I expect much more commitment from my PhD-supervisor. How do I communicate this to him?

Realise your own commitment first. As a PhD candidate, you are training to become an independent researcher. Ideally, you aim to reach the stage when you are able to tell good results from bad, proofread and edit your own writing, prepare the PhD thesis for publication and defence. Many PhD candidates struggle because their advisers are over-protective and micromanage every step, leaving them little chance for self-reflection and self-improvement. Embrace the freedom to do your research your way and to learn from your own mistakes in the process. Own your work and own responsibility for making it better.
Use others. Many questions can be answered by people other than your PhD supervisor. Use online resources, such as Stack Exchange, use other peers and colleagues, use support systems in your department. Ask questions, try to understand answers, find and use the relevant literature. Do not sit and passively wait  for your adviser to come back to you with suggestions - use this time to find the answer yourself.
Do not wait for your supervisor's approval of your work. Assume that silence  is a sign of approval and move on. If in doubt, show your work to someone else and ask for their advice. Politely cc your supervisor in the email.  It may work wonders.
Understand the process of submission and clearly distinguish the points when your supervisor is essential to move forward, from those when their advice is only desirable. Politely ask your supervisor to give you feedback by a particular date, but be prepared to move forward regardless of whether or not you receive the response. Depending on your University structure, you may even be able to submit your thesis without your PhD supervisor's approval. Know the people who are in charge of the PG education in your University - such as Research Office of Head of Department - and cc them in all really important emails (but only in really important ones). They may help to encourage your supervisor to find time to give you feedback or approval when it's critical.


How to find original conference of the paper on arXiv?

In short: arXiv is a repository for scholarly research articles (in certain scientific disciplines) that allows them to be recorded and distributed widely without paywalls. The articles should be genuine attempts to produce scientific contributions, and be "refereeable" - which means that it should be in a state that it would be suitable for submission to a peer-reviewed venue, but it need not actually have been submitted to one, nor does it need to have been accepted by one.

Papers on arXiv are not required to be published anywhere (conference, journal, or otherwise) - some are submitted before even being sent to a venue for review at all, some are in review progress, some may have been rejected by peer review and may or may not be in the process of revision for sending to a new venue, etc.

You may want to read about arXiv a bit more, such as here https://arxiv.org/help/general (see the disclaimer):

  Disclaimer: Papers will be entered in the listings in order of receipt
  on an impartial basis and appearance of a paper is not intended in any
  way to convey tacit approval of its assumptions, methods, or
  conclusions by any agent (electronic, mechanical, or other). We
  reserve the right to reject any inappropriate submissions.

And you may wish to read the primer: https://arxiv.org/help/primer

In practice, papers found on the arXiv are in every state of the process, from before-submission, to accepted-but-not-yet-appearing, to being the home for the pre-print or even final version of the article appearing in some peer-reviewed venue (see How many arXiv papers are uploaded in their final (refereed) versions? for more on that). And you'll even find some "submitted but rejected" papers, too - it's not a bug, it's a feature.

It is ultimately up to you as a scholar to decide how to interpret the credibility or usefulness of any given paper. Appearing on arXiv is proof of availability of a paper, which allows you to read it and judge for yourself.


License of code accompanying a published article

Copyright only protects the expression of a work that is written down or otherwise placed in a "fixed medium." It does not apply to ideas or concepts.

In the case of a published article where copyright is transferred to the publisher, that copyright only applies to the written content and images in the article. It doesn't apply to the concepts in it.

If you write source code based on concepts described in a paper, you can apply whatever license you want to it - the copyright status of the paper is not relevant. (If the idea is patented, you may have to deal with that... but that is not related to copyright of the published article.)

See Does copyright protect the author's creative ideas? for more information.


Are authors of papers okay with receiving questions from people in industry?

I certainly don't see anything immoral about asking questions.  You may want to mention your affiliation, which will clarify the issue and perhaps also help the author give a more useful response.

The author doesn't have any particular obligation to respond to your questions or anyone else's, but probably will if they are interesting and well thought out.  Academics generally would want to encourage anyone who is interested in their work.

If your questions get very involved, to the point where an academic might consider suggesting a collaboration, you may want to consider offering the author a consultant contract.


What is exactly the role of a phd advisor?

The quality of your relationship with your PhD adviser is one of the biggest factors in determining your quality of life during grad school.  I strongly encourage anyone in your position to consider switching advisers (which it sounds like you're doing).
I don't know what field you're in, so I can't authoritatively speak to "the way it goes" in that field.  However, speaking as a mathematician, there are a wide range of management styles.  Often, even the same PhD adviser will manage different students differently, depending on their abilities and desires.

Some schedule a weekly hour meeting without fail; others say "come see me when you have something".  Some coauthor most of their students' papers, some rarely do. Some students, like you, feel micro-managed.  Others wish their adviser gave them more attention and cared more about their research.
 My adviser essentially let me pick all of my own research problems, which was what I wanted.  It took me longer to start publishing than some other students, but I also felt well-prepared for life on my own after grad school.

So in short, stubborn micro-management is not "just the way it goes"; rather it's just the way it goes when you're working for a power hungry egomaniac.  Run, don't walk, to find another adviser!


I have been pigeonholed, how can I solve it?

It is clear from your recent questions that you feel exploited in your lab, and it is good that you want to do something about it.

However, first things first. What is your agreement with your current mentor / lab head / whoever? Essentially, what is your "job"? If you have been specifically hired to "help out with the programming", or something like that, it will be difficult to convince whoever is paying your salary that you now actually would like to do something different. Not impossible, but maybe also not easy.

On the other hand, if you have actually been hired to do research, but now end up being more of a scientific programmer because that's what the lab currently needs, it is time for a good one-on-one meeting with your lab head. You wrote in a comment that you do not foresee this going well, but I really see no way how you can change your situation without talking about it very explicitly to your lab head. It should be easy to see for most sane persons that not only your lab has needs, but you and your career have needs as well (and working as a scientific programmer can easily be a dead end for an academic career - no first-authored publications, no faculty job). Try to make a plan for a suitable compromise between you helping out the lab with your programming skills, will still being able to progress your own career. Should your lab head really not be willing to compromise at all, it may be time to move on.

Possible compromises could include:

Hiring an actual scientific programmer, perhaps with funding that you help acquiring
You training some of the junior staff to do their own programming
You helping others in their programming problems, but ultimately let them do the majority of it themselves
You supervising some undergrad or master students that can help out with programming tasks
etc.

  that they appreciate more (because they are their own PhD students and now postdocs, it's emotionally logical, I'd say)

That's not logical, that's BS. A lab where people "coming from the outside" are valued less than those that "have always been there" is a terrible, toxic environment.


Is it okay to reference something well agreed by only one source, [e.g. 1 source]?

If something is considered common knowledge in the field (for instance, Newton’s second law in a physics paper), then no reference is required. If it’s been developed multiple independent times, though, I’d use more than one reference to establish it.


Is qualitative method welcomed by editors/reviewers?

Every research method can be thought of much like a movie genre. What makes a good comedy doesn't necessarily make for a good drama, and anytime genres combine deciding what is good can be different (as with mixed methods). Judgements change over time, and vary between sets of critics as well. Research works like that - what makes for a good paper is devilishly hard to pin down, and what one community loves another community can hate.
People with more than 20 years of experience in this process have told me they are still surprised how some of their favorite papers end up poorly reviewed, while others they thought were marginal or unlikely to be accepted won awards. Sometimes they feel that what was unacceptable one year suddenly became hot the very next year. Reviewers are conducted by humans, and lets face it - humans are a wild and messy lot!

Everything I've been told and seen points to only one solution: develop your own tastes and judgement in research to use to guide your own work, try to learn what sort of things some people like and some don't, and write what you think will be good - but then get other people's opinions (formal reviewers or informal colleagues) and revise according to what you think makes sense, but taking into account what other people tell you. Try a lot, get rejected a lot, keep at it.

Some things people have in common - almost everyone wants to know why out of all the possible methods you could have taken, these are the ones that are appropriate the research topic, and that the conclusions you derive are supported and valid given the methods you used. Some people care about rigor more than others, but both quantitative and qualitative methods have their own standards and methods of being rigorous, so you have to know your method and learn to speak about it clearly and convincingly.

Try different styles, different techniques, different venues. Read what other people like, what people criticize, and what they praise. Accept that there is a heavy random factor in both the sampling of who you get as a reviewer as well as how the weather made them feel that particular day they reviewed your paper, and get use to a whole lot of rejection and noisy signals. Improve what you know to improve and try again.

In the words of a cartoon scientist, "Sometimes science is more art than science".


What citation style allows the author to reference sources with superscript numbers?

I am presuming this is a coursework assignment. If you're that tight for space, are you sure you haven't written too much? Be careful that your finished piece doesn't "feel" cramped.

