Advantages and disadvantages of doing PhD research at a non-academic lab

Throughout graduate school I worked at and was funded by a university-run laboratory that operated somewhat like a government laboratory and was largely funded for applied research. I now work at a UARC (which is similar to an FFRDC).  Given that my graduate school lab was already affiliated with the University, though, my situation is slightly different than yours.

At least in the US, it is relatively hard for non-academic laboratories to find funding for basic research; funding agencies like the NSF have a prejudice toward funding degree-granting institutions.  Therefore, in my experience, much of the flavor of the funding at non-academic laboratories is geared toward applied research.  This might not be a problem, but it can be a challenge to find a deep, Ph.D.-level problem to solve when your sponsors are interested in seeing more concrete results.

In my case, working at an applied research laboratory to fund my graduate degrees was actually somewhat of a benefit.  Due to the reasons I listed above, it was difficult for me to latch onto a deep problem to solve for which there was stable, direct funding.  Therefore, I used my position at the laboratory to basically "pay the bills" (it covered my stipend, tuition remission, &c.).  That gave me the freedom to work on related—but not directly funded—problems that interested me.  This of course had the overhead of essentially working two jobs at once, but it had the added benefit of providing visibility to my "side" research to the sponsors who were funding my "pay the bills" research.  It also paid for my trips to relevant conferences, at which I was able to present both flavors of my research.

Now that I am working at a UARC, I see others here who are also pursuing part-time Ph.D.s.  Most of them seem to have found a similar model to mine: They use their position at the non-academic lab to "pay the bills", and then focus their actual research on a related but independent problem.  If you are able to fund yourself (i.e., if your Ph.D. advisor doesn't have to worry about finding funding for you), then many advisors will be willing to take you on as a student.


How long are typical letters of recommendation for grad school admission?

An LOR is typically one to two pages.  If it was five pages, that would be odd.


Problem-based learning is one approach that fits your description. From wikipedia

  Problem-based learning (PBL) is a student-centered pedagogy in which students learn about a subject through the experience of problem solving. Students learn both thinking strategies and domain knowledge. The goals of PBL are to help the students develop flexible knowledge, effective problem solving skills, self-directed learning, effective collaboration skills and intrinsic motivation. Problem-based learning is a style of active learning.

A related approach is inquiry-based learning, which allows the idea to be used on a much smaller scale than problem-based learning, which, based on what I have read, tends to be rather resource intensive and require vast amounts of planning from the teaching staff.


Is it possible for reviewers to ignore papers?

Let me expand a bit on Thomas comment.

By its very nature, peer review is a guaranteed item of discussion in all academic discussions. Every author has stories to tell about unfair reviews, reviewers that missed the entire point of the article, reviewers that rejected a paper only to publish something similar themselves, and so on. What is much rarer talked about is that the vast, vast majority of rejected papers are simply not good enough! Indeed, this surely also includes a large percentage of those papers that the authors are sure were handled unfairly.

An important point is the following:

  My only argument is that authors believe that their paper is a breakthrough paper and it has a very good contribution.

Clearly, all (ethical) authors believe their paper has merit. Otherwise, one would likely not submit it. It has to be said that the author's own opinion is not a good indicator of the actual qualities of a paper.

  Is it possible that reviewers ignore papers? Maybe because the authors are not known or maybe they did not write the paper well?

Somewhere on this site, I have previously listed reasons why a paper can get rejected, but to be honest I think "the authors are not well-known enough" is very low on this list. The second reason ("the paper is not well-written") is more common, but it should be noted that rejecting a badly-written paper is not unfair. It is the responsibility of the authors to make sure that their paper is graspable. However, again, I suspect the majority of papers are well-understood by the reviewers, and just rejected because the reviewers were of the opinion that the contribution was not substantial enough.

So why do papers sometimes get very short, high-level reviews, even if the reviewers read and understood the papers? One possible explanation is that many reviewers follow the golden rule "spend your time on manuscripts that deserve your attention". In practice, a reviewer has finite time to invest into reviews. When receiving (say) 5 papers for review, two being borderline and three being clear-cut rejects, it is an understandable decision to spend more time scrutinising the papers that still have a chance, and only provide high-level feedback on the ones that the reviewer sees as clearly too weak.

Now on to your questions:

  How can one be sure that their paper is well treated?

