spreading your attention well, which often means picking up on the overviews, and accepting that interesting details are just the sort that will need later study

Excellent answers here already. I will try to add a little.
Part of the reason for attending a conference like this is to learn what's out there that you may want to learn - not necessarily to understand it there. So read the abstracts and decide which presentations to attend (if the conference is large there will be simultaneous ones).
You may find times when no  talk  is even close to your interests. Skip those. Take the time for a cup of coffee - maybe with someone you introduced yourself to at an earlier time. Other junior people like you will be easier to connect to than senior featured speakers. Making connections is as important as learning from the talks.
This is from https://www.conference-service.com/conferences/graph-theory.html about the 25th Ontario Combinatorics Workshop
15 May 2021 - 16 May 2021 • Queen's University, Kingston, ON, Canada
(maybe it's the one you're going to)

The objective of this meeting is to have an atmosphere conducive to
research discussion and collaboration. The setting of the meeting is
informal to provide a friendly environment for students and
post-doctoral fellows to present their results, to exchange ideas, and
to gain exposure to various topics in combinatorics. It is also a
place where students and faculties meet, which may foster future
collaborations.

There's a saying that each talk should contain a part that everybody understands, a part that only the experts understand, and a part that only the speaker understands (some also include: a part that the speaker does not understand either). When you're not an expert (as most people on most subjects) the point of going to a talk is to understand the first part and get the general flavour of the argument from the remaining parts.
I would advise against trying to prepare for a conference. To me, conference talks serve as an invitation to read the corresponding paper(s) or study the subject. If a talk catches your interest or turns our to be relevant to your research, then it's the time to study. Plus, there's a fair chance the recordings of the talks are going to be available online so you can revisit them later, and if not you can always ask the speakers for a copy of the slides (they're almost universally happy to comply).

You don't go to conferences to hear things you already know. You go to conferences to learn about things you don't know yet.
In that respect, you are in the perfect situation: You have lots to learn, and you will learn a lot. You should look forward to the conference, rather than being stressed about it.
Of course, the stuff you learn will be different from what people who are experts in the field will learn. But this is not the point: You will learn lots of things which are new to yourself, and this is what counts. (In fact, you will likely learn much more than the people who are familiar with the field: The conferences where I learned the most new things were certainly the ones which were out of my own comfort zone.)
Of course, you should try to do something to increase your learning experience. As far as I would say, this mostly means talking to people at the conference, in particular about the things you would like to understand better.
You will notice while at the beginning, there will be lots of things you won't understand, this will get better by the end of the conference, since you will have learned a lot of new things.
And if you feel like you don't understand a word, keep in mind that at most conferences most of the attendants can't follow a non-negligible part of the talks!
Enjoy the conference!

"You will notice while at the beginning, there will be lots of things you won't understand, this will get better by the end of the conference, since you will have learned a lot of new things." - I think this is quite an optimistic view, and depends on the structure of the conference. Things don't necessarily feed off each other at a conference they way they do in a structured course, and it may be that OP only gathers a little bit of something here and there and may be totally burnt out and unable to process anything more by the end, and that's okay.

@Bryan I never claimed it would be like a lecture course, and I didn't recommend doing homework! But after hearing the same introduction for the 10th time, one starts to understand and things start to make (some) sense, even if it is only about the basics of the field. Again, let me repeat what I said above: I learned most at conferences which were clearly outside my comfort zone, even though the things I learned were of course more basic, and it was super exhausting. If the OP wants to relax, I recommend a vacation at the beach.

I don't know how conferences you've attended relate to ones that I have, but I certainly have not heard the same introduction 10 times at a conference. In any event, I think most of your answer is good advice, especially about appreciating the potential of learning a lot as a novice, and of learning something different from what 'experts' will learn. I just think that my own experience and the experience broadly shared by people in my own orbit both more and less experienced than me is that by the end of a conference they're pretty exhausted and it gets harder rather than easier to learn.

@Bryan I'd say whether you consider an introduction the same or not basically to a large extent depends on your distance to the field. From the further away you look, the more similar the things you hear in the beginning will sound.

This is a non-math perspective, but similar problems are faced in other fields as well.
As correctly mentioned in another answer, nobody can know everything. As a corollary, nobody at a conference will attend/carefully listen to all the talks (even if it were possible to). Time and mindspace are both limited, so it is a good idea to plan beforehand which talks/presentations to attend. I personally don't like to attend more than 3 in one session (assuming each is 20 odd minutes). This allows time to absorb and network, which is an important part of conferences.
Once you've chosen the talks to attend, it may help to do some background reading on the speaker rather than the topic itself. If you read some of the recent work done by them, you may get a better perspective of their direction, way of approaching the problem, and this may help you follow the talk better. The same topic can be interpreted quite differently by different speakers (again, I don't know if this is true in math), so reading up on the subject will not necessarily going to equip you well. Knowing the general research interests of the speaker will atleast facilitate a discussion with them (most speakers are happier to talk to you if you have some familiarity with their work).

The first thing is I think it's important to have low expectations in terms of how many talks you'll really get something out of.  When I go to a conference I feel like it's been a really good day if there's one talk that I really got something important out of.  And that doesn't mean I understood the whole talk!
The other key thing (both as someone going to a talk and as someone presenting) is that a large function of a talk is to serve to advertise and introduce a paper.  Sometimes that means the talk leads me to go read the paper, sometimes it just means I'm aware that a certain result is part of a certain authors work and then I can find it if it turns out that I need it down the road, and sometimes it lets me understand a paper that I tried to read but failed to understand.  So don't think of the talks as something that you need to prepare for, but rather the talks are the preparation to read papers at some later point.  As a grad student its fine if you don't understand any of the details of any of the talks, if it means you've learned a bit about what kind of questions which people in your field are working on.  Then you'll learn who would be interested in your results and where to look if you need certain kinds of techniques.

Personally I go to talks I don't understand all the time. I love diving in over my head and getting to know a new field. If something looks really cool, then I go read the paper. Or sometimes I just read the interesting papers that the speakers cite, rather than the speakers' own papers.
Many people do the opposite --- they read in advance the abstracts of all the talks and then the papers of the talks that seem most to their research and then go into the talk prepared to either learn or ask questions. This is just a matter of personal choice and style of learning, and maybe discipline as some may be be easier to communicate in talks than others.
Other people only go to the conference to pick up the proceedings and schmooze. They think you never learn anything from talks, you should just read the papers, and you get the real work done at conferences through meeting people and collaborating.
Sadly, some people go to conferences only to be seen, or perhaps as some weird ritual of academia, and don't seem to be trying to learn at all. I don't understand that and I'm glad you aren't in that category. You are off to a great start to be asking this question!