The Nature journal uses superscript numbers for in-text citations1 and then references them in the bibliography like so:

Hynek, B. M. Implications for hydrologic processes on Mars from extensive bedrock outcrops throughout Terra Meridiani. Nature 431, 156–159 (2004).


How do I get "promoted" as a PC member in a conference?

I am not sure if this is the same in your field, but in mine (software systems) PC member and senior PC member are actually different roles with different tasks. It's not so much an honour badge to be a senior PC member than being assigned for a different job in the selection process (typically, PC members do most of the reviewing while senior members do less reviewing and more "meta-reviewing", similar to an Associate Editor for a journal). It's also not the case that, once "promoted", you will always remain in that role - every team of program chairs is free to assemble their own PC, and they invite people to the different roles. This often, but not always, includes re-inviting previous committee members.

I know of cases where people who used to be senior PC members were asked to serve as regular PC members in the following year (or not at all). Also, many senior PC members are actually more junior (in terms of academic age or rank) than some of the regular PC members. This has to do with PC composition - you want to have good coverage of all topical areas that you receive contributions in, and of course past performance and the subjective impression (of the PC chairs) of the different people plays a big role as well.

That is all to say that there typically is no defined promotion process between different levels in a program committee. You need to do good work in previous years and gain sufficient notoriety in the community that the next batch of PC chairs sees you as somebody who they trust to oversee the selection of papers in a specific niche topical area.


How do research papers differ from research articles?

Research article refers mainly to research published in a journal, whereas research paper refers to a research report whether it is a published one or not.


The legality will depend entirely upon the nature of the intellectual property agreements you have signed or agreed to at your local institution, or that are otherwise in force in your local jurisdiction.

But based at a quick high-level read of your description, you seem to indicate you were paid to perform work as a research assistant, and during the conduct of that work you spent a significant portion of time planning a research project. By any definition I have ever seen, this would count as "work product" as part of that position, unless it somehow greatly differed from the nature and subject of the work you were being paid to perform. Even if it was different, most IP agreements tend to be very favorable to the "employer" part of the relationship (because of course, guess who writes those documents).

You'd have to speak to a lawyer for specifics, but in general you would be expected to provide any working materials, artifacts, or other creations/documents you have regarding the project to your former employer if requested (and really as a matter of practice). I have not heard of any situation where this requires extensive new creation, though - so creating a plan and description beyond what you had during that time would be beyond the pale.

From the perspective of this disinterested third-party, however, it kind of sounds dangerously like you want to have been paid to perform work, then keep that work to yourself for your own future advantage and benefit while shafting the people that paid you by not providing to them all the benefits they paid for in good faith. This is certainly not a pro-social behavior, and sets off alarm bells that you don't sound like a kind of contributor I'd be comfortable working with. At the same time, telling someone else to give up an idea so you can assign it to someone else so that they can be the first author and the person who came up with it will be in some subordinate position is also not pro-social, and is a big red flag that I wouldn't want to work with a person like that in the future either!

You are most certainly in your rights to decide ongoing involvement with a project, however, so if you want to turn in your old work ideas, wash your hands of the situation and tell them you don't want to be involved as an author further as you will be pursuing a similar-but-different line of research than what you had initially planned, you could do that. But I would really, strongly suggest you get any new advisor involved in your new lab involved before you decide on any such course of action, because if a professor did this to another professor it would likely be seen as quite aggressive and possibly the start of a long rivalry. Very dangerous for a person in a more fragile position to try to do!

I would tend to err towards "I have lots of ideas, no need to get hung up on one single idea that someone else was paying me for". If the check cleared, I prefer to give people what they paid for and part ways, wishing them the best of luck and removing myself from ongoing entanglement if the relationship is no longer a positive one.


Doing research toward a Ph.D. degree versus doing research for commercial purposes

(computer science perspective here)
Research in grad school differs from industrial research in a few key ways. First, research in academia can be more abstract - you can focus on fundamental research and not feel pressured to produce, say, a working prototype or a product.
Second, the type of research you can conduct is dictated by company needs: if your company is interested in deep learning then you're gonna work on that even if you're really interested in graph theory.
Third, since companies have an incentive to provide products, you may be under more pressure to produce within tighter timeframes.
Finally, often enough companies limit your capacity to publish results due to confidentiality/company interests. Companies won't like it if you publish results on a new method for competitors to use (you may not publish anything for years if you sign an NDA), or publish things that present the company in a negative light (Timnit Gebru's ousting from Google is a notable recent example of such a conflict).
There are of course exceptions. Some industrial research divisions offer more academic freedom, but even then you are expected to contribute to the company's bottom line (which is not unreasonable in my opinion).
That said, companies have a clear advantage when it comes to access to resources. Generally speaking, academia simply cannot compete with the resources and datasets that tech giants such as Google/Amazon/Facebook/Intel/IBM have at their disposal (I don't know enough about other fields, e.g. how the NIH compares to big Pharmaceutical companies).


As MadJack says in the comments, this is really something that you and your advisor need to sort out with the department.  Part of an advisor's responsibility to their students is to make sure that they don't end up in easily avoidable bureaucratic screw-ups like this.  So yes, you've failed, but your advisor has failed as well.

First thing to do, then, is to sit down with your advisor and figure out how serious a problem this is.  If it's something like JeffE suggests, and due to recent regulation changes, or if it's a requirement that is more pro-forma than serious, then there are likely good ways to deal with it.  For example, you might end up following the letter of the law and in fact having the proposal exam be essentially a dress rehearsal for the defense (and that might be considered to be OK).  Or the proposal exam might end up finding some problems that really do need to be addressed before you defend, and you will be grateful---you might be delayed, though, and that might or might not be a problem (you don't say where you are: in the US, delay is generally not a problem if your advisor can fund you; in some other countries it can be a major issue).

If the department is not flexible, however, and wants to make an issue of your failure to comply with the letter of the law, then the resolution will be very particular to the department, and that is something that you and your advisor will need to navigate together.


What to do if I have found a major issue with my model before a conference presentation?

Things like this happen. No one should be ridiculed for honest errors. It's a good thing that you found this one before someone else did.
Your description suggests that some (even much) of your work is still OK, since you say only that the problem  might affect your conclusions.
If you can describe the problem (even with no solution) in advance, you should.
Does the conference format allow you to introduce your talk with some preliminary comments, either via zoom (or some such) or with a short new video upload? Ask the organizers.


Should workshop papers be cited (computer science)

Don't cite bad quality work as evidence.  Judge the quality yourself.  Only cite things if you think they are of a sufficient quality to demonstrate the claim you want to reference.  Don't rely on peer review (whether in a journal or conference).  Lots of poor quality work gets into journals, too.

Work in progress and early results do not equal bad quality. Something that is still in progress, or hasn't been rigorously demonstrated yet, may still be worth reporting.  This doesn't make a bad quality paper, as long as the paper is honest about the interpretation of what is presented.  Falsely claiming that early results are definitive is bad, but "Our early results seem to show this, but we aren't sure yet" can be a perfectly good paper.  There is nothing wrong with citing such results, as long as you similarly are honest about what (and how much) they show.

In short, There is no reason for a blanket refusal to cite conference papers.  Such a practice might make you miss important evidence.  Do consider the source and the quality of the work, and try to cite the strongest source(s) when possible.  This will often (but not always) mean preferring a journal article.

I'm assuming you are thinking of cases where you are searching for evidence in a particular area and can choose what to cite. Of course you also have an obligation to cite anything your work relies on or uses, regardless of the source.


Yes, a graph theory paper is just as relevant as an algebra paper for graduate admissions, even if you plan to specialize in algebra.  There are several reasons for this:

Many people applying to math graduate school don't really know what they will specialize in.  (This is true even for the very strongest applicants.)  It's OK not to know, and everyone realizes that you may change your mind in a year or two even if you think you know now.
Undergraduate research is generally limited by the availability of supervision.  You may not have had the opportunity to work on your favorite topic.
Undergraduate research is not intended as a head start for graduate school.  Even if you had written an algebra paper, you would almost certainly not end up building on that work for your Ph.D. thesis.  Instead, the real purposes are learning about research and demonstrating your talents, and the research topic itself is not so important.


What matters most for Grad school admissions ? Practical grades or Theory grades?

I may be suggesting the obvious but it will depend on your program and your level.

For a course based masters program with a practical bent I would imagine they would look upon your grades favourably. These tend to include some sort of practical capstone project required to earn the degree. If it's thesis based, it would tend to imply some theoretical work.

For a PhD, expect theory. Really, why else would they be PhDs?

Further, most of the applications I've seen (and submitted) tend to speak to a well rounded applicant profile. They want to know about the work you've done, volunteer experience, publications, and your academic history.

But perhaps most importantly in your situation, they tend to want some form of personal statement outlining why you both want and deserve to be in a program. This would be your opportunity to convince them; much like a cover letter.

I'm in the western world however, and cant speak to institutions beyond that sphere.


Is it self plagirism if i use the same assignent twice in the same course?

