Who should I ask for reference letters for academic positions?

Short answer: Extra letters do not improve an application, but could undermine it.

Elaboration: One advice often given in career center presentations or online articles about post-doc/TT applications is that the application packet should only contain the documents (and the number of documents) requested. If the announcement asks for 3 letter of reference, it means the hiring committee expects 3 letters, not 2 or 4. This is a simple yet often overlooked fundamental criterion of a successful application.

Assuming you are planning to supply only the requested number of letters and the issue is which letters to include, I recommend sticking with the traditional approach of letters from the individuals who you have worked with in subordinate capacity with during your PhD studies. This typically includes your dissertation advisor/committee chair, perhaps another committee member, or (if different) a PI on a grant you worked on, whether in or outside of your department (e.g. an affiliated research center).

I would advise against letters from very junior faculty at other institutions (e.g. your recent peers) as they carry relatively little clout and the hiring committee might get the wrong idea if they suspect your choice of using them as reference may have been forced, to some extent, by circumstances that prevent letters from more reputable/senior colleagues (in other words they may come across as less convincing and perhaps even suspicion-provoking reference choices - and you don't need that).

Generally, I would advice including letters from the individuals (faculty) you have worked with most recently. The dissertation advisor is an unavoidable choice and a must. Beyond that, if you worked with other faculty who were PIs or partners you have collaborated/co-authored with, choose the individuals you have worked with on most recent projects/publications as consistent with the chronology of your academic appointments/experience in the CV.

It is also a well known and accepted (if not publicly advertised) practice to pre-write letters of recommendation to save your references' time. Whether you have done this already or not, good to keep in mind. Just ask your reference in a matter-of-fact way if they prefer to author the letter or could use a summary draft (or at the very least, a current copy of your CV).

Good luck with your apps! Let us know how it goes!


Is it moral to propose work that's already partly done?

Let me make two points. The first is that in order to write a research proposal you have to understand the area well enough to describe it. This implies that you have already explored it and have done some work to get it ready for submission. Even after you submit, you aren't likely to just forget about the problem until you get funding. The alternative would be just saying random things in research proposals. So, there is no alternative, in my view, to making proposals on partially done work.

The second point is at the other extreme. I've heard that some very successful researchers, though the stories may be apocryphal, work like this. Do research problem A. After you are nearly done, write a grant request for problem A and if it is funded, write the report but use the funds to do problem B, that wasn't mentioned in the grant request. If B is successful, write a grant for it (B) so that you have funding for problem C, etc.

You might question the ethics of this, but the realities are that the funders get what they funded, and the researchers get the funds they need to do research that the funders (and society) like. If you think about doing it any other way, what you wind up with is a lower success rate for funded research (hence less funds for students, etc) and lower reputations all around. That is because there is no guarantee that your initial thoughts on a research topic will bear fruit. So you try to solve more problems than you can reach conclusion on. Lower "success" doesn't serve anyone very well and turns research into a sort of jungle - eat or be eaten - situation.

But, I'll also note that if you apply for a grant for a piece of work and tell the funders that it is nearly done, you won't get funded. That should be pretty obvious, I think. On the other hand, if you ask for funding for a wild idea you just had, you won't get funded (unless you are already a superstar). So there is a tension here. So maybe there is a sort of "sweet spot" in which it all fits. But certainly the work is partly done before funding is contemplated by either the researchers or funders.

Even if the real situation isn't quite as extreme as this, a researcher funded for A and working on A would be foolish to completely ignore problem B if it occurred along the way. S/he would be wise to follow the threads for at least a while to see what potential there might be. People, including researchers, aren't machines that work on only one thing at a time to the (mental) exclusion of all else.

The reality is somewhere in between these extremes, though both extremes exist, I'm pretty sure.


Reporting negative results/failure of experiments in thesis/papers

I agree  with you but suggest that you follow your advisor's advice about your dissertation. To a fairly large extent you are limited by the standards of your advisor until you finish your degree. Even when their advice isn't optimal.
Research is a search for truth, not for results. Negative results can be just as important as positive ones in the search for truth and should, in principle, be reported so that, just as you say, others don't follow blind alleys.
But too many people, I think have the opposite view that a negative result is a failure in some sense, even when it contributes to knowledge. Your advisor may be one of these.
But the purpose of the dissertation is to get it approved and get the degree. After that, the standards you follow can be (more or less) your own. So, a tactical retreat here may lead to a strategic victory. Your dissertation won't be your last, nor, hopefully, your best work.


How do professors usually discover "new" research interests?

Here are a couple ways that have resulted in new research directions for me:

Reading a paper/book. Reading a paper/book can inspire new ideas. You may find that a paper is missing something, or you think of a way of doing it better, or perhaps you can combine the ideas in the paper with something you already know.
Obtaining funding. Often funding is obtained in groups, generally to inspire collaboration and cross-fertilization of ideas. As a result, one is forced to venture into new territory.
Talking to a colleague (generally from other institute). Simply chatting with someone at a conference or when visiting another institute can inspire new research directions. They may have a problem; you may have the tools to solve it.
Changing job. This brings you in contact with new people who have new problems. Collaborations my result from conversations in the coffee room, or by going to research discussions within the new department.
Following up on something a student has done. You may set a masters student, for example, to look at something you find interesting, but have not yet had time to explore in depth. The student may come up with something useful, but then leaves.


How should I stay in touch with the professor with whom I have arranged an internship?

Well, you don't really want to start the internship now, on a remote basis. So just send an email once every three months or so with some news about yourself and your studies.

If you want to write a bit more often, that's okay too.  I wouldn't write more than once a month, though.


I would recommend not batching up assignments to a common deadline, because that makes it even more challenging for students to manage their time properly. If someone waited to the last minute on an assignment in the prior regime, now they'll be waiting until the last minute on 3 assignments and be in even worse shape -- compounded by the mental effort in prioritizing which one they should work on first. Under the original regime, they have more opportunities to engage in this cycle and get feedback on how their study skills work for them.

My response to these types of problems is to have a blanket policy of dropping a certain number of grades from consideration; for example, in my classes, there are 12 weekly online quizzes, and the lowest 3 are dropped for each student at the end of the course. There are absolutely no makeups or past-due work allowed for any reason, which massively clears out my own time (absolutely no chasing students or managing late work after my grading process is completed). Plus, the "drop N grades" is automatically supported by the Blackboard management system.

In my classes, I don't give any special allowances to students who first show up later in the semester (but this may vary for your institution). I had a student join my class in the 2nd meeting last week, and he had already missed the first quiz submission; he asked "Can I make that up?", and the answer was simply, "No", and being pointed to the syllabus for the drop allowance, which in the years I've been using it has always been accepted quite gracefully. In my opinion, it's the most efficient use of your time as an academic.


"If multiple papers are accepted for presentation, each paper requires a separate registration fee." -> Why?

For most conferences, the primary costs are:

Venue
Catering
Society fees
Program and proceedings
Keynote / scholarship travel sponsorship

The price of these is wildly variable depending on the arrangements that have been made.  At the low end, consider a conference using university meeting rooms, asking people to go out for lunch on their own, using volunteer labor and keeping program and proceedings electronic.  This can be extremely cheap, on the order of a couple of dollars per attendee, even for a rather large meeting.

When a conference meets in a hotel, the expenses go up like crazy.  For a week-long conference in a major city hotel, the venue and catering expenses can easily run as high as $500/person.  These are often required to be booked far in advance, based on the number of people expected to register for the conference, and there may be limited flexibility to change these numbers if attendance falls short.
Hotels also frequently ask a conference to have attendees book in the hotel, and will ask for "insurance" from a conference in the form of a commitment to get at least a certain number of rooms booked and to pay for unbooked rooms if the conference falls short of that commitment.  This can add thousands of dollars of expenses.  These factors can operate at universities too, which sometimes demand high venue and catering fees even when their own professors are organizing.

With an expensive venue, then, a conference's organizers can thus get very nervous about whether they will have enough money to cover their anticipated expenses, if registrations are less than anticipated.  This is especially the case if the conference has had difficulty meeting its expenses in the past, and may be in trouble with its sponsoring society as a result.

Forcing people to register per paper is one response to trying to avoid this type of shortfall.  Not only is there the fee, but if you're registering a second time, you're more likely to send a second person from the group, who will likely have their own hotel room.  For a conference that may be facing a shortfall in its hotel commitments, a single registration easily can be worth $2000 in increased income and decreased hotel penalty.

Personally, I still don't approve: I think that a conference operating at such a razor's edge would do better to take other approaches to trying to make up its budget shortfall.  I can understand, however, why the organizers of respectable conferences sometimes choose to do it: it's not that they are getting rich, but that they are trying to keep from going bankrupt while they make their venue rich.


How can one know if a paper award decision was made with the award committee not having access to the author names?

In some cases the award committee or sponsoring organization may describe its procedures on its official website.  Otherwise, you can write to the award committee chair and ask.

I don't think there's any more general way to know.  In particular, I doubt that there is any central place where you can find this information for many different awards.  (It would be a pain for someone to collect it and keep it up to date.)


