aggressive co-worker and bullying at the lab

It is unlikely you can fight this culture, and academic settings have practically no good ways to address bullying of this nature. If you find what seems to be one, look for evidence that it has worked for past students. Recently.

Alternately, make the bully your friend. This is not advisable.  Alternately, work with people the bully cannot impact, which is a version of leaving. This may be unavailable, depending on your situation.

Calling out this bully may help, but if it does not it will make you a target.  Again, it is highly unlikely your institution has any kind of meaningful recourse available.

Your best strategy? Leave. Keep your head down, and start planning your exit now. After you have an exit, cite the bully as the reason to both your PI and HR; it may help others.


How to assign authorship when publishing with Bachelor's and Master's students

...but they might also consent to not being given authorship.

No, no and no. If it is your students' BSc or MSc thesis, they should be co-authors. Period.

  ...I will have to write up the article.

You are right. That is why in those cases, you may be first author on the paper (according to your discipline's norms).

Also, you should always discuss BEFORE assigning the MSc and BSc theses' topics, that ideally you want to work on the suggested topic so that you will get a publication out of it. Also you should make clear that if a student's thesis results in a paper, then the student gets to be co-author on the resulting paper and additional work might be required from him. Earlier discussion always leads to fewer disputes later-on.


Advisor drops MSci student suddenly in final semester

Advise your colleague to take this up with whatever graduate student support is available at your institution.

As a fellow student, there probably isn't a productive way for you to intervene directly.  You don't have any official role or reason for involvement, and any action you can take could be taken more effectively by the student herself.

The situation you describe is quite troubling.  If this is the whole story, then action ought to be taken (and hopefully the university will support the student).  But she really needs to be her own advocate here.

However, keep in mind that you only know one side of the story.  Even though you think quite highly of this student, you need to be cautious in jumping to conclusions.  Sometimes (though not always) when something seems inexplicable, it's because there is more to it than meets the eye.  So I would be careful not to take any rash actions.  Don't let this unduly affect your professional relationship with your adviser.


Should I include publications where I am a "team member" in my CV

Looking at the CV that's linked to your website, I don't see anything inappropriate about what you've done. The only thing to make sure of is that when you have a team listed explicitly as the author in a paper (e.g., "Author X, Author Y, and The A-Team"), you will need to make sure that there is a publicly available listing of the team members available for reference. This could be as a supplement to the paper online (as "supporting information"), or it can be on a permanent web site for the team's endeavors. However, people should be able to confirm that you are a member of this collaboration beyond just what's on your CV.


Where to upload a reprint (post-print) of my publication?

arXiv is not only for preprints (actually, updating after publication is highly encouraged). So if you can self-archive*) and you have an intersection with an arXiv discipline, it is the best place to place it.

*) The only objection to post-publication is in case where you are not allowed to self-archive and don't wan't to mess with it.

For other disciplines, see Preprint services other than arXiv (for other fields).

Or (maybe even better) just - putting them on GitHub repository. It is a stable service + makes it easy to upload work with source code (tex + figures) (much alike arXiv, but on GitHub it is more convenient). Just make sure to link the pdf file in the README.md and reference it properly (i.e. the full citation, the best with a DOI link) so to have its status clear.


Quitting Physics PhD to become engineer?

There are actually a few areas where you might stand out more than someone with a straight up engineering background.

Look at specific types of organizations like Space research and exploration organizations. These typically have other PhDs in Physics in their program and you might have a better shot. A collection of such roles is here:
http://tapwage.com/channel/space-doctor
Another area are interesting startups. Something like 3D Printing focused startups are looking for bright scientists. Given your experience with mechanics, electronics and tools like Matlab, that could be an interesting area and startups might be more amenable to looking beyond very structured educational experiences as they look for good talent
http://tapwage.com/channel/engineer-in-3-dimensions

Ping me via the tapwage.com site if you have further questions or clarifications and I'd be happy to answer.


Who pays for travel for a conference paper completed at previous job?

First of all, I would recommend that one never submit a paper to a conference unless you have some idea who will be going to present it and how their travel will be supported.  I would thus have advised you to discuss the possibility of travel funding with your current advisor before you submitted.  Of course, it is too late for that now, but it may not be for others who read this answer.

That said, depending on the particulars of arrangements, it could easily be either institution that pays for travel.  I have often known people to have one last trip paid for by their former advisor, since it is the completion of their last piece of work.  More often, however, I have known the new employer to foot the bill, as presenting at conferences is generally part of their work as a researcher---it's worth noting that the new employer will be paying for the trip in terms of your salary, even if they don't cover the travel expenses.  I have also at some points known people to end up having to pay for their own travel on a junction like this, but that is unusual and can indicate trouble building with the new employer.

Bottom line: it could be any arrangement.  The old employer may be willing, especially if you arrange before you leave. The new employer is more likely to be willing, if they are truly interested in your training as a postdoc and not just exploiting you for cheap labor.


Bulk download of arXiv (or other publication data set) with metadata AND citations

arXiv's metadata does not include any citation information.

If you are interested in citations in arXiv documents, your best bet is probably to extract them from the PDF files using a dedicated tool (Cermine, pdfx or pdfextract for instance), or from the LaTeX sources, by inspecting the .aux files.

You can download PDF or source files using the dedicated bulk data interface. Using the OAI interface for this purpose is not recommended as it generates a lot of traffic on the main arXiv site.

You could extract a similar dataset from PubMed Central using their API. If you are looking for something broader (not restricted to a particular topic), you could use COnnecting REpositories (they have full texts from a variety of sources, with an API).

You can also use a pre-curated dataset such as the Microsoft Academic Graph.


In general, a PhD is the highest degree you can get. A postdoc is simply a research position that is not permanent, i.e. no fixed contract or tenure. There are some exceptions, for example in the German system where you can get your Habilitation, which is a degree after you get your PhD. But in most systems there is nothing beyond a PhD in terms of degrees.


What should I do if I hate engineering, but my parents want me to become an engineer?

I hate engineering (too practical, too far from physics)

This in an unfortunately common misconception, which can bring nonsense answers like this one on Meta Physics SE, where it is said:

  If I pose this question to an electrical engineer, I will likely get design rules, possibly in the form of immediately useful formulae. If I pose it to a physicist, I may learn something about the physics of electromagnetic fields near dielectric boundaries, diverging fields at conductor corners, and maybe even something about conformal mapping.

As an electronic engineer who specialized a long time ago in engineering electromagnetics, I can tell you that, yes, I've studied all of the theory above and much more than design rules. And I have also studied Langrangian and Hamiltonian mechanics, chaotic dynamical systems, quantum mechanics, quantum optics, statistical mechanics, relativity. Indeed, with an engineering flavour, which I have actually come to appreciate along the years.

Said another way, engineering can be as theoretical as you wish it to be.

  I don't enjoy fixing things

Most engineers don't fix things.

  What should I do?

Some thirty-odd years ago I was somehow in your exact situation: I wanted to study physics, but my parents wanted me to do engineering because they felt that there were more job opportunities.

I studied engineering, but I chose my curriculum to have a good blend of electronics and physics and, now, I cannot be happier than this about my education.


How to teach to an adult person that is not used to study?

Life is dependent many times on being motivated to succeed. There is not a magical formula for having no motivation and yet having success. If your mother cannot find the motivation to learn, it is rather hard to force learning down her throat. If you can make learning matter to her, she will want to learn.

Perhaps you should look into hiring a professional tutor if your mother needs to learn this material for her employment (or the like). Removing the family element could allow for her to feel more motivation. In certain countries, there are programs for adult learning. One can obtain an equivalent to basic high school education from these programs.


My MA thesis has flaws. How do I present it during PhD application?

Do not mention anything related to the master thesis being flawed or of poor quality. It is supposed to be a degree rather than a big contribution.
The situation would vary depending on the selection procedures. Perhaps nobody will even have a glance at it, especially if you have already two papers. Those would be probably scrutinised in more details, or at least taken into greater consideration.


How to get a book indexed by Google Scholar: How to upload to Google book search and what makes a book scholarly?

As at the time of writing, the other answers here are incorrect: you certainly can manually add entries, including books, to your Google Scholar profile. That is done directly on your Google Scholar profile page: there is no need to use some other indexing system.
When you are logged in to the Google account that corresponds to your profile, you'll see this "+" icon on your profile, which allows you to add records:

Select "Add article manually", and when you get to this dialog box, select "Book", and enter the appropriate details:

Perhaps just as importantly, you can also select records to delete (when Google Scholar's algorithm incorrectly adds someone else's publications to your profile), or you can select records to merge (when Google Scholar picks up slightly different citation details and thinks that a single publication is actually two, very similar, publications).


How to write an aside in a journal article?

There are sometimes "remark" blocks that some authors use for discussing aspects that are of substantial interest to some readers but do not strictly belong to the core of the story that you are telling. If you are preparing your document with LaTeX, then such text blocks are called "environments".

An example is given in the Springer Lecture Notes in Computer Science guide for preparing papers, page 4 at the bottom.


Should I include research stays in my CV?

Yes, listing them would add some more value to the CV.