Pace.  This applies even with ACCESSIBLE, enjoyable conferences (like chemistry).  Go through your book and make a list of the talks and do some selection of them. Not 100%.  Something well short of that.  You just don't have the capacity to get use out of the stuff anyways.  Look at the list and decide which ones are interesting or comprehendable or close to you or cute speaker or whatever criteria.  (It won't be perfect and you will miss something interesting and go do something not, but forcing a selection process increases investment and you will have some Bayesian effectiveness also.)  When taking a break, grab a longer coffee.  Check email, whatever.

If it is a several day conference try and sneak off and do a half day golfing.  Or at least look someone up in town (outside the conference) for dinner.  Obviously don't completely ditch the conference.  But get a little non-binded-oxen-mouth grain.

Emphasize coffees, beer drinking, etc.  CHITCHAT!

Make it a goal to come back with at least one collaboration.  Make it a game and see what you can do. Cool things happen at "boundaries".  Preferrably something small, tangible. (Not some grand collaboration that we read about here with sob stories of not getting published.  But just some human "connection".  Shit is so lonely otherwise.)

There's a helpful approach that I've heard ascribed to Uri Treisman with the Emerging Scholars programs he developed in California and Texas.  This is for students from various groups who historically don't do well in calculus.  In addition to extra sessions with specially trained TAs, the students in the program also attend math research talks!  Here's the advice they were given.
There are people who love going to the opera.  It's usually not because they speak the language of the libretto, know the plot well, or have memorized the score.  Rather, they find it a beautiful experience and enjoy whatever they get out of the evening---the staging, the emotions, the melodies, the costumes, the orchestra...  Going to a math research talk is like going to the opera: Almost certainly you won't understand every idea presented, just enjoy what you can---the overall structure, examples, small details, how it's similar to or different from other talks, possible connections that pop into your mind...

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Being told a conflict of interest is acceptable for paper review
I was recently asked to review a paper. I feel like there is a conflict of interest as (i) I frequently collaborate with one of the authors, (ii) I discussed the paper with the authors while they were working on it, and (iii) I am currently doing follow-up work (i.e. extending the work of the paper in question).
I told the program committee member who asked me to review the paper all of this. I was surprised when she responded saying that this is not an issue. Specifically, she responded that this is unavoidable as there is a small community of experts who all work together and that this just means I'm the most qualified expert to review the paper.
What should I do? Should I accept the PC member's assertion that this is OK? (I have been honest with her.) Or should I insist that I am not able to give a fair review?

You're always able to follow your own conscience and decline. If you strongly feel like this is a bad situation, it probably is. If you strongly feel like you couldn't be  impartial and objective, you probably can't. If you are concerned your colleagues would frown upon this if they found out, then they probably would.

If you did decide to review it, being as impartial as you can be, put the above statements in the review.

@CramerTV: That's not good enough, since no one will know other than the authors and the PC chair. The paper will have made the conference/journal without a proper review. This may be fair if the same is true for most other papers, but is quite unfair otherwise.

If you can be unbiased, then I think that points (ii) and (iii) mean that you can understand and review the paper much better than most other reviewers. If you can be unbiased.

How small is your community? If you decline, how many others would have the relevant expertise to perform this review, and how likely would they be to have problems similar to yours?

From an outsider's perspective, both choices are now ethically just. You've declared the potential conflict of interest and been assured that the authority in question doesn't see one ( hopefully you did this through a means which let you keep a record).
So now it pretty much comes down to whether giving the paper a fair review makes you feel uncomfortable. If it does, then get back to the committee as soon as possible, and tell them as clearly as possible that you can't do the review. Otherwise, review the paper, making full use of your deep understanding of the context of the work.
If you're wondering whether the committee member's statement is ethical, then consider whether you, as an obviously knowledgeable person in the field, could think of three other possible reviewers. Of course, if you can, then maybe one answer is to say no, but pass on those names instead.

Disagree with the first part of your answer. The fact that a reviewer consulted a PC chair does not make this fair to the authors; they do not and should not care about the internal deliberations of the PC and the reviewers.

I agree with @einpoklum  in one sense and not in another.  I think that consulting with the chair is necessary but not sufficient, in the sense that if it really weren't too bad a conflict, and OP felt it could be reviewed objectively, it would be OK to proceed.  Here it seems clear the conflict is too great and the chair should be ignored.  The part where I really disagree though is the question of who it would be unfair to.  It seems like the bias here would be in favor of the authors/collaborators and unfair to the other authors who are competing with this work...

@FredDouglis: I meant all authors. Should have made that clear. Of course it would be unfair to the authors of other papers, who get a not-biased-in-their-favor reviewer; but it would also be unfair to the authors of the paper OP got, because now it would appear they inappropriately got a paper into a conference - even if it wasn't their fault. So everybody gets hurt some way... Also - see my answer.

@einpoklum, fair enough.  The reason I didn't interpret it that way was because it would be unfair to other authors on its face. So I'd read it as "the other authors don't care whether the PC or whoever thought it was ok, it isn't"... the authors who would benefit aren't going to be tarnished due to inappropriateness if no one knows a reviewer was biased.  Only if it somehow came out.

And I'll add I agree with your answer, "anonymous reviewer" must not review it and seems to know this.

This answer is completely wrong: a conflict of interest doesn’t go away just because some person erroneously believes it does, even if that person is in the program committee. In fact, that person has acted deeply unethically, at least OP’s description strongly implies this. The conflict of interest in this case is egregious, and asking a committee member for guidance, while potentially helpful, is ultimately insufficient for excluding a conflict of interest.

I've occasionally been in a situation where I was asked to review something I thought would normally be a conflict. I was told it would be ok if I felt I could be unbiased. It sounds like you think you can't be unbiased... so just say no.

The main requirement with a conflict of interest is that it must be disclosed to the editors.
Reviews aren't processed automatically, but by an editor. The editor is supposed to read your review - in particular if you indicate a conflict of interest - and may then decide whether your review is fair, or may need to be ignored.
So just do a very thorough review (in your case, probably a very much critically thinking review, because this is also a chance to reconsider foundations for your own work!) and in the confidential remarks, repeat your conflicts.
I have also reviewed papers where I had prior collaboration with one of the authors. It turned out the other reviewers liked the paper, but I found flaws in the proofs. My review "won", they had to fix the proof to get it accepted. Sometimes, a reviewer with a conflict may be the most valuable, because he puts much more effort into the review. The editors just need to know and pay attention to potential bias.
Personally, I would not do the review because you are already working on a follow-up and seem to be quite close to the authors. This most likely makes you too "blind" for the actual problems of the approach. And in the worst case, imagine that you find a fatal flaw when doing the review, which may even kill your own current work? Imagine you find some weaknesses, they need to resubmit, and your own work cannot get published until theirs is, so you end up delaying your own work... so by doing a good review, you may hurt your own research? It's probably better to have someone else do the review - or they missed some weakness, or if they delay publication, neither is your fault. Also, will you be able to remain anonymous to the authors? Imagine you find a weakness, and 'kill' their submission, and you somehow give away you reviewed... will they take this well?