How is a Masters different from the first two years of a PhD in the same field?

There are two different types of Masters - taught masters and research masters.

In England, a research masters allows you to work, on rotation, around 3 labs in the year, and you can pick and choose from different sub-fields. This is hugely beneficial because it exposes you to different sub-fields, but more importantly because it exposes you to different work dynamics and environments, allow you to cope better in your PhD; furthermore, you'll make more contacts (which is all that matters in research - reputation and recommendations) and learn from different people. It'll give you the confidence to know, during your PhD, whether you are right or wrong.

The downside is that it takes you one more year and there is no guarantee you'll get a PhD after, and there is also the extra cost - most funding bodies do not fund a one year masters. However, if you apply for a 4-year Masters with PhD, funding options are more generous.

I can only speak for England, unsure about other countries, but the same principles apply. (my own opinion is that MRes is good if you can afford it)


Writing REU Recommendation: Should I mention the student is an underserved demographic?

As has been said in the comments before,

1.a) Most REU specifically say they encourage underrepresented minority students to apply. I understand some of the grants the NSF gives out require that the research group be diverse.

1.b) However the REU application the student must fill out already contains a question regarding this subject, and as @Tom Church pointed out, the student is not obliged to disclose this information. So I would say you should not mention it in the letter

2.a) Again, most REU's specifically encourage this type of students to apply,

2.b) However it is something the student should mention in the personal statement, so again it would not be your place to mention.

3) Yes, you and the student should mention his/her interest in graduate school, as again this is something REU's look for.


One concept/approach, which is what I try to keep in mind in addressing a heterogenous audience in a not-required more-advanced course, is exactly to not try to be "systematic", much less "complete". As noted in the question, it would be easy to use all the available time for "general theory", without ever getting around to the points of interest that motivated the course in the first place. So, instead of "laying a systematic foundation...", I try to get to interesting phenomena as directly as possible, and then back-fill "general theory" as relevant. For that matter, "general theory" is more widely available in textbooks and on-line notes than are interesting examples (since the latter tend to be written in "research papers" aiming at more-expert audiences), so students can more easily do further back-fill themselves if desired.

For that matter, some "general theory" is somehow over-hyped as a big deal, when, in fact, the introductory parts of it are really very elementary. For example, in an introduction to modular/automorphic forms (my interest...), one could position the thing as having prerequisites of "Lie theory", "algebraic number theory", "representation theory", and/or "algebraic geometry". It is certainly true that all these things are relevant and useful, but (I claim) it is not the case that one must have "systematically" studied all these things prior... For example, "Lie theory" at the entry level can be simply a study of behavior of two-by-two real and complex matrices. "Algebraic number theory" at a basic level is just about integers, or perhaps Gaussian integers, and so on. "Representation theory" (infinite-dimensional unitaries, etc.) relevant to automorphic forms will not even be found in "basic" representation theory books (which tend to do finite-dimensional and more combinatorial things), but can be approached in a down-to-earth way (for real rank-one groups) as Bargmann and Wigner did, by looking at asymptotics of solutions of second-order ordinary differential equations. (Indeed, the later work of HarishChandra and Casselman-Milicic might be construed as adapting those classical asymptotic techniques via Deligne's PDE version of the old ODE asymptotic results, as in the appendix to the C-M paper about it.)

In particular, to my perception, far too often students think that they have some moral-professional obligation to be "completely expert-prepared" in the alleged background material before starting the next stage... which is (to my perception) substantially misguided, since that way one has no inkling of what the use of the "background" might be. Trying to short-circuit this impulse a bit by directly drawing attention and explicating the applications is a good anti-dote.

And, to repeat, one has no obligation to "prove everything in class"... That's a recipe for not getting anywhere.


Chose name for first publication (special characters and compound names)

+1 for thinking about this before your first publication. Have you read through the other questions tagged personal-name? They may be helpful.

In your case, I’d go with Alan võn Neumann, or võn Neumann, Alan if your target journal uses this format.

If you include Chúrch, then I’ll guarantee that you will start being referenced as “Chúrch (2015)” - maybe not on this publication, but later. (You do plan on using a consistent name throughout your sciencific career, right?) Bibliographic databases may be smart enough to pick this up, but they will need to rely on journal editors including your correct name in their journal databases, and this is where noise will creep in.

Conversely, I wouldn’t worry too much about the diacritical characters, as long as their mapping to basic characters is straightforward. Search engines understand this, so it won’t make a difference whether your name is listed as võn Neumann or von Neumann. One exception would be German ß, where it is not obvious that this should be transcribed ss. IIRC, people have legally changed their names over this.


Can you be co-advised by 2 other faculty instead of 1 for PhD

Yup.
I know it’s quite common in Israel (and I know of someone else who has two advisors). No idea about the US though.
I personally think this should be more widespread- with the way research is going these days, most impactful work span multiple domains and it’s not possible for a single professor/lab-Group to develop expertise in all these domains.
So multiple advisors bringing their expertise is a win-win for everyone involved!


To ask such a question, just ask. Don't worry too much about "polite". Just be direct. Let them know that your potential letter writer won't create an account for this and prefers email. Ask if it is possible.
Some institutions will agree and find a way. Others will not. Then you have to consider other options. Try harder to find letter writers or find institutions that have a more compatible/reasonable application process. You have little control over either the rules of the institution or the reservations of your letter writers.


Job after post-doc - Whom to list as referee?

List all 4!

People will find it odd if you PhD advisor is not under the list of referees. The same holds for the host of your last position. If you are limited to 3 references then get rid of one of the "superstars", but typically job descriptions say "at least x referees".


How to write large numbers in a scientific thesis?

If it's a measurement, or another number where precision is key, I'd prefer just numbers, possibly using powers of ten, or standard prefixes - e.g. a resistance of 3.4MΩ. Otherwise, I don't think there are any solid rules on this. Some do indeed suggest consistently writing numbers like "1 million", whereas others say "one million" for the round numbers.

Personally, I wouldn't worry too much about achieving consistency throughout an entire thesis. Focus instead on making the text flow well from one instant to the next. Maybe using words in the introduction, and numerals in later chapters would fit your thesis best? The style should be certainly be consistent within a sentence, and possibly a paragraph, to avoid confusion. However, unless you have to follow a really strict style guide no one  really cares beyond that.


IEEE membership for academic and professional career

Student membership is for students only. Once you lose that status, then you will require a professional membership.
Student members have access to the IEEE digital library through the library of their institution. Professional members have access also, but it requires fees, perhaps a subscription.
But one can gain access if the employer holds an Institutional Subscription to the library.
This is similar to the ACM which has its own digital library, available on similar terms.
But, otherwise, a student membership has most of the advantages of a professional membership but at a lower cost while you remain a student. There isn't really a distinction between Academic and "Professional" membership.


Graduate school admission advantage if offering instrument time

That might certainly catch my eye if I read your application, but I'm not sure how much weight it would carry. I would be a bit nervous offering it quid pro quo - that seems to get into a dangerous or at least gray area in the vicinity of a bribe for admission.

My suggestion, if you include such information, would be to limit your disclosure to a demonstration of your commitment to the topic of interest, or to talk about ways you have already used the equipment for outreach purposes to demonstrate your value to the community as an emerging scholar - and not as a condition on accepting your application.

The problem is the perception, and whether you offer it directly or not you could be perceived as trying to sway the admissions committee. For example, a police officer has some leeway in choosing whether to cite you or not; offering the officer $100 is going to get you in trouble, whether you say "I will give you $100 if you let me go" or if you say "Hey I just wanted to let you know how much I care about police officers in general, so I am going to put this $100 on your car, you can take it if you want."

Your situation is different because the legality is much less clear than the example I just gave, but I would be uncomfortable accepting a student who wouldn't normally meet the expectations of the university because they were offering the use of some equipment.


How is feedback process done after submitting an article to arXiv?

There is no official protocol or formal procedure. Here is how I handle it.

I skim the arxiv submission in my fields of interest every day (headlines and abstracts). Every few days I find some things that I read in greater detail and if it happens that I find something that I'd like to discuss with the authors, I write a joint email to all of them. Could be a question for clarification, a hint for further reading or something like "look here, I've done something related". Once in while I take the time to write a blog post for some article and then it sometimes (rarely) happens that one of the authors comments on my blog.


Responding to different requests to contribute a book chapter

This is not an ethical issue at all. You are free to contribute to whatever book / project you like. There is no obligation that you can't join a different book project just because you turned somebody else down before.


For each of these cases which is the designation that best describes my role in class

Teaching Fellow (which is a title usually reserved for an instructor who is also otherwise affiliated with the institution as a student, usually graduate), alternatively, I have seen a few graduate students who taught classes in their own right and were given the title of Lecturer, which is analogue to "adjunct" at some institutions--generally, though, even at institutions that use the title "adjunct" and not "lecturer" for their adjunct professors, graduate students who teach courses in their own right will usually still be referred to as a "lecturer". The reverse, as far as I know, is not true though--at institutions that use "lecturer" over "adjunct" or where both "adjunct" and "lecturer" are in use, students that teach are not called adjuncts, but are usually identified as "instructor" or, though rarely, "moderators", or even, the difficult-to-cv pseudo title of "Course led by...".
Teaching Assistant. Your overview might literally be the definition of a teaching assistant.
Monitor. Proctor. Or, more specifically, Lab Assistant or Lab TA.


confused after accepting PhD offer? Your experience or advice is very much appreciated!