This is how I would list it in my CV under a section called Research Visits.

Research Visits

Visiting researcher, ABC Laboratory, University of Alphabets (Duration: January 01 -- January 09, 2018; Supervisor/Collaborator: Professor A. BCDEG)
Visiting researcher, ABC Laboratory, University of Alphabets (Duration: January 23 -- January 30, 2018; Supervisor/Collaborator: Professor A. BCDEG)


Notable academics or departments ranking list?

I think the American Academy of Arts and Sciences might be a good place to start, at least if your focus is primarily on academics in the U.S. Two criticisms of the academy: it tends to be clique-y. Harvard is always going to have the most new fellows every year because they've already got the most fellows. Second, not everybody who deserves to be a member is one. They're really good about not giving memberships to people who don't deserve them (at least in my field, Philosophy), but there are some people who clearly should be members but aren't.


What are the most common ways international students secure funding for graduate school in the U.S.?

In the physical sciences (which in the Survey of Earned Doctorates includes mathematics), the primary source of support for international PhD students in the US is:

32.0% via teaching assistantships
52.3% via research assistantships or traineeships
12.9% via fellowships or grants
Very small portion via other sources (e.g. self funded, employer funded).

Across all fields, the primary source of support for international PhD students in the US is:

22.2% via teaching assistantships
49.9% via research assistantships or traineeships
20.4% via fellowships or grants
Small portion via other sources (e.g. self funded, employer funded)

Source: Survey of Earned Doctorates, TABLE 35. Doctorate recipients' primary source of financial support, by broad field of study, sex, citizenship status, ethnicity, and race: 2014

In STEM fields in the US, both US citizen and international PhD students are generally offered admission with funding, which will be provided via teaching assistantships, research assistantships, or some combination of the above. US STEM PhD offers that don't come with funding are generally not worth accepting. So it's not about specifically trying to get funding, it's about getting a real offer of admissions (which should come with funding).


Vague paper submission guidelines - can I use double column if not specified?

I would look at past editions of the conference proceedings to see what style they were ultimately formatted in. Double-column (like IEEE) is typically denser than a single-column, so by picking a two-column format, you may be giving yourself some extra room that other submitters won't have. But you may lose this advantage if your paper is accepted and the format was intended to be single column, since you may have to cut something like 20% out of the content if you are already pushing the limits.


Teaching a class because advisor bought out and advisor input

In the long term, how much control should my advisor have over my class

None, for the duration of this instance. The advisor bought out. You're in charge. End of story. Now you might need some help in standing up to your advisor, and you need to bring in the chair of the department (who's already shown a willingness to help) and/or other senior faculty who manage curriculum activities. Don't do it confrontationally: merely say that you're really uncomfortable expanding the class size and don't feel like it's right to selectively admit students who have access to your advisor, but that you'd feel more comfortable with a faculty intermediary to help mediate.

  In the short term, should I admit this waitlisted student?

No. you're right that this is both setting a bad precedent as well as being unfair. Again, as for how to proceed, see above. You haven't indicated exactly how the advisor is pressuring you, but I think it's fair to point out to them that this undermines your authority as the teacher, and you really need to maintain your independence because you're "only a student". Anyone with teaching experience should understand the importance of establishing authority and presence in the classroom.


Is an interest in the Philosophy of Biology a good reason to pursue grad studies in Evolutionary Biology?

My understanding is that taught MSc in evolutionary biology will likely differ in course content from university to university. So whether its a good idea / is going to interest you is hard to predict.

Secondly, what would be looking to do after the masters? That's another way to frame whether masters study is a good choice.


Is it standard that universities in some countries don't give affiliated students/faculty email addresses?

Many universities, especially private universities, in  India do not provide an email address to its students. This is due to the cost of maintaining email server, ensuring confidentiality etc. Even in top universities in India such as the IITs, where everyone is provided with an email address, the email server is suspect and fails.
While I was teaching a graduate class, I circulated a sheet in which they were supposed to write down their email address. I would then make a group and circulate any class related notes or ideas. I noticed that 90% of the students gave gmail or yahoo address and not the institute email address. When I inquired further, I was told they never had an institutional email address at their undergraduate university and are not accustomed to it.
Many faculty in Indian universities also do not use official email address due to reliability problems. You can notice this from noticing their publications. The address of the corresponding author refers to an university while the email address is generally yahoo/gmail.


How should I publicize a university event of wide interest?

Not sure which of these things you already tried, but here goes (note you don't have to do all of these -- I'm just brainstorming here):

create flyer (letter sized)
create poster (not sure of exact dimensions -- I think it's about 11 x 17, somewhat glossy)
ask the people on the list you were given to put up copies of your flyer (attached to your email)
put flyers and posters up on bulletin boards and in elevators
involve students in your publicity efforts
get an article in your campus newspaper and your town or city newspaper, in advance of the event
do direct outreach to target relevant sectors of the community
liaise with relevant student organizations
plan to serve refreshments, and mention them in your flyer and poster
arrange a back-up larger venue in case your publicity efforts have too good an effect


Can I have a PhD in mathematics or physics after having a bachelor degree in medicine?

The hard answer is a straight no.

Doing research level Mathematics or Physics requires a broad set of knowledge and maturity that takes years to achieve. GRE exams are quite crappy, they just ask a lot of questions on basic knowledge and arithmetic; but you won't see an integration by parts (first year maths).

But not everything is lost. There are fields where medicine and maths overlap, and definitely your expertise on one field and interest in learning the other can definitely help. Look at Biomathematics, Bioinformatics, and perhaps, Biophysics. I myself am a Physicist working in Bioinformatics. I do pure analysis of the data, but in the group we also have a wet lab, where my colleagues are trying (among other things) to come up with new creative ways to gather data more suited for our purposes.


What concerns does a scientist have in studying their own data?

I can think of two aspects that might be problematic depending on the exact details of the study:

If identifying your data would also allow you to identify anyone else's data, then clearly you having access to the dataset might violate someone else's privacy. This could happen if there is any familial data stored (e.g. in a twin study), or if experiments were conducted in smallish groups and you met the other participants in your group.
If the stored data include anything of a highly sensitive nature (e.g. information regarding disease susceptibility) then those running the study may want to have control over how that information is delivered to you, so that support can be provided in terms of correct interpretation or counselling. This would almost certainly have been discussed with you at the time of the original study (unless you were very young or did not have mental capacity for some reason) so it's likely to be a formality, but still worth disclosing.


I think it is very unlikely that any reputable publisher won't review your changes and get back to you if anything seems wrong.

However, if you have contacted the copy-editor, they are also warned that it needs a look. Relax for now, I think. You may have more work to do, of course.

They likely deal with similar things about once a week (day?).


Are physics and natural sciences considered liberal arts?

There is little consensus, I think. But mostly it is a matter of convenience and organization at colleges and universities. I studied mathematics. I earned both a BA and an MA at different places, one of them an R1 university. Just by asking, the degrees could have been designated BS and MS. Other places the math department is in the School of Engineering. But that is just an organizational convenience, though it might let some departments share faculty more easily when it comes to budgets and such. Some places CS is part of the math department and is a "liberal art". Other places it is part of an engineering discipline. Still other places it is different from both.

But in the US, at a liberal arts college, the student is expected to gain a broad and well rounded education. It will include both literature and science, even though it might focus somewhat on a single area.

But, your question, itself, details that there is no consensus on this.


As you alluded to in your question, there are several things to be gained by being a journal editor:

Greater familiarity with ongoing research in your field
Credit for "service" within your department institution
Greater visibility within your research community
In some cases, monetary compensation (some editor positions are paid, some are unpaid)

Being a journal editor can be a very time-consuming job, and it's certainly not for everyone. However, it can also be an interesting and rewarding experience, even if it's not a journal at the level of Science or Cell. (Then again, many of the journals at the level of Science have in-house professional editors, rather than part-time staff from academia!)

Editing a minor journal can also offset other forms of outreach service, particularly if you are still developing a tenure dossier. In those situations you may find editing more (or less) rewarding than the duties you would take on (or be assigned) otherwise. (You should check with your department chair, however, that such service would be considered acceptable before committing to a position!)

Whether or not the connections are worth it at a particular level of journal is not something we can directly answer. You should consider the time commitments relative to other priorities that you might have, and make a decision accordingly.


Asking for official e-mail address from ex-employer University for publication?

I'd say whether asking is appropriate depends on whether the paper is still related to what you did at that university.

Whether the university gives you such an email address is quite a different question. My experience is: probably not.

That is, when I moved to my new institute I asked whether I could have a .forward to my new institute for some time. This was not possible, not even with the prof's statement that he would like this, too (the address got prolonged another 6 months, then it was deleted).
The reason for asking was that I wrote a software at my old university and published it with that email address. So it would have been quite in the interest of the old university to stay associated with the software.

I'd think re-activation of an already deleted account is even less probable.


Should I use Japanese title for Japanese people instead of English title?