The more important question is whether this would be accepted by your professor. If you cite the earlier work it isn't plagiarism and you put the professor on notice about what you've done. But it would be much better (safer) to get permission first.

Whether it is technically self plagiarism or not depends a bit on whether you have, in some sense, published the earlier work. Probably you have, just by giving it to your professor. But even if it doesn't meet the technical definition, the professor could still penalize you for it.

And it isn't just the issue of copy/paste of the same words. Even paraphrasing without citation is considered plagiarism if the definition applies.

I'd guess the professor is already aware of the situation and will have a ready answer for you. They may want you to go deeper into the subject than in the first assignment.


Is it possible to write a masters thesis in 10 days?

If by "writing" you mean to do the research/experiments/studying and then write the thesis then no.

If by "writing" you mean transforming your well organized notes into one document, then yes, maybe if you have great discipline.

If by "writing" you mean to start to write-up from not-so well organized notes, then most probably not.

If you want to try to make it, stop hanging around on the internet and start working.


Knowing when the code is good enough, for research

As the

  code I write is almost always only used by myself

you only have yourself to please. So the only sensible answer is to balance things to minimize the frustration to yourself. Don't do things you see as frustratingly slowing you down until you are more frustrated by the problems caused by not doing them.

However, the more strategic question is whether you want to continue writing code that will only be used and seen by yourself. If you want to advance your career through collaboration with peers, or by building a group of researchers to work on and with your codes, then it will be better to do more earlier.

You then know you've found a good balance when the collaborators you want to work with still want to work with you after they've spent some time with your code.


How to introduce multiple authors of a research paper in content?

This is completely dependent on your citation style. Two examples:

For APA, if there are only two authors, cite both each time; if there are between three and five, cite them all the first time then cite as "First et al., 2014" in subsequent citations; if there are six or more, use "et al." every time.
For IEEE, use of "et al." begins at three authors, and you use "et al.".

As you can see there are wild variations. Check which style you're supposed to use, and check how multiple authors should be cited with that style. As a general rule of thumb, maybe use "et al." when there are too many authors.

As another user pointed out it's also dependent on your field, and it's even possible that author names shouldn't be cited in every reference (just a numeric reference like [42]) -- I just checked a math journal at random and this was like that.

PS: If you're writing something in LaTeX and are using biblatex, I want to advertise the commands \textcite, \parencite and \footcite. They are able to automate most of this (for example with the APA style, they correctly detect which citation is the first).


If I'm understanding the answer correct, professors need funding to do research, but once they get it, the university takes some of the grant as overheads (to pay for office space, electricity, etc), and the cut the university takes is substantial

The number of services provided by a university is substantial, of which space and electricity are the least of them.

Maintenance, janitorial, and IT services - machines break, rooms get dirty, and technology has inexplicable problems.  Universities have infrastructure in place to deal with all of this.

Access to literature - Universities maintain subscriptions to the journals, standards, and other references a researcher needs.

Laboratory equipment and specialists - Most scientific research requires specialized equipment, which can cost anywhere from a few hundred dollars to several million.  Universities can afford to maintain such equipment, and the expert technicians needed to run the equipment at maximum efficiency.

Other researchers - A university department provides ready access to and familiarity with other experts in your field for potential collaboration.  Additionally, it provides a way to find potential collaborators from other fields for the times when you find your research leaving the bounds of your expertise.

Students - an unfortunate amount of research is tedious.  A university provides a ready framework for delegating simple but time-consuming work to students so that a researcher can focus on the parts of the research that only they can do.

Contacts - Universities maintain contacts with businesses, governments, and other research institutions that can open more doors than any one researcher could do on their own.

Reputation - Being a member of a respected university means that people who trust that university will afford some measure of that trust as well.

Legal services and other expertise - While it would be nice if research could exist completely separate from the outside world, this is not the case. Universities have systems set up to support and advise their researchers when problems arise during their research.

Many of these things could be aquired by a solo researcher, of course. But doing so would cost time and money, likely amounting to more than a university takes in overhead. And things like contacts and reputation are difficult to purchase.


How aware are grad school application readers of differing standards internationally?

Repeating a bit other remarks: in the U.S., exams in upper-division courses are usually designed by the individual instructor, and vary widely.

There is a tradition in top-tier places in the U.S. to "challenge" students on exams, and students seem to expect this, while, yes, in some local cultures students expect/demand exams that contain no surprises.

For that matter, it is not clear to me that "testing cleverness" is necessarily an important goal for timed exams. I am well aware that there is a huge tradition in which quickness and cleverness are construed as fundamental skills/talents. Certainly these are important for math contests, and occasionally useful in the practice of mathematics, but I don't think our classes teach these things, in any case. Thus, testing for quickness and cleverness is testing for something outside the course content. Thus, in many regards it is an irrelevant challenge to the students.

That is, substantial mathematics often has genuine complications and difficulties that exist despite examples and forthrightness, and it is sometimes (often?) counterproductive to create "challenging (surprise) problems" from material that should be straightforward.

But, yes, people on admissions committees are well aware of such traditions and their variations, don't worry.

For me, the letters of recommendation from math faculty are far more important than grades on the transcript, in any case. Similarly, the statement of purpose of the applicant tells much more than the transcript. And, one more time, the skill set relevant to surprise questions on timed exams becomes ever less relevant throughout grad school.


How to gracefully step back from academic administration duties during the pandemic?

I have to admit to some ambivalence about the issue -- which may be what many of your colleagues might feel as well, and that might affect how they see your decisions.
On the one hand, I think we all sympathize with your situation, and your desire to go back to be a "regular faculty" with a life that revolves around teaching and research. I get that a pandemic is not what you had in mind when you took the job of graduate coordinator, and that the resulting upheaval in all things academic (and non-academic) lead to a workload that is not what you thought it was going to be.
On the other hand, however, you did get a promotion and (I assume) a pay raise that reflects your increased level of responsibility and leadership. By accepting these, you are also accepting the fact that your job becomes less predictable and that you become a more direct subject of the whims of the higher-ups wanting you to respond to this or that. That's really no different than nearly any other promotion: If you work at McDonalds, you can have a low-stress job by flipping burgers Monday through Friday 9-5; just don't accept the promotion to shift manager, because then you have to deal with workers not showing up, unhappy customers, etc. So while you say "this is not what I signed up for", I'd argue that in a sense you did actually sign up for it -- maybe not in such explicit terms, but the uncertainty comes with the job, and it is rewarded in certain ways.
So while I assume that your colleagues will have personal sympathy, they might also ask you why they paid you more (or gave you teaching reductions) if you jump ship when showing leadership is actually required. I suspect that it might also be difficult to find someone to replace you during these times, and that might also factor in how your colleagues see your decisions. A department actually needs its graduate director, so not having one is going to be a problem.
In the end, talk to your department head and your colleagues how they see the situation. You might also discover ways in which you can lighten your workload somehow, and become happier with your role. For example, if you find that during the day, you stomp out the really urgent fires and in the evening at home deal with the mundane and boring stuff, consider whether one could hire a student worker to do at least some of the work that mucks up your cogs. Delegation is often possible, and your department head might recognize that it's going to be cheaper and easier to find ways to make your more comfortable with your role, than to replace you.


In principle, you can use any professional name you like to sign your papers.  I have a few colleagues whose nom de plume (or perhaps nom de LaTeX?) is not the same as their legal name.

But by default, I would recommend signing your papers precisely as you sign anything else, including spaces and accents:

  Jorge Fernández de Cossío Díaz

It would be helpful for people citing your papers to state, somewhere in your CV and on your professional web page, that your last name contains three spaces.  And you'll have to correct copy-editors who incessantly abbreviate it as "J. F. C. Díaz", but you'd have to do that with the other suggested variants anyway.   Modern search engines have no trouble with accents.


Will non-research but relevant extracurricular help me get into graduate school?

Yes. Participation in all types of scientific competitions is appreciated, even if not directly relevant to your research area. Even if you don't win them, participating in such events show inclination to scientific activities.

But if you know what you want to pursue in research, and you're able to do that early, it is definitely better than joining random scientific competitions and internships.


Do I inform my Professor that our digital exam isn't recording us?

From your comment, I note your concern that if you report the matter, you might be required to sit the exam again.  I think that is unlikely.  It is unlikely that your professor would impose additional work on the students due to a technical error that was not their fault.  It is more likely that your professor would be glad to have been informed of the technical problems, and would use this information to try to have the technology run correctly in future exams.  It's really up to you, but as an academic with experience in teaching, it is certainly useful if students report problems, so that you can improve future iterations of your teaching.


Is copying the exact statement of a definition or a theorem considered plagiarism?

In mathematics, often there are highly optimized/perfected statements of theorems. It would be silly to alter them (introducing damage?!) just for the sake of avoiding exact quoting. Cite, that's all.
That is, unless you have something to add to their idea, there's scant point to changing the wording... apart from the risk of mis-stating them!... just to meet a sort of fake goal. Cite and acknowledge. Be honest. With citation, what could possibly be the objection to quoting a perfected assertion of a good theorem?


