Do people need to have their PhDs at Harvard to get tenure at MIT (and vice versa) in STEM fields?

I have never sat on a tenure case at either Harvard or MIT, so my answer is purely conjecture. While it is possible the first thing the tenure committee does is look at where the PhD is from and throws out everyone not from Harvard/MIT, that seems very unlikely. Tenure decisions are about teaching, service, and research. At the point of tenure decisions, the school your PhD is from is essentially meaningless although there may be some correlation between research productivity and where your PhD is from any longer term causative effects are probably pretty limited.

Where the PhD is from plays some role on initial hiring at all universities and if you don't have a TT position it is much harder to get tenure. Additionally, where you work probably has some causative effect on research productivity giving Harvard and MIT PhDs additional advantages (or at least preventing disadvantages). Therefore it is not surprising that lots of tenured faculty have PhDs from Harvard and MIT.


Can I re-apply for a new PhD position of a better university if I am currently full funded international student of another university(both in US)?

Yes: You can drop-out, give-up funding, and start-over with a new supervisor.
Albeit, that's probably ill-advised given the current climate.


When asking research-based questions, what are some good practices to maximize the rates at which people reply to emails?

All of the points in the linked article are very true in academia as well. Some points which may be specific to academia which he didn't mention:

If you're referencing a specific article or talk, reference it very specifically ("In your presentation at SfN 2012 entitled 'The Amygdala and You', ..."). If you can quote a specific slide/paragraph, all the better.
Mention (concisely, one sentence or less) why you're interested in knowing. Your problem may very well be something which the researcher is interested in, and s/he may be more interested in responding and following up later on.
If you're working for someone in the field, mention it at the beginning ("I'm a postdoc working for <Mr. Bigshot Fancypants whom the professor likely knows>, and...")
Note that researchers are more often than not interested in talking about their work, so the very first point from the article ("Don't email") is likely bad advice here. Definitely try to get in touch and talk about your mutual interests (if you have a valid question, of course).


How to obtain research data about IT related subjects?

Statista.com claims to be what you're looking for: a statistics aggregator. However, I don't think there's a general well-defined methods to get any statistics.

The way I usually proceed is that I attempt to find as many statistics as possible from multiple sources, I eliminate the ones that are too old / really inconsistent with the others / describe a shaky methodology for data collection, and I present all the remaining statistics. So instead of having one reference for a peer-reviewed document, I get 3 or 4 concurring non-peer-reviewed documents.

EDIT: one other important aspect is how 'fresh' the data you use is. First-hand accounts from Microsoft about Windows apps are arguably trustworthy. Second-hand accounts that don't indulge too much in interpretation and who publish rigorous documents (the difference between Financial Times and BuzzFeed) can be used, too, ideally having multiple sources. For any other source or things that are more than second-hand, you want a large consensus over multiple sources.


When an academic researcher decides to file for a patent, where does the budget to pay for the patent-related costs typically come from?

In my experience, in the United States, patenting is typically provided as a service by the university, budgeted to its intellectual property office (or equivalent).

Since the university typically owns the rights to all work done by its employees, it is more or less compulsory for them to use its services if they wish to patent.  Moreover, many of these organizations will actively solicit interactions with faculty and offer them assistance in patenting as otherwise many faculty will not bother to patent things the university might be interested in licensing.

For most universities, this office is probably able to effectively pay for itself via licensing fees, though there might be any number of complexities in how the actual accounting might be done.


What to do when your supervisor is not really supervising you?

Given the constraints and assuming that you can't move to another institution, I think you are stuck with coming up with your own plan. A well known and respected advisor is an advantage to you provided that he signs your thesis and writes a good letter of recommendation, even if he doesn't do anything else. Sad? Yes. Probably true.

My suggestion, in your huge lab, is to try to start up a study group in which a group of three-six students decides to meet regularly and discuss their work and any blocks they have. Study groups are a feature of Law School, of course, and some other disciplines. Perhaps you can adapt the idea to your work. It would depend on how closely your work aligns. If too different, it probably wouldn't work.

I will also note that some professors consider letting students work almost entirely independently as a feature, not a bug. This is probably more common at the doctoral level, but the large lab you are in makes it almost mandatory. But the ability to work as an independent researcher is an important skill for any academic, though being forced to do it too early is a disservice.

The best advice, however, is to get the thesis done, get it signed, and move on. Look for a better situation in the future.


Yes. The simple answer is that a research master's degree is, all being equal, a higher degree than a taught master's degree. Just like a PhD is higher than a research master's degree, and a taught master's degree is higher than a (implicitly taught) bachelor degree.

I don't think we can comment on "downsides" in having a higher or lower degree. It depends on ones preferences in life.

EDIT: This is an answer to the original question: "Is a master's with research "better" than a taught one?".


At what point does a PhD student have to commit to a research group (US)?

This can depend a bit on field and even by institution. It would also make some difference if you are applying with a BS or an MS already in hand. If you are early in the process then the early part of the doctoral program will likely involve advanced coursework, so choosing a specialty can typically be put off.

But starting later, ready for research, it will probably be an advantage to know, going in, which group (or groups) you are most compatible with.

But overall, your assessment in the question is correct. People choose a bit later than first contact and some people change. In math, for example, there is less reason to choose early than in, say nuclear physics, where expensive labs might be part of the process.

I changed groups because I changed institutions. The old situation didn't work out for me. I joined the new group relatively soon but held an MA at that point and knew who I wanted to work with. But it wasn't a choice made in the first weeks.


Does a low GPA in an unrelated (second) major affect math PhD admissions?

For a math PhD program, the GPA in math is by far the most important.  Your overall GPA still counts for something, but GPA in a different major may not count for anything more: if you applied to my math PhD program (UGA), I don't think your philosophy GPA would specifically be considered by us.  If your overall GPA were something like 3.5 and your math GPA is 4.0: well, then you look like an overall good student who is outstanding at math.  That's what math PhD programs want!

Having said that: I note that (i) you intend to go to a math PhD program, (ii) you have a perfect(?) math GPA and a (perfectly respectable but) significantly lower GPA in your second major, and (iii) you describe your second major "as a spare time interest in high school".  I don't quite get it: you're not in high school anymore, so....tell me again why you're majoring in philosophy?


Given a downloaded PDF of a publication, is there any way to detect if it's a journal or conference paper?

Just search for the title of the paper as a phrase, online. That will almost always lead you either to the journal, or to the conference.

If that doesn't work, go through the list of authors one at a time, and find their university home pages, if they exist; from there, look for their list of publications: that will often have the full citation, and that will let you know whether they are journal or conference papers.

You could also try searching on one or more of the online reference compilers, such as CiteULike, Sparrho, Zotero, Mendeley, or even serial spammers ResearchGate

There are also existing tools such as Mendeley Desktop that will try to find a pdf's metadata for you, with varying degrees of success.


Can books be included in literature reviews?

Note carefully the word scholarly in that description.  It refers to works whose intended audience is experts in the field, and which either present novel research or interpret existing results in a novel way.  Books can fit that description; often they will have been published by an academic publisher and reviewed for academic merit by expert editors or referees, prior to publication.  Scholarly books are sometimes called monographs, especially in the sciences.

The books you mentioned by Kaku and Sagan are not scholarly books.  They are intended for a non-expert popular audience, and they don't present new research or expand the state of the art.  The same goes for the online sources you listed; they are newspaper articles or blog posts intended for a popular audience.

A literature review is how you show that you are familiar with the state of the art.  It convinces the reader that they should believe you when you say that your proposed project is feasible, novel, and interesting.  You want to show that you are an expert, or are on your way to becoming one. Citing a popular book won't achieve that; it puts you at the same level as any random person interested in science who can read a bestseller list.


KAU is accused of hiring well-known professors to boost university rankings by adding affiliation. Is it ethical to accept this kind of offer?

This behavior seems just as unethical as to put someone's name on a paper while he has not worked on it, and for the same reason: it provides the academic world with a wrong information about attribution, and the academic world wants to use this kind of information. Less abstractly, it means that students or scholars might be fooled into going to a university expecting to be taught by or to work alongside high-profile professors while the university really has much less to offer than it pretends.

Now, it could be argued that it is the job of the rankings to design them in a way that is not so easily played, not the job of the professors to act according to such ranking.

Also, we currently do not have clear and well-admitted ethic rules for affiliation, while we do have such rules for authorship. This makes the ethical lines much fuzzier, but in my opinion the conclusion to draw is that we should give ourselves such rules.


Should researchers disclose their political interests in publications?

The researcher should probably disclose any bias she knows she has, though outside of potential biases due to funding of the research (think drug companies funding studies for their products), I don't think this is done much. Prominent public intellectuals usually wear their biases on their sleeves, so reviewers are often pretty aware of them. I'm not sure matters as much for less well known academics unless there's a worry that they were cooking the data.


Must my ex-advisor be a co-author in new research after the defense?

The traditional role of authorship is to clarify who (significantly) contributed to the work being published. Doctoral advisors often contribute actively to the research being performed, and thus are included as co-authors on that particular regard.