The philosophy I try to communicate to my students is to stop worrying about optimizing manuscripts for peer review and start doing the best research they can. I am convinced that the best way to ensure that your papers are treated well is to write good research papers.

  How to write papers that make the reviewers do not throw the paper away.

Make sure that your papers (1) have a clear contribution, which is evident from the abstract and the introduction, (2) are written as clearly as you can, (3) are correct in terms of grammar and spelling (try to have a native-speaker spell-check your manuscripts), and (4) have a compelling and relevant contribution. If Your paper is technically sound but boring as watching grass grow, you are not entitled to complaining that the reviewers did not read the manuscript carefully.


Academic home page with low maintenance burden

tl;dr: Wordpress (installing a Markdown plugin), if you are a techie, Jekyll.

(My website is in Wikidot, I created for my group with Wordpress.

EDIT: Now I use Jekyll; here's why)

See Software for Scientists: Website tools:

For personal homepages, lab notebooks and conference websites.

  WordPress - code  and WordPress - hosting

  Examples:

  https://johncarlosbaez.wordpress.com/
  https://gowers.wordpress.com/
  http://netsci2013.net/wordpress/

  Jekyll

  For writing blogs in Markdown and easily putting them on GitHub
  Tutorial for using LaTeX in it: http://cwoebker.com/posts/latex-math-magic
  Examples:

  Open Lab Notebook in Jekyll
  A homepage

  Wikidot

  e.g http://offtopicarium.wikidot.com/

  Wikispaces

  Simple wikis, very easy to create and manage
  Used as open science notebooks, for instance http://usefulchem.wikispaces.com/

  Site44

  Showing small site by putting files into a Dropbox folder

  GitHub Pages

  Static websites with Git

  Instiki

  Wiki especially for mathematical collaboration
  Examples:

  http://www.azimuthproject.org/
  http://ncatlab.org/

  WorkingWiki

  Wiki especially for mathematical collaboration

  Sphinx

  Great for writing documentation
  Example (in Polish): http://django.carrots.pl/

  Jekade

  Jekyll-like static pages with built-in LaTe support, in Node.JS


Is it acceptable to keep extending medical leave to prolong insurance coverage, when one has no intent of returning?

Assuming that you are in the United States, the ethics of the situation are not clear-cut, because the health care system is such a mess.  It may not be clear to either you or your former advisor who is actually paying for the health care. For example, the school may have outsourced responsibility to a third-party insurance solution, or it might be covered by some unusual provision of the new health law, or the FMLA, or who knows what.  Honestly, I have no idea, and probably you can't find out without detailed interactions with HR, and even they might not be in compliance with laws and regulations and might not even know it.

It's also the case that, while there is a clear conservative ethical solution of "better safe than sorry," it's not actually clear that it is the right thing to do, given the amount of financial and/or medical problems that can be caused by a short period uncovered in the US.  A colleague of mine, for example, who was actually continually covered with a good plan, had problems getting critical medical care for a child because her plan was late in handling paperwork on a year-to-year transition.  On the flip side, I kept using some of my university's medical services for years after I had left, because I asked about it and was told that my alumni status meant it was still OK: it turned out that I wasn't supposed to, but nobody including me knew that.

So it's a pretty mess to sort through.  How should you deal with it?
Let's lay out some principles:

You really don't want to burn bridges.  This means that if you decide that it is important to try to stay on the same plan, then you should make sure that your advisor is OK with it.  Some professors I know would tell you to do it, and some would be uncomfortable.  What you don't want to do is have the professor be uncomfortable and only find out later.
Second, how critical is the difference between the plans?  Are you potentially facing many thousands of dollars in extra cost or being forced to go untreated for your medical conditions?  If the difference is relatively small, then let it go.  If the difference could destroy your health or life, then it's appropriate to try to use the options that are available.

None of this is ethically squeaky clean, unfortunately, and I wish that it were so.  Unfortunately, because health care coverage is so tightly linked to employment in the United States, we have a system that sometimes forces people to choose between problematic options.

In sum: if you can afford to drop down a grade in health care, that's the ethically best choice.  If you can't, make sure your professor is OK with you taking advantage of something that is permissible under the system but ethically questionable.