Assuming you are writing in English, I would say

The expected* way to address university staff (non-faculty) is
generally "Mr" or "Ms" depending on their gender.
You can call
people who you would call sensei in Japanese by [family name]-Sensei
(note the position of the sensei as after) in English.
Calling people with doctorates "Dr X" is not generally expected in
    Japan. (Also, many Japanese faculty who are older don't have doctorates due to some vagaries of the system used here).
Similarly, they are much less used to "Professor X" than
    in American contexts.

I would say (2) is normal in day-to-day conversation, but for many of them writing = Mr / Ms

Separately, if he is truly "support staff," then he is not a sensei within the Japanese system. If he is over the support staff, that might not be true.

*by "expected" I mean the expectation of most Japanese users of English

Source: 1kyu (JPLT N1) and presently living in Japan working at a university


What should I do if I believe my former advisor is alleging to journal editors that I have copied his study?

I would talk to the conciliation board on your university and to the editor . Ask your colleague, if he/she will confirms that information in front of the conciliation board. Furthermore, I would do some research (or hire someone) about code of conduct on your university valid this case. Last but not least I would write down every single accusing in a chronological form (kind of factual report).

Maybe you can prove by the timestamps of your files, that he copied ideas from you and not the other way.


Hearing back after an academic interview in the UK

Depending on the customs and practices in a particular University, it can take from one to several days before the decision is made, approved, and the first candidate is contacted. "Several days" is typically below a week, but in rare cases can be longer.
If you are not contacted within 2-3 days, you may not be the first candidate. However, there is still a slim chance that the first candidate does not accept (for whatever reason), and the offer goes to you.
If you hold another offer, it is usually the best to let both Universities know the date, when you will make the final decision, based on what you have at this date. Everyone understands that candidates are usually applying in several places simultaneously, and HRs/HoDs can be quite efficient when they must (i.e. if they are interested in hiring you), and inefficient otherwise.


What is the best way (terminology) for a postdoc (PDRA) to refer to their 'boss'/'supervisor'?

I've heard "supervisor", "advisor" and "mentor".  They can be clarified as "postdoc advisor", etc, to avoid confusion with a Ph.D. advisor.

There's also the simpler "I work with Professor Smith."


It’s winter time and many people are sick. Your email could have been caught up in a spam filter. She could be on travel. There are any number of explanations that don’t involve you having done something wrong.

Just send a follow-up email politely asking if the proposal had been received and proceed from there.


How to tell supervisor that you first want to do something else before accepting his offer?

Understand the specifics first: To make an informed decision, you clearly need to understand the specifics of the position you've been offered: Can the start of work be deferred? If yes, how long? Does the company have such openings frequently or is it an unique opportunity? I suggest to ask these questions to your potential supervisor first, before making an announcement  that you might later regret.

Honest communication: Tell him exactly what motivates you to defer your potential start of work. There is a non-zero risk that he will still be disappointed, but this risk cannot be avoided, no matter how good your communication skills are. Also, be prepared to negotiate the date when you're ready to start work in his company.


Will my "the finalist certificate of the best paper award" be underrated if I co-chair a session at the same conference?

I would propose to put both points into your CV.

The interpretation you're afraid of is a bit far-fetched, and while some persons may indeed come to such a conclusion, I think most will not. Even for those who would think there has been an influence, I would argue that putting both is better than putting only one of them.
This is because they are in different CV categories, and thus people who evaluate your CV will in their mental checklist tick off both "won a paper award" and "chaired a conference session".


Is it possible to give too much praise in a reference letter that supports a green card application?

Letters written for a green card application are very differently structured to letters written for other purposes. As was explained to me when I went through the process, the structure of a green card letter is usually

I am awesome
here are all the ways in which I am awesome
because I am so awesome, you should trust me when I say that this person should get a green card
and oh yeah, they're pretty awesome, which I can tell because I'm awesome.

I'm only slightly exaggerating here. The point is that GC letters are not read by academics - they are read by lawyers who don't evaluate technical skills so much as achievements and strength of recommender. So there's no way to go over the top really.


Rankings of the historic universities in Europe

First: Rankings are just rankings and are, to a large degree, arbitrary. (Shameless plug: Here is an article (arxiv version here) that shows that for some specific database many players can get to the top rank just by fiddling around with some weights.)

Second: Just as some universities gain reputation, other lose some. That's pretty normal, isn't it?

Last, some trivia: You are probably even more surprised that some universities of some fame in the old days do not even exist anymore. Stupid example: Gauß got his PhD from the University of Helmstedt, a town that has nowaday less inhabitants than some German universities have students… Another example I know of is the University of Rinteln. However, it is hard to judge the standing of these universities at that times. Alas, university rankings did not exist some 300 years ago…


Students and postdocs not asking questions

During and after the talks and seminars in our dept. (~80 people, ~10 groups, ~40 postdocs+PhD+Master students), it is extremely rare to see postdocs or students asking questions. 90-95% of the questions are asked by senior people (mainly PIs or experienced permanent researchers).

My first thought is that this a large group -- maybe too large.  In my department (mathematics, at a big US research university) if you count tenure track faculty plus postdocs plus graduate students you get about 100.  For this group of 100 people we don't have one research seminar, we have 8-10 different seminars.  (We do have a departmental colloquium, but not so often -- in part, I think, because the people who want to go to see talks already have plenty of talks to go to.)  I am a number theorist, and I feel a very high degree of "mineness" about our number theory seminar: I spoke in it today, as I do once a semester.  I gave a ridiculously long talk (90 minutes -- hey, that's what we're scheduled for) and most of the core audience stayed until the end.  When I miss a single week of the seminar, people ask after my whereabouts and well-being.  There are several other seminars in my department of interest to me, and I attend when I can -- but they're not mine in the same way.  And by the way, I am a tenured, full professor who has spent 20 years cultivating a broad, shallow knowledge of many different areas of mathematics, but for almost half of my department's seminars I would be too lost to want to attend regularly and too lost to ask good questions.  Math is indeed hard, but so are other academic fields: I am really skeptical that all 80 people are equally invested in any one talk.

I would suggest scheduling more and smaller seminars, both dividing by research area and also by seniority.  Can a talk really be pitched equally at senior faculty and students?  This seems very unlikely.  In the talk I gave today, I decided to pitch part of it at the students much more honestly than I often do.  So perhaps the first 15 minutes (of 90) were truly aimed at them.  The rest was aimed at faculty (including postdocs) and indeed the largest number of questions came from the most senior person in the room.  More or less we are expecting that to happen by collecting that audience.  Students are still there and still getting things out of the talks -- for instance, one of my PhD students attends the number theory seminar as faithfully as I do.  Only very rarely does she ask questions on the spot -- but we often discuss the talks afterwards.  She is also active in organizing the Graduate Student Seminar in my department, in which faculty are allowed but not encouraged to attend and usually do not.  In fact, I had a period of about one year where I often attended the Graduate Student Seminar, but I stopped going when I realized the extent to which my presence there was warping the proceedings in a negative way.

In fact, here is a parable from when I was a graduate student.  One of our seminars, the Basic Notions Seminar, had once upon a time been the "Graduate Student Seminar."  But it was the kind of graduate student seminar where the faculty would give talks -- nice talks, which other faculty members would attend.  After a while the students realized they needed their own "Graduate Student Seminar."  They gave it a name -- the Trivial Notions Seminar -- which made it clear and obvious that faculty were not wanted as speakers or audience members.  Both seminars have coexisted for many years.

  We want to find a way out of it. One possibility under discussion is to force, right at the end of the talk, the first couple of questions from them. But it's not accepted yet. Do you think this could be a good idea?

It could be a good idea, but I don't recommend it.  There are probably many reasons why young people are not asking questions.  As you made clear, young people who do have questions do not feel fully comfortable asking them.  If you want to address the issue, then actually address the issue by creating an environment that makes them more comfortable.  Forcing them to ask questions seems willfully dismissive of the reality that they are uncomfortable, which they probably actually are. As I said above, one of my students faithfully attends my seminar and rarely asks questions.  If it were my choice, I suppose I would rather she ask more questions.  But it obviously is not my choice: she is a thoroughly intelligent, competent, professional adult person, and one whom I know well enough to understand and respect why she behaves as she does.

Rather, I think that if you want students to ask questions, you need to actually create a seminar environment in which this is what they'll naturally do.  I gave some suggestions for this above in terms of who is in the room.  There are many other things you can do, if it is important to you.  One big one is to get speakers for whom interacting with the young audience is something they want to do.  When I teach graduate courses I get lots of interaction from the students, even though some are not so comfortable asking questions.  How do I do this?  By saturating the lecture itself with questions and interactions with the students. I will literally ask for students to complete my sentences.  If I need to make a definition, I will say "Someone must know this" and ask a student to supply it.  If the student gives the definition in exactly the form I want, I write it down quickly and we go on.  Any discrepancy gets incorporated into the lecture on the spot (and is not necessarily bad or problematic: there are many different ways of saying the same thing, and what could be a better use of class time than showing a student that the thing they have in mind is actually the same as the thing I have in mind, or should be the same except for one technical point they have missed...) When I give a seminar talk, I still try a bit of this kind of didactic Q&A...but it depends on what the audience wants.  Sometimes every single question will get snapped up by the people who know everything.  Sometimes people will say nothing and not look me in the eye, trying to pretend they know the answer.  Sometimes they will say nothing and look me in the eye, trying to get me to get on with things.  In my home seminar, the senior people will play along with me if they clearly understand the game we're playing...but in part because they know I'm mostly pitching things at them.