However, they should not be included as co-authors automatically. Only if they have actively contributed towards the paper's ideas, implementation and/or writing. The least that can be expected is that they contributed to the paper's ideas (during your supervision) and that they have read and edited the paper being published.

That said, it is usually expected that you invite contributors to co-write a paper, if they have contributed significant ideas. If your doctoral advisor did that for the research you made during your PhD studies, then you should invite them for those particular papers.


Postdoc position "on hold" due to covid-19

A signed offer letter is normally a valid contract.  Usually it is the only contract document.  Only someone who has read the offer letter can give you a perfect answer to this question.

They have announced their intention to break the contract.  That is illegal unless the offer letter says otherwise.  Moving on is probably your best option.

There are two possibilities:

The university is unable to pay you, so they are forced to do something that could potentially cause them a lot of harm in the form of bad press or litigation.
They did this voluntarily or out of incompetence, in which case the university is a bad place to work and you are lucky not to be working there.

In either case, you should look for employment elsewhere.


Median age at doctorate by field of study and country?

In my opinion, there are two approaches to answering this question. The first (which seems that the OP expects here) represents references to publications, containing global summary statistics on doctoral graduates across the indicators of interest, such as age, field of study and country. In this category, IMHO the most well-known and comprehensive is the Education at a Glance report by OECD. AFAIK, the latest such report is Education at a Glance 2014: OECD Indicators, which, along with supplementary materials (i.e., highlights), can be accessed in various formats from this page.

The second, open data, approach, which while not requested, I recommend to those wanting to perform their own statistical data analysis, which might be very interesting especially by combining the indicators of interest with other socio-technical and economical indicators, widely available from open data repositories. In particular, for this specific question / category, I would suggest analyzing the following two open data sets from OECD, which can/should be combined in order to perform needed analysis: Graduates by field of education and Graduates by age.


Code of conduct when proposing to open a new lab in a field new at the University

If I understand this correctly, you are asking if you should contact a university telling them (a), that they definitely need their first lab in field X that they currently have no lab in, or (b), what (a) says plus I’m applying for this to-be-created new position! Neither approach would have any hope in any country or field I’m familiar with.
Your question seems to be prompted by a colleague of yours being hired into a newly created lab (in an already present field) through personal connections. This combines connections with the new lab being in a field that already exists, and so does not really compare.
By and large, you can only apply to specific job openings, no matter how good your fit would be in a place. As you are in a new field, there might be neighboring fields with sufficient overlap that you can apply to openings in them as well. But the case at hand strikes me as fruitless.


Whatever the schedule is, it's almost certainly identical for all candidates.  You can't deduce anything about the school's interest from the schedule.

The way my department does tenure-track interviews, the only one-on-one meetings are with the department chair and the dean.  Other than that, there are, as in your description, group interviews with faculty and students, a research talk, a sample class, and meals with a group of faculty.  The schedule doesn't include one-on-one meetings with individual faculty.  And this is the same for all candidates.

(This is a mathematical sciences department at a medium-sized public university in the US.)


This is highly specific and might require reading between the lines. Your best and simplest course of action is to contact the admins in the funding body and simply ask them.


Professor wants to submit paper, but no real results

You have two options. First option: decline to be the author of the paper, second option: write and submit the paper as first author. In the second case, the paper will go under review and the reviewers and the editors will decide if it is a good publishable result. Personally I would choose the second option in a high-medium ranking journal. In this way, if the paper will be rejected, it will not be your fault and you will not enter in contrast with your professor.


What should I (a professor) do if a student keeps answering other students' questions before I start explaining?

This would, I think, depend a lot on how the "answering" student goes about it. Just interrupting a request to the professor is disruptive, but some people do this sort of thing by reflex. But yes, a quiet word is in order. Ask them to meet with you. But decide first on what you would like them to do to correct the action.

If the answers they give are generally correct then it is a different situation than if they are mostly irrelevant, I think.

One thing that such a student fails to understand, of course, is that often the best answer is a minimal answer. An answer that lets students develop insight, not just get answers. Saying too much in answering a student question may be worse than saying nothing.

One option is just to require them to remain silent, but another is to ask (require) them to raise a hand before saying anything and first getting permission. But yet another, that might be useful, depending on the student, is to require them to write out an answer when they feel the need, rather than to blurt it out verbally.

But the behavior can be a symptom of many things. Some are insecurities on the part of the student; a need for affirmation. Some would just be showing off for the professor. Without knowing what it is, it is difficult to formulate an exact solution.

You have a right, of course, not to have your course disrupted by outbursts, but think a bit about whether the disruptor has needs that also need to be met. So, as part of your quiet word with them, ask first why they think it important to do that. Depending on your view of the student, the question might be direct, or you might want to be a bit more subtle about it.

And sometimes it is actually useful to have students volunteer answers to the questions of others as long as you maintain control over the process. If one student is dominating a conversation, it might be counterproductive for others.


How to find the most relevant publications in field/topic

IMHO, it is difficult to say which search strategy is most reliable. The Google Scholar (as well as Web of Science, Scopus, etc.) citations are a good place to start but they definitely should not be your only guide.

Another item to look at are survey papers and research monographs in your field of interest (and, nowadays, Wikipedia, Scholarpedia, etc.; note also that sometimes plain Google search instead of Google Scholar search brings more helpful results) and the references therein.

There are least two reasons to do so:

sometimes an important result makes it straight into surveys and monographs which get cited instead of the original paper(s);
a paper with an important negative result (e.g. one which closes certain research avenues) is sometimes not particularly well cited just because people move on to other research directions.

Yet another way to find relevant references is the so-called snowballing method a good description of which is given at this answer (without using the term snowballing).

And, of course, it is a good idea to ask your colleagues, especially after you've already done some searching on your own and just want to make sure that the search results you have are reasonably complete.


Statement of purpose: how important is correctness of grammar and punctuation?

If the written question above is a genuine reflection of your English spelling and grammar abilities, then I strongly suggest you seek professional services to assist if you are in any way concerned about your abilities having an adverse impact on your application.

This application is clearly a very important step in determining your future, and if it is so important and you have concerns, it is not worth leaving it to chance. If you have no suitable friends, use a professional service. Plenty of other native-English speaking applicants who are competing for spaces with you will have done so.

I can't say for certain how a selection committee will factor your English as a second language. It is likely to depend on the institution and the course you are applying for.


How to present (key) publications on personal website?

The most common solution which I usually see is having a section called "Selected Publications" or "Key Publications". Often people show the details only for these and you have to take some extra step (e.g. press some link or an "expand button") in order to get the full publication list.


How to describe a situation in which you "throw things at the wall and see what sticks" in a master thesis

It would be best to explain why such experiments were conducted along with supporting concepts that you would like to verify. It ought not to look like a random set of trials.

You may write something like this:

  Concept X follows from [explanation of X]. This concept formed the hypothesis Y to justify the following experiments. ... Although the experimental results were negative, it would be of worth to note them here as to why they were so.


In general, there was no central source of funding for research until recently.

If you were engaged in scientific research before modern times, you usually fell into one of a few categories:

You had an official position, such as Royal Astronomer in the UK and other countries, that provided you with a salary in exchange for doing research.
You had your own independent source of wealth that allowed you to survive.
You worked another job, and "dabbled" in research in your "spare time."
You were part of the church (e.g., Gregor Mendel) and did your studies and experiments in your free time.

Industry played at most a small role in funding research, directly or indirectly.


When should I send thank you letter or email to my thesis committee members?

After the defense will be fine since by then the committee members have completed their job. What happens between that and when you have the final paper work done is irrelevant. Pointing at the discussion you have just had and finishing with a few personal comments/reflections will be fine. But, do not overdo it since long and talkative mails can be either too long to read or in the worst case seem constructed. So be yourself and be happy for what you have achieved ( I take it you will or have passed?)


Can I thank websites that host illegal book downloads in the acknowledgements section of my thesis?

You can thank whomever you want in the acknowledgments of your thesis, but there may be consequences that you have to live with.

In my opinion it is a bad idea to admit to illegal activity in a formal document like this.  Once you write that, you cannot unwrite it: it will be archived for the rest of your career.  I don't really think you'd get in any trouble directly, but by doing so you're advertising the fact that you are willing to break rules that you don't like and do so entirely openly.  I think that a lot of potential employers prefer employees who when they break the rules for a good reason, do so more quietly.

I also don't really see what you're gaining by doing this.  A thesis acknowledgment is not a step toward legal free downloading of texts.  I happen to agree with you that "a way to make them legal should be found".  One way I work towards this is that I make all of my lecture notes -- some of which are very close to being textbooks -- freely available on the internet.  Whenever I have spoken with publishing companies, I mention at the first meeting my requirement that my material be made freely available on the internet.  To my surprise, they have not walked out of the room.  I also have largely stopped assigning expensive required texts.

In summary: an acknowledgment to the providers of illegal content is a microscopic flouting of the establishment, not a helpful act.  I recommend that you think a bit more carefully about what you can do to actually improve the situation.