In writing a paper, how far can criticism of previous works go?

Generally speaking, any critiques should be brief and directed (i.e., "the cited works failed to consider <X> in their analysis", "to simplify their model, they assumed <X>, whereas in reality <Y>").

If you're criticizing assumptions, be sure to specifically state which assumptions you challenge, and clearly deliniate (with references) why they are incorrect. Note that many papers use incorrect assumptions to begin work in a new field, and your critique should recognize that (i.e., "The seminal paper assumed <X> [1]. We extend this work by removing said assumption.")

If you're criticizing conclusions, again state specifically which conclusion you disagree with, and be sure to provide data/analyses to back up your conclusion.

If you're challenging their data, note that (in neuroscience, at least) this is perfectly common; findings differ all the time. Progress often stems from finding the cause of these differences between data. You should note the difference and mention something along the lines of "Our findings differ from those of <X> [1], and we believe this is because <Y>". Note that it is almost a requirement to mention something like this; if you don't, (1) the researchers whose paper you missed will probably mildly insulted, and (2) people familiar with the field will assume you didn't do your basic literature search, which makes you look stupid.

Needless to say, ad hominem attacks are always inappropriate and should never appear in scientific literature.


Including articles in submission in "refereed publications" section of CV?

If you submit them to a journal that will referee them then put them in the refereed publications and mark them "submitted - under consideration" or similar. Just make it clear.

And update the CV as needed if you get accepted or rejected.

An alternative, if permitted, is a third section for submitted work under consideration or even work in progress with submitted works tagged as submitted. My preference (for myself) would be "Work in Progress". Sending that signal can help you.


The argument is a ludicrous one, defending a parasitic system that should have been buried a long time ago, and written by an individual with a blatant conflict of interest.

In theory there exist some attempts to measure scientific impact from download data. Example.

In practice, nobody cares, partly due to the fact that there are many ways to get an article without incrementing the counter. (and also because we already have enough stupid metrics).


You've not really commented on your thesis advisor's role as a research supervisor, which is quite different from being an instructor. Someone can excel in one role but be [almost] incompetent in the other.

Consequently, it's hard to give you solid advice. The basic question is if your advisor's unavailability is impeding your research progress. If so, then you should definitely explore other options, if possible. For instance, look for a co-advisor for your project with A'. If no options with A' pan out, then you should consider switching advisors.

However, if the teaching style doesn't carry over into research issues, then it may be worth your while to wait and see if things improve.


Switching research topics to something less interesting?

If you want to do research on X, you should go to a place where you can do that! Going to school A, working on Y, and hoping that you might be able to switch advisors does not sound like a good idea. How much the professor at school A wants you should not really matter, you have to do what is right for you; he will find someone else. Moreover, I would not already think about what to do if I lose interest in X. This is hypothetical anyway, and in this case, there might be some topic Z that is more interesting than Y etc.


How might changing topic affect a career in academia?

If you do a masters thesis on topic X and topic X is not too far from topic Y, for example, if they are both computer science topics, and your academic record is good and your background is sufficient to make the transition, then I don't see any problem making the change at this level. You can catch up on whatever knowledge you need while learning about and researching topic Y. This will not look bad. After you obtain your PhD, people will be less interested in your masters.

Changing later in your career is also possible, though a little more difficult.

One positive point about being able to demonstrate that you can change topic is to show that you are not a one trick pony, meaning that you are able to apply yourself at the highest level to different areas.

Indeed, as interests in the field shifts and technology changes and new topics open up, it will often actually be necessary to change topics in order to survive in the field. If people (or just you) lose interest in a topic, then you need to be able to change.

But it is also good to demonstrate that you can commit to one line of research. Apart from the advantages this gives you, such as having a deep knowledge of a specialised topic, it demonstrates your commitment and can be used to show that you have and follow a research strategy.


My adviser is hesistant about letting me graduate. How should I handle it?

Most departments have a faculty member who serves as the director of graduate studies. Talk to this person about the situation. He or she will have much more contextual information than any of us here, and it is this person's job to resolve such conflicts between students and advisors.


How many papers are expected a PhD student to write in order to be accepted on postdoc programs?

A post-doctoral position is not usually part of a "program."  It is not like graduate school, leading some kind of higher certification.  It is a job, doing research in a specific area.  Hiring is done individually by the senior researcher overseeing a position, and what they may be looking for is highly variable.  Some people may hire based primarily on people's publication output as graduate students; however, in most cases I am familiar with, hiring is done based on a holistic view of the candidate.

For example, when I applied for a post-doc in theoretical particle physics, I had only one publication out (and another one submitted), based on my graduate work.  However, I came from a top graduate program, and I had a very strong letter from my advisor.  I had to apply for a lot of jobs, but the one I eventually got was with somebody who had research interests very close to my advisor's.  (The two had collaborated once, briefly, some years in the past.)  I had a very broad background (having taken a lot more classes than most graduate students at my institution), and based on this and my advisors strong recommendation, I got a job.

One of my professors in graduate school had told me explicitly that it was much more important to learn a lot in graduate school than to publish a lot of papers.  You are not going to get the opportunity again to broaden your base of knowledge in the same way, and how many papers you publish is probably less important than learning and networking and making a good impression on senior people.  Once you have a post-doc, that is the time to really crank up your research output (to four or five papers a year in theoretical physics or applied mathematics, if you want to get a good faculty job).


How should I cite a paper that I've obtained by asking the author to send it to me?

It doesn't matter how you got the paper. Just cite it as you would anything else. I've had papers from Science sent to me from a friend when our departmental internet was down, but that doesn't change how I cite it. Yea, the journal is obscure and others will have difficulty finding it, but in theory they could given the info you provide. That should be sufficient.


Are IPython Notebooks code or slides? (for licensing purpose)

While CC licenses aren't really appropriate for code, and code licenses aren't really appropriate for text, there's no real downside to assigning both kinds to the same material. This is "dual-licensing" (reasonably common for software), and it allows the reuser to choose whether they wish to use and redistribute your material under license A or license B.

They can then pick the particular license which is most appropriate for their purposes without having to (eg) try and work out how to apply the BSD license to a graph.

For example, you could use a license statement that says something like:

  This material is copyright Piotr Migdal and made available under the Creative Commons Attribution (CC-BY) license (link). Code is also made available under the MIT License (link).


How do the completion of online courses impact a Master's application?

So if someone mentions those kind of course certificates in CV or application material for grad school, does it have a significant value for the applicant?

They are better than nothing, but it's unlikely that they would have significant value.  Courses are only a small part of what matters for graduate admissions, and elementary or low-level courses matter the least of all.  Only a fraction of Coursera/Udacity courses are at a high enough level to matter, and even those courses aren't likely to make much of a difference.

I would not recommend devoting any time to online courses for the purpose of graduate admissions.  If they are teaching something you really want to understand and have no better opportunity to learn, then that's a good reason, but the learning will have to be its own reward.

  Do you consider these kind of certificates at the same level with a grade on an academic transcript?

I'd look at a certificate of completion for an online course the same way I'd look at a traditional course taken pass/fail (i.e., without a grade).  It's evidence that you have done something, which shows some level of motivation and energy, but it's not evidence that you actually learned much in the process.

However, there's a bigger issue than grades here.  Ultimately, good grades don't mean that much: standards vary dramatically, the ceiling is rarely high enough to distinguish between excellent students, and even if the ceiling is high enough it's not clear that this is a meaningful comparison.  Letters of recommendation are crucial for supplying the information grades alone can't supply, and this is something MOOCs are currently unable to help with.


In my field, Physics, I have only focussed on a single, yet detailed, hypothesis.  This has been true for my thesis and published papers.

I find that it has been and is easier for me to concentrate and explore one single hypothesis thoroughly, any new hypotheses that arise from from this form the basis of several sie projects and further research.


How much say does an associate professor have in accepting a foreign intern into his lab?

Different schools have different procedures, but as far as I know, a formal offer of admission will come from an admission officer (or a graduate officer), not from a professor.

Usually, the most a professor can do is to recommend a student for admission to a program, and possibly indicate that she/he has already met the student.  The admission process itself is usually handled by a separate officer, which will check if all the admissions requirements are met.  Those might include various academic requirements, suitable background in the primary or a cognate field, language requirements etc.  (These requirements might be checked at the departmental level, and a recommendation then forwarded to the appropriate admission officer.)

In some cases, admission may depend on the availability of funding, so that a student who applies knowing a professor can guarantee funding has an advantage.

Funding is usually the trickiest part, but I am also aware of cases where a student had found a willing supervisor but the file was rejected on academic grounds.


What are the 25th-75th percentile ranges for the annual income for graduate students in the United States?

Note that those statistics are often averaged over all possible disciplines, and therefore, since there is such a wide disparity of stipend levels between different schools, and between different disciplines at the same school.