Some doubts are pretty natural. While the bird in the hand may be worth two in the bush, those others look pretty sweet from a distance. I don't think any of the issues you raise should cause you to really want to switch except, possibly, the language issue. However, you should note that academics nearly everywhere are English speakers even if imperfectly. If the other country is, for example, in Western Europe, you will find that nearly every working age adult (and all kids) speak English very well. The issue will be in group situations in which they might prefer their native language over English. Then it would depend on their willingness to accommodate. If you are in a field in which large groups of people much interact it might be an issue. For daily life you can get along pretty well nearly everywhere.

I've not been in your situation but have colleagues all over the world and language has seldom been an issue.

For everything else, I'd just suggest you relax.


Compressing figures for paper submission

The upload limit is clearly a stricter requirement than the image resolution threshold since you can't submit a paper over that size. As you have done, I suspect most people would compress the images to meet the file limit.


Why is my paper constantly being rejected despite supervisory team being very happy with it?

This can happen when a paper is sent to the wrong journal.  This may often happen with an inexperienced researcher.  A Ph.D. student normally could get advice from the advisor on which journals to try next.  When there is no one "very involved" with your research area to advise you, what to do?
Look for journals that have recently published papers on topics similar to yours.
After being rejected from a top journal, try a less prestigious one.  In the future, after you have more experience with publishing, you will be better able to judge what level journal to send your papers to.  But also note: if your papers are always accepted by the first journal you send to, then you are aiming too low.


Asking for recommendation letters for math PhD applications

Many, if not most, successful PhD applicants in mathematics have no research experience, and even when an applicant does have "undergraduate research experience, " it's usually not worth much as an indication of talent. If the first three letters are from the same project, it's probably better to skip one of them and go with the course professor instead. Rank, or at least reputation, of the recommender does matter, but what's most important is what they have to say about you.


How can I check which Bachelor's degrees are offered by which institutions in Israel?

There is a searchable database of degree programs at the website of the Israeli Council for Higher Education (which governs the accreditation/recognition of such programs and conducts periodic academic evaluations of them).

The search keys are a free string for the degree name, an optional geographic region, and an optional "level" of degree: "First", "Second" or "Third" (effectively - Bachelor's, Master's, Doctoral).

For example, a search for First-level Math degree programs yields 81 results; some are pure Math, others are Applied Math, and others are Math Education.

Caveat: The search mechanism is in Hebrew, as are the results.


Three given names, the second being my calling name: what to put on paper?

I would not base such a decision on the fact that it is funny or not, as funny depends by the person that reads.
Naming it is not a big issue as long as you are consistent during all your career.
I would suggest you to pick up one of your three names, your surname and use the composition of them. As far as i understood, you are known as John Harris, so just go with this.

Cheers!


For a new assistant professor in CS, how to build/manage a publication pipeline

Here two pieces of advice:

As a mid/long term perspective you should build a large network with
bright people. In the beginning talk to as many as possible. Tell
them about your ideas and ask them about theirs. This will lead to a lot of collaborative papers. Don't waste too much time with people who are reluctant. Most people will be very open (especially the younger ones).
Do this also with people who are not working in exactly your field. There might be a lot of low hanging fruits to collect i.e. something that is easy for you to do but not for them or vice versa. There is hardly any type of research field that would not like to get some input from CS (buzzword "data science"). e.g. Experimental biologists here or people working in business or geography etc. This will not lead to first-authorships but possibly get your name on many papers by putting only few days of work in.


Is it reasonable and ethical to apply for two PhD positions with two different professors at the same faculty and the same institution?

Yes, it's ethical. Everyone applies to multiple positions. Everyone knows this. At least this is my impression from the US. You don't say which country, so it's unclear who might be funding your position if you're eventually accepted. It's also unclear if you apply to the university, department, or professor directly. This might have some slight influence on whether you tell A and B about your cross applications. If they are going to be meeting together in committee to decide about applications, it might be better if everyone knows that you've applied to work with two different professors but really only once to the university. If each professor has sole discretion as to whom they hire, and only they see the application, then it probably doesn't matter.


Is it possible to ask offers of admission to extend the deadline?

Yes, it's definitely okay to ask.  They're certainly not going to rescind the offer because you ask for more time.  Depending on the school, their applicant pool, how bad they want you, and (probably) how rigid their administrative structure is, they may grant or refuse your request.

You should, of course, word your request very politely and recognize that they have the right to say "no".


Do I need to inform my PI about every single project I am working on?

In your comments you mentioned that you are funded by your PI, which changes the dynamics and expectations somewhat between you and your PI; and I think he needs to know how you are spending your time.

My suggestion would be to seek approval from him to work on these. This is to show him that you are respectful and value his opinions on if these are worth working on. It can be in the form of I have some ideas I would like to develop with Prof xxx and Prof yyy, can I go ahead and discuss with them?

Your PI would probably also need assurances that working with them does not compromise too much in your abilitty to support his lab. And lastly remember this. It is in your best interests that relationships between your advisor and you remain cordial.


Citing books: international edition or the original edition?

A citation represents a source. Authors should cite sources they used. (I'm sure many don't, but that's besides the point.) Your assumption is correct:

one should cite the version/edition that they have access to

As you rightly note, citing an edition with limited circulation may cause readers difficulty. By contrast, citing an unseen edition will surely cause readers more difficulty: Authors cannot know whether an unseen edition contains the same material. They certainly cannot know whether page numbers remain consistent.
As a compromise, authors can cite section numbers, perhaps even noting the section name when inconsistencies are known, e.g., because tables of contents (available via Amazon, Google Books, or publishers, for instance) differ.
Authors may sometimes have access to multiple editions (e.g., via Amazon or Google Books, for instance), allowing a more widely cited edition to be cited.


How long should the background section of the literature review be for an engineering thesis?

Style is very discipline, department, and even person specific. So this is really up to your supervisor. We can tell what we think, but when (s)he thinks differently, then it is her or his opinion that counts.


How should I ask my PhD advisor to let me work remotely...permanently?

Bring this up directly and immediately.

You mentioned in the comments that your advisor is out of town for a week but your wife must respond to the offer in a week. This doesn't leave you much choice, so email him immediately and ask to have an urgent phone call.

Tell him openly about the situation and get his feedback. It is up to you whether to frame it as asking for permission or informing him of your decision.

However, you have to be prepared that he will not be willing to work with you remotely. You are putting your advisor in a potentially difficult position without much time to discuss it and basically giving him an ultimatum. I would have had an involved discussion about this before my spouse went on the job market (informing him that your spouse will be looking for a job and that you will be moving away if she gets an offer).


Is it a good idea for a prospective MS student to mention in his SOP that he has good expertise on software like Microsoft office?

No, because it does not distinguish you from other applicants nor explain why you would a good fit in the program to which you are applying.  The expectation in 2015 is that everyone likely to be in graduate school, and even undergraduates, can use the standard desktop software with enough proficiency to get things done.  If specialized software, something like Mathematica or SPSS, is needed in your field, the assumption is that you either already know about it or you'll figure it out.

If you haven't already done so, have a look at this: (Master's Degree) What are they 'precisely' looking for in a Statement of Purpose, and does a SOP matter when one has excellent GPA?


Ibid is not a proper noun, so it's not capitalized as a matter of course. (Your own question contains several examples where lowercase 'ibid' is used correctly.) Whether it should be capitalized at the start of a footnote depends on the style guide used. For example, OSCOLA uses lowercase 'ibid', whereas the Chicago and Harvard styles use the capitalized form. When used for in-text citations it is typically lowercase, however.
Finally, when used with footnotes, 'ibid' doesn't necessarily occur at the start. In books I've seen 'ibid' occurring after parenthetical remarks, such as "For X, see ibid p. 50". Sometimes a single footnote is also used for multiple references, as in this example from the Physical Review style guide, where 'ibid' refers to the journal name:

J. M. Smith, Phys. Rev. B 26, 1 (1982); R. Brown, ibid. 24, 3 (1981); C.
Green, ibid. 24, 22 (1981).


Criteria for acceptable integrative research

You need to make sure your project can be finished within the time limit available. The main problem beginning researchers seem to have is delimit their project such that it is possible for them to get it done.

The other challenge will be to find a structure for your text that would make it readable. If everything depends on everything, then where do you start?


How should references in non-Latin script language be treated in English paper?

In general, this would depend on the style prescribed by your publisher (journal, conference, etc.) For instance, a blog post cites the Chicago style manual explains how one should go about sources in Chinese and Japanese:

  10.108: Inclusion of original characters

  Chinese and Japanese characters, immediately following the romanized version of the item they represent, are sometimes necessary to help readers identify references cited or terms used. They are largely confined to bibliographies and glossaries. Where needed in running text, they may be enclosed in parentheses. Computer technology has made it much easier than it used to be to typeset words in non-Latin alphabets.