One final idea: you can keep the seminars entirely as they are now -- again, please understand that the senior people are probably largely happy with them -- and add an additional component afterwards which is just for the junior people.  Or talk to your junior colleagues, find out what they want and what environment would make them more interactive, and see if you can create that environment.  But don't force the issue, and don't assume that everyone will feel the same way about it that you do.


I will fail 1 (or 2) classes this semester as a master's student. Should I forget about PhD applications to schools in US?

If getting a PhD is something you really want to do, I suggest applying. If your failing those classes is truly not a reflection of your abilities or motivation, but - as you said - relating to effects of the pandemic/quarantine, then hopefully the rest of your course grades and other application materials will make up for those two failed courses.
When I applied to PhD programs, my own bit of insecurity came from the fact that I had graduate credits from another university where I didn't receive a degree (it was my first attempt at a PhD and it just wasn't a good fit). I decided to address it in my personal statement. I acknowledged that I attempted my PhD before but quit, explained why, and quickly moved on to explain how it was still a learning experience for me in terms of coursework, gaining teaching experience,and learning more about myself and what I valued/prioritized in a PhD program.
I would suggest you do something similar in your personal statement (if engineering programs require them), and to keep it brief. Acknowledge the failed courses, offer an explanation for why you failed the classes in such a way that they understand that this was an atypical experience for you, and then come back with a statement of some sort that illustrates why - despite what you just shared - you're still a great candidate for their program. None of this should dominate the personal statement, I would keep it to just a few sentences.


Is it possible to get a PhD in field X with research that isn't really in field X?

It is possible, usually, to work in another field on your thesis at least in the sciences. However, the thesis defense and dissertation will have to relate to the program you are in.

i.e. I had friends in physics PhD programs who worked in biology labs. The research had to be tied to physics for the dissertation and defense (light diffraction, computational modeling using physical concepts, etc.)

There will always be people who look down on specific disciplines, but I would think that usually it is acceptable if you can make it work.


Is it legal to ask an intern to write a peer-review report?

The only ethical concern I see here is possibly one of deceit. If the supervisor or yourself misrepresented who the author of the review is.
But you didn't mention the destination of the review or where the original request came from.
But there are many situations in which such a thing would be perfectly fine. For example, a review used only internally. Or a situation in which the supervisor wanted the intern to learn enough to do a good job and get the experience of a review. This isn't especially rare in the case of advisors asking doctoral students to write reviews either as a form of practice or to provide a "first draft" of something.
But you can't expect that every reviewer on every paper is completely knowledgeable about what is in the paper. That would imply that science doesn't actually advance at all and that only "known" things appear in articles.
But, submitting your work under their own name would be a form of deceit. And, sadly, this happens in the case of doctoral students noted above.
Another form of deceit would be misrepresenting one's qualifications to do a review, though I don't see elements of that here. That would be an issue between the supervisor and the editor.


How would I judge the status of a researcher without talking to them or reading their papers?

Assuming the question is about status and not quality:
Job title is a strong indicator of status.  The meaning of each title typically depends on the country.  For the US, as an example, named professorships have the highest status, followed by professors and associate professors.
The status of the university is also a strong predictor of status of the researcher.
"Status" is not quantitative and attempting to rank status is not productive.


How far can one expect a external examiner to travel to be on defence/viva committee?

If your university is paying the expenses, then it's quite plausible for an examiner to come from arbitrarily far away.  I myself have gone from the US to Europe to serve as an external examiner, and it was no more a burden than traveling to a foreign conference.  You can also combine other things into the trip: for example, when I served, my colleague also asked me to give an invited seminar, and we took the opportunity to work on some collaborations as well.


How long does it usually take for published articles to show up on Google Scholar?

My article showed up in a few days. Since google is crawling, I believe (although I am not certain), that updating other sources such as policy, government, medical repositories and other resource hubs that allow you to update fields, add links etc, without needing to upload the article, increases the external links with the article page. This might not be necessary to expedite the process, but if the article is not showing up within the normal period of time (which could be a week), I believe this would be a good step to take. This advice also applies for anything else such as websites and blogs. Actually my repository link showed up in google before the actual journal page did!


Can I submit a paper to a conference if I have presented it at another conference earlier but it wasn't published in proceedings?

I am aware that in some fields conferences are the main repositories for new contributions. I don't know how it works and I do not want to enter into this aspect.
In other fields* conferences are rather venues to disseminate and discuss results and ideas, and, at the best level, doing it in a more interactive fashion than the one permitted by papers.
Moreover "political" motivations play a big role. Note the quotes... It can simply mean an authors is curious of meeting others, or seeking collaborations.
This means that

the same talk maintains its practical novelty for an indefinite time. It is up to the authors and to the organising committee to decide what is worth a presentation;

one can desire to enter in, or present to, a slightly different community.

As such, if your research is in *the other fields and you think you should submit you can surely do it.
Often one encounter the opposite problem. Namely the author already has a paper (paper or proceeding) and is barely interested in attending /presenting, while the committee asks for a paper to be published. This is a problem easily circumvented (everyone knows that it is not the case of self plagiarism) but it seems even not existing due to the loophole (?) you mention.
Summary: hard to say if you should. Most likely you can.


What sentence is suitable for thanking a professor?

Hint: professors are people too. You can thank them just like thanking anyone else. Your email may go something like this:

Dear Professor X,
Thank you for the information about your PhD project. I look forward to submitting my formal application to your department.
Best wishes,
maryam


Is it advisable to email director of graduate studies inquiring about the application status?

From my experience, you may if you think it is long overdue, as in if the expected deadline for your school "xxx" to send out all offers of admissions has elapsed. If that is the case, then it is okay to send in an inquiry email regarding the status of your application.

Most schools usually send out the first round of admissions to very outstanding applicants first, then in that order. Also, domestic students often receive their admission offers first before international students do. These are the most obvious graduate school admission process but other applicant-unique factors may account for the delay in hearing back from your school. So you may have to factor all these in to see if you should have heard from your school or not regarding your application status. Contacting them before the given deadline for admission offers to end may paint a rather not so good image of you to them.

In my case, apparently the school had received more applications that year for that program than anticipated and so the selection process was rather complicated. I waited for the given time (month) all admissions (both international and domestic) to elapse before I contacted the graduate secretary. They immediately replied explaining the difficulties they faced that given year and the status of my application. Apparently I was placed on their waiting list. I hope this helps :)


BSc in CPSC or CIS: How will this affect Grad School applications (Stanford, UBC)?

The obvious answer here is: if you have very specific programs in mind, and a specific set of constraints that may hinder you, check with the upper-level programs you're interested and find out what their requirements are. If the master's program requires a bachelor's in computer science, then you have your answer. If not, then they may list what degrees they accept as "equivalent" or "sufficient" for their program.

But, in general, when in doubt, ask. That's what graduate officers and admissions staff are there for!


How can I make use of iterative "work in progress" versions of papers

Not sure if I understood you correctly, but if you need a better workflow for managing the progress and evolution of your drafts, then I think the question you've linked to actually answers your question.

A combination of git and modular LaTeX can help you to:

track changes in your draft(s)
make sure new versions (and new versions of new versions) start with everything that was in the version they were started from
merge changes between versions
split your draft(s) in such a way that it is easy to include different bits and pieces in different versions
greatly simplify collaborative work
reuse parts of your projects (e.g. git project setup, LaTeX macros/environments/styles, any compilation scripts)
and many more things


At the author proof stage, you are expected to not make any more substantive changes.
Thus, if the copyeditors introduced these unwanted references, there is zero problem in asking for them to be removed.

If you realize that you messed up any put in things that you should not have or wish that you had not, however, it's a bit more iffy.  You can ask to have them removed and the journal staff will make a judgement call of whether it requires reconsideration or not.  If it's a simple mistake, don't worry about it.  If you were to try to remove all references to prior work, on the other hand, they would be right to consider that a serious substantive change and to strenuously object.

Bottom line: just explain why you want the references removed, and if it's reasonable don't worry about it.


There is a language/cultural barrier between me and my supervisor, what can I do to improve this situation?

It will be much easier for you to learn German to conversational level than all of your co-workers learn English. Even if they are some-what able to talk in English, conversational English is actually pretty tough, whilst German is pretty structured and easy once you know the rules (and the many exceptions ;) )

More importantly, you moved to Germany. Whilst English is expected of all Scientists, there is probably more of an expectation in your lab that you will, eventually, learn German.

Personally, I would tell everyone you are going to German classes on Monday mornings, etc, and that should not only fix this issue, but also give you a positive perception among your co-workers as someone who is a fixer.

Also, speaking from experience as someone who didn't take their own advice when doing a PhD in Germany - if you dumb-down your English for non-native ears, you very quickly find yourself not being able to speak English with natives. Whenever i go back home my parents think I have some kind of brain damage...