For all intents and purposes, I can see no way of distinguishing between a preprint that is not intended to be submitted and a preprint that just hasn't been submitted yet.  Thus, if a template is useful to you for formatting, by all means use it.

One caveat, however: some templates also include statements of copyright or material like a journal's logo that do not apply to a paper that has not yet been published.  Whether or not you intend to submit, I think it would be poor form to publish such things in a preprint to which they do not apply.


How should I list my advisor's name on a talk I am giving about our joint work?

A common way to address this kind of problems is to highlight on the title slide who is the speaker among the authors (e.g., by underlining, bolding or by assigning a different colour).

For instance, you can write the list of authors as

  A. Boss, H. Student


It it appropriate to request a letter of recommendation via LinkedIn?

If someone is on LinkedIn, especially if they are active on LinkedIn, I see no reason why they would be offended if you sent them a message on LinkedIn. LinkedIn is a professional networking site. That would be exactly what you are doing. I would write something straight forward:

[Salutation]
I am applying to graduate programs at a few schools. I enjoyed your class in Underwater Heavy Metal Guitar and felt I did well in the class. Would you be willing to write me a letter of recommendation for my graduate program applications?
Sincerely,
-bron10

Three weeks is a long enough time that this professor has likely not seen (or has forgotten about) your email. There is no reason to cower in fear about asking for a letter of recommendation from a professor who said he would write you one. If he is at all reasonable, a simple message on LinkedIn will be just fine.


At what point should I no longer include my former professor as a coauthor?

I'll copy and paste my answer from another question earlier today:

Everyone who makes a sufficient contribution to your paper for authorship should be an author on your paper (and no one else).
It doesn't matter what institution they are at nor does anything else: everyone that contributes at a level appropriate for authorship is an author.

Probably the best person to judge this is your former professor. Have a conversation with them about where the project is at and how you see their contributions and ask whether they think it is appropriate if they are an author or if you should be a sole author.


Do GRE verbal scores matter for graduate admissions in mathematics?

Yes, a decent verbal score is definitely desirable.  I mean it: I have done graduate admissions for my math department, mentioned low verbal scores as a point against the applicant, and had the point taken by the rest of the committee.  But I would think that spending three-plus years in a university would be the best possible way to study for the GRE verbal: if after all that you need separate study in reading comprehension, sentence completion, and so forth, something has gone wrong!

(I remember the GRE as the SAT all over again, to the extent that my GRE scores were each within 30 points of my corresponding SAT scores.  The GRE has been retooled multiple times in recent years with the unfortunate effect that a lot of people doing graduate admissions, like me, are now a little vague on what it actually contains.  We tend to assume that the changes are cosmetic and that the exam is more or less the same as the one we took years ago.)

The math subject GRE is not a hard test in the sense that you need to devote much (or any, necessarily) time to study for it.  I remember contemplating studying for the Math GRE (circa 1997), learning that the study guide was really pretty miserable, and maybe spending a weekend flipping through a book on differential equations because I had never taken a course on that.  More pertinently, I remember that at least one third of the test was rendered trivial by my deeper study of subjects like topology and analysis: e.g. I think there was a question like "Which of the following properties does the real line, as a topological space, not have?  Hausdorff, compact..." To me this read more like a mathematical joke than anything else.

Here's the bottom line: please don't spend six months only, or even primarily, studying for any/all of the GRE.  What a terrible waste of your time.  If I am honest, the fact that you think this might be a good use of your time makes me concerned that you might not be a good candidate for a graduate program in mathematics.  I would not say this if you provided any distinguishing or identifying information whatsoever, but as you are completely anonymous it is something to think about.  The way you prepare for graduate school in mathematics is by learning math.  That means absolutely mastering truly basic, undergraduate level topics like linear algebra and deepening your knowledge of algebra and analysis.  This knowledge and mastery will serve you well at every step of the graduate process, starting with admissions.


Is attending a more expensive and prestigious foreign university a good financial investment?

Ok, I have answer to this as I did finish all my higher education in the UK, and still living/working here.

Money Buys you a Place But Not a Future: Yes, you can spend money and get to very decent universities; but:

Exceptions: The Oxford, Cambridge, and Edinburgh are very wealthy and well known and funded, so they don't care much about anyone's money to be honest; however this might differ based on your field. But, the general rule, don't count on getting a place over there by flashing money.

University: Not so many universities currently looking for hire from postdoc level, yet alone PhD level. There is a mayhem over this, just talk to an academic living in the UK.

Conclusion Back to your question, no by paying extraordinary amount of money you will not get a better financial future compare to finishing your studies within Italy.


What should I do about my previous self-plagiarism?

This following response is highly personal and does not claim universality: it is my personal 2 cents, and my opinion is that your approach sounds perfectly fine. You do not claim other people's results as your own and you do not claim previous results of yours as novel.

I do not know where this fashion that one has to rewrite everything from scratch comes from, even unchanged aspects in a new paper. Perhaps it comes from humanities where language and formulation is central. But in technical topics it does - in my personal opinion - not really make sense to reformulate obvious intro sections; as little as it makes sense to rewrite code for which there is a library.

Personally, I like to rewrite even intro material sections because I do not like to bore my readers that have read other papers of mine, and also I sometimes discover novel aspects just by writing. However, as long as above conditions of 1. attribution and 2. clearly delineated novelty are fulfilled, I would not join in a negative judgement about repeated sections.


Test answer rejected for saying more than asked for

I know from personal experience that it's very frustrating not to get proper credit for knowledge that you think you demonstrated correctly, so let me start by saying I sympathize with your situation. Now let me address your questions:

  Is it justifiable to reject an entire answer because more was said,
  without even partial credit?

To give a literal, completely general answer: obviously yes. If the correct answer is, say, one sentence long, and your answer quotes the complete works of Shakespeare that happen to contain that sentence, I personally would not give you any points (but I would still be very impressed :-)). Of course, that is an absurd example, but it illustrates the point that what likely matters to your professor (or if not, certainly what should matter to a reasonable professor) is that your answer demonstrates an understanding of the topic the question asks about. It is certainly possible, and happens pretty frequently, that an answer Y contains the correct answer X but by adding more irrelevant things demonstrates a less good level of understanding than just the shorter answer X. The way this typically happens is that a student doesn't understand the material well and upon being asked about a certain topic, regurgitates everything they memorized about the topic, not knowing which part is relevant to the question. Clearly that does not leave a very good impression.

Now of course, the above does not address what happened in your specific situation. It is completely possible that your longer answer Y still demonstrated as good of an understanding of the material as the official answer X, and deserves to get partial or full credit; or not - you haven't given us enough information to say.

  Is it justifiable to reject an answer that gives something better than
  what is required, perfectly equivalent, even if relying on the
  student's intervention? (in this case, it would be a compiler
  optimization, thus not an entirely direct interpretation, but an
  elegant and industrially valuable workaround)

I think this question is too specific for anyone here to be able to answer without knowing more details. As I said above, the points you get for the answer should be correlated with the perceived mastery of the topic being asked about that your answer demonstrates. If including the optimization demonstrates that mastery, you should get the points. But I can imagine a situation where using the optimized method instead of the official method actually demonstrates less mastery, for example if it appears that you used the optimized method to avoid revealing that you don't know the simpler, less sophisticated method the question asked about. In that case, it may make sense for your answer to be rejected.

  Is it acceptable to direct students to example answers and not allow
  them to explain why they think their answer is correct?

I think it may be acceptable in certain cases. For example, if you have already asked many questions of the professor, argued with him in a way that he thought was unreasonable, overly argumentative, or delusional, and if the professor is very busy, for example is also teaching a class of 500 students in addition to the smaller class you're taking with him, at some point he may decide that spending more time discussing your exam with you can limit his ability to perform his other duties effectively, and be a disservice to the other students.

Summary. As you can see from my answers above, whether the professor's behavior is unreasonable depends on many details that you haven't provided. It's certainly possible that it is unreasonable, but it's also possible that it is less unreasonable than you may think. Statistically speaking, I've found that students often overestimate the extent to which they understand the material and the degree of correctness of their exam answers. That doesn't mean it's what happened in your case, but it's a possibility you should keep in mind as you consider your next steps. In any case, good luck! As for what steps you should take to address the situation, this answer is already quite long so I think it makes sense to save that for a follow-up question if you care to post one.


What incentives have professors to teach a large class (vs. a small class)?

At my institution in my department, I think there are two major external incentives:

The number of teaching assistants is a function of the number of students in the class. Critically, below some threshold size n, a professor will not receive any teaching assistants.
Offering the class in the future may depend on enrollment in the present.

In some other departments,

Professors who teach classes with more than N students get double credit for that class, so if they typically teach 4 courses a year, they could instead teach 2 small courses and one large course with >N students.


Information with no reference in literature review

If you're confused about whether information comes from a citation, the clear solution is to go to the source being cited and look for it there.

You will then find that one of two cases applies:

Yes, the information was in the source, and the citation was just confusing. Now you've read the source yourself and can cite it in a less confusing manner.
No, the information was not in the source, and you have no idea where it came from. Then the author either made a mistake or was dishonest. At this point, you either need to disregard the information as unreliable and unsourced or else try to contact the author to get a source.