Only one supervisor but two reference letters required

For the second letter find someone who knows you well enough and has a high enough opinion of your work that they can recommend you without qualification. They need to make a prediction about your future success. Someone recent is better but absent that, an older relationship should work, generally. And someone in academia is better than someone else.
But there is probably no reason to delay your application to do another project. At worst, you could apply in parallel with starting another project as a backup.
Note, however, that my perspective is US, not Germany.


Is it possible for an international medical graduate to take their residency and fellowship training in Singapore?

I cannot find anything about fellowship yet. But, about the residency training,
The Singapore government agency says

Enrolment into Training Programmes

...
Graduands from overseas must secure an offer of employment as a doctor from MOHH or a local healthcare institution before they are eligible to apply. ...

For more details, please contact them directly.


Why there is a lack of transparency in US tenure-track job searches?

There are several factors at work here:

Remember that there are several thousand colleges and universities in the United States. A central database of such jobs would be significantly harder to publicize and organize.
Most universities in the US are private. They are under no such compulsion to post their jobs on any particular web site, unless constrained to do so by the funding sources that are supporting a particular position, or legal requirements to do so. (To my knowledge, there is no such requirement.)
The more deadlines and constraints you build into the cycle, the more pressure you put everyone under—applicants, recommendation writers, support staff, and departmental faculty involved in the search.

So I think there are multiple reasons not to publicize the results of a search, and I think most hiring committees would be reluctant to do so. There could be a better job done of announcing searches, certainly, and that would make things easier (but again, the places that currently advertise would likely complain about losing their business to a central source!).


How to avoid theft of potentially patentable IP when trying to obtain a Ph.D?

Let me describe fairly typical practice at reputable US universities. When someone has a patentable idea, the university itself will take over the patent process, paying lawyers and fees. The university will probably be the patent holder of record, but will make arrangements with the actual creator(s) to share any income that results from exploiting the patent.

This can be good or bad, I suppose, but the good part is that the university covers the cost and also provides backup if anyone challenges the patent at any point. This can be very difficult for an individual to do on their own. The bad part is that the patent is probably in the university's name, though that may vary.  Another point is that the university may take it upon itself to find ways to monetize the patent if it is awarded. Again, this can be a large expense for an individual.

But one protection for you, a student with an idea, is that if the university is, indeed, reputable, it won't try to steal your idea or let a faculty member steal it.

But faculty at the (reputable) institutions that do a lot of patentable research normally require this (or a similar) process as part of the contract with the faculty member. Such agreements might also be necessary for a student to participate in such work. And there is usually an office, full of lawyers, dedicated to shepherding such work. So a further expectation is that the university is not only reputable, but also large enough to support that office.

And the sharing arrangement may be standardized or, possibly, negotiated, so long as costs can be expected to be covered.

The situation and the rules will also probably vary by a lot in other countries.

For completeness, I'll note that large companies doing important research also tend to have (and require) some similar arrangements with their own researchers.


CV for Ph.D. Applications: how long is too long?

You should list all relevant experience in your C.V. and application. Two pages is a rough guideline for the typical master's or Ph.D. candidate coming directly out of a university with limited research experience. This does not describe your situation. So if you need more than two pages, it's certainly appropriate to go over that limit. Where I would try to save some space is in the presentations and posters section—perhaps you could list invited talks instead of all your talks.


How do admissions committees evaluate coursework?

This is more of a general answer.

Graduate-level coursework should carry additional weight in a graduate school application, because it normally suggests that you are capable of doing work at a higher level than the standard undergraduate curriculum. However, it should be pointed out that more weight will be given to a full graduate-level course than a "shared" course that regularly offers both undergraduate and graduate enrollment.

The primary red flag would be poor performance in one or more "core" courses in your discipline, while encouraging signs are taking more or harder classes and doing well in those.

As for the relative importance of this in an application, I'd put coursework in general somewhat behind the letters of recommendation and research experience. However, this is something that may vary from school to school, and even department to department.


How I add a co-author to my Google Scholar profile?

The recipe is this:

Sign In to Google Scholar.
Click on My Citations.
Type your co-author name in the search box provided (top right).
You will get a list of authors that match the search. Click on the "Add co-author" button on the right of the correct person.

If your author is not found, you will get a failed search.

If you click on the wrong person, you can remove them with the edit button at the top of your co-authors list.


submitting two papers (the second depends on the first) simultaneously to the same journal?