I think your last comment is the weakest. If there is s flaw, whoever finds out BEFORE publication, they should be grateful the paper was killed/delayed. Better than being published and find a flaw afterwards.

That is what is should be like, but you'll learn that people feel otherwise. People will rather get their work published, then find out it's useless. You may even get to write another publication on the problem.

While it's true that a potentially-biased review might be the most valuable, this is actually an argument against anonymous and impartial reviews in general. Now, you can make this argument, but not - I believe - as a justification for reviewing one paper out of many in an interest-conflicted impartial way.

Well, it is not anonymous to the editor, and what do you mean with impartial?

TL;DR: I think (iii) is your strongest problem.
(i) and (ii) can be mitigated by the editor by having other reviewers not collaborating with the authors balance with your likely deeper expertise; this requires a legitimate judgement call.
However, as for (iii), separating the contribution of your own work from theirs under the influence of a review cuts into your own flesh. It is similar to be asked to review proposals for a funding call in which one submits oneself. One can never win: either one violating ethics by damaging other submissions, or one is generous in giving proper credit to others, thereby endangering one's own submission (kill one's own child). And it looks bad if you were on the committee, no matter what you do.
Your case is probably not quite as extreme, but requires careful handling. If you feel compromised by your current extending work on the topic, you probably should tend to decline.

I believe that the reason the committee gave you for giving you the go-ahead anyway (small community of experts and therefore any reviewer would potentially have a conflict of interest) is a common one in this situation. However, if you believe that you are unable to give an unbiased review, I suggest recommending a new reviewer to the committee. This will alleviate the burden of the committee to find a new reviewer and they will be more accepting of you declining to review.

Suggesting someone else is a good idea (I also mentioned the option of finding someone else in my answer), but a reviewer suggested by a very biased reviewer suffers transitively of some bias too... also you're assuming it's the OP who needs to convince the PC chair of something, which is not the case. Finally - you didn't write you, as opposed to OP, believe about OP's situation - and I think it's important to do so.

TL;DR: You mustn't review the paper; escalate to force the PC to devise an alternative course of action.
It would be unethical for you to review this paper. If your research community is so small that the only person to be found who can review a paper meets your conditions (i) - (iii) (especially (ii) and (iii) ) - then it is not a field in which proper peer review is really possible at all. Or at least, some of the field isn't.
For such (sub)fields, the first thing that has to go is anonymity (which seems to be in effect in your case): The authors would actually know it is you who wrote the review (or perhaps another similarly-interest-conflicted member of the PC). The second thing is the pretense of publication selection by fair peer review. There should be other arrangements, either simply including in all papers into a non-reviewed section (since there should really be very few of them), or enacting some kind of collective decision-making process regarding which papers make the cut, that involves most/all stakeholders within this small community.
But I doubt this is actually the case. I'm guessing the PC chair was brushing you off to avoid more hassle - as I'm sure she's swamped with other work. I'm almost certain there are people - perhaps not on the PC - which can review the paper and are less conflicted. The PC needs to reach out to them to ask for help with the review. And a last resort for the PC (again, assuming she doesn't face the same situation for many papers) is to accept this paper without review: The committee accepts, but notifies authors of its failure in the effort to find an impartial reviewer, and the reason for this failure. Such an action should probably be taken after consulting all PC members to form a consensus.
Now, there are other ways to handle this situation, I suppose - those were just a few alternatives; but what the PC chair cannot and must not do is brush conflicts of interests under the rug. And the same goes for you: Her authorization does not justify your actions (it merely partially shifts responsibility for a misdeed).

Reviewer anonymity is by no means a core requirement of ethical peer review, it’s merely a (fairly debated) property of the currently prevalent form of peer review. I do agree with the rest of your answer though, especially the bolded part, and the last paragraph. I’m a bit dismayed at the community’s blasé attitude towards this flagrant ethical violation.

@KonradRudolph: I didn't argue reviewing anonymously is a core requirement, but it looks like that's how things are done in OP's specific case - since otherwise the authors would probably be "in the loop". Edited to make that a bit clearer.

As far as I can tell, there are two potential problems if you review this paper. (1) You might be biased. (2) People might think you're biased (even if you really aren't).  The program committee member's saying it's not an issue indicates to me that (2) won't be a problem.  But (1) is something only you can decide about.  If I were in your position, I would first reflect very carefully on whether I can write a completely fair report.  If so, I'd go ahead and review the paper. If not, I'd tell the PC member that I can't review the paper because I'm not confident that I wouldn't be biased.


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Lack of motivation-Changing PhD
I know there are different posts about changing PhD, but with such an important decision I would like to ask the same question but including the details of my personal situation.
I am in the first year of my PhD (now starting the 8th month). I did my masters in my home country, Spain, where I did research in computational protein dynamics although my background is about computational chemistry at atomistic level (Quantum Mechanics). I really enjoyed my masters, but I decided to look for a PhD position in quantum chemistry again. I got this position in Stockholm University. I though I would enjoy it, but after 7 months I am not enjoying at all, I do not trust my own research and my interests are moving far from this field. The thing that my group is the only computational group of the whole department is also a big point, because all other groups are experimental and this make me feel quite isolated.
I already had a talk with my boss, where I expressed all my concerns and where we agreed to look for new things. He was really open-minded and comprehensive, and I will try my best for the next months to see if the change fits me. However, my apathy feeling is still present and I think I should start considering the possibility of changing PhD. Do you think I must change only considering this personal feelings? In the past I was really passionate in science, but this feeling of apathy is keeling me. I want to make clear that there is not any problem with my boss or my group mates (all of them are really fantastic), just with myself and my motivation.
Any opinion and advise is welcome


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Community College/College Teaching Certificates
I have both an MA and an MS in Mathematics and would like to teach community college or college level mathematics. The problem is that I have no teaching experience, and so far I have not even been able to get adjunct positions. I would go for a PhD for the purpose of increasing my chances, but am not really interested in research.
I recently discovered some certificate programs for community college/post-secondary teaching which include a one course teaching practicum.
I am interested in knowing about experiences candidates may have had with such programs and if such a certificate would be taken seriously when it comes to being hired.
Also, would high school teaching experience have any weight in obtaining community college/college teaching positions?

Did you not TA for classes when you were in grad school?

I did a post-secondary teaching certificate and I thought it was very helpful.  But I cannot comment on how it is viewed in the job market.