  Hua Linfu 華林甫, “Qingdai yilai Sanxia diqu shuihan zaihai de chubu yanjiu” 清代以來三峽地區水旱災害的初步硏究 [A preliminary study of floods and droughts in the Three Gorges region since the Qing dynasty], Zhongguo shehui kexue 中國社會科學 1 (1999): 168–79 . . .

  Harry Harootunian and Sakai Naoki, “Nihon kenkyū to bunka kenkyū 日本研究と文化研究, Shisō 思想 7 (July 1997): 4–53.

  That year the first assembly of the national Diet was held and the Imperial Rescript on Education (kyōiku chokugo 敎育勅語) issued.

Harvard style and reference guide requires a translation, followed by the original name:

Milani, F. (2001) The Phantom of the Opera. [Le Fantome De L’Opera] Paris, LeRoux.


How to define methodology for two different approaches?

The best way to go about this is to be very clear about what you're doing. Label one as Methodology A and the other as Methodology B. Write them up separately and if then if you feel it necessary, write how they are similar.

When moving forward in your thesis be sure then to refer to each methodology explicitly in the context of what results were achieved et cetera.

As long as the reader is fully aware of what you're doing throughout, it shouldn't be a problem.


The answer to you question is that it varies both within agencies and across agencies.

I have seen program coordinators write solicitations by themselves. I have seen them ask for scientists working within the agency to help write them. I have seen them ask for external feedback on research priorities. I have also seen scientists working within agencies write their "statements of work" for small, project driven proposals.

To answer your question for a specific agency and program, I would ask their coordinator or someone within their agency. You might also be able to ask a faculty member who has served as a reviewer for an agency.


Distinguishing "Presentations" and "Experience" in CV for application for Ph.D

How can I distinguish the two sections? Should I emphasize the content of the presentation more in the "presentation" section, and my day-to-day routine more in the "employment" section?

Answer #1) I would distinguish the two sections by calling one, "Presentation Experience". The ability to execute lengthy and quality presentations is a very valuable and rare capability. Not many people can do it well. I consider myself to be a poor presenter and I've personally witnessed people who present worse than I would. By all means, accentuate your presentation experience by providing as much context as possible. Let the reader feel like they can almost "see" the presentation as it took place.

Answer #2) I don't think it's detrimental if there is a little overlap between your job duties and your presentations. Simply don't provide much or any information about your presentations in your job duties section. You might mention that one of your current job duties is to make oral presentations as required/needed.


Don't do anything without more information. In particular:

Why were your papers rejected? Was it because of some analysis you did not do? Was the entire approach bad? Was it correct but not interesting enough for the journal? These rejection reasons all reflect differently on your ability as a researcher. Remember as well that your supervisor was almost surely heavily involved in the paper, so at some level it's not just you being rejected. If for example the entire approach was bad, then your supervisor is just as responsible (arguably even more responsible, since they're supposed to be guiding you).
If you quit, what can you do? Don't just say "I can still find a good job". Make sure you know what kind of job you can find. Look at your local job portals and see what's out there for people with your qualifications. You may have a CS Master's degree, but can you program in the languages that people want, or perform the types of analyses that is asked for?

From the answers to these two questions you can make a much better-informed decision. If your conclusion is you are an idiot and not suitable for pursuing a PhD degree (are you sure? I would at least talk to your advisor to confirm that you are underperforming), then quitting makes more sense. On the other hand, if you quit now when you're actually overperforming your advisor's expectations, then you'd have metaphorically shot yourself in the foot.
Get the information first, sleep on it (so you don't make emotionally charged decisions), talk to your advisor, and then make a decision. Either way it'll be a life-changing moment.


Green card or student visa (J1) for a post-doc in the US?

Get your green card as soon as possible, do not waste your time with J1 visa. As Patricia said, you have to go back to your country where the visa was issued and you can't come back to USA for period of time (there is 2 years rule) stated on your visa. It is very restricted visa. Talk to an immigrant attorney and find the quickest way to get the green card.


Why writing about experimental results is difficult?

It's difficult to write about other people's work because:

It feels redundant repeating the same introduction that appears in all other papers over and over again.
Oftentimes it's impossible to get an in-depth understanding of other people's work, but yet you're expected to describe their work as if you fully understand it.
The way other people explain their work in writing can be difficult to understand because of terminology, background or perception differences.

It's difficult to write about your own work because:

Quickly after you start writing, you realize that there are so many more experiments you could have done to confirm your results, and that your readers may expect you would have conducted in the first place.
Explaining your results is easy only when they match existing theory. When you have unexplainable results, you actually need to come up with an explanation (= theory), which is not easy.
The way you end up ordering your text only rarely matches the actual chronological order of the work you've done. Creating this somewhat fake narrative may feel dishonest and demotivating.
A typical pattern in presenting information is hierarchical organization into mutually exclusive abstract groups. This could be difficult to do, simply because the world is very complicated.


Question about arXiv replacement restriction and contacting moderators

My best suggestion is to stop making replacements so frequently and wait until you think you have a ready pre-print, before you submit to arXiv. The arXiv is, after all, an archive for pre-prints and articles, and not a server for uploading new drafts on a daily basis.
I honestly fail to see the need to make updates to an arXiv entry, more frequently than monthly, on a regular basis. My own work-flow - for an article with many replacements - is roughly the following:

Pre-print ready, upload to the arXiv.
(+2 weeks) Get comments on the arXiv pre-print from colleagues, incorporate then, make a replacement, submit to journal.
(+1-2 months) Get comments from journal referee, incorporate, make a replacement, resubmit to journal.
(+1 month) Possibly final comments, final proofs, replacement to final version.

I assume that you upload your work to arXiv to allow other people to read it. Consider that it only serves to confuse your readers, if you make too frequent updates. I would never expect that a pre-print I have once read, will change drastically on a weekly basis after I read it the first time.
Perhaps you should re-consider your format? If you want to be able to write down thoughts quickly, and release them to the world, perhaps a blog would be more suitable?


Lab-meetings: How to establish a good setting?

This is a fine strategy. See how it goes, and discuss afterwards whether it was helpful or not. You should not allow your meeting to run any longer than ninety minutes though on any account. Most people will not be able to concentrate for that long. Also consider inserting a break if it is going to exceed 60 minutes.

Some other thoughts: Instead of having every contribute every month, consider having only one or two presentations each week. You will probably find that some people assume that 45 slides can be presented in eight minutes and you have to cut them short or cancel the later presenters.

Keep the first session very positive and upbeat, don't be afraid to step in as the moderator if anything is going wrong. If the students make a hash of things, so be it. The first meeting will set the tone for the rest, so if someone spends thirty minutes dissecting the student's presentation, no one will want to come to your next meeting.

In that respect consider giving a short presentation on your own work/goals yourself, so that everyone has a good example presentation to emulate.

I would say it is not really fair to insist that everyone prepares some food for the group to consume. Your team are scientists, not caterers. ;) My advisor used to contract external caterers for our team meetings but I think he was a bit over the top there.


One alternative would be to use a corporate author.

Using Harvard referencing for an undergraduate course I did a few years ago I cited annual reports like this with no problems.

Taylor Wimpey, 2014. The Taylor Wimpey Annual Report, High Wycombe: Taylor Wimpey.

The Berkeley Group, 2014. The Berkeley Group Annual Report 2014, Cobham: The Berkeley Group.

Standard Life Investments, 2015. The UK Stewardship Code- Compliance and Contacts. [Online]
Available at:
http://www.standardlifeinvestments.com/governance_and_stewardship/the_uk_stewardship_code
/index.html
[Accessed 15 March 2015].

Key Note Reports, 2015. Bellway PLC. [Online]
Available at: https://www.keynote.co.uk/company-report/ownership/01372603
[Accessed 3 March 2015].

If it is a team of authors and you are adamant to put an author if there are many authors the Harvard system allows you to put Smith et al. even in the even reference list.

Microsoft word is great for references and should not be overlooked for a simple and effective referencing tool.


Will having a mediocre undergrad GPA ruin my chance getting into a PhD program

Mediocre grades don't help, of course, but a doctoral admissions committee will look at much more than your GPA. Many things are considered, especially the things people say about you in your letters of recommendation. Your statement of purpose, which is often required, can also be a big factor. You need to show that you are both highly qualified and a good candidate for success in the program.

So, yes, you have a chance, but the competition will also be fierce. If you want to continue in organic chemistry, or something that depends heavily on it, then you need to explain those grades, but, depending on the field you choose it might be a relatively small factor. But your record will be judged by humans, not an automaton, so many things can affect what happens.


Become not interested in my research topic after two years of my PhD?

This is a conversation you need to have with your supervisor. If they are any good at supervising, they can help with strategies to either reignite your interest in your topic or salvage what you have done and apply it to something else. If you dislike your topic now, writing it up will be even worse and you may not be able to produce something passable. This is exactly what PhD supervisors are for.