Should I write a thank you note to a professor for his recommendation letter even if I didn't get the scholarship?

Absolutely. He probably feels bad that you weren't selected. Not as bad as you, of course, but he will want to know that you are ok in spite of a setback. Moreover he may be in a position to help you in future so you will want to make sure you keep lines of communication open.

Beyond that, however, a professor who thinks enough of you to write the letter in the first place, probably is the sort of person who wants to be kept in the loop as your career progresses. He will greatly appreciate your thanks, I assure you.

I once had a mentor in grad school. He was not my advisor, but I always used him as an example of a great professor, just as you describe your professor.

Many years after I graduated I had occasion to revisit the campus, where he was still teaching (Dept Chair, I think). I told him how much is model of a professor and his mentoring meant to me, not only at the time, but over the intervening years. He thanked me and also said that professors don't hear such thanks very often. That saddened but also surprised me. He died not long after that, so I've been happy that I was able to express that to him in time.

As for the words to use. Thanks is enough, but fill him in on your current plans and what has happened to you since you were last his student. Wish him well.


The short and to the point answer is that no currently existing licence does what you want. If you wanted to do as you say, you'd need to write a new licence. That would probably mean employing lawyers.

The long answer is that I doubt whether any such licence would be enforceable in practice. Further, in general scientific software that is released under restrictive or unusal licences is generally not well used by the community. See Lior's Pachter experience. Important here is not that this was about for-profit vs not-for-profit use, but that when people are unsure about a licence, they just won't use your work.

If you don't care that people won't use your work you must ask why you are releasing it in the first place. One hopes that you are releasing it because you wish to further the horizon of human knowledge and believe that your library has a role to play in doing that. If nobody uses your library, you are not meeting your goal any better than if people used the software in non-reproducible science. I you do not want people to use your library then you are not doing science, anymore than those that refuse to release their data or methods are.

Putting all that effort and cost into inventing a new licence, which in the end might lead to people not using your software is a poor use of resources to achieve your ends. Much better to expend that effort convincing journals not to accept non-reproducible things, reviewers to actually review the reproducible of the code and into creating infrastructure that makes it easy to do.


How should I sign myself on poster if I am a student?

I suspect that any of them would be fine. Instead of an institution, it is also acceptable to describe yourself as "Independent Researcher" or the equivalent, depending on the venue. But listing the university could be taken as identification only.
There is an exception, of course. If you are doing something that the university would object to for some reason, then it is better not to name them unless you clarify, somehow, that you aren't suggesting they authorize or subscribe to what you have done. But even then, "Student at Moo U." is an accurate portrayal.


If I already have a master's degree, can I use it to apply for another master's degree (UK)?

Yes, of course you can, since you are changing fields.

A friend of mind never finished his bachelor degree and had years of work experience and wanted to get into a master program (in the US). The program he wanted said they would take him if he had a bachelor degree but since he did not have one, he could not enter.

He went to the UK, got accepted into one master program based on his partial completion of his bachelor degree COMBINED with his real-world experience. Once he completed that master program, the program in the US (in a different field) did accept him.

So, yes, it is absolutely possible to do this.

I think what your real question is whether an admission committee will overlook your poor performance during your undergraduate since you have a master degree. It would help to know what your performance was during your master, and how 'top' of a school you want to get into.

The publications should help, especially if they are from reputable journals. The best course is to actually submit an application. However, you should consider what you really want to achieve. If you want to do research, perhaps going into a PhD program would be better for you. If you just want to change fields, but don't want to do a lot of research, then a new master degree might be just what you need.


Which are the best journals for letters in mathematics (bordering with mathematical physics)?

As Pete L. Clark, I do not quite know what a letter is: short papers are usually quite similar to regular paper, only shorter and usually called notes.

Concerning the venue suitable for short articles, there are quite a few. First, you should now that most journal could accept short papers, but certainly you have more chance to get accepted in a journal specifically targeted toward short paper (except if you solve a known problem or reprove a notoriously difficult theorem, in which case no reviewer can use the length of the paper to argue it does not have much merit). Let me give my impressions on the journal that come to mind (to remind that this is from a biased perspective, I will often refer to the French mathematical community), limiting to journals that to not claim being restricted to a subfield -so called generalist journals.

CRAS (Comptes-Rendus de l'Académie des Sciences, Paris): this journal publishes both research announcements and complete short papers. The announcement part is less and less relevant, but I do not know whether it is less present now. Sadly, while CRAS published top-notch papers, it cannot afford to be very selective anymore. It also suffers from the research announcement role: French hiring committees often blankly dismiss CRAS papers, partially because they may be only announcements.
PNAS (Proceedings of the National Academy of Science, USA): this journal is not very well-known from French mathematicians, but publishes some quite good papers. I think it has a particular taste, but I cannot find the word to describe it. Beware that even if it has a page limit, the format is very dense so articles are not necessarily that short overall.
PAMS (Proceedings of the American Mathematical society): this journal is explicitly for short papers, but the page limit recently moved from 10 to 15 (AMS format). As far as I can judge it is selective, and sometimes publishes excellent papers. It is reasonably well regarded, benefiting from the sisterhood of Transactions AMS.
Bul. LMS (Bulletin of the London Mathematical society): this journal is the LMS counterpart to PAMS, and is somewhat similar (although a little less known and considered, maybe). Since the LMS series has three journals (Bulletin, Journal and Proceedings in increasing order of paper size) instead of two for the AMS, I guess that the average Bulletin paper is somewhat shorter than the average PAMS paper, but the different format makes it difficult to judge.
AMM (American Mathematical Monthly): this journal is well-known and extremely selective. It publishes papers of general interest, of varying length. The notes are typically a few pages long. It is even possible to publish mathematical facts of a few lines, in a grayed box. Since it is considered somewhat recreational, publishing in the Monthly gives less weight to a CV than its harsh selectivity would do for any other journal.
Elemente Math. (Elemente der Mathematik): this is a Swiss cousin to AMM, much less known and much less selective.
MRL (Mathematical Research Letters): this does barely belong to the category of note-publishing journals: it does not usually published paper more than 30 pages, but the average paper there is not a note as far as I can judge.


Can both a grad. student & faculty member cosign a recommendation letter?

Like Noah, I had a situation where two advisors co-signed a letter of recommendation. I should mention that the people reviewing the letter found this an unusual situation—and had claimed that they had not seen that in twenty years of reading recommendation letters. So this is definitely not standard practice. I suspect it would be memorable, but I am not sure it would be actually useful.

However, the difference was that my two co-signers were equal in rank. Your situation has a professor with a graduate student providing most of the insights. I suspect you will need to have the professor adapt the graduate student's comments, and then sign the letter. In the case where feedback is needed, the professor would then need to get the relevant details from the graduate student.


How should I put a disclaimer in my thesis indicating that I am not responsible for any misuse of my work?

Talk to your professor.
Your professor is going to be the one marking your paper, so they're the natural one for you to ask. As the comments pointed out, it's unlikely that anyone's going to be reading your thesis besides the professor who's marking it, so asking your professor about the best way to ethically address the potential for your research subject to be misused is probably the best way to go.
Your university would also have some form of ethics committee or institutional review board (IRB) that you could talk to, but at your level, if you were doing something that required the IRB to sign off on it, it's likely that the professor has likely already done so before proposing this as an area of research for your undergraduate thesis.


What are the benefits and purpose of presenting a paper in an academic conference?

The answer depends on the discipline.

In many disciplines you can do both. There are conferences where you can present work that has been published in a journal (or at another conference) or that shall be published in the future.

In other disciplines, conference publications are as "valuable" (or even more prestigious) than journal publications.

To know what is the case for your discipline, talk to your advisor.


Generally it would mean a tenure track assistant professor position. There might be exceptions, but for Columbia, I'd expect it to mean just that.

But they might even be willing to entertain a lower level (non tenure) or higher level (associate professor) position for the right person. I can't think of any other reason for a US university to be non-specific.

But even an associate professor offer would likely come with some probationary period prior to granting tenure. Probably two years or more, but less than seven.

Contrast it with "senior faculty" position. Here it would mean a full professor, even a distinguished full professor or someone able to take over a leadership role.


If there is academic dishonesty, can I temporarily withdraw from a paper until the dishonesty is removed?

It is difficult to play hardball when you are a student. I never recommend playing it against your advisor, but this is a bit different as you say. If the person has no effective control over your future then you might consider it, despite the possible blowback.

What is being demanded of you is unethical. No one can publish your work without your permission. If they publish it without you it is plagiarism. Even publishing it without you as an author but acknowledging your contribution is unethical if you don't agree to having your name used. You have a lot of power here, actually.

The actions open to you are an ethics complaint to the department or the university. You can also offer to inform any journal to which they submit it without you that they have plagiarized your work. Hardball indeed.

But a better way is to ask (actually require) them to split the paper. Write a paper that everyone is happy with and make no contentious claims. Have those that are interested write a second paper in which they try to support further claims. The second paper should cite the first, obviously. This isn't the same as "temporarily withdrawing".

Of course, you can also write another followup paper explaining why the further claims are unsupported by the evidence.