When should private tutors communicate with course professors?

Academic integrity is the responsibility of the student.  Everyone has a responsibility to decline to knowingly assist cheating.  Only the instructor and university have a responsibility to actively discourage cheating.
So no, you do not need to contact professors unless your employer requires it.


on a CV do you list both a paper and an associated oral presentation?

I generally see people break their CV into peer-reviewed and non-peer reviewed contributions. Then within those categories they indicate whether or not they were the presenting author.
The presentation is really presenting the work in your paper, so they are one and the same. Plus consider the fact that the proceedings of the conference are what people will be able to find your work in, and therefore you want to give them the information for your paper. For example:

Peer Reviewed Contributions
Your Name, Co-Author, Co-Author, "A breakthrough in a big question", The International Journal of Great Answers, vol. 42, no. 0, pp. 3141-5926.
etc...
Non-Peer Reviewed Contributions
'*' Co-Author, Your Name Co-Author, "A very novel and important answer to a very big question", The 9th World Conference of Very Big Questions, Conference paper and presentation.
Your Name, Co-Author, Co-Author, "The smallest possible answer to the biggest possible question", The 42nd World Conference of Very Small Answers, Conference paper and poster presentation.
Note: Contributions with an asterisk '*' indicate that Your Name was the presenting author.


Correct way to cite paper that is published as part of a book

The references are there for your readers to be able to hunt down the reference, be it to check what you say or to follow a different thread of research. For their sake, do find out as complete bibliographic data as you can, and add them to the citation.


Most journal articles are often a revise and resubmit before they get published.The final article that you see in journals is often never the first submission attempt but rather, crafted through continuous revising and editing.

You should revise and resubmit, you would be doing yourself a disfavour if you don't.

The editors had two very contrasting reviewers for your piece, one who suggested a minor revision and the other an outward reject, so a Revise and Resubmit is a pretty good outcome from that, but also highlights a stark contrast of views.

When you receive harsh comments, it's good to take a step back for a few days and let the anger and frustration that you undoubtedly feel to disappear. At the moment you might feel like it's a bit of a personal attack, and have used language such as 'it's unfair' and 'he hasn't read the article completely.' These are emotional responses and are not helpful for your success.

Why are the comments unfair and how can you determine whether they've read the article completely?

When you are ready, sit down and read them with fresh eyes, highlighting what you can do to improve the article. There will be things in there (difficult to find) that you can utilise to strengthen the quality of your article. You don't have to address everything the second reviewer says but you might be surprised that once those personal feelings die down, the number of things you might find helpful from that second reviewer.

When you do your revision, you'll need to prepare a summary report regarding all the comments, highlighting what you changed, and what you didn't. The things you do not change you provide justification for in your summary report.

You would be surprised by the number of academics who never bother to revise and resubmit a paper to a journal, the numbers are outstanding. Revising and resubmitting allows for you to continue to improve your ideas and produce something of high quality.


How can an assistant professor have a much higher salary than an associate professor in the same department?

The phenomenon you describe is known as compression and, in the case where salaries are actually reversed, inversion. Unfortunately these are very common especially at state universities. The principal cause is that faculty get hired as assistant professors at market rates, but the university salary structure fails to keep up with inflation and any other sources of increases. Given the severe funding cuts, salary freezes, and so forth that have plagued public higher education over the past few decades, this situation has been almost inevitable. The result is a salary structure such as you describe.

The only ways to fix this are either explicit allocation of funds to correct compression, or for individual faculty to obtain raises via retention packages to fight off outside offers.

In general, salaries are basically set by market rate at hiring (which for assistant professors is largely independent of citations and papers, conditional on getting the job in the first place) and by outside offers received later during the career. Both the availability of outside offers and their magnitude will depend on stature in the field. Even if one does not actually take an outside offer, receiving one or more such offers can prompt the home institution to put together a retention package. The willingness of the home institution to put together a top package will also depend on stature, and similarly the magnitude of the retention package depends on the outside offer and is thus also based on stature.

In principle, regular merit raises could also reward faculty in accordance with their productivity and impact. But for whatever reason (I blame self-governance, but that's another discussion), merit raises and such tend to be allocated in relatively egalitarian form, rather than proportional to differential merit and productivity.

Other answers provide additional important information. Some salaries are 9 month, some 12 month. Some faculty on 9 month appointments can cover summer salary off of grants; others spread 9 months salary across 12 months. Public databases often list total salary received rather than 9 month salary; this considerably increases the variation among faculty.


Research faculty I would like to work with not in my department

Yes, it can hurt your chances of admission if your application focuses on a desire to work with people in a different department.  It's fine if you list some people in other departments, for example if they collaborate frequently with members of the department you're applying to (or even if they don't, provided they aren't the sole focus of your application).  However, you don't want to submit an application that looks like it's a substantially better fit for another department.  You might still get admitted if your application is strong enough, but there's a real risk someone on the admissions committee will try to make room for another candidate by declaring that you really belong in the other department.

This generally isn't a problem if you take it into account while planning.  If the best advisors for you are all in applied math or operations research, say, then you can apply to those departments in addition to computer science.  The only tricky case is if your advisor works on two very different things, one of which falls into the other department while the other is more traditional computer science, and you want to do the latter.  In that case you should explain in your statement of purpose why the computer science department would be a better place for you despite your choice of advisor.


Should I have a fourth recommender in PhD Application

Provide the number of letters of recommendation requested.

Some systems will not allow you to add additional ones. Even if they do, I agree with the assessment that adding further letters won't reflect well. Either you didn't follow the rules, or you didn't figure out who'd be your best recommenders.


How many credit hours of mathematics does an average successful student take before applying to graduate school?

This tends to vary a lot, but here's what I'd consider reasonably good preparation for pure math graduate school in the United States:

Three semesters of calculus (possibly less if you've had calculus in high school)
A semester of linear algebra
Two semesters of abstract algebra
Two semesters of real analysis
One semester of complex analysis
One semester of topology
At least 2-3 more semesters of advanced electives.  These can vary a lot, but it helps to have some expertise in a few different subfields of math before attending graduate school.

So it seems that I'm recommending at least 12-13 semesters of mathematics.  Assuming 4 credit hours for a one semester course, this is 48-52 credit hours of college mathematics.


How often do you get to "play with" scientific instruments?

It depends to a large degree on who owns them.

If it's your lab group, and your supervisor's happy enough, you can probably use them whenever you like.

If they're owned by the department/division/etc then there's likely to be a formal booking system. Once you've booked a slot, though, I'd imagine you can do whatever work you like on them.

Provisos in this are cost and safety.

Cost, because some of the stuff you're talking about is pretty pricey. An fMRI session can be charged at over $400 dollars per hour.

Safety applies to you and the equipment. You may well intend to be safe and not damage the equipment, but that can be easier said than done. As such, you're never going to be allowed to use certain items without having gone through the necessary training - so you'll have to convince your supervisor that doing such training is a good use of your time/funding.

So in your lab, play around time will I suspect be limited, save on equipment you use daily. But if you must get your hands on a piece of kit, fear not, for there are workshops and courses you can attend! These often occur in conjunction with a conference/meeting/etc of some kind, where a sponsoring vendor will kindly 'donate' a piece of equipment (in the hope you'll buy the same brand later down the road) and as a group you get the opportunity to spend a while using it under the company representative's watchful eye. Keep an eye out for these, and try to arrange to publish a paper in the conference, or give a talk in the meeting, and I'm sure you'll be given the funding to go.


How to publish under a Creative Commons license?

Let me build upon excellent Wrzlprmft's answer, adding a few things:

there is a de facto open access standard license, and that is CC-BY. It is similar to public domain, and I'd strongly suggest not to use CC0, as you would waive also the attribution of your work. CC0 it is used for databases and data, where CC-BY licenses are trickier.
institutional or disciplinary archives as ArXiv are heavily used in some academic communities (eg. math, high energy physics) but they do not provide peer review. It is customary within those communities to archive pre-prints. You should try to understand the customs in your very own community: it's very important if you want to make the best choice (and if you want to foster open access publishing in your discipline).

As per your last question:
why do so few researchers seem to be concerned with these ethical problematics?

Because their priority is their academic career. Academia is built on personal, scientific reputation, and the current system (with Impact Factor and other scientometric indicators) is completely unbalanced towards old, authoritative closed-access publications that provide the "authority" a young researcher needs to gain reputation between its peers. You need to publish a lot, and in reputable journals. You will advance, get grant, get tenure on your publication (and citation) record.

Open access publishing (as a model) is relatively young, thus it is difficult for open access publications to gain the same reputation as those other journals; thus researchers don't want to publish there, thus the old, closed-access system survives.

Often, the rational, selfish choice of the researcher is enough for the ethical choice to be bypassed. Ignorance of alternative models (and ignorance of the intrinsic flaws of the current closed access system) do the rest.


What is the difference between digest and extended abstract?