What productive academic work can you do with minimal attention in a small (<30 minutes) block of time?

Given that you can't do something that requires your full attention during this time, I would at least advise to follow Matt Might's advice to procrastinate productively on meta-work:

Read articles (or answers on Academia.SE!) about how to be more productive as a grad student.
Read a few pages of a book on data analysis, visualization, academic writing, or some other research skill.
Use the time to review your schedule, make to-do lists, schedule a meeting, etc.
Try a relevant Coursera course that has video lectures broken into small bits
Put some thought into a tiny bite-sized aspect of your research or research presentation: How should I organize this manuscript? What is the best way to visualize this data?
Unfocused literature search: check in on your favorite journals or conferences and identify interesting papers (to read later, when you can give them your full attention)
Do a favor for someone else: Even if you're not teaching or grading this semester, I'm sure someone in your department is, and would be happy to give you a pile of quizzes to grade.
Update your CV and/or web page.
Start preparing a presentation on your current work. You'll present it to someone, somewhere sooner or later, right?
Think about your ultimate career goals.
Use the Internet to look for promising potential collaborators at other institutions.
Try out a new programming trick, LaTeX package, or software tool.


Supervisor getting another PhD student with the same project?

Having a close colleague with whom to discuss tough sticking points, potential research ideas, etc. will be INVALUABLE for you.

There is nothing quite so lonely as being one of the experts of the world on a very narrow subject and never having the opportunity to discuss that subject with another person who shares your understanding.

You will likely produce better work as a result of having this other student around. And you two can collaborate.  Don't think of this as zero sum. Think instead about collaborative potential and about this student as a sounding board. Some of the greatest research I can think of was produced by pairs or groups.


Can I edit my name on a submitted paper if I changed my name during the review process?

If your paper has not been slated for publication yet, you can probably change your name on it.  I would contact the editor about making the change immediately.  Depending on the system the journal uses, this may simply require the editor to edit your name in single file; or it may entail quite a bit more work, so you want to given the editor and production staff as much time as possible to make the correction.

You will probably not need to provide proof that you have changed your name.  Name changes are not particularly uncommon; they happen when people get married or divorced, and less frequently (but uncontroversially) for other reasons as well.  If you have decided that it is definitely in your professional interest to change the name under which you publish, that is unquestionably your prerogative.


How to find "original papers" on some topic?

As much you deepen your read of papers on a topic, the "first papers" will be cited recurrently.
However, the first paper candidates could be extracted computationally. You could use scientometrics techniques that map most cited works, for example. The most cited works are good candidates to be considered an "original paper".
Another way is to map the history of a field using visualization techniques. You extract a relevant set of papers in a topic, and then draw citations networks. The papers on the root of the network probably are good candidates to be original papers. And not necessarily have many citations.
A good book to see these techniques is Mapping Scientific Frontiers, from Chaomei Chen. The author presents an interdisciplinary view on science study, focusing on found the scientific frontiers - including finding papers that are disruptive or initiated a whole study field.


Mathematical creativity: better a high profile or a "laid back" department?

Let me focus on the question in the title.  In my experience, a vibrant mathematical community is the best environment for creativity.  More prestigious universities/departments tend to attract creative and passionate people, who create vibrant communities, and being surrounded by them will help you be more creative and passionate.  While this is not a rule, and some departments just have bad atmospheres (you need some individual knowledge of the department to know about this, so visits etc are good), you're more likely to find inspiration at a place with cutting-edge research, than at a place where most of the research is "pedestrian."

There is a caveat, however.  If you can barely keep you head above water, it's hard to be creative.  Fortunately, most places won't admit you if they don't think you can handle it, though it does happen.  Again a visit, or browsing student/faculty webpages/blogs may help with this. See also this related question on MSE.


Can I use the same PhD application for consecutive years without paying extra fees?

This is tricky, because in the US there really is no standard/universal handling for this sort of situation. It's probably going to be different at every department you are thinking of applying to.

With that said, there are a few common outcomes, to wit:

Some programs will simply say no - you must pay in full at the time of both the original application, and re-application.
Some programs offer fee waivers with a variety of requirements. Some programs will waive fee for US citizens with demonstrated need, some programs waive fees for people who participated in certain programs (often which target helping certain groups get to and succeed in college).
Some offer waivers/reductions to countries where the relatively reasonable fee to US citizens is just an absurd expense (especially ones where $75 is 2-4+ weeks of average salary). This does not apply to every country, however.
I suppose it's technically possible that a program will allow you to pay the fee once and reapply the next year at no additional cost...but I've really never heard of that and I'd be pleasantly surprised if any program you were looking at would offer you that option.

I'd suggest you contact a few of your target programs right away and ask their graduate coordinator what your options specific to the fees are. That's really the only way I can think of to get a real answer that's certain enough to help you decide on what to do.

But barring answers from your target programs, I would absolutely suggest that you do not simply rely on them being willing to let you reapply at no extra cost or automatically not pay the fee - or even to waive the fee more than once. They are not required to do this by any external rules or laws, and being a foreign citizen or having limited finances are not protected/privileged groups under most US laws.

Get direct answers from schools you care about, and then decide for yourself if you absolutely cannot afford to apply two years in a row if it comes to that.


Applying for a tenure-track job at my undergraduate alma mater

I've seen job talks of people applying for tenure-track jobs at their alma mater. These talks tend to be more tailored more closely to the research within the department.

For example, these applicants tend (more so than others) to make references to specific projects conducted by professors within the department. I've also seen applicants make light-hearted jokes about the department's culture within a job talk before.

They also tend to be more savvy at answering soft-questions about why the department appeals to them and how they would improve it.

Showing that you're an 'insider' or 'one of them' is a useful strategy that I've seen.


Is it common to express interest in post-doc positions well before you are qualified to apply?

One semester into your PhD is probably a little too early to start contacting potential post doc advisors and future employers—the crystal ball is way too fuzzy, and their plans almost certainly aren’t known. (They may not even be doing the same area four or five years from now!)

You could certainly contact them about your interest in your research and introduce yourself, but I would wait until you’re slightly further along to start discussing future jobs; I’d say serious discussions about that are appropriate when you’re about two years out from graduation.


How to italicize technical which is explained in Introduction but defined in another section later according to APA?

In general, you should italicize a technical term when (or right before) you define it. And you should define it when it appears the first time. If you don't need to define or explain it, then you are implicitly assuming that your audience is familiar with it, in which case you don't need to italicize it. The difficulty arises here because you are essentially defining it twice, once informally and the second time formally.

I would recommend italicizing the first use in each of the sections. Clearly, you should italicize it the first time you use it. But if you are defining a lot of other terms in the "Definition" section, leaving it unitalicized might make it look odd next to all the other italicized terms you are defining.

This is not what the APA rules actually say, but I would assume that they also believe that informed decisions in exceptional cases should override their rules where it is appropriate.

Another thing you could do is say something like

  we now give a more technical definition of thingamabobs

in the "Definitions" section, and implicitly point out that you've already  defined it, which is why you're not italicizing it.


Do PhD admission committees prefer prospective professors over practitioners?

Yes (but it's usually an unconscious bias, and not openly stated).
Many academics consider failing to become a professor actual "failure". An academic career is supposed to be a vocation. PhD students are supposed to be passionate about the topic, so much so that they'll want to continue to work on it after graduating. The best graduate students go on to become professors; the not-so-good ones are eliminated and "get a job" (because being an academic isn't actually a job!). The belief is pervasive enough that many academics who quit felt compelled to write blogs about why they're quitting and why they don't consider themselves to have failed.
Viewed this way, a prospective PhD student openly states they want to work in industry is a red flag. They've already ruled themselves out of being the best, they're likely to fail. Admission committees might not think this crassly, but they'll come up with the closely-related reasons "not passionate enough" or "applicant is not motivated by the subject, therefore when things inevitably go badly in the PhD they might drop out", both of which stem from the idea that the only way to be sure the applicant is passionate/motivated enough is for them to want to be a professor.
Granted not all academics think like this, but unless you are certain otherwise (e.g., you are applying to work under Phillip Greenspun, or the program description explicitly says they have an eye on preparing students for industry jobs), I think you should err on the side of caution and say you will consider an academic career even if you are almost certain you will join industry, or at least be non-committal about your future plans.


What happens if the grant requirement for open access publications is not respected? [small & short-duration grants]

I'm most familiar with the US NIH.
They write:

Non-compliance will be addressed administratively, and may delay or prevent awarding of funds.

For the most part, NIH seems focused on awareness and trying to encourage compliance, rather than strict enforcement. It seems many are not fully aware of the guidelines, which are quite new for some researchers who have published a different way for decades.
More generally, big funding agencies like to act through the institutions researchers belong to in encouraging compliance, whether for policies like this or for ethical policies like those for human/animal subjects research.
They can threaten to withhold their funds and even government funding more broadly from entire institutions, not just individuals. While cases of this threat actually being carried out are rare, it may mean that researchers find themselves more directly responsible to their institution rather than the funder. The institution has a large incentive to ensure local compliance and likely has more resources than the funding agency to follow up, as well as a broader range of sanctions.
For your particular situation, I have a hard time imagining a funding agency feeling too bad for your circumstance. If they're funding your work and demanding open access, they're implying that they expect you to use their funds towards those costs in addition to all the others (either directly or through the fungibility of money). "I spent my money on other things and now can't afford to comply with your publishing requirements" doesn't seem like a very good argument, since everyone they fund is in the same boat and since you've accepted their terms by accepting their funding.