But before you take irrevocable action, make sure your own advisor is in agreement and will back you up in the likely ensuing shoving (and kicking) match. Don't let it come between you and your degree.


How do I distinguish a Private college from a government one in India?

A little bit of searching online turns up many lists that others have compiled that can help you distinguish whether the nature of a university in India, including whether or not it is private.

A good starting point may be Wikipedia's "List of private universities in India"


1st year Ph.D. student in Computer Science - want to switch fields

First of all, it's better to make the exploration now than later. Having a good place to apply your CS knowledge can be very powerful, and now is a better transition time than you will ever receive in the future.

With that said, there are several bioinformatics courses online that you can try out; one popular one is Coursera. This allows you to spend a few hours per weekend exploring the topic from a well known professor, and can help you decide whether or not you are truly interested. From there, as @ff524 stated, it is best to ask your advisor for information on how to continue applying your skills to both your PhD and bioinformatics.


Where does the title Dr come from for PhD?

It's actually exactly the opposite: "doctor" is Latin for "teacher" and the title originally had no special connection with medicine.  Instead, a doctor was anyone qualified to teach at a university (in medieval Europe teaching qualifications were typically determined by the church).  The concept of a formal PhD degree came much later, but it continued this earlier terminology.

The confusion in English is irritating, but not problematic enough to make universities give up a 1000+ year old tradition.  It's not clear why this situation arose.  One natural explanation is that if you want to emphasize your medical skills, you can do it by explaining that you are not just a healer, but in fact someone qualified to teach other people the healing arts.  In other words, you're a doctor of medicine in the academic sense of the word "doctor".  Until very recently universities were fairly exotic, and most people didn't talk about academic doctors very much, so the medical usage was much more salient for the general public and for most people it became the standard meaning of "doctor".

Of course this difficulty with this story is that it doesn't explain why, for example, German does not confuse the terms the same way English does.  Maybe it's just chance, or maybe there's some cultural reason.

In any case, though, academia had the title first and is reluctant to change it.


For applications where prospective students upload transcripts, is there a preference between scanned official vs unofficial transcripts?

If an "unofficial transcript" is requested, generally they just want something that contains the relevant information: courses taken, grades, any disciplinary sanctions, etc.

It might be most convenient to scan an official transcript, because then it will be in the most familiar format, but as far as I know it is also fine to, for instance, retrieve your own records from your university's system and print the relevant pages to PDF.

On the other hand, transcripts are usually printed on special paper that causes words like "COPIED" or "VOID" to appear on any copies or scans that are made.  Of course if the department only wants an unofficial transcript, they should not care that it is a copy, but sometimes it's hard to read a transcript if it says "COPIED" all over it.  So whatever you send, make sure it's legible.

Of course, as you say, an official transcript (sealed, by mail) will usually be demanded if you are accepted and/or decide to attend, and woe be unto you if it does not match the unofficial transcript you provided with the application.

It can't hurt to contact the department and ask what they would prefer.


Research on career path after tenure denial?

In the German academic system, assistant professor positions were introduced only in 2002. Recently, there have been studies evaluating how well these positions have been established, and how it affects the career paths of junior researchers. One example is a project by the Center for Higher Education (CHE), which is described here (in German unfortunately): http://www.che.de/cms/?getObject=260&PK_Projekt=1292&strAction=show. Scrolling down to publications shows references to articles where data from this study have been published (again only in German).

One difficulty in interpreting this data with respect to your question is that tenure track positions are rare in Germany (an estimate I remember, but don't have a reference for now, is that 10 % of assistant professor positions are tenure track). On the one hand, that means that "being denied tenure" is almost the norm for these positions. On the other hand, it's also possible that professors become tenured even though they haven't been on a formally tenure track position.

Also, the statistical population for this study are persons who have been assistant professors in the past, not only those who have been denied tenure. Thus, the study does not give directly the percentages for all the positions in your question, and some data (e.g. field of study) was not collected or published, but still, the results can be used to estimate some of these percentages. So let's get to the key conclusions that can be drawn:

For 1., 85 % of former assistant professors have a tenured professor position now (either through tenure track or at another institution)
For 2., 6 % of all former assistant professors have a non-tenured academic position
Summarizing 3. - 5., 9 % have a position outside academia.


A general strategy you can try here is "respond to amateurism with professionalism".  Even if it looks like he's being unreasonable (as it currently seems to you that he is), just suspend disbelief, and, in a completely non-confrontational manner, engage his questions as if they were serious:

  I always appreciate constructive criticism [true statement!  you don't
  have to say that his was constructive, let him think what he
  wants...maybe he actually did think it was].  I didn't quite
  understand what led you to wonder whether I did enough testing of X.
  Did you see something in the results that made you suspect this
  specifically?  Just want to make sure I'm not missing anything.

  Thanks for your input!

Treat it exactly as if it were a sincere attempt to help, that you had a question about.  It's possible (though I'm thinking you think it unlikely) that he really is sincere and has something to offer you.  If so, wonderful!  You get useful feedback from someone smart!

If he doesn't actually have a real question, this technique may make that obvious in a relatively non-confrontational way.  Part of the value of it is that you are not simply being the victim of stalker-y behavior, but professionally and politely holding your ground.  It is to be hoped that this will lessen the feeling of exasperation that would otherwise normally accompany this kind of childish bullying, if that is indeed what it turns out to be.

There are very intelligent and successful people in academia who are nevertheless  woefully underdeveloped emotionally; one way this will be manifest is in the need to tear down other people who seem to be having success, or demonstrating skill, or garnering attention comparable to their own. This can catch one off guard when it's coming from a successful and respected person, because you would think that their success would be all they need to feel good about themselves.  That, alas, does not turn out to be true.  If it's a chronic emotional problem, you are unlikely to get him to change his behavior; hence the advice to concentrate specifically on blunting his ability to make his problem your problem.

If the cerebral approach doesn't work or becomes too time consuming, you can always set up a filter to send email from that address straight to trash....

Escalation (adding this section after your clarified and expanded examples indicate that mere polite discussion may not work here)

[Fuss level: zero] Gather evidence.  You don't have to do anything with it yet.  Later steps I will describe will talk about possible uses.  It's just good to have in case you ever get into a he said/she said situation and need to be able to back yourself up.
Note that there is already a "fuss", to some extent.  Not your doing.  You can't choose to have this situation be "fussless", because the behavior is happening in public.  The question is to what extent you wish to participate in the fuss.
[Fuss level: low] A body of evidence might be useful for you to have handy if you wanted to petition a site administrator to block him from contributing comments.  The sites hosting your research results and facilitating discussion don't want their work compromised by trolls.
[Fuss level: medium] Does he work at an institution with a published policy regarding academic ethics?  Spuriously calling into question the validity of your results seems like it would violate ethical standards.  It might be enough for you to obtain a copy of the institution's standards, highlight the part that you consider him to be violating, and send that information to him, asking for him to comment on whether he agrees his behavior violates those standards.
[Fuss level: high] Same as 4, but with more fuss.  Contact the institution.  Ask to speak to someone about the fact that you feel that one of their employees is violating academic ethics.  Do they have a published policy?  Can they send you a copy?  Can you send them some redacted examples and have them confirm that they would consider that in violation?  You would like to resolve the matter with the individual privately if possible, but you want to be sure that you are interpreting their standards correctly.  Then, email the stalker and tell them that you've been in contact with the ethics office, not having mentioned any names of course, we can resolve this between ourselves, can we not?, and they agreed that the behavior is in violation of standards.  Would he be willing to simply stop commenting on your work altogether in the future?  It seems it would be better for both of you if he did.  You don't have to threaten exposure--you should be careful not to threaten, actually (to avoid any possibility that you could be charged with blackmail or whatever)--just state facts.
[Fuss level: nuclear]  Put all the evidence on the web, unredacted, and send a copy to his boss, his wife, and his students.  Let them know you really hate to bother them, but you need to ask them if they can contact his psychiatrist because he apparently needs his meds adjusted.  (<-- not a serious suggestion, but it was cathartic to type!)

Serenity

Reflecting on others' answers and comments, I feel that one more section should be added here, because there are practical things you can do to help the situation, from your side only, with zero direct interaction.  Although I would still gather evidence in any case (since it might be of value later should a dispute come to the surface), it is possible for you to improve your experience here by improving yourself.  It's easy and natural to focus on the fact that he is the aggressor and by rights he should be changing his behavior, and to forget that, completely independent of whether he stops or not you can choose to become better at not being affected by baseless criticism.

Give yourself a mental picture of a small child attempting to attack an adult who calmly holds himself out of harm's way by virtue of having arms twice as long as his attacker.  Your stalker has mastered the art of playing the flailing child--you can grow long arms.

Mentally rearranging your perspective on the whole situation can help.  You can say "I am going to end up better for this by learning the valuable skill of ignoring trolls.  Think what I would have had to pay a trainer for this, and he's providing me all this learning experience for free."  It is, after all, entirely possible that you are going to run into other situations in life where the ability to be calm in the face of baseless or childish criticism helps you out immensely, and this is an opportunity to learn that skill in a relatively risk-free environment (as the stalker really has no actual power over you in this situation).