In regards specifically to the value of a post-secondary teaching certificate, this would help you as the practical teaching portion of one course - as well as hopefully the pedagogical teaching portion - at very least moves you from "no experience" to "some experience", and signals that you are interested in teaching. Both are certainly very important at teaching-focused institutions. If you also had TA experience at all during your studies, of course, you should include that under teaching experience (but I was assuming you'd mention that if you experienced it). It is in no way guarantee of getting a teaching job, but you can reasonable ask the program if they can direct you to people who gained the certificate and took jobs at a community college to see if you can email them, ask about any stats they keep on people who've obtained the certificate there, etc.
For teaching high school, yes this would certainly help in terms of community colleges and would absolutely count as teaching experience. Most instructors I know at community colleges actually were high school teachers at some point. My own undergraduate University actively recruits high school teachers - including retired ones - who have a masters degree in their subject to come and teach introductory classes for them. They need a masters because the state/institution requires it, but otherwise they just want the teaching experience.
One of the reasons teaching experience in high school can be of interest is because...well, there really isn't a world of difference in freshman taking first year math and high school seniors, because most of them just got out of high school anyway. There are certainly differences, especially the part where some of your students are older and may have been out of high school for years, but the experience is expected to transfer at least partially. It isn't as good as previous experience teaching in college, but it beats zero experience by far.
Your area may have substitute teaching programs which need willing, able, responsible people (read: people who will show up when told and won't be an embarrassment, and accept the humble pay), so you might check into that as well to help you move from "no experience" to at least "some experience". If you are interested in high school teaching you might need to ensure your area doesn't specifically require teaching certificates (high schools in some areas require more specialized certification in teaching than Universities), however - and admittedly how to get a job as a high school teacher is well beyond the scope of this site.

This answer seems to have no understanding of a post-secondary teaching certificate.  It has nothing to do with a secondary education teaching certificate.

@AnonymousPhysicist I actually mis-read the part where it explicitly mentioned post-secondary teaching certificate with a practical portion, which changes this part of my answer. I'll update appropriately.

@AnonymousPhysicist I've edited the answer to more properly reflect OPs situation, and not my misunderstood version of it. Let me know if it more correctly reflects your experience with post-graduate teaching certificate courses, etc.

I think I understand what you're trying to say with "For teaching high school, yes this would certainly help in terms of community colleges and would absolutely count as teaching experience" but maybe a little more editing would make for an easier read?


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Conclusion of an Important Article
Let's say I solved a million dollar problem [for instance P = NP] and wrote a paper describing my proof. Let's assume the conclusion starts like this:
Proposed algorithm, as far as our analysis goes, achieves polynomial time on an NP-Complete problem, showing that P = NP.
Should I add a sentence like this to the conclusion?
All the proofs in this article need to be checked by experts, to make sure that they don’t contain any logical flaws.
Given that no one can be sure about a lengthy proof, and given the importance of the P = NP problem, I feel like it should be added. But it may also weaken the conclusion. What do you think?

One presumes that you have checked the proofs. And, one presumes that you are an expert. So, no, don't include that wishy-washy sentence.

I'm not a mathematician, and I haven't read a single mathematics paper in my life. But I would assume that every proof that is published will need to be checked by experts, starting with the reviewers. So, my concern would not be that it weakens the conclusion -- pointing out potential flaws in a paper is a question of scientific sincerity, so that's good. My concern would be that you might be stating the obvious, which might even sound a bit patronizing to some of your readers.

@Schmuddi, IMHO it does weaken the conclusion.  Of course it will be reviewed.  Any paper that included that sentence though would be casting so much self-doubt on it that I can't imagine it not making any reviewer think twice even if they'd thought it was OK.

No, leave it out.

It's redundant, because obviously any paper that claims to solve a major open problem should not be accepted by the community unless it has been carefully checked.  You don't have to tell people that.
It's arrogant, because it's not up to you to tell experts what to do.  They will decide for themselves if the paper has enough merit to be worth their time to check carefully.  The vast majority of such papers are actually just garbage, and they do not need to be checked by experts.
It makes even less sense in a manuscript being submitted for publication.  Just by submitting it, you are asking for it to be checked by reviewers; and when it is published, it will have been checked (though the community may still expect further checking before they really believe it).


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How to handle one doctoral supervisor being unhappy over a doctoral student's preference for the other supervisor?
For my doctoral programme, I have 2 supervisors: 1 academic (i.e. a professor) and the other an industrial.
Over the past few years I've found that my industrial supervisor isn't really able to contribute to my research that much. It's not that he isn't smart or anything like that, its just that he doesn't seem interested in me producing actual research and would rather I just implement existing literature or settle for something that doesn't fulfill my research aims.
I don't really want to go into too much detail but essentially my industrial supervisor has a low opinion of me because from their perspective it seems like I just do whatever my academic supervisor tells me. This isn't true at all.
Before knowing this (he told me himself in no uncertain terms) I felt like I could respect my industrial supervisor and talk to him about my work but now I don't really want to talk to him unless I have to.
What is the best way to deal with my situation?
For context, the current contact arrangements are that I speak/video call my industrial supervisor every weekday. With my academic supervisor its a back and forth email chain with a video call when we can't express things in an email. Prior to COVID, I would work at my industrial supervisor's company everyday and have to arrange skype calls from the office to my academic supervisor. This was difficult to do, so I only really spoke to him once a month and saw him in person every other month (its a 600km round trip).

There is always a conflict between academic blue sky type research and industry research, where there is a problem that requires a solution 'immediately'.   Your academic supervisor needs to discuss the expectation of your research with the industry supervisor.  Your industry supervisor needs to understand what is academic research, and that you won't get a PhD from doing industry work; i.e., you are not a low paying staff member he/she can exploit to get things done.

What is being discussed on these every-day calls with the industry advisor? That seems excessive. I'm used to hearing people on this site struggle to speak with their advisor as much as once a month. Especially if the industry advisor is not usefully interfacing with your research, then what's the point of those daily meetings?

I could be really snarky about it but I don't want to out myself by accident. He just wants to keep tabs on us. We don't get anything productive done in these daily meetings. Its a "What are you going to do today?" sort of meeting.

While there are lots of ways to go about this, one is to have your primary (academic) advisor intervene in some way with the other person. The industrial person needs to understand that your doctoral research comes first and shouldn't be compromised.
But, this assumes a few things that might not be true. First is that the industrial person can't put a veto on your work somehow. But better that the two "senior" people have a discussion about priorities than you fighting with a more senior person.
But analyze the situation before taking any advice, including this one. It is you that is at risk.
And, for what it's worth, your preference for the academic advisor is certainly appropriate.

This does seem to be the right thing to do.
The only concern I have is that I could lose a significant portion of my stipend if the industrial leaves. Aside from that, I don't think they can veto anything or prevent me from graduating.
The industrial person needs to understand that your doctoral research comes first and shouldn't be compromised
My director of studies has had to do this already for a different yet related reason. I'll speak to them to let them know what has happened recently so if things get worse it won't be a surprise.


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Scientific Research Publishing - Unspoken Rules
I would like to know more about some (unspoken) rules in scientific research publishing. More precisely, i am interested in computer science field.