At the institution I attended for graduate school, engineers had stipends approximately 30% higher than the science majors (chemistry, physics, math, etc.). Similarly, at the undergraduate institution I attended, a similar disparity existed between science and humanities graduate students.

It is also important to ask if master's students, who often don't receive a salary at all, are included in that average. (And, since humanities students tend to stay longer, they may skew the statistics even more than one might expect.)

(One final note to directly address the question: competitive national fellowships in the US currently pay between $30,000 and $35,000 per year as a stipend. I would estimate, then, that most stipends are significantly below that amount. I'd say something in the range of $20,000-$30,000 would be appropriate in STEM fields, and probably $15,000-$20,000 for full-time humanities PhD's.)


Is it necessary to add mentions such as "Any opinion expressed in the paper does not necessarily reflect the view of the funder"?

It depends on the grant that you receive to do your work. Most if not all grants require you to acknowledge the granting agency. Some grants give you very specific language that you must use in your acknowledgement (ranging from the request to include the grant number and use the full name of the agency to very pedantic requests for particular wording).
And some grants do require you to specifically disclaim the granting agency from your conclusions and opinions. For example, NSF requires the following:

An acknowledgment of NSF support and a disclaimer must appear in publications (including Web pages) of any material, whether copyrighted or not, based on or developed under NSF-supported projects:

“This material is based upon work supported by the National Science Foundation under Grant No. (grantee must enter NSF grant number).”

NSF support also must be orally acknowledged during all news media interviews, including popular media such as radio, television and news magazines.
Except for articles or papers published in scientific, technical or professional journals, the following disclaimer must be included:

“Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.”

The NSF example is interesting because you don't need the disclaimer for academic journals -- presumably because the readers aren't presumed to be idiots.
In any case, this is all part of the grant letter that you receive when you get a grant -- and part of the contract you sign when you agree to receive their money. There may be other terms inside the grant contract that are not visible (rights of first refusal in licensing technology, etc.) but by their very nature, acknowledgements are the most visible.


Applying for a Physics Masters as an international student

You can pose these questions to the institution you are most interested in applying to.

I doubt you need a Masters in order to apply for a Masters.

In general, I recommend applying for a PhD.  If you decide to stop with a Masters, that's okay.  Check this with the particular institution, of course -- but in general, I think that applying for the PhD program would give you the best chance of financial support (research assistantship or teaching assistantship).


The position that I have applied is being advertised again. Should I be worried?

Should I be worried about this?

Nope. It is totally out of your control and impossible to guess what it means. It could mean they have already written you off and are just wasting time (and money) bringing you in for an interview. It could also mean that they are hopeful about you and need to satisfy some HR requirement. It could also mean lots of other things.


How do I ask a professor at a different department whether I can attend his classes?

Don't act yet.

There's no need to ask yet. You aren't enrolled at the university, so there's no need to ask. If you must ask, then ask an administrator, rather than the professor. (Professors are busy, they'd rather have fewer emails.) Assuming you're accepted, then you have several options.

Exception: You should ask if your decision to enrol depends on the answer. (See comments for further discussion.)

Just turn up.

You can sit at the back of the class and ask the professor afterwards, e.g., Hi, I sat-in on your course today and I really enjoyed it. I'm not formally registered, but I'd like to continue attending, is that okay? You can answer any follow-up questions in person. For large classes, this approach is fine. For smaller classes (or tutorials, lab sessions, etc.), you might want to ask in advance.

You needn't ask: Attending an occasional class on which you aren't registered is fine, but it is courteous to ask. (See also Allowing a student to sit in during class.)

Ask in advance.

You can attend the professor's office hours and ask something along the lines of, e.g., Hi, I'm studying ..., but I'd like to attend your class ..., is that okay? Again, you can answer any follow-up questions in person. The same question can be asked by email.

What's better?

It really depends on the professor. Personally, I'd favour a student just turning up to my class. It requires the minimal effort on my part.


PhD supervision in the Netherlands: what ranks can supervise?

There is a difference between supervisor and promotor. You need a promotor, who is going to sign off your thesis. This needs to be a full professor (not associate or assistant). However, your main supervisor can be any PI (comparable to assistant/associate professor). Your daily supervision can even be handled by postdocs, and to some extend even by senior PhD students.

Depending on the status of your PI, if he or she isn't full professor (yet), a promotor may not be involved in a PhD students work at all.


Can one's professional degree (e.g. Masters, PhD, MD) be revoked on the basis of an academic offence committed during their undergraduate studies?

If the offense committed as an undergraduate was severe enough as to cause the undergraduate degree to be revoked, then it is possible to affect graduate enrollment under the guise of "fraudulent admission." (You shouldn't have been admitted because you knew you had committed an offense which would make you inadmissible, and therefore you are ineligible to enroll in the graduate program.)


Do US professors/group leaders only get a salary, but no group budget?

Certainly the US and German systems are very different. For starters, there is no US national system for higher education (or for lower education, either). The individual states here all have individual systems of higher education, but funding can be problematic there and can vary with the political climate. Also, many of the top institutions, including MIT, are private institutions, without regular government funding. It is too broad to say that no US professor gets a budget, but generally speaking, in most fields, it would be rare to get a budget beyond salary that comes from general university funds.

Instead, those fields that require such things as laboratories rely heavily on grant funding from NSF and other, similar, agencies as well as private funding. Grant writing becomes a treadmill. In some places your tenure decision may be heavily influenced by your success in getting grant funds for yourself, your lab, and for student support.

It is true, however, that some departments in scientific disciplines do maintain general laboratories. Chemistry and physics labs, for example. I know of one cyclotron run by a physics department, but I assume they require lots of grant funding to keep the particles going round and round.

Many, probably most, graduate students are funded as teaching assistants, paid, modestly, by the university for the services they provide. Research assistants might also be paid that way, but, more likely, are paid by grants of the PI of a lab.

There is very little secretarial and staff support in most fields in the US unless it is grant funded. The once exception, I think, is that universities have offices that manage grants awarded to faculty as assurance to the funders that funds are properly spent. This office may even be responsible for managing private grants, as has been my experience. It is also likely to offer help in obtaining grants and for seeking out grant opportunities.

Postdocs and other limited-term positions might be paid out of grant funds or out of general departmental funds for faculty. This would depend on the field. But, I would guess that it leaves an individual some room for negotiation, being less regulated.

I'll make a guess that Germany, as a society, puts a higher value on education generally than is true in the US. Certainly relatively few tax dollars go to education at any level. This wasn't always the case, but seems to be a continuing and increasing trend.


How detailed should proofs be in a mathematical PhD thesis?

I usual give the advice

  If something is clear, just write it down clearly.

Of course there is a caveat: What is "clear" clearly depends on the reader, and also what is considered a "clear explanation" certainly depends.

But the message is: If you are tempted to write "The case $n=0$ is obvious." think a minute about the explanation and how to write it down. If you then think that writing down the explanation does not add anything, leave it out.

But in general, I would say, being more verbose is the better option.

Another test you could apply is: Write down "obviously…" but note down a longer explanation somewhere else. After a week or two reread that part and try to recover the result again. If you don't have any problem than you are probably fine without a longer explanation.

Some resource that may be helpful for your proof-writing skills is the talk given by Leslie Lamport on proof-writing last year at the Heidelberg Laureate Forum: Here is a blog post about it and the whole talk is here.


Translate the laws abbreviation of non-english speaking country in English written paper?

I seriously doubt the translated version you've shown would make any more sense to the reader and so would just leave them as is.

If the distinctions in the various abbreviations are important, you may want to explain them by including them in a spelled out fashion and mentioning that the abbreviation used comes from the original language. But the reality is, it sounds like the people reading your paper will be familiar with the laws of both countries, and so such information may be entirely superfluous.


Difference of professor salaries between different department in the United States

Here's one that's readily accessible, though the full data isn't public (but can be obtained).   Here's another one in a much more concise format, though a bit older.

At least for public universities, it's not too hard to do such a survey since our salaries are public record.  I haven't actually checked but I would imagine that the groups that have done these surveys keep them updated every so many years so you can use the ones I linked to to find more.


Can I cite a paper published after the initial submission of my paper?

There is nothing special about the initial date of submission.  As such, it is entirely acceptable to add new citations, including for recently published papers, at any stage except for some journals' final proofing (where they really just want to confirm their formatting and copy-editing).

Moreover, in many cases it is not just acceptable but required, especially given that review may be a very lengthy process.  For example, I am in the middle of a revision right now of a paper that had an unusually long initial review for my field---from first submission to submission of the revision will be nearly 18 months.  In the revision, we will most certainly be citing new work, including some of our own other recently published work, as a necessary part of addressing the comments of the reviewers.

So, in short: yes, cite whatever is useful to cite, regardless of its publication date.


Am I taking a wrong approach while looking for an academic position in applied areas - brutal criticisms appreciated!