Conference format varies. Some conferences ask for more than just a short (up to one page) abstract, but something like a short paper containing some of the preliminary results. Some ask for a short abstract, screen the abstract, and ask for a full paper which will then be reviewed before the conference starts. Some others ask for an abstract and only ask for the full paper once the conference is concluded. I believe this is more of a tradition of that particular conference rather than the preference of the chairmen or reviewers.

It is important not to exceed the page limit, but make sure that you are not way below the limit.


How does one properly indicate a translator's explanation of a word within a translated passage

Any time you need to give additional information for readers, and you do not want to interrupt the flow of reading, footnotes are generally considered the best way.

This is common for translation notes or any other information which the reader might need for a fuller understanding of your text.


Giving a career talk in my old university, how prominently should I tell students my salary?

I agree with you. I feel the request to put your salary on a slide (on the first slide, no less!) is rather unexpected, and quite frankly does not speak highly about the professionalism of your contact. I would decline this, for multiple reasons:

Your salary is nobody's business. Not sure what more there is to say about this.
Students are, for the largest part, intelligent adults. Many would take this exactly for what it's meant to be - rather crude marketing and hype generation. This would detract from the message you actually want to transport, and would undermine your following talk.
Focusing so much on how much you make is arguably not the best way to motivate young people for a specific career path anyway. If you talk about why you love your job (if you do) will encourage more people than a six-digits salary number. More importantly, it will probably encourage the people who will actually be happy doing your job, not the ones who would end up wealthy and miserable.

You can of course provide a salary range as proposed by other answers, but I would not emphasize this point much (and base it on third-party data, such as Glassdoor, not just your own experience).


Can one excel in graduate school with a demanding family life?

I feel for once I am somewhat qualified to give an answer here.

A bit of background to know where I am coming from and hopefully give some insight to my situation.  I am currently finishing my second year in a MA Mathematics program and beginning my first year of my Ph.D. in Mathematics in the fall.  I am married with two children(a 3 year old and an 8 month old).  I had my first child during undergrad and my second child came two weeks before the current school year started.  I attend a smaller department that is most certainly less intensive in regards to the expectations that another school would have(such as a top tier research university).  I've been a Research Assistant for the past two years doing active and successful research with an amazing supervisor.  This past year has been the most stressful since I decided to take three core year long sequences, which is a great deal of work to keep up with.

Above all, put your family first.

I would hope this goes without saying, but it can be easy to lose sight of this when you're up to your neck in homework/deadlines.  When something comes up with my family, I drop my schoolwork to deal with it.  I make it a point to always put my family before school.  I'm sure there are professors out there who would argue otherwise, but I'm grateful that my professors seem to (hopefully) understand the situation and that I just can't put in the hours that other students can.  I generally score lower on average than other students but I think I do fairly well.  Could I do better?  Absolutely...if I were to put in the hours and sacrifice time with my family I could score better on my tests and homework, but that isn't what really matters in the long term to me.  Of course I want to do well in school(and I generally do!), but sometimes I have to make a choice and school gets the axe.

In the end, you choose your own priorities, and I would suggest opting for spending time with your family over finishing that HW.  You just can't get those moments back.

Having a Strong Support System

I would absolutely not be able to do this without the support of my wife, family, and friends.  Without my wife to help out with the kids and pick up some extra housework when studying for tests/finals/my oral MA exam, I would certainly have dropped out or (worse) ruined my marriage or become a terrible father.  I make sure to try and do extra work whenever the stressful times pass and try to make it up to her as I can.

We are lucky to have family close that can help out with childcare and babysitting when I need to go in on an off day or want to stay late for a seminar.  Without the support system we have in place, I'm not sure I could physically do it.  If you have a similar support system, then it will be a huge relief to your stressed.

I should also mention that without some amazing people at my department, I wouldn't be able to succeed.  Professors have been amazing with deadlines if the time just wasn't there for me some week.  My RA supervisor has been absolutely amazing as well.  She's extremely understanding with the kids and even being cool with me bringing the little one to meetings if everything just fell apart for that day.  If I had a less understanding supervisor, I probably wouldn't have made it.

Time Management

This is probably the trickiest part.  Time management is always important, but it's extremely important to successful manage school and family.  You just don't have all the time that other students do so when it's time to work you need to remove all distractions and get as much done as possible.  I arrive at school between 8-9am and in between classes I work nonstop on homework or studying until I leave at 3-4pm.  I have a computer in my office, but I purposely keep it off unless I absolutely need it on.  I disable the wifi on my smartphone and removed nearly all the time wasting apps(facebook, games, etc..).  I check my e-mail probably twice, once near the beginning of the day and once around the time I'm getting ready to leave for the day.

I do take small breaks from work to socialize with other students or check in with professors as needed, but I strive to make sure that I don't waste an hour doing absolutely nothing in someone else's office.  Socializing is an important part of graduate school, so don't neglect it but don't let it consume all your precious time.

When I come home after school I shut off school mode.  I spend the rest of the night with my family, eat dinner, and help get the kids into bed.  Once the kids are in bed then I'm free to do homework.  I don't always go straight into homework though because it's important to me to spend time with my wife relaxing and watching an episode or two of TV shows to wind down.  It doesn't happen every night, but I usually make an effort to take it easy on weeknights when I don't have school the next day.  The "school nights" I usually retire upstairs to work on homework.  I'll work until midnight or later depending on how early I have to get up and I'll average around 6 hours of sleep.  It's not great, but sacrifices have to be made somewhere.

Finally, in my opinion, give yourself the weekend.  Once I leave school on Friday, I'm done with math until at least Sunday night.  The weekends are prime family time and we spend every weekend visiting the zoo, science center, art museum, the park, or virtually anything else the kids would enjoy.  I initially thought it would be impossible to take the entire weekend off schoolwork and still succeed, but I've been doing it for 2 years.  This past year was the worst, but I stuck to it and I can safely say I managed to survive it and do just fine in my courses.

Dealing with Stress

Let's face it, you'll be stressed.  Grad school is stressful as all hell to begin with, but then you go and toss kids into the mix?  It's insanity, and you have to handle it somehow.  I'm a fan of exercise, which takes up that precious time but is totally worth it.  You have to feel as good as you can and any sort of activity is a great way to relieve stress.  You could also do another hobby, or something that you do to relax.  I'm also an avid reader, so losing myself into a book every now and then is great.  The time I have to read varies, but it's one of my top hobbies.  Find something you enjoy and do it frequently to relax.

Sometimes it just can't be helped.  If you find yourself really freaking out, you really should seek out the school's counseling center.  They are no doubt used to overworked students and having a place to lay all your problems on the table and have a trained therapist help you sort it out is probably exactly what you need.

To sum it up, I put my family before everything else.  School takes a high priority but there are far more important things in my life than getting an A in every course.  Schedule your time wisely, remove distractions, and work when it's time to work.  Do something relaxing for yourself on a regular basis.  Give your family the attention and time they deserve.  You can't get those moments back and no letter grade in the world is worth that sacrifice.

Above all, make sure you are happy.  It's such a small thing but I've seen students absolutely miserable hating what they are doing.  Don't be that person!  Life is too short to waste it being miserable.  I suggest every 6 months or so, take a step back and evaluate how you feel about your situation(this should apply to anyone, not just graduate students).  For instance, I vow to myself that if there ever comes a time when I begin to genuinely dislike what I'm doing, I will quit and find something else.

Good luck and don't forget what's really important.  Grad school has a way of giving you tunnel vision and destroying you emotionally...just don't let it do it too often. :)


Why do most science classrooms use similar black-covered desks?

I found an article that explains the reason quite clearly: the black top is a resin laminate that is chemical and stain resistant.

Not all bench-tops are black: there are alternate materials that are white or metallic. Presumably those substances have different resistances for different purposes; for example, some of the white benches I saw while searching were anti-static materials for electronics work.  For anything with biological and chemical substances, however, it seems that the black resin laminates are often the preferred material.


Does anyone know of an international postdoctoral association?

It's a great idea Scientist/Tommi but there's none yet that I'm aware of.

A lot of issues are common to different countries, but there are many important differences too. A good reason to look up your national/sector/discipline association, and a possible roadblock to the establishment of an international group.

In Australia it's the EMCR Forum*. They recently asked about similar international groups that advocate for and represent early and mid-career researchers and got a few bites: https://twitter.com/EMCRForum/status/950530138491400197

full disclosure: I am deputy chair of the EMCR Forum in 2018


How important are graduate courses to a successful PhD and beyond?