Can someone expect his papers to be published in any top level journal (M23, M22, M21) without completed bachelor studies or master studies?
Is it true that professors have better chances their papers to be published than graduated students or it is just a justification for academic exploitation?
Can someone who works in IT industry or is unemployed expect his papers to be considered or even published?
What are the differences between the first author and other authors? Taking the academic exploitation into account, is it profitable for a student to be the second author after the professor?

I have no idea what you mean in 2).

In the case of computer science, a couple of venues (conferences and journals) have recently introduced a double-blind review process, which means that the reviewers do not know the identities of the authors. That being said, a professor typically has more experience in writing publishable papers than an undergrad, which may be helpful when trying to write a publishable paper.

Related: http://academia.stackexchange.com/questions/3010/does-one-need-to-be-affiliated-with-a-university-to-publish-papers

#4 is rather different from the rest of these and should really be asked in a separate post.  In general, Stack Exchange works best when one post contains only one question.

Please ask one question per post. Also, some of these questions have already been asked and answered on this site.

See: What does first authorship really mean?, Does one need to be affiliated with a university to publish papers?

It sounds like you're asking about a specific situation you are in. It's probably better if you briefly describe your situation in your post, rather than asking questions without context.

In order:

Theoretically, sure. Practically, almost never going to happen. The chief reason for this is that graduate studies are designed to instruct you on how to conduct and report on original research. Even a bachelor's degree alone will usually not be sufficient; anything less than that, and you probably don't have enough expertise to conduct cutting-edge research.

As @lighthousekeeper pointed out, being a professor usually means you have more experience in producing papers. As with most things in life, practice makes perfect.

Someone in the IT industry -- most certainly. Researchers at Facebook, Google, Amazon, HP, and many other companies have dozens of papers (if not more) published every year at top CS conferences.
An unemployed individual certainly could get published. But see #2 for why this is unlikely to happen. In addition, not having access to research databases and journal databases will stymie most individuals looking to conduct independent research (though not all).

Entirely depends on the field. In some fields, author names are listed alphabetically, so it doesn't matter who is first or last. In other fields, the first author is usually the researcher who wrote the majority of the paper. As a student in CS, there's nothing wrong with having second authorship on several papers. You'll want to eventually have first authorship on at least one or two publications, but any authorship is valuable when you're starting out.

Even in CS author order may be purely alphabetical (depending on how theoretical the field).


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How to deal with discussion of poor performance due to personal issues?
I am an undergraduate student on an integrated masters degree, currently getting started on the journey of looking for potential PHD projects/supervisors. I have just written up my academic CV (by the way - this wasn't the point of this question, but one page or two? Do people care?), and I had a thought after putting the year-by-year breakdown of my grades.
My first and second year percentages are mid 60s, whilst my third year percentage is 77. This is due to the fact that during first year I experienced the onset of a relatively severe mental health issue (I hear voices in my head from people who aren't there), in second year I was undergoing treatment and trying to find what was/wasn't working, and by third year things were sorted out and I'm somehow "back on track".
I'm imagining the question "Why are your averages in first and second year so much lower than third year?" being thrown at me. This is a fair question, because third year is really quite significantly harder than the first two years, and I was also just back from a year long work placement which I undertook after second year.
How should I answer? I'm sure the answer "Personal problems" would be acceptable, but what if the question is asked "Would you mind discussing those?"? I have no problem discussing my mental health issues, and I no longer consider myself somebody who "suffers" from them, but I am aware of the possibility that in terms of PHD applications this can somehow be a red flag.
I also have no problem giving the answer "I would rather not discuss those, but they are no longer issues for me" or something along those lines.
I also thought "That is something which I would be happy to discuss with my PHD supervisor, if I get one, but is not something which is easily explicable in the time we have here." could be a reasonable answer. What would be the best way to deal with this potential scenario?

Shortly, for your CV: One or two pages is okay where I am from. But if you could put the information on one page, the question is why would you have two? If, on the other hand, there are a lot of accomplishments to be listed, of course do not omit them just to make it fit on one page.
But now to your general question, and to discuss that I would like to quote you.

I have no problem discussing my mental health issues, and I no longer consider myself somebody who "suffers" from them, but I am aware of the possibility that in terms of PHD applications this can somehow be a red flag.

Personal problems could mean anything, not just health issues. If it were me, I would maybe try to inquire how "expertly" you have figured them out, as there is a difference between "I just started to feel better." and "My mom recovered fine from her illness/ I dealt with the problem adequatly/..."
Although, if you are fine discussing it in a little more detail anyway, a "red" flag might become a "yellow" flag.
For example, if you tell me you had mental health issues, I will try not to judge you, but without further information, I have to face the problem that I am treading on eggshells. I would not want to trigger a trauma in you or something similar. Can I work with this insecurity? I don't know.
On the other hand, if I know at least a little about the problem, it will give me a chance to watch out for you, to recognize a reoccurring problem early and be able to warn you, to not trigger said trauma, to generally be able to have an idea how to treat you right.
I don't mean that you have to throw your history at everyone, but if you are in an interview that is going well with a person that you judge to be well-meaning, it might benefit you to be honest about it.

How about "I had some medical issues", or "I was diagnosed with an illness, but things have been going much better since I got treatment for that"? Mental illness is just an illness, you don't have to specify the mental part if you don't want to.

Honestly and truly, you're overthinking things.
I don't think you will be asked about your first and second year percentages- and this is coming from direct personal experience (you don't say, but I'm assuming, like me, you're in the UK, applying for UK PhDs).
I also completed an integrated Master's course. My first year grades were worse than yours, and although my grades did improve over the years, I was still nowhere near a 77 average in my third year. My "low" achievement was also partly due to mental health problems. I never mentioned this once in any of my application materials (CV, personal statement etc) and it was never brought up in interviews.
Provided your grades show an upward trend i.e. they get better over time rather than worse (which yours do) you have nothing to worry about. This is especially true if you do well in a course that has a subject you did badly in as a prerequisite e.g. you got 54 in Calculus I but got 75 in Calculus II.
In the unlikely event that they do ask about your previous low grades, answering that it was due to personal problems or illness is perfectly acceptable. If they press you, just be honest and tell the truth (as you should when answering any interview question!). However, in my experience of PhD interviews, they are much more interested in finding out what your current skills and research interests are, not about some low grades a couple of years ago (quite a long time for a young academic!) which you have since compensated for.
At a tangent to this, I would strongly recommend that you get some research experience before applying- I expect that as part of your Master's you will be doing a final year dissertation. Be ready to talk about all aspects of this project in great detail at interview, as well as your future research interests and how they link to the project (if your Master's and PhD will be in the same field).
Good luck and try not to worry too much about PhD applications- it's a stressful time and you'll be very glad when it's over!