If you are making a mistake, it may be in narrowing your focus, closing off opportunities. Especially if it is you who is giving a too-narrow definition of your capabilities.
A math PhD should be able to teach (nearly) any undergraduate math course and many MS level courses. Every college and university teaches math and so needs people to teach those courses. The market is enormous. But for, say, medical imaging, there are few places that are truly interested. While it is also true that your skills should, and do, enable you to work on a vast range of problems, if you exclude those from consideration, or seem to, then your opportunities also close.
In a lot of ways a mathematician is like a Swiss Army Knife, being able to attack many problems, pure and applied, since they have a facility with abstract thought and how things fit together synergistically. But be careful, in any application, that you define yourself in a way that is flexible enough that others can see your potential.


Do I need permission to use an image from a book from 1942?

It depends on whether or not the book is in the public domain in your specific country.  In some countries, copyright extends to some amount of time after the death of the author, for example 50 years.  However, your country's copyright laws may be different.


Supervisor gets PhD student to do his entire job

It is really hard to judge a case like this. It could be anything from a wonderful academic training situation to extreme abuse. It would depend on a lot of things not stated here. What is the agreement between X and the professor, now and for the future? What does the professor actually do with the time freed by X? Is it to X's benefit in any way - say via joint research? Does the professor have such a stellar academic reputation that anyone standing in his/her aura is bound to be a success. Or, such a stellar reputation that they can get away with abusing students without anyone complaining?

If the professor treats the student like a colleague and they have agreed between them that the extra work will put the student into an excellent position for the future, then all is well. If the situation is delaying the student in some way, or impeding his/her research or future then it should be condemned.

But if you are to step into such a role, you need to make sure that you agree to it and accept whatever tradeoffs there are. If they are to your benefit, then it would be worth considering, though not necessarily accepting.

You should have a conversation with X to see what the long term view is. You should have a conversation with the professor to set appropriate limits and expectations.

One of the extremes, of course is Stephen Hawking. His students were willing to do everything for him. Happy to do it. Thrilled to be there. Even when it was hard.


How report of reviewer travel through editorial system?

The report goes to the editor.  Once the editor has all the referee reports (if more than one reviewer is involved), the editor makes a decision about acceptance.  Then the editor sends the decision and the referee reports (which are occasionally redacted by the editor) to the author.


Dismissed from PhD program and reapplying; how to answer question about dismissal?

The fact that you were not allowed to continue toward the Ph.D. is not "dismissal" in the sense that that question means.  (I can certainly see how the terminology could be confusing though.)  The question is there to identify students who have been involved in academic (or other) misconduct.  Academic failure does not fall into the misconduct category, so you should answer "No" to the question.  Doing so will not imperil your application in any way.


Should I take threats from a former professor seriously?

This sounds terrible, and like you said, I definitely think asking her to write a letter of rec was a mistake.  However, regardless of whether she tried to sabotage you or not, you've been admitted!  Congratulations.

Now is the time to sever all contact with her and move on.

You left a record with your previous university about your issues with her, and if she was going to create problems at your new school I really think it would have come before you were admitted, especially since she was a letter writer.  Whatever she did or did not say, they gave you a big vote of confidence in offering you a place.  Time to focus on the next stage.

Good luck!


The safest course of action would just be to take it.

Each department at each university has its own policy on the TOEFL.  Usually international students from non-English speaking countries are required to take it, but there may be exceptions.  It is common for there to be an exception for students who have attended a university in the US, but that does not apply to you.

So you'd have to check the policies of each department where you want to apply, to see if they have an exception that does apply to you.  Or, if there is no written exception that applies, you could contact them directly, explain your situation, and ask them to waive the requirement (of course there is no guarantee that they will agree).

So unless you can verify that every department you care about will accept you without a TOEFL score, you had better take the exam.


How detailed should I describe my actions regarding code?

In general it is good to be complete, if you can do so without being overly pedantic. But the example you give (multiple data sets) seems like an especially important one to include. This is especially true as a single data set is seldom definitive (if the analysis relies on statistical data - sampling). Multiple, similar data sets gives general confirmation.

If you say too little, you leave yourself open to questions about what you considered and didn't or whether your results are too sensitive to extraneous factors.

Give enough information so that someone else is able to independently confirm your conclusion.


What suffix should you use when you are a PhD Scholar filling out membership form for IEEE Xplore?

Names are complicated, and some people are very touchy about getting theirs exactly as they want it. In English-based naming, this can often include prefixes (e.g., "Sir" in "Sir Walter Scott") and suffixes (e.g., "Jr." as in "Martin Luther King, Jr.").

This form is making things more complicated and confusing by combining two orthogonal categories of suffix:

Generational suffixes:  I, II, III, IV, Jr., Sr., V.
Academic suffixes:  M.D., P. Eng, PE, PhD

And what should you do? Just leave this field blank.
If your name had a generational suffix, you wouldn't be asking this question.
From your comment, you don't have an academic suffix yet.

Even if you did have an academic suffix, you might not want to add it anyway. In many parts of American scientific or professional society, for example, people do not bother to use their academic titles (it's always a little weird to me to be addressed as "Dr. Beal", and I would never ask somebody to call me "Jacob Beal, Ph.D.").  In many parts of Europe, on the other hand, such titles are used much more commonly and comfortably.


Didn't Pass Final Course for Undergraduate Degree - Already Have Full Time Job

You're going to have to find a way to retake that class, or an acceptable substitute, if you want to get your degree.  So that's the starting point.

I would suggest you begin by speaking to your academic advisor.  They will know about possible options for retaking the class, or other classes you might be able to take as a substitute.  You can also ask about the possibility of taking an equivalent class through another university (which might include online options) and transferring the credit - but be sure to get the specific course approved by your university in advance.

Ultimately, you might have to consider rearranging your work schedule, or even looking for a different job with more flexible hours, in order to retake the class.  Which is more important to you in the long term, this specific job, or having a college degree?

(Another thing to keep in mind - if you were offered your current job on condition of having a degree, you would likely be obligated to inform your employer that you haven't yet graduated.  If that's the case, then going on with your current job and forgetting about the failed course may not be an option anyway.)


Must an "academic reference letter" be from a university-employed researcher, or will other researchers do too?

Better safe than sorry: check with the institution you're applying to, they may have formal requirements about this.

However, I don't think it's likely to be very narrow. The important points are that the recommendation letters come from people with a good track record, i.e. people who clearly perform high-quality research, and that they have worked closely with you in the past. Whether they're affiliated with a university, a meteorological agency, the NASA, a museum, or even (may God have mercy on your soul) The Industry… it doesn't matter much.


How many papers should I be reviewing as a referee?

I have wondered about the same question.  One thing that I've noticed is that there is an incredible amount of variation in the amount of reviewing done.  I have two good friends who are strong, active mathematicians.  The last time I spoke to them they were each at least six years past their PhD and had never reviewed a single paper.  This seems bad, but it's not their fault: they are not being asked.

I suspect that the lack of coordination among journals in the same field causes the same small number of people to be asked to referee papers over and over again.  I am not a journal editor, but I have begun to wonder how editors choose referees: I am someone who is getting (what I think is!) a large number of referee requests.  I submit maybe 2-4 papers per year.  Not so long ago I used to get that number of referee requests per year, and they were all from people who knew me directly and pertained to topics related to my thesis work or to the areas in which I have written multiple papers.  Now I get at least a dozen referee requests a year, and in addition to the above I get some very strange-looking ones.  Not so long ago I got asked to referee a paper in (what I think is!) control theory.  This was so baffling that I assumed it was some kind of email crossed wires situation and asked the editor about it.  It turned out that the paper on real analytic solutions to Bezout equations had been sent to me because of a question on math.SE that I answered, in which I explained why the ring of analytic functions on the complex plane is a Bezout domain.  This is distressing: I can see why google would make a connection like this, but in the realm of academic experts, is it not obvious that we are on different sides of mathematics?  Experiences like this make me wonder who is refereeing papers.

I'm not sure that counting papers is the right way to gauge whether you are pulling your weight referee-wise.  As I mentioned in a comment to another answer, many -- I think most -- papers are refereed by more than one person, either simultaneously for the same journal or sequentially, as many (most?) papers are submitted to more than one journal before they are accepted.  Here are some things that I have thought about:

1) It cannot be appropriate for everyone to referee the same number of papers.  More experienced people should referee more papers, but also should referee more important / difficult papers.  People who have permanent / senior positions in academia (especially: tenure) should have more obligations than those who are struggling to stay in the profession.

2) Not all papers take the same amount of time to referee: not even close, actually.  I try to make a point of quickly processing especially short and simple papers: I probably do 3-5 of those each year, and I often process them in a week or even a day.  But it would be silly to equate this kind of referee work with the long, difficult papers that you spend weeks or months working on, perhaps having to do considerable outside reading in order to adequately evaluate.  Doing 2-3 substantial papers a year is what really keeps me busy as a referee.  I suppose I try to keep my eye on the total amount of time I've spent refereeing rather than on the number of papers, although I admit that I don't do this in any formalized way.