I am worried that if I start my PhD without having good courses I will be under-prepared to handle challenging problems later, and [various bad things]

There are a few things to note here that might put you at ease.  Firstly, while it is true that the quality of the material and instruction in a course certainly matters, even more important is the drive and work ethic of the student.  Depending on your willingness to engage deeply with the material, and search out other material, you can pretty much make your course as rigorous as you want it to be.  If you find that there is a gap in the material in some respect (e.g., some mathematical assertion that is not proved and that you don't know), look up other material to supplement what is in the scope of the course.  Since you are a PhD student now, one of the things you should be getting good at (or at least practicing with a view to getting good at it later) is looking up other sources of material to supplement gaps in knowledge.
Beyond taking courses as a student, a very effective way of learning a topic is to teach it.  Since you are a PhD student, you should have some opportunities to tutor some of the early undergraduate courses in your field, and maybe even some of the later undergraduate courses.  If you become an academic, you will probably end up teaching both undergraduate and postgraduate courses.  Teaching a course requires you to fill out a deep and systematic knowledge of the subject that goes well beyond what was required of you as a student (even as a high-performing student), so it is a very effective way to solidify your knowledge.  Obviously right now you will not be teaching your graduate courses --- you are the student here.  But you can look for opportunities to teach into some early undergraduate courses, which will get you on the path to solidifying your knowledge of foundational material at a deeper level.
Finally, don't make the error of thinking that your learning ends when your coursework ends.  Even after you have finished all your courses and you are doing pure research, you will find yourself exposed to thorny problems that necessitate learning new material, or going back and relearning material you have previously studied and forgotten.   Often a formal course undertaken in graduate school is just the first iteration of learning a topic --- you do the course and learn a bunch of things, and then if you don't apply them for a long time (e.g., years or decades) you forget a whole bunch of it, and then when you need that material you relearn it, and so on.  The main advantage of doing the formal coursework in your training is that when you find you need to relearn it later on, it is a lot faster.


Differences between the introduction of a sandwich thesis and a paper

From a structural point of view, there is no major difference. An introduction should set the work in a wider context starting by establishing the wider context and showing the need for the work done and identifying the knowledge gap that is filled. What is different concerns the matter since a thesis introduction should focus on the thesis not the individual studies (articles/manuscripts).

If the articles/manuscripts all are very tightly tied, then it is probably easier to write the introduction. If the articles are more disparate, which is not uncommon, then trying to tie everything together can be more challenging.The stumbling block for most is that they have not thought about the wider perspective and some do not even manage well to include it in the articles/manuscripts themselves. So I would say that the difficulty does not lie with the fact that it is a thesis introduction per se but rather that many do not see the forest for all the trees while they write the articles/manuscripts to be included in the thesis.


Is it a good idea to use Octave to teach an Intro to Matlab course?

As suggested also by SiXUlm in a comment, if you want to avoid being committed to a specific software, rename the course, e.g.,

  Introduction to scientific computing

or

  Introduction to scientific computing with Octave/Matlab

During the course, outline possible syntax and library differences.

  when my students make it out into the real world they will most likely have to use Matlab

Most of your students will likely not use Matlab at all in the real world. A few of them will, but they would be able to fill the gaps by themselves.


Is there a university that has only graduate programs?

There are some universities that offer primarily postgraduate degrees; Wikipedia has a list. Some notable examples on this list are Rockefeller University (US) and the Weizmann Institute of Science (Israel).

However, this doesn't necessarily save money; undergraduates in the United States typically pay tuition, after all. Other sources of income for universities in the United States (such as federal Pell grants) also apply only to undergraduate students. Furthermore, having a local population of undergraduate students allows budding academics (PhD students) to get teaching experience.


When can a thesis get rejected or asked for a major revision?

This very much depends on which system you are in. I can answer from the point of view of the UK system.

It is very unlikely your thesis will be outright rejected.

It is very likely you will be asked to make some corrections.

Yes, you will have to make the corrections and send the thesis again.

Requirements for a thesis are generally set out by the university. They normally specify you must have made a "novel contribution to the field" and the work is, in principle, of publication quality.  Or something similar.

Yes, a good examiner will read the thesis line by line.

There are five possible outcomes from the examination of a thesis.

Accepted without corrections
Minor corrections - generally textual changes only - 3 month time limit
Major corrections - might involve some reanalysis, but no new experiments - 6 month time limit.
Resubmit - this thesis does not pass, but contains sufficient material to convince the examiners you are capable of passing. You are giving leave to rewrite and resubmit the thesis. May involve new experiments - often 1 year time limit.
Fail (either with or without a Master of Philosophy degree).

Almost all students are given minor or major corrections - I'd say 90% fall into these categories. Slightly more in minor corrections probably. Maybe 8% get no corrections, and perhaps 1.5% are asked to resubmit. Very, very few fail outright.


What happens if an IRB mistakenly approves unethical research?

Since researchers are not allowed to trust their own understanding and must seek IRB approval even in the most obvious "there's no way that could be unethical" scenarios, it stands to reason that the opposite is true - that if research has been IRB approved, then researchers may go ahead with a clear conscience even if they personally feel that the research still has ethical issues.

I don't see it that way.  The IRB doesn't replace the author's judgment, it supplements it, and the ultimate decision should be based on the "logical AND" of the author's and IRB's approval.

Since conducting unethical research seems clearly worse than not conducting ethical research (a Type II error is worse here than a Type I error), it makes sense to have an asymmetry between approval and rejection.

So in my view, even if the IRB has approved the research, the author should not go ahead if they do not believe it is ethical.

  If research turns out to be unethical, but it received IRB approval, who is held responsible? Is it solely the responsibility of the IRB for misguiding researchers, or does the researcher bear some responsibility for not recognizing the ethical infirmity?

Practically speaking, the researcher would have some cover because of the IRB approval, but I would still hold the researcher primarily responsible.  After all, it is their name on the paper.

  Another way of asking this is whether researchers have a duty to police their own IRB, potentially second-guessing their approvals.

Well, the researcher ought to make sure they think the work is ethically OK before submitting to the IRB in the first place.  But if they start having doubts later, or they are ethically uncomfortable with changes recommended by the IRB, they should not proceed until those issues are resolved.  So in short: yes.


What is the purpose of letter of recommendation?

I hate that this is a legitimate question, but it is. Yes, letters are weighted heavily, in my experience. The fact that you (and many others) are often asked to write their own letters is very troubling. For one thing, it's biased. Secondly, confidentiality is absolutely violated despite most such letters being assumed as such. Now you are in the awkward position to have to write 3, and feign separate ghost writers.

It is impossible to defend this from any logical or ethical standpoint, particularly if confidentiality is assumed.

The best course of action is to thoughtfully ask the recommender to write his/her own letter. But you can make it easy on them by providing a CV, papers, manuscripts, etc. Give them the information you'd like to highlight but not the words.


In a yes/no question, a student gives the right answer and an unnecessary but wrong explanation. How to grade?

You asked for a yes/no answer (which, as you've discovered, has its disadvantages) and got one plus some other stuff. You should grade the yes/no answer and ignore the other stuff. If you like, you could add a note like "You got lucky! This is actually because..."

The whole point of yes/no or MC questions is that you grade only the answer, and assume that type-1 and type-2 errors cancel out or are normalized out. That paradigm doesn't work if you don't uniformly ignore everything other than the answer.

More concretely: other students likely got this question right using the same incorrect reasoning, but didn't write their reasoning down. There is no way to identify these students; so, you need to make sure they get the same score as this student.


Applied to two MS programs, but one wants a decision before the other has made a decision

Would it be wrong to accept the offer to University A, and then
  withdraw later?

Ethically, I think this would be wrong unless you expressly told University A of your consideration when you make the decision.  When you accept an admission offer you are taking up limited resources and potentially depriving someone else of admission to the university.

  Or, would it reflect poorly on me if I asked for an
  extension to make a decision?

Not at all - just tell them that you are very interested in A but also have other possibilities and would like to make a fully informed decision.  The worst thing that will happen is that A says "no".

  I find it strange that University A
  wants a decision so quickly, seeing as how you can apply for admission
  for the fall quarter up through mid-August.

Presumably, University A has a limited number of slots that they can fill, and, if you say "no", they would like to extend the slot to someone else before decisions are made.  I'm a bit surprised that these universities are making fall MS decisions in June - these decisions are typically done by mid-April.


Colleague gaining majority credit for largely my figures/analyses in their scientific poster

If this would have been a paper, Jim's doing would certainly have been unacceptable. As we are talking about a poster, I could imagine that Jim had no bad intentions. Given that you come from two different disciplines, you are probably not directly competing in terms of scientific merits, and you could both greatly profit from collaborating further in the future.

In the past I always tried to resolve these kinds of conflicts on the lowest level possible before escalating it to the professor / PI. This helps to keep the work environment poison-free and often resulted in surprising insights on both sides. More often than not people do not have bad intentions. Maybe he considers these figures as a team effort by the two of you. Maybe you are overreacting. In these cases a discussion from face to face often helps to sort things out.

I would probably talk with Jim and ask him why he did not ask for your permission to use your figures. Maybe also ask him how much, in his opinion, were your and his original contributions to the poster. If he considers your input as important, you could also argue that your contribution helped him to receive the price. I would certainly try to discuss the terms of your future collaboration.

Only if that discussion is not fruitful I would go to the PI and explain the situation.


How much overlap is permitted between a submitted journal article and a thesis?

Generally, many publishers and fields have rules against reuse of one's own text if that use is a (a) substantial; (b) not disclosed/attributed; (c) published.