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Is "How good am I?" a reasonable question to ask a supervisor?
I have recently completed my undergraduate degree, in mathematics. As part of the final year, we had to complete a "project", which was effectively a 40-page (ish) dissertation on a topic of our choosing. This was done with the aid of a supervisor, one of the researchers in the department, for the duration of the year.
During the undertaking of this project, I felt like I developed a good relationship with my supervisor (who I met once a week, and who provided a reference for me for PhD applications).
At times, particularly when knee deep in PhD application stuff, I started to get a little negative/worried about my long-term prospects. This seems to be a fairly common problem, from what I read here. On more than one occasion, I was seriously tempted to ask my supervisor whether he honestly thought I was any good, had any reasonable prospects doing maths/a PhD/research, whether I should do something else, etc.
I never actually ended up doing that, because I always decided that it was a bit of an unfair question, and that I my supervisor quite possibly wouldn't know anyway.
My question is: In a scenario like the above, is that ever a question that one could expect a supervisor to answer/answer well? Is it easy to tell, from a supervisor's point of view, what a students prospects are in that field?

They will have a more well-informed opinion than yours, but it will also be influenced by their own particular background and particular experience with you (which is only a slice of your overall life).

A better question to ask would be, compared to other students he advised, win which upper percentile would he place you. That eliminates a potential unrealistically high expectations (e.g. in his opinion you did just ok, but he would not say say  you did great to any of his students)

@50k4 which upper percentile would he place you — I'm sorry, but that is a really stupid question.  Every student has their own set of strengths and weaknesses; different students are good fits for different subfields, different working styles, and different career choices.  There is no global ground-truth total order of students (or researchers, or departments).

I would welcome such a question from a student I'd worked closely with, but I'd also like a bit of time to consider before answering.
But even better, is to ask - also - what you can be doing in the short term to get even better. Make sure the advisor understands something about your long term goals so he/she can best assist.
However, this implies that you have more than a transactional relationship with the advisor and each of you recognizes and respects the advice of one another. Some people are "brutally honest" and will say things you really don't like  to hear. Others are too "conflict adverse" and will tell you things that sound nice but aren't helpful. You will need to judge for yourself the quality of the advice.
But that is the reason for asking how to improve. It helps you directly, avoids personality issues to some extent, and helps you better judge the "raw" assessment.
In any case, if you are good enough to ask the question, you are probably pretty good anyway, even without knowing much more. I had professors in my background of whom I would gladly ask the question, others of whom I certainly would not, and still others for whom I'd think long and deeply before asking. But that was more personality than anything. If trust is there, it should be fine.
My own background somewhat influences my response here. When I was in secondary school I was told, on the basis of some standardized test, that I didn't have very good prospects and shouldn't set my goals too high or I'd be disappointed. This was largely based on mathematics. It wasn't a request to an advisor for guidance, however. The episode made me so angry that I decided to prove them wrong and later earned a doctorate (among other degrees) in math.

Yes, this is a reasonable question to ask any supervisor and it's reasonable to expect a thoughtful answer.  But to ensure a fruitful and helpful discussion, it's helpful to add a little more structure, explaining the kind of feedback you're seeking.  For example:

You've had a chance to observe my work up close and over a longer
  period than my other professors, so I'm hopeful you might be willing
  help me take inventory of my strengths and weaknesses, what I do well or
  not so well and, considering all that, the academic and career options and
  strategies you'd suggest.
I really value your advice.  Could we find a time to meet in your
  office?


text:
Emailing a student corrections to their typed notes
I study undergraduate mathematics at university. In one of my units, the lecturer does not provide any notes (typeset or otherwise), but has said that if anyone else who attends the lectures wants to typeset some notes, he'd be more than happy to check them over and then share them with the class.
Remarkably, one of the students is actually doing that, and is actively typing up notes for the course as it goes on, and those notes are being shared via the online course page with the class.
Unfortunately, the notes have some errors. These are often, rather than just being typos, completely incorrect assertions. I don't blame the student who's writing them at all; I completely understand that having written the notes it's very difficult to then check them over properly.
I want to email the student with a large number of corrections to the notes he's typeset, but I don't want to come across as overly assuming. I feel that emailing the student who's taken the time to make these notes to such an effect might come across as condescending - or worse, "I'm better than you, do it like this". Should I email the lecturer instead? What's an appropriate way to approach this situation without upsetting anyone?

Email them offering to provide comments and corrections first. Then mail them the corrections if they take you up on it. Obviously congratulate them on their effort, show interest in their work and offer help (who is doing the notes if that student cannot attend one of the lectures?)

Are the notes shared before or after the lecturer checks them? If you find errors in a "lecturer-approved" version, maybe you can ask him to clarify; it is also possible that you are wrong or that there is a misunderstanding.

It is said that the lecturer checks them over before they're put online, but I'm not sure what that actually entails - from some of the problems I'd imagine that the check is not more than a brief skim (especially at this time of year, lecturers themselves are obviously also very busy). I do account for the fact that I may well be wrong in what I think are typos/corrections, I will be sure to try and make that clear in my email too.

Since the notes are shared via an online system, it seems like a good idea to collect all found errors and typos in the very same online system, e.g. if the system provides a kind of a forum. This would have several benefits:

Everybody who spots an error can report it right away.
Everybody who suspects an error can check if it actually is one.
The author of the notes or the instructor can answer in the forum and indicate if this is an actual error and announce when it has been fixed in the notes.
There is the possibility of discussion around the issues - sometimes one thing appear as an error for one person, but not so for another one and in the end it may just be a matter of convention (this is also true for mathematics…).

Note that the etiquette of the forum is very important: Everybody has to be polite, ask and answer in good faith and no blaming shall happen. But if this is supported by a moderator (e.g. the instructor) this can work very well.
I used a system like this for the lecture notes I typed and I even announced and awarded bonus points for everybody who found an error in the notes (this seemed to be a good idea as it makes it pretty clear that all lecture notes may contain errors…).


text:
Is it reasonable to report another student for cheating when it has no impact on me?
I currently am studying on an Undergraduate Maths course, in my third year. At my university there are various modules from which students can pick to make up the required number of credits for the year.
5/6 of my circle of friends take a particular (popular) module which I do not. Recently, they had a piece of coursework due for submission. They had about two weeks to do it, and the submission deadline has now passed.
One of the students, with whom I am friends, has informed me that she took pictures of her answers and gave them to another student (with whom I am not friends) three hours before the deadline, because that student had done little/no work and was going to fail. This was not a group piece of coursework, and she essentially gave the other student her answers.
I'm not entirely sure why I'm so upset about this, considering I don't take that module and it has nothing to do with me. I have my personal opinions about the student, but I feel like that shouldn't be relevant to the situation.
I do want to report this as cheating, but I'm also well aware that it's effectively hearsay. None of the others of my friends (who do take the module and who are also aware of this incident happening) has reported it.
I'm wondering whether it may even be out of line for me to report this incident, given that I have absolutely no evidence in my possession of what happened, and I do not take the module, and I wasn't involved in any way.
Is it appropriate in these circumstances to report what I've heard to the lecturer of the module?