3) Unless a paper is clearly of the "one day" variety as above, I try not to let my queue exceed 2 papers.  This is also out of respect to the authors: if I have to read two papers before I get to yours, then you'll be waiting for at least six months, probably more.  If at any given time every sufficiently experienced/qualified academic had either 0 or 1 papers to referee and made a point of processing papers faster than they submit them, then things would work relatively smoothly, I suppose.


Is it reasonable to ask for access to an advisor/supervisor during summer time?

Supervisors are employees just like everyone else. They have duties (to supervise you), and they have vacations and business trips. Both vacations and business trips (conferences, field trips, probably archive work in your line) will be more common during summer. Specifically for academia, many people will use summer to spend more time working from home while they don't have to give lectures, but they may designate certain days when they are in the office, specifically to meet with everyone on a single day.

That said, I see no reason whatsoever why email contact should decrease during summer, of course except for known vacation or trip periods, where everyone can agree that emails may take a little longer to be answered.

Face-to-face contact is also important, but given that many people will spend more time at home, there is a case to be made that you may not meet quite as frequently with your advisor during summer, even after accounting for vacations/trips.

Nevertheless, I see no reason why a request for email contact and (possibly somewhat less frequent) face-to-face meetings should be unreasonable. It would of course be optimal to work out a schedule before summer, taking vacations etc. into account. "I'll check in every day with a short email, and I understand if you reply later to email questions. Could we set up at least some face-to-face meetings, perhaps not every week as during the semester, but every other week, except for the week you are at a conference?"

After all, your supervisor will be just as interested in hearing from you and knowing that you don't spend all of summer at the beach...


How do researchers affect the funding opportunities of their department

A few quick points:

Many grants have evaluation criteria that incorporate the research environment of the investigators. Thus, the research ranking and status of researchers in the department and the university of the investigator can influence the chance of getting a grant.
Researchers within a department can help each other do good research in a wide range of ways. Senior researchers often mentor and teach more junior researchers. Researchers often collaborate within a department. This is both easy, because you are collocated. It also often aligns well. I.e., an academic is not only helping his own research track record, but he or she is helping the research output and capacity of the department.
If you do good research and increase the prestige of the school, this can have a range of other beneficial effects for the department and other researchers. Academic visitors may be more keen to visit. Good PhD students may be more attracted to the department. And so on.

So in general, the contribution of a single academic to a department's research status is often only modest, but it is still meaningful. And in extreme cases, where the department recruits a research superstar, the effects can be profound.


How can I migrate a library from Calibre to Zotero?

Discussion here suggests that you can export a Calibre catalog as BibTeX

  click the arrow next to convert books and create a catalog in bibtex format.
  ...
  (you have to select at least 3 [books])

You can then import the BibTeX into Zotero. Whether that transfers PDFs, comments, and tags depends on the ability of Calibre to export that metadata (all of it is supported by BibTeX).

A thread on Zotero forums indicates that Calibre may sometimes assign "silly dates", so you may want to look over your library after import.

  I have identified the origin of these silly publication dates (Jan. 1st, year 101): that's the metadata I have in my calibre database for some e-books, probably a default value assigned by calibre when a specific date isn't available in the imported document and designed to stand out when sorted in ascending or descending order.

Alternatively, if you want Zotero to try and find the metadata for your books, you can just drag and drop the PDFs into Zotero and use the Retrieve Metadata function to look up metadata. May even want to combine both approaches and merge duplicates at the end (by selecting the best metadata from both software).


What do reviewers mean by "broad readership" when rejecting paper?

Though I haven't seen this language used, if it was the editor saying "broad leadership" rather than a reviewer, I suspect what they mean is that they did not feel your paper was sufficiently revolutionary for their tier of journal. The editor would likely base this decision on lukewarm reviews, even if those reviews are not fully negative.

Your options in this situation would be to

A) publish in a lower-tier journal, to make sure your work takes precedence in the field even if it lacks some exposure, or

B) better emphasize the novel aspects of your work in a future submission.

I also like the suggestion by @Ian_Fin that "leadership" may have been a typo from "readership" which I think would make much more sense, but my conclusions and interpretation are the same: this is the editor saying your work is not sufficiently groundbreaking for the tier of journal and either belongs in a more specialty journal or you would have needed to improve the writing to clarify the significance to the broader community.


Do people who work at research institutes consider themselves "academics"?

I don't have statistics, but I'd guess that if you asked the question of individuals working in such institutes it would depend on exactly how you asked the question. I would think that the quick answer would be no, but a more reflective answer, when provided with some "definition" of academic might be yes, but would depend on that definition.

I'm also going to guess that only a small proportion of members here are from such institutes but not associated with a university.

Of course, if a person moves from an institute to a university they would then likely self-describe as an academic.

But if you just ask "what are you", you'd be more likely to hear "researcher" than "academic".

But, as you say, it is mostly semantic, given that many academics do just about the same sort of thing as institute based researchers.

The situation is complicated a bit, of course, since many such institutes are associated with universities - some very closely. It might be further complicated in situations in which industry researchers have some "training" duties, even serving as committee members for graduate students.


How should I avoid being in the shadow of my PhD advisor after I have my own faculty position?

I find a little radical to stop collaborating scientifically with her (in part because there is no one around working on this area!), but as the time goes by it seems to me that the best option is to start working alone on this common area, or some similar solution...

There is some truth to the often-heard advise that one should stop regularly collaborating with one's PhD advisor after getting a PhD. I would argue this is doubly the case when you and your advisor work at the same place. To the outside world, you will always appear to be the "junior" in your collaboration, independently of who does how much work, who has had which ideas, or who is where in the paper author list.

My impression is that in the career stage that you are in, you should prioritize collaborations where you are the most senior person in the team, or where you are at least not overshadowed by somebody much more famous than you. Work on papers with your students, or with other people in a similar or earlier career stage than you. Avoid collaborations where you do all the work and some other eminent figure in the community (your advisor or some other senior professor) could be seen as the strategic brains behind the work.


Is it normal to not understand things from undergrad?

I want to ask if other people experience similar things about not understanding many things and eventually filling in the gaps later (I mean a lot of gaps :)? Or is it a debt of a student who didn't properly go through their education?

I do very often feel the same way and asked my advisors their opinion. Here is a batch of answers fused with my commentary on the subject.

There is a big gap between getting an A and actually understanding the subject.

It is normal to not understand something in your first try. It takes few tries for some people.

Those gaps will be filled over time as you work on those subjects further.

You can't really fully understand something before teaching a course on it (verbatim from my advisors).

I personally feel like I really understand 2-3 subjects and have a passing understanding of other 4-5. Unlike your case, I did not graduate early. I personally approach this with solving textbook problems without rereading the text. It really help, at least to me, to figure out what I do or do not understand. Another method is taking more advanced courses which inevitably require, at some point, some of those gaps you are missing. That is a good time to go back and repeat, learn in context.


How many years after MSc graduation, am I able with possibilities to be accepted from a PhD program?

In many places you have a chance until you die, so don't lose heart.
But you might want to evaluate why you haven't been accepted. For many people it is just too few applications. For others it is only applying for positions in a very narrow range of institutions, such as "top 20 in the field". And there might be ways you can improve your application materials as well, including letters of recommendation and your statement of purpose.
But a year is really nothing.
Don't lose contact with those that can support your candidacy. After ten years, it will be much harder if no one in academia remembers you.


Is it lawful for a fellowship linked to a permanent faculty position at a British university in the STEM field to only be available to females?

In the UK, there are a number of fellowships exclusively for women (e.g., L'Oréal WISE fellowship). The Equality Act of 2010 allows for positive action outside of recruitment which these fellowships likely fall under. The Equality Act of 2010, however, does not allow for positive action in recruitment (apart from giving preference for equally qualified applicants).

The Anne McLaren Fellowship is a little strange in that it is a fellowship that is linked to a permanent job. If you view it as a fellowship, it legal positive action. If you view it as a job, it is illegal positive action. I think the key thing is that when the school is making a decision about the job, the gender of the applicant is not considered. It is obviously very relevant to the school that the applicant has a fellowship as generous as the Anne McLaren fellowship, but the fact that the fellowship is limited to women does not matter in the hiring process. So the Equality Act of 2010 is likely not being violated.

Providing fellowships that only women are eligible for may go against the university charter or may be illegal in some other manner, but I do not think it runs afoul of the Equality Act of 2010.


Ethics approval for an independent project akin to a survey

Let an IRB or equivalent make the call on this, not random strangers on the internet. I suspect, but haven't seen the research design, that you would get permission. But if you don't ask them, you don't have permission.

But, if you do it without permission, and are asked by a journal for your documentation on ethics approval but don't have it, you are a bit stuck as retroactive permission is (many places) not permitted.

It isn't you (or us) that gets to judge this. It is whatever ethics board is appropriate and whichever journals you might want to submit the research to.