How these terms are interpreted varies among publishers and disciplines. Most publishers would not consider a thesis or dissertation to be a "publication" for this purpose (hence the still widespread practice of converting dissertations into "book"). However, to avoid misunderstandings and keep definitively within the rules it is good practice to cite one's thesis, and to provide a brief summary of what content was reused and the extent it was updated, in the cover letter and in an introductory footnote.


Here is a first attempt at providing some short suggestions:

You need to identify the scope of the journal and it is best if it does not directly compete with others. Competition is more detrimental if the scope is narrow, it is unavoidable if the scope is wide. You need to make sure it has an international audience (a local journal would probably not end up prestiguous). Find a set of editors that is international in composition, preferably with well known active researchers at the helm. And then you need to look for publishers. I would say that Open Access is what you should go for. Many government funding agencies in Europe now request researchers to publish in Open Access.
Financial in what sense? If you manage to get a commercial publisher to publish your journal they will most certainly set up a budget of some sort. This question is the most difficult to answer. You need to get some finances in to support review systems, type-settings (and by the way, LaTeX would be your way to produce consistent high quality journal papers most easily; you also need someone to design the journal for you). In Open Access journals people usually pay to submit papers, in commercial cases, published papers are charged per page. Many review systems take a fee for each paper submitted. So there will inevitably be some finances involved but they will be determined by the systems you chose.
Yes, without having the journal stamped as serious by established scientists, it will not be easy.
Scientific Society would help but they will probbaly then take over the journal. A publisher/distributor (commercial, society, other body accepted by the community etc.) is a must. You need systems for submitting, managing and publishing manuscripts as well. Getting branded through a publisher is a good way to become recognized.
I would argue that it is only a matter of time before all journals are on-line only. Printing is no longer necessary and really only a waste of time and funding (not to mention resources). Any new journal will almost certainly be on-line only.
A strong line-up of editors and then try to get established scientists to commit to publish in the journal to set a good base-line. You need to work up citations to make the citation index, which takes effort and some time. The citation Index, whether you like it or not, is a hurdle that will make or potentially break any effort. In the long-term people will not published in journals that are not ISI listed.
Chosing the editors should probably be done as publically as possible. I can imagine getting names of persons that are willing to run together and then put them up for a public vote within th ecommunity. This way everyone (who will hopefully send their papers to the j) can feel they are part of the process.
Just make sure it is a communal effort and not a private enterprise. Get as many as possible involved by starting discussions early on in public. Use conferences and listservers (if the community has one) as vehicles for this. Facebook, twitter etc. might also be possible to involve.

EDIT: The journal The Cryosphere is a good and successful  example of a new journal (Open Access). It became ISI listed after a very short time because it received the support of the community in terms of good papers to establish it. It is now a key publication in the field. (and I am not paid to say this!)


How good do master's rec letters have to be?

Unless you want an MS for its own sake, in the US you should probably just apply to a few doctoral programs. Most applicants here hold only a BS/BA degree. Few programs require significant research in that case. It also gives you the opportunity to earn a stipend as a TA to support your studies, including paying for your tuition.
One problem with taking a break and then getting an MS is that you still need to pass comprehensive exams in most programs. The MS may prepare you well for that or not. Starting a doctoral program after a BS leads you through the required advanced courses to enable that. In many such programs you can earn a masters along the way for little effort.
In the US, letters of recommendation are quite important as they give information beyond the formal record, including making it possible for an admissions committee to make a fairly accurate prediction of a candidates likelihood of success. Without good letters, admission is difficult for any graduate degree program, but especially if it is research focused.
The implication is that you should stay in contact with your professors if you need to take a break. Visiting once a year to "catch up" with professors who have worked with you is a good plan. Keep them up to date on what you've been doing and your goal evolution.
Some of the "top 40" programs are State Universities with relatively large programs. Don't restrict your search too narrowly. There is a lot of competition and any of the R1 universities will likely do a good job.


Professor wants to expropriate submitted code for commercial use

You seem to be asking about two different things: (a) is it OK to assign coding assignments based on the instructor's real-world experience, and where the instructor isn't sure how to solve it himself? (b) is it OK for the instructor to use your solution/your code in his company, without your permission?  You should keep them separate, as they're likely to have very different answers.

Is it OK to assign this sort of assignment?  Yes, absolutely!  It sounds like it could potentially be a great project, if designed well.  A course project that's based on a real-world problem?  Sounds wonderful.  The instructor isn't sure what the best way to solve it will be?  Open-ended projects can be great, too, as a way to boost creativity.

Of course, it's the instructors responsibility to design the course project so it will inspire learning and meet the pedagogical goals of the course, but nothing about "based on the instructor's real-world experience" or "the instructor doesn't know how to solve it himself" is incompatible with that (and those could even be beneficial features).  So, your negative reaction to that aspect is unjustified.

Is it OK for the instructor to use your solution in his company, without your permission? Almost certainly not.  There are both ethical and legal concerns.

From an ethical standpoint, this seems like a potential abuse of the instructor's position of power.

From a legal standpoint, this could run into intellectual property issues for the company.  At the university I am most familiar with, the university has an official policy on copyright.  It explicitly states that student coursework remains the student's property: the student retains copyright in essays, code, etc. that they write in their course.

So, look into your university's official policy.  If the university has a similar policy, then the situation is very clear: this is a great assignment, and the instructor has every right to offer this assignment -- but he cannot use your code at his company (without a written signed agreement from you transferring copyright, and it would of course be highly improper for him to expect/demand this as a requirement of the course).

Also, depending upon laws in your jurisdiction, it's possible that this abuse of the instructor's position of power could itself pose legal issues.

In his enthusiasm, your instructor might not have realized these issues or thought through them very carefully.  Don't assume bad faith -- this could well be a situation where the instructor saw a great opportunity for learning, and failed to recognize the issues with this aspect of the assignment.  I'd suggest you start by talking to the instructor in person and very respectfully having a discussion about this: you could start by mentioning that you are not comfortable with him using your code for anything beyond the course, and his statement that he would use solutions makes you uncomfortable.  Have a meeting in person -- an email is too easy to misconstrue.  Assume good faith, share your concerns, and see what he has to say.  It's possible that this might be a misunderstanding or that he might be entirely receptive to your concerns.


Chances of getting a postdoc with low number of papers

In the UK and Scandinavia at least, provided you show that those papers are in review you should be ok except for very highly competitive labs. The 'well-known professors' are most likely to be running those kinds of labs BUT you may well still get in if you are experienced in a topic or technique they are looking for.

I honestly doubt the professors are lying or trying to brush you off; nearly all postdoc positions only come up when project funding comes through. Bear in mind that the professors are probably answering several such emails a week so they do indeed keep a 'stock' reply and that is fair enough.

So don't wait for your publications to happen but look for advertised positions in your specialism and/or with your skillset named. Good websites are jobs.ac.uk and Euraxess.

Side note: I am aware that candidates from not-USA-or-Europe often get a harder time which is regrettable. My answer stands but I wanted to acknowledge that you do have it tough.


How to encourage students to attend and participate in class?

Learning tools are substitute goods - don't be afraid if students choose their favourite tools: This is an excellent question, since it raises a common issue with teaching, and it is an issue where some academics (not referring to you) take an irrational and overly defensive view.  Here are a few points that I think are worth bearing in mind in these situations:

The goal of any university course is to give students the best possible assistance to learn the skills you are seeking to impart in the course.  The lectures and other materials available to students are generally "substitute goods" in economic parlance, meaning that use of one tool assists in learning the course content and thus diminishes the demand for the other substitute tools.  Thus, if the digital tools you are referring to are of high quality, they may be very helpful for students to learn the course content, and thereby diminish demand for your lectures.
Students appreciate having a range of teaching tools they can choose from.  When I was a student, the best lecturers I had were the ones that gave us lecture notes, practice problems, and other teaching resources of such clarity and high-quality that attendance at their lectures became virtually unnecessary.  It was a pleasure to be able to teach yourself the material directly from lecture notes, etc., without the assistance of the lecturer.  In some cases this meant that you learned some part of the course so easily that you could skip the lectures and still feel that you had good command of the subject.
If lecture attendance is dwindling due to the provision of useful outside tools, this can be seen as a signal that the quality of those outside tools is relatively high.  The fact that you are offering outside learning tools that the students perceive to be sufficient for their own learning should be seen as a good thing.  Of course, you should want all the learning tools you are providing to be the best quality they can be, so if your lectures seem to be lagging behind in demand, you should certainly do what you can to improve them.  Since you already have good outside resources, the use of a flipped classroom would be one obvious thing you could try.  Another thing to try would be increasing student questions and other interactions that cannot be substituted by digital materials (e.g., recorded lectures).
Unfortunately, some academics take it personally when students don't attend their lectures, and so they try to encourage attendance by removing outside learning tools that compete with their lectures.  (I am not suggesting that you are thinking about doing this, but I want to raise it anyway, since this is something I have seen other lecturers do in university courses.)  This creates a kind of "race to the bottom" where a lecturer tries to increase demand for one set of tools by diminishing substitute tools.  In the worst-case scenario, a lecturer who gives bad lectures ends up removing other material that could have substituted for those bad lectures, and the students end up with no good learning tool for the course.  In my view, this is a petulant and irrational strategy, which represents a failure to appreciate that the goal of the course is student learning, not affirmation of the teacher's ego.  So whatever you do, I would encourage you not to remove the digital tools that seem to be working successfully.