What to wear to a tenure track faculty Zoom interview (men)?

I hope this doesn't come too late to help you, but, for the possible benefit of future readers....
Let me suggest that appropriate wear for such an interview, assuming it is with faculty and possibly students, would be something like what you would typically wear to a face-to-face teaching session or lecture in that place. I don't remember ever wearing a tie to teach in a forty year career, for example. And yes, this might be somewhat less formal than you would wear to a face-to-face interview, but not necessarily.
For an interview with a dean or provost (which might happen at a small school) step it up one notch. A jacket over an Izod, perhaps. (I've dated myself with the Izod ref, I realize).
You need to project professionalism appropriate to your field and the position you seek, not formality. They aren't the same.
But there is another issue I'll mention for the ZOOM generation. Pay attention to the background of what is seen in your session. It is much better if it has a scholarly look (bookcases, say) than a messy room. And try to arrange it so that there won't be interruptions (family, pets, phones, ...) during the session.
Finally, note that this is a US perspective. There are other places that are more formal and others less formal than here. But if you consider what is typical dress for teaching (and/or research) in that place you should be fine.
If you are interviewing at a place with a different academic culture than what you are familiar with, note that many colleges and universities have  set of faculty pages with photographs. That can give you a guide as to what that particular faculty is comfortable with.


Right time to start applying for PhD - Germany

I'd recommend that you start applying a few months before you graduate. The process may easily take several months, and if you want a direct transition, you need to find something before you actually graduate.

In most cases, it will be possible to delay the start of a position by a few months. So by all means, if you find an interesting position that starts a bit before you expect to graduate, you should still apply. Just state the date of you expected graduation (month/year is fine) with your application.

Note that many potential employers, especially if they don't know you from earlier activities, will want to see results of academic work such as a Masters thesis (or at least a draft for it) or other academic texts. If you can't show anything in that direction, it would be good to first focus on positions where you know the professor.


How do you approach your professor if you do not understand or know how to do the homework at all?

To address the part of the question "what do I tell the Professor" to help with the problem "I do not understand the lecture material":

Clear your head
Start reading your notes, word by word
As soon as you get confused (even a little bit), stop reading. On a piece of paper, write down what you are confused about, and why.
If you can, skip over the confusing part and continue with step 2. If you have hit a brick wall and can't understand anything that follows, stop.

Take your piece of paper to the office hour and work through it with the Professor. This will give you both a better idea of precisely what you are confused about, and how to resolve it.
Hopefully, when confusion about the lecture material is resolved, the homework will start to make sense.


Publishing a paper as the sole author (undergraduate)

It seems that it is not an ego issue for you even slightly and so if it's easier you might grease Professor B by offering him a co-author credit if he'll handle the revisions and creative changes you hint are needed.  If nothing else you will learn if he is missing the work ethic in addition to completely missing out on integrity already.

You might ask B if he would edit the paper and make the needed changes in exchange for a co-author credit.  As a courtesy you might also consider mentioning that idea to give Professor A a long distance call first so he won't be surprised by finding out about the two you you sharing credit and not including him after the fact.  Men of integrity are not missing from professional teaching completely but i wouldn't say they are not all that common either so I would want to grant him that small courtesy I think he is due.

Life can be easier when you let the Professor B's of this world help themselves to some of what is yours on occasion and getting in their way can make life unnecessarily complicated sometimes.

Then again sometimes telling them to stuff it is just too much fun to pass up.  (You end up having to deal with them anyway though, about every fourth time or so you can get knocked on your ass by these guys.  Either way you'll have done the right thing for at least one good reason.


Is it immoral to show new students how to use Wolfram Alpha?

I always like to show the students Wolfram Alpha in freshman math courses. (Many will already know about it, whether you show them or not.)

There are several reasons for this. The first is that it's a useful tool, both for checking solutions to homeworks, and also for later in life.

But the more important reason is that many students are skeptical of why they have to take a course in calculus. I double down on their skepticism by demonstrating to them that a computer can solve most computational questions on a calculus exam in about 0.05 seconds, and can even "show its work". Having gotten their attention, I now have a good opportunity to make my case for the value of a math education.

As far as exams go, I recommend prohibiting the use of all electronic devices. Some students will cheat on their homework, but that will be true no matter what and in the end they are cheating themselves.


Do physics graduate programs recalculate undergraduate GPA's for admissions?

I would guess that, independent of field, most places do some recalculation, even if informally. Some people/committees just put more emphasis on some things than others.

There is also the situation that grading systems vary widely, especially if there are international students involved.

However, if you have a specific worry that you took a course and did poorly, but then later re-took it and did fine, then that may show up, but it may not be the devastating issue that you fear. It might raise questions, but such things occur often enough that you aren't unique. You may need to explain the situation adequately and indicate that in spite of past problems you are a good candidate and likely to be successful.

There can be a lot of reasons for a bad grade. But most people will look at the entire record, not just something that is anomalous.

The only exception might be if the institution has so many applicants that it has to use crude measures, such as GPA cutoffs, to get the pool down to a manageable number.


What to include in a Festschrift (memorial publication)?

A couple of memorial papers in particular stick in my mind, from my field.

These are:

"A tribute: Professor Dr. Paul Hoffmann (March 28, 1931–July 10, 2008), a scientist with a great collaborative spirit"

and

William A. Arnold by Govindjee and Srivastava (2014)

If you can't find either of these then I'll link you to them. What sticks out for me when reading them is just how personal they are. They can go into quite a bit of family history and life history, telling some anecdotes, whilst showing happy, relaxed photographs of them. At the same time, they can cover the most important achievements of that person's scientific career.

There are plenty of examples out there for you to draw from but at the end of the day, this is your tribute to the person so make it how you think is best fitting to them and their legacy.


How can I find if my viXra paper is cited?

Most established academic journals are indexed in what are logically called “journal indexes”. These indexes commonly record all publication metadata, and usually also include a record of all citations. Such indexes are thus called citation indexes.

Now, the problem with viXra is inherent to its “alternative” nature: it is most definitely not indexed by conventional players (Web of Science, CrossRef, PubMed, CAS, etc.). You thus have two ways of looking for citations to your paper:

Google Scholar includes content from viXra in its results (see this search’s first hit, for example). It probably also records citations of such articles, but the quality of citation matching is limited by Google's heuristic algorithms. They're good, but not as good as DOI-based mechanism that commercial databases nowadays employ.
A regular web search with you name, or the title of your paper. This is not as automated, but it may give good results as to who is citing your work, especially if this is one of your first papers and you don't yet have a large web presence.

(Obvious caveat: if your name is John Smith or Li Wang, web search will not help much.)


How much assumption relaxation : journal review

I think you're right. The most straightforward interpretation is that the reviewer wants to know how good the trade-off you have made is. Are you just shifting assumptions around, or have you made a fundamentally important relaxation of assumption A1 such that assumptions A2' and A3' are not much of a big deal.


Constructing a Mathematics CV - what am I trying to portray to a graduate school admissions committee?

First let me say that I have a lot of experience with math department admissions, all of it in a department which is separate from the statistics department.  The title question is "Constructing a mathematics CV": I'll answer that.  I would not assume that it's the same for statistics.

For a math admission -- either master's or PhD, it doesn't matter -- the CV is just about the least important part of the application that I can think of.  At many places, it is probably being asked for as much out of force of habit as anything else: in academia, CV's are ubiquitous.  However, most information that is provided on your CV is also provided elsewhere on the application: grades, coursework, research experiences, relevant personal experiences all have other outlets.  I can only remember reaching for a candidate's CV when something was missing from some other part of the application (possibly because of a clerical error on our part) and I wanted to quickly put my hands on it.  I absolutely don't care how the CV looks, how it is formatted, or anything like that.  In fact I don't care about that stuff for any level of academic job.  And in fact I myself have one of the more unimpressively formatted CVs I've ever seen, almost to the point of being unintentionally "unbusinesslike".

So I would say the key is this: whenever you're wondering whether to put something on your CV, also ask yourself: "If I do put it on my CV, how do I highlight it elsewhere in my application?"  Because your CV might not even be specifically read by some (or all) committee members.

To answer your specific questions:

  if I volunteered as a TA, should I throw this experience in teaching instead if I don't have any other volunteering experience?

You should certainly include all TA experience, volunteer or otherwise.  (Whenever you do something as a volunteer that one might reasonably think you've been paid for, it is only honorable to clarify that you were a volunteer.)  I find your concern that you don't have any other kind of volunteer experience misplaced: we're not looking for volunteer experience, and volunteer experience that is not math related is not clearly relevant at all and should probably only be included if it is truly notable or substantial.  Honestly, we're not selecting for candidates who are unusually socially conscious or unusually well-rounded, so your volunteer work would have to be successful enough to show exceptional drive and/or administrative skill.