In short, you have, effectively, been focusing on the question "How can I get him to stop this behavior, without making a fuss?"  But you can get an excellent result by instead asking the question "How can I get this behavior to stop bothering me?".  The second question can be pretty much entirely in your own hands, and the things you do to work on it will help you in other aspects of your life, even enabling you to help others deal with similar issues, etc.

It's more than just ignoring (which, I think it should be said, is fantastic advice if you can do it--I haven't gotten to that point yet personally)--it's a conscious decision to rise above the behavior of the other party.  Rather than "he's attacking me and I feel powerless to stop it without escalations that I am not comfortable getting into" it can be "he's attacking me, but I am using this as an opportunity to practice, and therefore develop the power, to not be affected by this behavior".  From the outside it may look the same, but mentally, this kind of approach can make all the difference.

I think this is both the best option and the hardest to execute on.  In the times when I have implemented such measures myself, I've found it to be incredibly empowering, and even in some cases ended up with unexpectedly good relationships with people that at one point had occasion (they felt, at the time, at least) to attack me, simply because I consciously decided that I didn't need to fight back.  I don't think I've faced exactly the same situation as you are here, but I believe this might help you and sincerely hope it does--best of luck.


The primary reasons for the continuation of academic journals are correlaries to some of the things you've mentioned as negative.

Peer review. This a key driver for academic publishing in general. It provides a way to control the quality of published material, and an enforcement of accepted standards, and (for the author) feedback prior to publication.
Communication. Journals provide a means of communicating research to a targeted audience. Conventional subscription-based models do so for a fee, while the rapidly growing open-access model (which I highly commend) provides even broader and easier access for researchers, students, and others.

In short, journals serve to curate content to meet the needs of a particular audience, and thus they are unlikely to completely disappear in the near future.


How should I deal with need-to-define terms in introduction?

There are at several possible ways, actually.

First is to avoid the yet-to-be-defined term in the intro and use a descriptive phrase instead. This assumes the term isn't frequently used in the intro.

A second way is to footnote the definition or an pointer to it when it first appears in the introduction. Putting the definition itself in the footnote repeats it, but a pointer doesn't require that.

You could also just add "... frytopper (defined in the next section)..." at the first appearance.

Yet another would be to write the intro as: "... frytopper (italicized terms defined in the next section)...". For this you would only need the pointing phrase at the first of the later-defined terms, but just italicize all of them - at least for the first appearance.

Some of these require the reader to hop about a bit, but it should work.


how much benefit is there of working as a predoctoral research assistant

In many circumstances, yes, predoctoral research experience is an asset, in particular if you can get a strong letter of support for your graduate application, and can contribute to some publications.
Financial aspects are a consideration also, but it's hard to judge given the available information in the question.


How can a conference paper publication be guaranteed? Is such a "guarantee" even possible?

It isn't that difficult. All that happens is that a private university pays an association (IEEE or something else) to host a conference. Then since they host it, they can choose to publish conference proceedings, with a journal sponsor. That is how most special issues work.

A more comprehensive answer is here


First, I hope this has not already happened, but is only a potential concern.

Thus, I'd first address "how to avoid having this happen". As with failing oral prelims and such things, this results primarily from failed communication between the junior person and one or more relatively senior people. Ignoring for a moment department-politics-motivated tenure-vendettas, which do occur, departments are not collectively happy to deny tenure, since it reflects a kind of failure on their part, as well. Although the details of the expectations are different at "research universities" versus "small colleges", departments have expectations. Usually these expectations are communicated fairly clearly, although sometime not too forcefully or formally.

A pre-tenure person should have senior people to talk to about their situation in the department, about expectations, and about progress-so-far. Unfortunately, often there is no systematic implementation of this sort of mentor relationship, and the default is that the dept chair has a yearly talk with pre-tenure faculty. If this defaults further into an absolutely pro-forma, content-free interaction, there is potential danger, especially with a pre-tenure person who is oblivious to exactly these issues.

The worst cases I've witnessed, apart from those involving some political motivations, involved pre-tenure people who were surprisingly disconnected from the department in which they worked. Plausibly doing worthwhile work, but not interacting with local people.

Another kind of disconnection is that the pre-tenure person does receive fairly blunt advice from the dept chair, but decides to ignore it, as though some abstract notion of "virtue" would supercede the dept chair's recommendation!

Nevertheless, even if one has paid attention, it might be that one's research program just didn't quite measure up to hopes... Or there might be political/scientific shifts in the dept which (rightly or wrongly) marginalized your field/work "out from under you". In such cases, the external perception usually is fairly well informed, and the stigma is not too great, and there is hope for other academic opportunities.

If one hasn't paid attention, and, in some sense "rightly" was denied tenure, then this situation is externally understood, too, and it is in this case that one's academic prospects are dim.

Although I've had the good fortune to not need to look for non-academic employment, my several students who have deliberately (or due to vagaries of the job market, grudgingly) found non-academic positions emphasize that it's possibly not your specialized knowledge that you can "sell", but the point that you can learn very complicated things, and do things with them.


What incentives do professors have to serve on dissertation committees?

The professors serving on one committee will also have their own students, who they will want to see graduate (even if you assume pure selfishness they want their recrords to look good). Those students will need to be examined as well so in a sense it's mutual assistance, but time-deferred.  Also good relationships between academics are how a lot gets done: this is a fairly easy way for an academic to build relationships with other (perhaps more senior) professors.  So while generosity is important in this sort of thing, it's not quite that simple.

As an aside, you might like to ponder the effect on such well-established networks and systems of treating academics and their research groups as business units in a corporate entity.


Is it pointless to bring up poor supervision during PhD viva?

I'd suggest that the viva is possibly the worst time to do this. Almost anything you say could be interpreted as whining and trying to deflect responsibility for any shortcomings. Many things you might say would be countered in the minds of the reviewers whether expressed by them or not.

Whether you bring it up yourself or just reply to questions or comments with complaints about your advisor or others would seem, to me at least, as unprofessional.

If you have issues about the performance of your advisor, make it a separate issue in an appropriate venue after the degree is in hand.


What is a "residency requirement" in the context of Canadian and US PhD programs?

Generally, in the context of a doctoral degree, "residency requirement" refers to some minimum number of credits that must be completed at the degree-granting institution, or minimum duration during which the degree candidate must be enrolled full time at the degree granting institution. In contrast, work completed at another institution and applied toward the degree does not count towards the residency requirement.  See e.g. policy statements here , here, and here, which make it clear that this is the kind of residency requirement they're referring to.

But "residency requirement" is occasionally used in other ways - for example, here it refers to students being considered in-state residents for admissions and tuition purposes.

It is very unusual but not unheard of for doctoral students to be required to live on campus for some time. See this Google search. I am not aware of any US or Canadian universities that have this requirement.


Dealing with an unhelpful and unresponsive thesis advisor?

Ideally, you should make an appointment and meet in person with your advisor. If this is not practical you could send an email to propose a skype meeting or a phone call.

If they don't answer your emails, wait at least a few days and preferably a full week before sending a reminder. If there's really no answer after a couple weeks and the matter is urgent, then try to call them directly in their office (during office hours).


Are students allowed to read recommendation letters written for them?

Legally, in the USA, students are entitled to access their educational records.  (I assume that there are similar regulations in some other countries.)  This poses an obvious problem with letters of recommendation, the contents of which may ideally be unknown to their subjects; this makes it possible for the recommender to give completely honest evaluations and discourages students from "shopping" for the most positive references.

The solution is that students normally waive their right to view the recommendation letter.  Most colleges now have online recommendation systems for references to use, and there is always a prominent notice that the student has waived access to the letter.  I have never had to write a letter when this waiver was not in place.  I know a couple colleagues, however, who have gotten recommendation requests that did not include the waiver; their solution was to write a polite e-mail to the student, reminding the student to waive access.  (That the faculty involved would not be willing to write the letter without the waiver may or may not have been made explicit.)


Is it ethical for a journal to reject an accepted article because they decided not to publish the issue

If you gave up your copyright then get it back. If you still hold copyright then you can publish it elsewhere.
Even if the issue weren't cancelled, but they put out a call for additional papers to replace the removed ones, the time to "print" would probably be about the same for you as submitting to a different journal.
It is unfortunate (and maddening), but it may not be the journal at fault here. There isn't enough information to judge. And there is no ethical violation provided that you haven't given them something of value that you can't get back. They just may not have a suitable place for your paper.
It is also unlikely that anyone else will "blame" you for the fiasco, but it will help to get the paper published in a reputable place.
Just make sure you have the copyright. All else will flow from that.


Which limits to draw for speculations in an scientific publication?

The legitimacy of such extrapolations is, as far as I know, among the topics studied by statisticians.  If I'm right about that, it would be good to ask a statistician about your extrapolations, both to check how valid they are and also, if they are valid, to get some citable support for their validity.


Sending reminder for LOR and asking them to do it early?

You sent "all the information" - including deadlines?  You can expect that they will submit by the deadlines that you told them, but not necessarily before.