Making myself an attractive candidate for a research lab (no prior lab experience)

I'd like some suggestions on how to improve one's usefulness in the lab without actually working in the lab.

This might not be possible, but I would love to be wrong.

Experience in the (chemistry) lab is about using your hands to perform specific and often complex tasks with dexterity and proficiency. Many of these tasks also have associated hazards, which through experience can be avoided or minimized.

I am afraid that if you are interested in pursuing a career in chemistry or another lab science, you will need to get some experience in the lab. The easiest way would be take a few courses. Given your interests, you should at minimum take and organic lab course and a microbiology lab course.

Let's take as an example a simple distillation, a common organic lab technique. No amount of reading about the technique prepares you for the many things that could go wrong. At least one of these has potentially disastrous consequences. If you take a course where you do several (as a good introductory organic chemistry lab should), you have the opportunity to learn how to do distillations in the presence of another person who will catch your mistakes. At the graduate/professional level, you are supposed to know what the common mistakes are and avoid them entirely.

Things that could negatively impact a simple distillation:

The joints are not sealed and the vaporized liquid escapes.
No means of encouraging nucleation during boiling is used and the liquid in the still pot bumps.
Your still pot has a star fracture and shatters when heated.
Your variable transformer blows a fuse, and you have no heat.
Your variable transformer is set too high and you superheat your liquid (and it bumps) and apparatus.
Your thermometer is not placed low enough into the neck of the 3-way adapter and you do not record accurate temperatures.
You forget to turn on the water in your condenser and you collect no distillate.
You (against someone's better judgement) try to distil something that thermally decomposes and the apparatus catches fire, explodes, or something otherwise disastrous occurs. At the very least you do not get the distillate you though you were getting.
You distil to dryness, and the apparatus superheats.
You distil an ether to dryness and the residual peroxides explode.
You start to take apart your apparatus before it has cooled (hot glass looks identical to cold glass and has a high heat capacity so it does not radiate a lot of heat) and give yourself second degree burns.
You fill your still pot more than halfway, which prevents there from being enough room to establish a good liquid-vapor equilibrium, causing the liquid to superheat and bump.
You get the idea.

I don't want to be a total downer. If you had told me that you were interested in theoretical or computational chemistry, I would have told you to read up on analytical and physical chemistry and apply to a program in theoretical and computational chemistry. You do very little wet-lab work in those subfields of chemistry. However, since food science involves a lot of wet-lab work, you need to have some preliminary hands-on experience.


Is it allowed to submit accepted and published journal articles in Elsevier, to arXiv?

You can easily find the answer following the author guidelines of Elsevier, starting from the link you provided. On https://www.elsevier.com/about/company-information/policies/sharing they explicitly state:

  Authors can update their preprints on arXiv or RePEc with their accepted manuscript .


Before interviewing at a grad school, how much background research should I do into its research groups?

My experience interviewing was in the US, so it might or might not apply to you in Austria.

None of the schools where I interviewed expected me to know the details of their latest work. I read a few of their recent papers so I had some idea what the groups did and I could have an intelligent conversation with professors and other students. It seemed to go well.

Good luck!


How are department budgets funded and disbursed at undergraduate institutions?

(not US, but Europe)

Some money comes from the government, some comes from students, some comes from research grants (overhead, quite a big part of a grant, sometimes).

Overhead costs are department specific, that is, overhead at the physics department might be more than at the social science department.

Some of the money is to be distributed according to needs, but a lot will be up to discussions among the different boards along the hierarchies.

For purchases, most are done through grants that researchers/faculty obtained, general stuff (paper, pens, ...) is financed through overhead. There are also grants that can be used to buy special equipment exceeding "normal" amounts.

Another part is going to things ranging from cleaning personnel to journal subscriptions. Sometimes, universities have to rent the facilities they are using, some own them (country specific laws apply). This is financed through overhead, which also pays administrative staff.

Your university should have information for researcher/grant applicants, on overhead costs, and what it is used for. This might give you more details (and nightmares).


Do workshop publications hold the same value as conference publications in CS?

No, workshops are generally (at least in my area of CS) of much lower value than full conference proceedings. (Especially when held before a more major conference.) Even though workshop proceedings are published, they are not always considered archival, and usually are stepping stones to full publications later on. A workshop is a good place to get feedback on ideas that can then be upgraded to a "full" publication in the future.

But, I'd strongly advise you to attend the workshop in order to meet and interact with people in the area! You can get great feedback for taking a weak conference submission and making it a strong accept.


What is the difference between Masters in Engineering Management vs. MBA?

I haven't heard much of an MEM before, but it sounds like a quirky, industry-specific degree, which I think is the key here. An MBA is more established, general in scope, and applicable for management careers outside engineering. So recruiters would know what an MBA entails without needing to ask. Not so much with an MEM.

To me, the question isn't which to get, but whether you should be getting a management degree or not. The traditional advice for getting an MBA is don't, if you're a fresh grad or new worker/hire. From your question, it sounds like you fall into one of these categories.

Typically, the merits of having an MBA for job recruitment are vertical, not horizontal. It's key to moving up within a company, once you're in one, but it doesn't improve your chances of getting hired off the job market a great deal.
So the time you should consider getting an MBA is when you've been with a company for a while, and within the company, are ready for a promotion. In some cases, companies would even fund your MBA studies at this point.


How to cite software used to produce data/images?

Some software may have citation requests in their web-pages. The following are a few examples

Matplotlib: Hunter, John D. "Matplotlib: A 2D graphics environment." Computing In Science & Engineering 9.3 (2007): 90-95.
MATLAB: MATLAB <version> and <toolbox>, The MathWorks, Inc., Natick, Massachusetts, United States (<year>).
Origin: Origin (OriginLab, Northampton, MA)

Otherwise, you may adopt the following format:

  Software [version], Company, Year, Link, Last visited: Date.

Also bear it mind that you may not need to cite the software used for image production unless the software itself produces some data used for scientific inference in your work (as mentioned by @DSVA's comments).


Difficult adviser and personal improvements: How do I move forward?

First of all, even good writers find academic writing somewhat difficult to learn. But it can be learned. Judging from your post, you can write coherently, and don't struggle with spelling or grammar. So I don't think it would be that difficult to learn the skill.

I'd like to recommend a book. It's entertaining, and gives really good insight into what makes academic writing different from other forms of writing. I think you will find it very helpful.

Here's the book: Scientific Writing 2.0: A Reader and Writer's Guide [ISBN: 978-981-4458-75-7 (ebook)]. If you buy it direct from the publisher, you can get it DRM-free, but you have to download each chapter separately. (On Linux, you can use pdfjoin to join the chapters into one big book.) Or you can buy it in one piece from other places, but with DRM.

Another thing I suggest is that when you read other people's academic writing, pay attention to how easy you find it to understand what the author is saying. When you find an article that is especially clear and easy to read, try to figure out what about the writing works. Likewise, when you find an article difficult to understand, identify the writing problems, and think about how the author could have made it better.

I'm a PhD student myself, and one thing I found helpful for my first few papers was to write a rough draft in an informal, conversational style, as if I were writing an email to my advisor. Then I would go back through the paper and make it a bit more formal. It's a lot easier to make clear writing more formal, than to make formal writing more clear!

Finally,  point to consider: when your advisor complained about your academic writing skills, are you sure that he or she was really talking about writing, as opposed to how you structure the article, or whether or not you incorporate suggestions, or even the methodology you used in your research? The reason that I ask is that, again based on your post, you appear to have reasonable ability for non-academic writing. Advisors can have students who are less than fluent in English, or have poor grammar. Getting that worked up because a student is struggling a bit to learn academic writing this early in the game seems a little surprising.


What to do when you think a student is incapable of using certain vocabulary?

Thesauri are a thing.  The internet is a thing.  As such, everyone is capable of using all vocabulary and dialects at all times. They're also capable of changing their minds about how they express themselves at any moment.  One could write a serious mathematics paper entirely in Middle English (modulo terminology a bit, which will be hard to adapt, unless the mathematics is historically appropriate to the time) if they were so inclined.

If the words are used correctly in the student's work, then in the absence of actually substantive evidence of plagiarism or academic dishonesty, then there's nothing to do.  At best you can comment on whether the choice of phrasing is suitable for the topic or not, and if it helps or hinders the clarity of the exposition.  That Middle English math paper is fairly unsuitable and inappropriate, and almost certainly unspeakably unclear, unless, say, the assignment was specifically concerned with writing in Middle English (in which case maybe the math is the inappropriate and unclear thing).

Furthermore, academic writing is often a dialect of its own.  In mathematics we often say things like "We will show..." even in single author papers, because that's the history and convention.  It is entirely reasonable that efforts at serious academic writing will not sound like natural conversation, and that anyone familiar with how a person sounds in only one of those will be surprised by how they sound in the other.