  Am I missing anything?

No, I don't think so.  Your research experience -- if you have any -- is one of the more important things to go on a CV, and you mentioned it.  But in keeping with what I said before, it is really too important to just hide in a CV: if you had any research experience at all you should certainly mention it in your personal statement (and if you haven't had any at all, it would be a good idea to address that, at least by saying how excited you are and how much you welcome the opportunity).  If your research experiences resulted in actual product, then include the product itself: papers can be part of the application, and you can also include links to websites.

  how much detail am I expected to put in for my experiences? Am I expected to talk about "excellent communication skills" or "teamwork" in any of my experiences, if applicable?

At this point I wonder if you're confusing the CV and the personal statement.  You don't "talk about" anything in a CV: it just displays information.  There is not a single complete sentence in my (eight page: yours should probably be one or two) CV.  Information about relevant experiences should go prominently in your personal statement and you should do what you can to ensure that these experiences are also discussed in your recommendation letters (along with your coursework, these are the most important part of the application).  I have no desire to hear about excellent communication skills or teamwork from the candidate herself, no.  In fact, writing a personal statement that is literate and moderately compelling is your big chance to show your communication skills.  Openly boasting about skills is something that academia largely frowns upon.  This can get tricky when in certain contexts -- grant applications, introductions to papers -- you really need to describe your achievements, but in a way which is factual and not openly self-promotional.  In a grad school application I would strive to look competent, eager and (reasonably) humble.

  are there any online forums where I can get feedback on my CV (mathematics-specific would be extremely nice)?

You should ask your recommenders for feedback on your CV.  They are natural candidates, because (i) they're reading it anyway and (ii) they have already shown an interest in your academic career.  The right way to do this is to first give them a CV and make it really clear that you want critical comments and that you've saved plenty of time for it -- more than a month! -- and then after that you would like a recommendation letter.


Why are women even less represented in engineering than in other STEM?

I suspect that this is yet another example of the fractal nature of the gender binary. STEM may be coded masculine in general, but within STEM different fields are coded "more masculine" than others.

I'm very familiar with this in my own field: IT in general is masculine, but UI/frontend is more feminine than backend, on the backend system stuff is more masculine than application stuff, writing it in C is more masculine than writing it in ruby, ... This is sometimes even explicitly expressed as "your beard has to be this long to write/understand this code"

I've never found a good explanation for most of these associations, they seem fairly random to me (and apparently change between cultures as well).


In terms of the points you raised concerning publications and research opportunities, it's pretty common for an undergrad not to publish. You ought to publish during your Master's though if you want to continue on to do a PhD, or to keep that option open for the future. If you would like to publish in an academic journal or conference before embarking on your Master's, I believe that you'll need to team up with some sort of R&D or academic institute. In terms of what you could work on, that's really up to you. There's plenty of open-source projects out there, and each one is linked to a field with plenty of open questions. Being an electronics engineer that can program puts you in a pretty good position; there's a lot to do in 'making hardware work' which requires both of those skills.

In terms of coursework, 6 credits (2/3 of permitted load per semester) + research + full time job should keep you well busy. You'll lose friends, you won't have time for a relationship or pets. You'll also have many, many 24 and 36 hour working days, especially towards the end. If you want to finish your MSc on time, so that you're on the same track as your competition (read colleagues), I suggest you negotiate a part time shtick with your employers, or that you take a hiatus from work for the first year of your MSc and focus on getting as many courses as you can out of the way. Overload whenever possible. Once you have the topic settled and the hardest courses out of the way, you can refocus on your career, your research, and getting published during your second and final year. I hope I made it clear how much discipline this needs, and how much you'll be giving up.

The last point: I think I've covered that above, but to reiterate; it's mostly about discipline and time-management. Learn how much time you really need to rest and recharge and don't overdo it, and see how much you can dedicate to maintaining your career to the level you deem as 'just enough for me to be satisfied with my work' and put all of the rest into your research. That means:
 Instead of GoT with dinner = Technical conference video.
 Instead of 9Gag on the subway = Reading technical papers, magazines, or even fiction to stimulate your mind.
 Slow day at work and your boss doesn't mind = Write your papers, find solutions to that problem that's nagging you, etc.

But, please, do not neglect yourself. Exercise, rest when you need rest, and maintain a healthy diet; it makes a huge difference.

Finally, please frequent this site, it has plenty of good advice and also visit 'How Not to Suck at Graduate School'. It's a blog by one or more McGill-ians who have some pretty good advice to give on managing your time, not losing your soul, etc.

Good luck!


Career options for an astronomer outside of academia?

I moved from a PhD in Astrophysics to an industry job some years ago, so I can share my experience, as well as the experience that a number of my fellow grad students had.  This was in the United States, so things may be different in other countries.

The basic idea is that as far as most industry is concerned, a PhD in astronomy/astrophysics is the same as physics, so any job looking for a physics background will do.  Jobs looking for a mathematics/statistics background are probably close enough as well, and worth applying to.

Your most marketable skills are your ability to code and do math/statistics while working with data.  This is EXTREMELY valuable in industry.  Your knowledge of astronomy and physics is likely not very valuable except in some very specific jobs.

Some specific fields that aggressively hire people with PhDs in astronomy in large amounts:

1) Quantitative Finance - The financial world hires a lot of people with PhDs in math/physics/stats to be quants.  There are a lot of pros/cons to this field, but it pays well at least.

2) Defense Contractors - This is very much a research type environment.  However, this almost always requires that the applicant have US citizenship in the United States in order to obtain security clearance.

3) Software Engineering - A background in coding, data analysis, and mathematics is very desirable. You will likely want to brush up on your programming since scientific programming is not usually software engineering, as well as your statistics.

You can try for more specialized fields like medical imaging, but it is often difficult to compete with the physicists with specialized backgrounds in that specific niche in my experience.


How to politely negotiate working conditions/expectations in an ongoing advisor/trainee relationship?

I think you should absolutely have a conversation with your PI.  I also think that you can discuss your needs in a mature, polite, and straightforward way such that there is no ultimatum and no negative feelings.

Step 1.  Email your PI requesting a meeting for this discussion specifically. "Hello PI, As you know, I have to make a decision about transitioning into the PhD program by March X.  I was wondering if you could meet with me to discuss this. Thanks, Azzzzzz." This will eliminate the surprise element regarding your conversation with her about these non research related things. That is, if you unexpectedly brought this all up during a regular meeting, it could catch her off guard and lead to a less than positive outcome.
Step 2. Be open and honest with your PI. But do so in a way that leaves room for your PI to be the mentor.  That is, your post has several hints of arrogance and also suggests that you are really worried about there being a potential for confrontation. That is not the right mindset.  You need to focus on what you both want. Your PI is a mentor, and as such wants the best for you, but you have to actually allow her to mentor you. The tone of your conversation should not be: "I need this and this," but instead, "I'm concerned about my growth in this program and so I want to get your insight about these things..." Be open and honest and humble. Keep in mind that you are on the same team.
Re: continuous guidance. Ask your PI to schedule weekly or maybe 2x weekly meetings with you. This way you have a dedicated timeslot with her regardless of how busy she is. Again, do not present this like, "I want weekly meetings," but rather, "one thing that would really help me is if we could dedicate a time for weekly meetings."
Re: constructive feedback.  I once worked with an amazing PI who would often withhold feedback. But a trick I learned is that if I asked them, "Would you do it like this?" or "What do you think can be improved on XX?" Once I specifically asked, they gave it to me! I appreciated that I had some independence to make my own mistakes and learn from them, but at the same time, whenever I needed a little more guidance I just had to explicitly ask for it.
Re: constructive feedback (part 2). In addition to using the above method in a more day-to-day kind of way, you could also just tell your PI that you want more constructive feedback. Your PI sounds pretty open to suggestion.  It's entirely possible she doesn't know that you feel like you aren't getting enough. Have this meta conversation with her. Again, frame it in a way that does not point fingers at her for not providing it, but instead in a way that humbly asks for more of her input so that you can grow.

This really shouldn't be just the one conversation.  You should use this initial discussion as a starting off point where you can be more open and honest about what your needs are and what expectations your PI has. When something comes up address it sooner than later, don't suck it all up with a smile--no one benefits from that.

A final thought is that if you are harboring thoughts related to pay and job offers while in a PhD program, it's possible that pursuing a PhD is not the right fit for you. Even more generally, thinking about "what could be" or "what if" seems unhelpful at best and detrimental at worst. Still, having these thoughts might be a hint about what is the best decision for you.

I hope this helps. Best of luck.


Can I accept an offer from a MS program, but continue applying to other schools?

Actually, to behave in a completely ethical manner, if you don't intent to honor your acceptance, then you should withdraw. But that is based on the basic idea that failure to do so could deny an opportunity to someone else. And, in light of the other things you say, I'll have to guess that the probability of that in this case is small.