Wrong assumption: your colleagues' cheating does have an impact on you. If the amount of work needed to obtain a degree is low, and if people with that degree are less well prepared, then that degree is effectively worth less in your CV, in the eyes of a possible employer.

Some institutions have an honor code whereby students are required to report instances of cheating by other students.  Does yours?  If so, then at least theoretically, you yourself are liable for punishment if it is ever discovered that you knew and didn't report.  One possible course of action, which at some places would be standard, is to tell this student that she needs to report herself, and that you will if she doesn't..

The evidence does not need to concern you at this stage, provided you are sure that the cheating took place. It is the responsibility of the department/university, during any investigation, to establish evidence. You are just a witness.

No it is not appropriate. You have better things to do.

I would take it to a department administrator, not the instructor. // Consider that you are part of the university community.  Also, the friend who told you what she did may be subconsciously asking you to intervene.

Some of these responses are categorically absurd. This is all you do, talk to your friend about how uncomfortable it made you to find out about this transgression. Then deny ever hearing about it.

It is perfectly reasonable to not want to associate with unethical people. You have a dilemma, as it is difficult to resolve this without yourself being ostracized. Most people just "go along to get along" but that isn't ethical either. Some people who cheat in small ways will cheat, also, in larger ways. Some people who condone cheating will cheat themselves. Cheating in general leads to bad overall outcomes eventually. The profession as a whole should work to eject its unethical members. You have to judge whether you need to help in this now, as a vulnerable member. It is a hard choice.

i would not have responded, but looking at all those answers I feel there is the need for an different oppinion ,) If you ruin an undergraduates career (and possibly the one of your friend) because you accuse them of copying some part of a homework you will be socially isolated at that university. I don’t know how that works on your university but solving problems with each other is a quite normal way to study (and pass homeworks). Besides that, it will be hard to proof.

As others have already mentioned, cheating is wrong and it's the right thing to speak up when someone commits a wrong. It may also indirectly affect you when someone cheats (eg. through grade inflation).
However, by reporting the cheater you are also implicating your friend who passed on the photos and facilitated the cheating. Your friend might feel upset (and perhaps rightly so) that you didn't put your friendship above some general (and perhaps minor) moral obligation. I caution that your obligation to report is not unconditional in the sense that you have to accept a disadvantage for yourself, such as a spoiled friendship. Moreover, I would argue that you also have an obligation of loyalty towards your friend; whether or not that 'trumps' your obligation to report depends on how close your relationship is.

As faculty members, we know that cheating is an ongoing problem - both for in-person courses and online courses. The reasons for students cheating vary, but it's frustrating for faculty.
I imagine other students' cheating bothers you, because you completed the work yourself and cheating overall compromises the integrity of the class. I agree with the comment stated earlier that if cheating is widespread, then students aren't leaving the course or degree program adequately prepared. In time, this can undermined the quality associated with your program.
That being said, you have observed academic dishonesty - it is not hearsay when someone admits to you that she shared her work with another student. You do not need testimony from the third party for this to be an observed case of cheating.
Most university Academic Honesty Codes do require students to report cases of dishonesty. That being said, the faculty member may not realize that his or her course has assignments or assessments where students can easily cheat. If you are unclear about the overall situation, you may explain to your professor that you believe that cheating could be a problem, but are not 100% sure. Then, it would be the faculty member's role to evaluate and take action for what is happening in the class. I'm sorry that this other student put you in this predicament.

The question of morality–is it right or wrong–that you pose is one that can only be determined by you. Some people might give you the opinion that it's never right to, for example, break the law; others are more lenient with exceptions. Ultimately, it is an exercise for you to discover your "moral compass."
In terms of the practicality of doing the report. No, it is not out of line for you to report. However, keep in mind that cheating is a very severe matter in most universities and your allegations will (or should) prompt the professor to conduct an investigation. It is likely that your professor will have to involve your friend (who took the pictures) both to uncover the student who took advantage of the answers, as well as her for facilitating them. The results of the investigation will depend on the approach your professor takes. If he/she is able to simply deduct that cheating occurred by looking at the two submissions, then perhaps you won't have to sit through a student conduct committee. However, if more evidence is required, be ready to testify against them in front of a committee (if your school utilizes one for such violations).
Finally, as mentioned in one of the comments, the impact of their academic integrity violation does affect you. In the long run, it can impact the quality of the course, the perception of your undergraduate program, etc.


text:
Two different abbreviations of your name in literature
I have been publishing in the past with a certain abbreviation of my name which I am unsatisfied due to draconian rules in my previous institution which wrote my name in the following way: X. Y. Z. lastname2.
Being my name composed of the following nouns: firstname1 firstname2 lastname1 lastname2.
For new publications I wish to change it to another format such as X. Y. lastname1 lastname2.
I wonder about the impact it might have in my academic profile, this is, whether articles databases would fail to index correctly both of the publications to the same person.
I also wonder what other complications this change of my name abbreviations might carry.

This may be field dependent since different fields use different software and systems to keep track of citations.

How many publications are under XYZ Lastname1?

@AzorAhai there are two works with that institution

A few of my early papers have my name in the form "A. R. Blass"; the rest of my papers have "Andreas Blass".The only effect of the change that I've seen is one letter, long ago, from Mathematical Reviews, asking me to confirm that both names denote me.  More generally, Mathematical Reviews (now MathSciNet) is very good at determining when two names denote the same person. I don't know whether fields other than mathematics have something similar.

One of the implications that will happen is that it will be slightly more tricky to cite your works:

general confusion when citing an author with the inconsistent spelling of the name
this and this talk about initials usage
inline citations of multiple works may become weird
reference manager systems might be confused, and organizing a library would be more complicated (it is already complicated with all other caveats)

However, I have to say that the problem of the different spelling of the name in cited works happens quite often, so I would incline to say that the author being happy with the way their name is spelled is much more important.