For the record, there are some exceptions under the law (some places) to the requirement of getting permission, but most things require it whenever human subjects are involved.


Am I not meant to be a software developer?

Lots of people (including me) get conflicted about what they want to do with their lives while in college.  So, the first thing I'd like to say is that your uncertainty is quite normal.  But, if you're getting anxious about it, you need to fix that.

I'd like to suggest that you consider going to an academic counselor at your school.  Find one that you trust to say all of the things that you have said here.  This is just the sort of thing that they are trained for.

I, personally, got my music degree a long time ago.  I didn't do very well at first.  I thought I wanted to be a famous concert pianist, but I really didn't.  I did poorly in school at first, but eventually I decided that I didn't care about being famous, I just wanted to play the piano well and get my degree.  I improved and managed to make it through as a solid 2.5 student. I got to be a good pianist and musician, but not good enough to be a pro. So, a week after I got out of college, I took a job at a ComputerLand store (a big chain back in the old DOS/IBM PC/Apple II days).  I have spent the last 30 years in the IT business, doing one thing or another.  I still practice piano regularly and take students from time to time.

So, a few observations.  If you decide to move to something else, you're not a failure.  If you think that you are interested in nothing but computer programming, you're letting your anxiety get the better of you.  If you "want to be a successful computer programmer" it sounds like maybe being successful is more important to you than being good.  If so, then you need to rethink your priorities.  You won't be happy in any field (or in life, for that matter) if  what others think of you is what defines what you think of yourself.  You need to care about doing a job well, and seek to feel that satisfaction that you get when you do.

I'll suggest again that you get with an academic counselor.  Helping you get in touch with what you really feel like you want to do, and then helping you do it, is their full time job.  Plenty of them are very good at it.  If you decide to switch majors, then you'll get plenty of help.

Above all, don't just sit and do nothing and let your anxiety marinate.  You don't need stomach trouble!  Go do something.  Start examining your desires, abilities and skills, and be tough with yourself about what your feelings and motivations are.  There's nothing wrong with tearing it all down and starting over; you never really do start over because you bring all the life lessons that you learn along with you.  Get to it, and persevere.  :)


Publishing as sole author on politically charged topic

I want to begin by acknowledging that I am stepping far outside my core expertise by answering this question: as a mathematician, the chance that I would write an academic paper on a politically charged topic is essentially zero.

I firmly believe that PhD students have the right to work on whatever they want in addition to their assigned thesis work and duties.  (In fact, everyone does.)  When I read other questions on this site in which students in the laboratory sciences say that their advisor tries to shut down their side interest in X, I got dismayed.

Being a PhD student requires a great deal of single-mindedness.  I think it's nice for a PhD student to have at least one project or publication which is not directly connected to the subject of their thesis work: that shows breadth.  However, this should not come at the expense of their thesis work.  Sometimes people with very independent personalities put more time into their independent work than their guided work, and this can be a good decision, but they should still get guidance on that decision!

In this case, I am a bit concerned that the OP may be going out too far on her own.  This is a side project which has some difficulties -- including political ones -- to the extent that the OP is wondering whether she needs more faculty assistance.  She also says that she has not published anything previously.  So the OP has chosen in my opinion a rather tough side project.  How much effort will it take to bring this project to successful completion (including publication)?  The OP doesn't know; that's part of the question.

I recommend that the OP talk to her advisor about this project, including the question of how much time to spend on it and whether to try to publish it now, later or never.  If the paper is sufficiently politically charged, then it has an unusual property among academic papers: publishing it may damage the OP's reputation in certain circles.  This is already worth a serious conversation with the advisor.

Finally: adding coauthors solely to increase the chance publication is both unethical and a suboptimal strategy for the solo author.  I have a different idea: if the paper is hard to publish because the author is so junior, the author can just put the paper in her pocket until she is less junior, and then try to publish it later.  (There is also something to be said for not having your first publication be controversial, at least in many academic fields.)  What a PhD student needs to do most of all is complete the strongest possible PhD thesis, and this strategy ensures that the OP is not getting derailed from that.


How to ensure adequate dissemination and wording of an academic job offer when the teaching language will not be English?

You cannot change the location of your university and the fact that the local language is not English. Moreover, the question focuses on tenure-track positions, so I will interpret that as positions where the goal is that the holder stays for a longer period of time (lets arbitrarily say 10 years), but correct me if I am wrong. Even if teaching in English was not a requirement, the holder would still need to learn the local language. You can survive in many places with only knowing English, but to make the best use of everything that is possible you often need to know the local language. So, in practice I find that the requirement to teach in the local language, with the accompanying support, actually helps foreign position holders adept to their new environment. So there is no need to be defensive about that.
Regarding your first question: I would say that there is continuum of candidates where on the one extreme are people who enjoy experiencing new places, and for whom learning the language is less of a chore and more part of the experience, and on the other extreme are other people for whom learning a new language is going to be too much. Your university will have trouble attracting people who are more on the "language-phobic" side of the spectrum, but that is not a bad thing as they would not be a good match for your university anyhow.
Regarding your second question: keep it short, to the point, and factual. Those who are not daunted by learning a new language, just want to know whether the requirements are reasonable for them. Is there a transition period, and if yes how long? What kind of support is there? In the advertisement, that needs to be very short, but you could include a link to a place that provides more information. Again, don't be defensive about it.


Who decides a university's stance on a topic?

Universities work like any organization. The stance of the organization is the stance of its leadership. It can be the president, the chancellor, whatever you call it, it can be the board of directors, it can be the faculty assembly… It can even be a university-wide poll as you suggest. It depends on how the university is governed.

The statement "organization X has position Y" is a very common one in English. For example, "country X is a friend of country Y". "Statistically", it's unlikely that every single inhabitant of country X is actually a friend of every single inhabitant of country Y. Saying that a group of people does something is not the same as saying that every single member of that group does something.


Would a professor write a bad letter of recommendation?

I would read these responses as: "I am happy to write you a letter of recommendation, I am busy, and just want know where to send my letter".

As a professor, I get literally hundreds of emails everyday, many of which, like yours, I want to reply to, but I don't have time to write elaborate or detailed responses. I read the responses you got as terse but professional.

If I am approached by a student I don't feel I can write a good recommendation letter for, I usually tell them this, and suggest they ask someone else. I think this is common practice.


Article awaiting reviewer invitation 6 months after submission

If you feel your paper is strong, then I would send one last e-mail in a week or so stating that if there is no response, you will be compelled to withdraw from that journal and resubmit at their leading competitor.

Note that sometimes the e-mail queues at journals are broken. If you can find an alternate way to contact the editor, you may want to try it.


How can I convey my concerns about a University graduate program to the director without sounding like a know-it-all?

Kudos to you for trying to improve the lecture! I was in comparable situations myself, but I'm a coward and didn't take steps. So this answer deals with how I would go about it, if I had to - I didn't test it in practice.

  However, these questions lead to more questions, comments, chatting, arguing, even talking about politics with the lecturers, to the point that the lecturers can't finish on time.

This is the important point and what you should focus on - the clearly detrimental effects (discussions/arguing, not being able to finish on time).

For sure, the usual etiquette applies

Be polite and friendly
Be to the point
Be concise
Keep it well-arranged

This applies to both, talking and email, e. g. in the latter case I try to write them in such a way, that what I want becomes clear already by glancing at the email. No unnecessary fluff.

I guess I would take the following steps

Praise the lecture (if you mean it, but you'll surely find something positive to point out) and especially the possibility to ask questions.
Describe how the way questions are handled interrupts the lecture, but not in an accusatory way. Say that it negatively effects you also.
Add suggestions on how to improve the lecture, e. g. by answering the questions directly only (and to cut discussions short) and your suggestions.

Explanation:

Gives them a good start and also makes clear, that you are neither just whining/complaining nor question the usefulness of asking/answering questions itself. After all, this is one of the advantages of attending lectures.
Explaining the problem situation and the effects it has on you, without blaming them directly, gives them valuable feedback. It's possible that they are already on your side, but if no one complains... Also, it is hard to not agree with you and the effects it has on you cannot be denied. How and that the learning experience suffers should be of great importance to them.
Suggestions are always helpful, and in this case you further emphasize, that you have no problem with questions themselves and are therefore not advocating something bad or having unrealistic expectations.

For sure, it strongly depends on them, how they react to your suggestions. It's possible that they don't do anything at all, or they may welcome them as an incentive to act. In the end, you are there to learn, and interrupting the lectures is detrimental to the whole purpose of such lectures, so it's good that you voice your opinion on that matter. Just avoid making it sound as if you were accusing them personally, rather that there is a problem and you needed their help to solve it.

I have good experience with constructive and polite feedback and my lecturers always seemed willing to listen to suggestions (usually by others, not by me) and actively encouraged feedback. The feedback was not always helpful (e. g. I noticed that, when the (anonymous) comments were discussed), but whenever it was, the lecturers were open to it, or at least explained why it wouldn't work.