In some programs, it would be very important that you withdraw. For example if you have been accepted into a program with limited slots that are difficult to fill and that require expensive resources - medical programs, say. But that isn't the case here.

In fact, the program that accepted you has probably accepted a few more people than they need to (course based masters) expecting that a few won't show up. It is fairly typical and is normally a good thing for them to do.

I think that in the narrow case that you describe you can probably go on for a while leaving it as it is. Any transgression would be small. But you should inform them when you know that you won't honor the offer.

I think the only consequences would be to your conscience.


Applying for postdoc in a mathematics department where no one has similar research interests

I sympathize with your situation - recursion theory as a whole is essentially the size of a sub-subfield in other areas of mathematics. Of the relatively small number of U.S. departments with logic programs, many are also extremely selective, and so getting a postdoc in any area of logic is challenging.  It certainly cannot hurt to apply to every program with a logic group that is hiring a postdoc, although if they are not looking for a recursion theorist this year your chances will be much lower.

On the other hand, the recursion theory community has at least one advantage due to its small size: many of the researchers in the U.S. know each other, and know each others' students.  I have always thought it is a friendly community, at least compared to the rumors about some other fields.

Two more things that are also worth note.

If you cannot get a true "postdoc", it is sometimes possible to find at least a temporary position at an institution with a logic program. Some of the logic departments are quite large, and may have another round of hiring for instructors later in the spring or summer. So, if you don't have a postdoc offer by the expected date, make sure you reach out (and/or ask your advisor for advice) to schools where you might be able to work while you apply again next year. It is particularly helpful in this case to try to get more research done in the spring, before you graduate, to strengthen your applications for the following year. I find it is always hard to get research done in the first fall at a new institution, while also applying for jobs.
Depending on the type of department you are looking for, you may want to consider broadening your search to less-famous schools. If you are interested in both excellent teaching and excellent research, by doing some internet legwork you can often find schools that are not prestigious but happen to have strong research programs (relative to the kind of school). These schools are often less picky about the "area" you work in, and you might be able to sell yourself as a discrete mathematician or mathematical computer scientist. Ironically, you sometimes have more research flexibility at these schools, for various reasons, which is a good thing if you are a recursion theorist. So look for choice tenure-track openings as well as postdocs. Just be well prepared when you give an interview - tenure track interviews are not like postdoc interviews.


My Professor changed my multiple choice answers. What should I do?

This is really tough to approach. On the one hand, it’s incredibly hard to prove this (also since there’s no clear incentive for the professor to do this). On the other hand, you stand to lose a lot if you’re wrong.

That said, paraphrasing Hanlon’s Razor: Never attribute to malice that which is adequately explained by incompetence.

Your professor might have mixed up something, or accidentally erased your answers (and then wanted to err on your side). You can simply approach them and nicely ask about question 17, that you distinctly remember putting another answer, but you could be wrong etc.


Does changing department affect my rank?

When you receive your job offer, it will offer you a specific position/rank. It would be unusual to offer someone a lower rank than they already have, but not inconceivable when moving between universities (i.e. moving from Northern State University to Harvard). It would be very unusual for a department within your university to offer you in effect a demotion.
You would always have the choice to not accept.


Can I publish my Master's thesis while my supervisor is marking it

I suppose your advisor will be coauthor in whatever paper you write that is based on your thesis. In such case, you need their approval of the manuscript before submitting it for publication.

If you are considering submitting for publication and you are not considering putting your advisor as a coauthor, I would strongly encourage against it if the norm in your field is to include your advisor. If your advisor has already signaled that they do not feel comfortable being an author, you should strongly reevaluate whether your work is worthy of publication before submitting it for publication.


Reflecting bad experience with previous graduate program in statement of purpose

It's tough to explain this, but here are a couple of things to note:

Explain the situation without being disrespectful to your adviser. If it were me I would not even blame him for anything, I would just make sure my writing leads the reader to that conclusion without me explicitly stating it.
I don't think that your immigration status issue would sit well with the committee as a reason for you staying in the program for five years. If you had the intention of finishing your degree despite your new-found interest you should mention it.
I'm getting the understanding that you will not be receiving any degree for your efforts over five years. I'm guessing that the school does not award M.S. degrees to PhD students who have not been able to conclude their research. However, if this is not the case, I highly recommend you try to get a master's degree. You mentioned that you completed most of the PhD coursework. You may be able to get a course-based master's degree even if your research has not progressed enough for a master's thesis. An SOP stating that you had difficulty with your research and ended up getting a course-based degree reads a lot better, especially since you seem to have a valid excuse for it.
Completing your PhD would disqualify you for being admitted to EE PhD programs at many universities (many schools do not award PhD's to people who already have one). I would assume if getting a PhD (in your new area of interest) became your goal at some point during these five years, this would be a good reason for you not to complete your current PhD, so you may want to mention this to justify not completing your degree. Again, if you are able to get a course-based degree, this will sound a lot more convincing.
Don't lie in your letter. Not that I'm implying that you meant to do this; however, it is usually pretty easy to detect an untruthful SOP.

Good Luck!


What information is mandatory depends on the applied reference style, e.g. APA6 oder Chicago Style. The reference style even sets the number of authors listed maximum in the reference. Most of the times, the journal/conference sets the reference style you have to apply.

Usually, the mandatory information for journal/conference papers includes:

Author(s) name(s)
Title
Year
Journal/Conference name
Page number
DOI

The only real option to shorten anything is to use the abbreviations of journals/conferences. But the applied reference style might even prevent this trick.


What is this 'tenure track' thing really about?

Why can't everyone who is doing academic research/teaching post-PhD be eligible for a tenure position, if they work hard and publish enough high-quality papers?

Supply and demand: tenured positions are pretty much lifetime positions. Not in the sense that the positions are fully guaranteed without having to work towards them once obtained, but in the sense that, absent misconduct or complete failure to meet expectations, there is a job there.

There are way too many PhD graduates in most fields for them to all have a permanent position in academia. I suppose you could start every researcher on the tenure-track and then make many more people fail to get tenure, but I don't see that as an appreciably better outcome than limiting tenure-track positions: there has to be a gate someplace. "Tenure-track" is really just a probationary period in which candidates demonstrate they are suitable for tenure.

Like hiring for any position with many applicants, there will be imperfections in the hiring process. There are too many "qualified" people, too many difficulties in determining objectively which of those qualified people are "best," and too few positions to put them in.

edit to address clarification in a comment:

  I don't understand why it would be less desirable to have more people failing to get tenure, as opposed to the 2-tier system that seems to exist. Why not put that 'gate' at the point where a tenured position needs to be filled, and then decide? Where is the incentive for the institution to not want to keep their options open as long as they can? Surely that would also be better for the majority of postdoc academics, who are currently on non-tenure-track and (apparently) locked out?

I wouldn't see them as "locked out" necessarily, there are lots of possible situations: a post doc (in some fields labeled a non-tenure track assistant professor; the distinctions are small though I believe more likely to include teaching for the latter) is someone who hasn't gotten a tenure-track job yet: their "clock" hasn't started yet.

Or, they are someone like me, with a semi-permanent soft money academic job, who likes research but didn't want all the extra stresses of finding money and earning tenure that a tenure-track position requires, and who is willing to take the difference in pay and independence.

Or, they work in a field like medicine where their primary responsibility is as a clinician, but they also teach, and they don't do enough research to fit their institution's standards for the tenure track.

In experimental fields, hiring a new tenure-track assistant professor is a big financial investment due to needed lab space, equipment, etc. Non-tenure track positions like post-docs let people build their research career in someone else's lab space and develop their independence more gradually.

The other side of the coin are the primarily-teaching adjunct-type positions; these positions are a tough topic that's been addressed elsewhere on this stack, but in summary they exist because people are willing to take them when they can't get another job (either to keep the possibility of an academic career alive, or just as a paid job), and they are a massive cost savings for universities. Whether that is ethical or not is unclear, but eliminating them would likely reduce the number of academics employed even if it increased the average salary/benefits.


How to quote from a source in a different language

Your method sounds good. Indicate somehow that you translated, either by saying so once at the beginning of your essay, or individually with each quotation.

General advice: Who are you writing this for?  If for a a class, ask the instructor.  If for a journal, consult the editor.


Cautions while writing non-specialist/lay versions of scientific articles

This is certainly acceptable. It is  probably a good way to practice your communication skills.
Unless it is really  well done and turns out to be useful for others
I think it unlikely that it will develop much traction for your own work.
The only downside might be using too much of your time on this instead of that work.
If you carefully cite all the sources you use and don't cut and paste large chunks of words you are   unlikely to ruffle feathers or encounter copyright problems. You should ask before reproducing images.


Criteria to evaluate consulting opportunity

Balance is always tricky but basically the guidelines that I follow are:

If the consulting will help me learning something new, +1
If the consulting will pay me a lot of money, +1
If the consulting will improve my reputation, +1
If the consulting will allow me access to something I want (new data), +1

On the other hand,

If it takes a lot time, -1
If it offers little or no pay, -1
If it could damage my reputation, -5
If it would be a bit boring, -1

In the end, I just do the math.