If you need the letters earlier than you originally said, you'll just have to ask them - no way around it, and the sooner the better.  If your new deadline is still at least a few weeks away, it shouldn't be too much of an inconvenience for the professors.  If you tell them "You know that letter I asked you to submit in December?  I actually need it tomorrow," they will very likely get annoyed, and may not be able to have it ready in time.


Should I send recommendation/reference letter to universities that don't require it?

Most organizations that have set requirements for applications refuse to look at any supplementary materials that are submitted in order to be fair to those who did not submit supplementary materials. The National Science Foundation, in many cases, reserves the right to return proposals without review that have certain kinds of unrequested or forbidden supplementary materials. I think it's best to only submit what was asked for.


Can I have a diagram from another book in my work with proper credits?

As with many questions here, there are two issues: plagiarism and copyright infringement.

By citing the work of another you avoid plagiarism, which is claiming the work of another as your own. So you have no issues with that.

Copyright infringement, however, is governed by laws that vary by jurisdiction. Normally (i.e. most jurisdictions) you can copy (with quotes) some words from the publication of another as long as you cite it. But there are (weakly defined) limits to that. Copyright law is usually civil law (I know of no exceptions) so infringement is subject to lawsuit and in a lawsuit a judge or jury gets to decide what is reasonable and what is not.

But in copying diagrams and images there is a special consideration. Even when produced inside another work, an image might be interpreted as a "work" in itself. So, copying it might be interpreted as copying an entire work, likely a violation. Another thing to think about is that "A picture is worth a thousand words.". That is more than just a cute saying as it has some truth. So, if it would be improper to copy a thousand words from another work, an image might just might be considered as "too much" to copy, even if cited and "quoted".

But let me give an example that might help you see the issue clearly. Take, for example, the book The Handmaid's Tale by Margaret Atwood. If I were to produce some work in which I quoted a complete chapter, it would very likely be considered infringement. But, as you can see, Wikipedia has provided a synopsis of the entire work without infringing copyright. The linked article explains the entire plot in some detail and lots of the reasoning and structure behind Atwood's work.

More deeply, however, suppose that I copy a complete chapter, but change a few words. Change names, perhaps, or locations, or phrasing of some parts. This is still almost certainly infringing.

So, in your case, if you take a figure and "change" it in insignificant ways, moving a few elements then you are on shaky ground. But if you take the ideas underlying the figure and produce your own, from the ideas, not just modifying the figure, then you are, in some sense at least, paraphrasing. But all that means is that you have a defense against a charge of infringement. Possibly a solid defense. So, if you do that and also, as you suggest, say that it was adapted from ... (avoiding plagiarism) then you are probably fine. But in the last analysis, neither you nor I get to make the final judgement if you are challenged. But do more than just mention the name of the author. Cite the actual work.

And you can avoid the issue entirely by asking for permission as GrotesqueSI suggests here.


Do two rounds of major revision lead to a better chance of getting the paper accepted?

I think of requests for revision as falling into three basic categories, sorted in order of importance:

New technical results (e.g., additional experiments, more theorems)
Large-scale text improvement (e.g., reorganizing text, dealing with pervasive language issues)
Localized text improvement (e.g., improving explanations, adding references)

Of these, only a request for new results should be of concern as a possible road to rejection: for the other two, if you want the paper published, if one cares to one can typically always put in sufficient work to address reviewer comments.  It may be hard, unpleasant, and unrewarding (depending on the particulars), but this is an area where any request for revision almost always has a clear path to publication, and of a stronger paper than you started with.

Requests for new technical results, on the other hand, might or might not be something that you cannot reasonable address.  If you can address them, then it's still a clear road to publication of a stronger paper.  If you can't, however, then it's a question of scope and may be worth discussing with the handling editor to see whether they are a sine qua non for publication.

In general, however, my feeling about requests for revision, even major revision, is that they're generally good news.  Once a paper hits at least a major revision, it's highly likely to be eventually accepted if the authors just keep answering the requests for improvement, and will likely be the stronger for it.  There are exceptions (I just had one rejected by a journal for the rather unusual reason that "they only allow one revision,"), but in my experience these most frequently reflect an author who has chosen to fight the reviewers rather than to improve the paper.


Depends on the journal and their layouts. Most will have a "Materials and methods" parts, this is where you write down which instruments and chemicals were used. At least in chemistry there are no common rules about how in detail this should be. You will read something like this very commonly:

  All commercially available analytical grade chemical reagents were purchased from Aldrich (St. Louis, MO) and used without further purification.

But you can include more information here, like CAS number, catalogue number and so on.

Sometimes this section isn't present in the paper itself and you might include it in the supplementary information.

In the end it's important to include all the relevant data in a useful way and it doesn't really matter how you do it.


Is it ok to copy/paste a section of a previous paper of mine into a new one?

Technically this is self-plagiarism and not OK. We had problems before where we published the 6th paper on a very similar topic and one sentence in our introduction was the same as in another of our papers (there are only so many ways to describe one thing) and it got flagged and we had to rewrite it, which in my personal opinion is just stupid.

However, if it's part of a methods section it is usually tolerated, since it doesn't make sense to rewrite technical statements all the time. For example in synthetic chemistry you would write something like

  All chemicals were purchased from Sigma Aldrich and used without further purification.

Which is fine to just copy/paste.


Does a supervisor have to read a thesis of his PhD student

Have to is a strong requirement. In the US, the supervisor is almost always part of the examining committee so at some point they will have to read it. Some departments may have rules about feedback on drafts and how quickly and how much feedback supervisors can provide.

In the UK, the supervisor is almost never part of the examining committee. While I have never seen regulations prohibiting feedback, but there is more of a culture that students should stand on their own. That said, I think most supervisorsuccessful read a draft of a thesis.


What is the proper method of citing from a video

It might sound odd to use video material as a source, but this is a frequent issue in modern History, to name one area of research. 20th-century propaganda is an example of a topic that would include primary sources that are videos, posters, or radio material.

The Havard citation includes guidelines, see here for a guide from the Open University. From page 33 on video sources:

  The Apprentice (2008) BBC 1, 14 June [Online]. Available at www.bbc.
  co.uk/iplayer (Accessed 16 June 2008).

On page 55 on (unpublished) interviews:

  Interviewee, A. (year of interview) Unpublished interview conducted
  by Interviewer Name, date of interview.

If you have the time, you could transcribe the interview yourself to make it easier to trace back the source. A good term to google is "Harvard Referencing for Visual Material". (Or whatever the appropriate referencing style is for your publication). I would cite it as an interview that you accessed online. The more you know about who conducted it, the better.

Imperial College London have an even more extensive guide on this, see page 12 here:

  Example:  Kirk, T. Interviewed by: Picard, J. News Night Live. (24th June 2001) 10pm Channel 6.

My approach would be to see which referencing is most common in the area that you work in, to ensure consistency.

Edit: including time-stamps:

  [...] the contribution of water damage can be seen at 2m33s in to the
  video (BBC, 2009).

See page 14 here.


Remote work employment opportunities for someone with chronic health problems

As you are asking this on academia.SE, I am assuming that you are looking for an academic job as opposed to working in industry. In that case, I am afraid your assumption

  However, as physics research is mostly a mental activity, I am still able to work remotely from home

may not be true for higher (post-graduate) academic jobs. I would say, being a postdoc or higher in physics is to a large extend a social activity, as much of your job will consist of teaching, training the next generation of researchers, and networking. In general, all researchers after a certain stage find that they spend preciously little of their time on actual research (which you may be able to do from home, depending on your concrete subfield). Most of the time is actually spent on activities that require physical presence, at least some percentage of the time.

That being said, many research labs are quite flexible in terms of working hours and (partial) home office. In my lab, for instance, I would not assume that anybody would take issue with an employee working about 50% of the time from home (under the assumption that one would actually work at home, of course). However, the remaining 50% would probably require physical presence, simply because the tasks would require it.


Can committees see the list of all recipients when I send them my GRE score?

In the past, at least, the default seemed to be that the list of all recipients showed up on the form of the records sent to graduate programs. I know this because I was/am on admissions committees and saw such information. On another hand, I do also know that it is possible to suppress it, since in recent years most GRE reports seem not to show this to admissions committees.

Unfortunately, I do not know how the examinee arranges to suppress that information. It certainly is not done automatically, despite the obvious point that it should be private.


Can a department revoke a degree, once granted by the university?

Absent plagiarism, fraud, or other academic sanction, it would be difficult to revoke an awarded degree. There would have to be strong evidence for doing so, and it’s not often attempted, in part because of the likelihood of legal action.

So, I would normally say don’t worry about it. However, in a dysfunctional department, anything could happen, and you should be prepared to act in that unlikely event.


Is it important to be a co-author when PI takes first authorship on your work?

I don't see any logical reason why you should withdraw your name from the authorship list. This only hurts you in the long run. You should want to have credit for your work.

You might politely ask your advisor why the "guest authors" have been included, and what contribution they have made (since you said 60 percent was your work, what about the other 40 percent), and then discuss it further if you don't like or aren't satisfied with your advisor's answer.