Orcid is a modern tool for disambiguating researcher identities.
You could also have a public Google scholar profile, Arxiv profile if appropriate, and profiles at any academic social networking sites widely used in your discipline and make sure they all list all of your articles, and no others. (Having falsely listed articles reduces the trustworthiness of the listings; many Google scholar profiles have random entries with no citations at the end, for example, due to people with similar names having written a bachelor's thesis at a professional higher education facility.)
Given these solutions, it should not be a huge deal to change the way your name is written. People do also change their names and survive the process, so you should be fine.


text:
Is it worth staying an extra year to bring up GPA for grad school (Master's)
I'm currently a junior at a Canadian university studying math. In my sophomore year, I got 2 Cs in two computer science classes, a D- in biology, and then in my junior year I ended up getting two Cs in two of my math (intro to analysis and DEs) classes.
I don't really want to make any excuses. My overconfidence and long term depression (I'm in counselling and on medication now) kind of were my vices for the past few semesters. I'm thinking about my prospects beyond undergrad.
I am hoping to apply to schools for physical oceanography, geophysics, and computational science and engineering. I'm particularly interested in UC San Diego (Scripps, CSME), UC Santa Barbara (MAT), University of New Hampshire (Marine Science and Ocean Engineering), and Dalhousie (Oceanography). Depending on how the rest of my academic career goes, I may apply to more computational mathematics programs.
I am just starting to study for the GRE and have a number of research projects under my belt and have presented an independent project at a math conference, which I hope to publish in the coming months.
Should I consider staying for an extra year or semester and maybe retake the math courses I did poorly in, seeing as they are important courses, and perhaps some other courses to boost my cGPA overall. I will be able to manage a 3.0 (B) average, which is what most (if not all) the schools I'm interested in are looking for... but I'm unsure if those sub-par grades will or can be overlooked.
Any help is appreciated! Thanks!

I'm sorry to say that I think this is off-topic for this site as being too specific to your situation (see here). That being said, I think that you're going to need to have a talk with your adviser - the research projects will work in your favor (especially with good letters of rec), but they may not be enough to offset the low GPA.

@tonysdg I don't think of it as off-topic. I too have similar circumstances. So do a lot of students.

My friend, you're being answered by a guy (me) who entered the engineering graduate school of his choice despite having several Cs, 3 course "withdraws", and an entire scrapped semester so that I could "find myself". All of this occurred because I was seriously questioning, in my junior year, whether or not I wanted to continue in my major. Working at a crappy, low-wage job for an entire semester made me get my head screwed on a little better. After all of that, I completed my B. S. degree with a 3.50.
Despite your comments, I think you might be in a better position, academically, than I was!
My gut feeling is that you should apply to all of those graduate schools because re-taking classes for a year would be a possible, sizable waste of one year. If those schools don't pan out, then you can re-group and decide on your next steps.


text:
Helping filter what really matters
So the other day I received an email from the department head stating:

Please list your highest degree.
Please list any professional development activities that you’ve done in the last 5 years.

He emphasized that it was for reviewing the department as a whole.
Now, I'm an adjunct so the same rules don't apply to me as the full time faculty, but it did help me focus a little bit. I thought about how my inbox is always full with professional development activities, but I don't think any of it could be listed in a cv.
Facebook? Really? But I do subscribe to 2 different Facebook groups in my area of expertise. I have since unsubscribed from them both.
Is reading the Wall Street Journal something that I can claim as a professional development activity? What about the myriad of other subscriptions? Discarded.
What should a person focus on in order to advance their career as a teacher? Is getting a PhD the bar that must be hurdled before anything else?
Here is my question: How should I approach my department chair and say that I would like to beef up my Curriculum Vitae, with the school's help?

Directly, as if he were a real live flesh-and-blood human being.

Note: just because your department head is asking about it doesn't mean it's something you would put in your CV. It might be useful for the department in developing professional development activities or for talking about how people in the department have access to professional development, but that doesn't mean it belongs on an individual's CV.

It's a pretty big topic and here are some cluttered and clustered thoughts:

How should I approach my department chair and say that I would like to
  beef up my Curriculum Vitae, with the school's help?

First, I would not advise going in bare hand. For i) most deans don't really know how to manage adjunct, ii) you may get advice that is not exactly up your alley but feel politically you should say yes. Instead, go with a plan.
It's hard to develop without a goal. So, think what do you want to achieve as a faculty member. And there are many things, just to name a few:
Teaching-related: pedagogical training (from general enhancement to how to deal with special students), use of new teaching technology or platform, (re)design of curriculum, organizing of local/foreign workshop.
Research-related: grantsmanship, training in new technology or skills, management, writing and publication.
More general: professional conferences, network building, public relationship/press.
If you're absolutely clueless, download their promotion package template and see what criteria are considered during promotion. While you are unlikely not in the promotion track, the contents will be helpful.
Pick 1-3 for next year. Then, before your next annual review (if you don't have one, schedule a meeting), frame them as:

In the next (6 months/ 12 months), I would like to achieve _______ (a goal). This would bring the benefits of _______ (at least one win-win benefit). In order to do that I'd like to know if I can _______ (your ask).

For example: "In the next 12 months I'd like to implement flipped classroom format in the course XY111. This would be a timely response to our university 2030 Teaching Goals announced last month. In order to do that I'd like to attend this 3-day workshop in DC. I'd like to see if the department can allocate some stipend for this development activity."
Simply put, just follow the SMART: Specific, Measurable, Attainable, Relevant, and Time specific.

For routine development, make sure to familiarize yourself with faculty benefit: tuition remission, access to library services, discount to other academic activities, etc. Milk that affiliation.

Think win-win or who would benefit other than you when justifying your arguments. For instance:

Is reading the Wall Street Journal something that I can claim as a
  professional development activity?

to that I would say no because staying on top of the field is more of a routine. But I would say yes to:

Developed 2 teaching cases using op-ed from Wall Street Journal and
  successfully applied them in course XY111. (See class reflection and
  evaluation in appendix.)

because in this case we used what we know to actively improve the quality or variety of teaching methods, while we get to experience using case teaching as a teaching development.
If these seem all very large and confusing I'd suggest talking to some other faculty members who has not vested interest in this matter.


text:
Hiring coder for parts of publication
I'm designing and implementing an algorithm for 3D mesh segmentation. Probably I'll publish the results. However, I'm also interested in using this for commercial means, and to do so I need to hurry with the implementation. For that reason I'll need to hire some coders to implement parts of my algorithm.
In my publication, Do I need to reference this coders? Is this allowed in academia?

You should certainly mention how you achieved results that are not your own work.  Not sure how you "cite" a coder but I think a simple sentence like "This result was attained with the help of [Xiao Smith] and [Mohammed Jones] who were paid for their work" is plenty.

@DaveKaye: For me, this would raise the question: "Why are Smith and Jones not co-authors?"  If they made a significant intellectual contribution to the paper, they should be.  If their contributions were just mechanical, I think this should be explained.

@NateEldredge no disagreement there.  I'm not certain from the OP's question how much of a contribution is being made here...

You would typically mention this type of help in the acknowledgements section, if at all. It is well understood that developing tooling requires manpower and that there are others on the team aside from the researchers, and it is up to the authors how to acknowledge that assistance. For what its worth, if their contribution was so significant to warrant authorship, that should be a discussion among the research team.
You mention "cite" in your question; this sort of mention would not go in your references, in case that was your thought.

For what its worth, if their contribution was so significant to warrant authorship, that should be a discussion among the research team. <-- This should be done before you hire coders, to prevent unpleasant interactions at publication time.