The problem is the part of "depends on each other" - if they are separate works, they should stand on their own, as they are going to be reviewed (and potentially read/published) separately. If one cannot stand without the other that's a pretty easy reject for each paper.

Now, it's perfectly acceptable to have two papers that build upon each other. I think I've personally seen a maximum of 3 papers, which end-to-end build upon each other, and were all presented at the same conference.

The key is that each paper must be worthy in its own right, and you must frame each acceptably. I'll use an example from what I witnessed working:

Paper 1: Establish a method fully described in Paper 1 to decide if a person is thinking of Object A or Object B. Mostly theoretical, describing machine learning algorithms and with only a small sample of data to establish if it worked.

Paper 2: Extend method described in 1 to an experiment with human participants, in two experiments which used different approaches of applying the method and tested on a good sized sample of participants. Starts to show potential practical applications of this method, and also highlights issues of accuracy, confusion, how to design objects that are more easily discriminated, etc.

Paper 3: Use methods from Paper 1 and lessons learned in Paper 2 and apply them to a live video game controller scheme, and report the findings on how it worked and what participants thought of the system, which was interesting because the system wasn't all that accurate and it made the games harder.

Each paper had their own unique contributions, and other than a similar intro, listening to all three talks was fascinating, and each paper was it's own accomplishment. If any of the three papers were rejected, the others would still have been appropriate for publication, and you didn't really need to read them in order or all of them to appreciate each one.

So, in the end it is fine if you submit papers that are improved by each other, and which are intimately linked, and even which are better together but which have a different focus and are better written up separately. But if both papers are inextricably linked and truly, strongly depend on each other, that is grounds for rejection of both of them (at least in fields I'm familiar with). This could vary by field, of course.

Ideally, you could make each one sufficiently self-contained as to stand on it's own merits, and still reference each other, making it clear how the papers are distinct and the focus and/or experiment is different. If that isn't possible, I don't know how approaching the editor would help as I haven't seen such a situation, so I'll have to leave it to someone else to advise about that.


If the paper has been already accepted, I am not sure that you are even allowed to add co-authors at this stage. So, the only option that you have is to mention his/her contribution in the acknowledgment (e.g., "I am grateful to XYZ for his/her help on data analysis"). Anyway, if I understood you correctly, the help was limited to 3 hours consultation. For such contribution a person usually will not expect to be part of the paper (unless you promised this explicitly).


How can I efficiently update a literature review (that got outdated due to being rejected three times)?

I recommend that you find another co-author who is willing and able to spend the time that you cannot. An good candidate may be a supervisee (PhD student, postdoc) who needs to get more familiar with the topic anyway. A fresh view may also help to address possible problems with the paper.


A quote that one has to be rich to engage in science?

I am not sure the quote actually exists. In Democracy in America, de Tocqueville posits a scenario where the absence of the wealthy would stifle science:

  It is possible to conceive a people not subdivided into any castes or scale of ranks, among whom the law, recognizing no privileges, should divide inherited property into equal shares, but which at the same time should be without knowledge and without freedom. Nor is this an empty hypothesis: a despot may find that it is his interest to render his subjects equal and to leave them ignorant, in order more easily to keep them slaves. Not only would a democratic people of this kind show neither aptitude nor taste for science, literature, or art, but it would probably never arrive at the possession of them. The law of descent would of itself provide for the destruction of large fortunes at each succeeding generation, and no new fortunes would be acquired. The poor man, without either knowledge or freedom, would not so much as conceive the idea of raising himself to wealth; and the rich man would allow himself to be degraded to poverty, without a notion of self-defense. Between these two members of the community complete and invincible equality would soon be established. No one would then have time or taste to devote himself to the pursuits or pleasures of the intellect, but all men would remain paralyzed in a state of common ignorance and equal servitude.

(Source: http://xroads.virginia.edu/~hyper/DETOC/ch1_09.htm)

However, he immediately goes on to dismiss this argument. There might be some more concrete examples regarding farms/farmers in the book, so you can try to take a look, but it does not seem too likely (or, as often happens, the popular magazine took the quote out of context).


What are the differences between a cover letter and an application letter?

Good question, and has been something that I have been thinking about also.

Digging around, I found a few articles that may be of assistance, This eHow article (Even though it is more trained towards work, rather than academia), and thi about.com article.

Both links state that there are subtle differences - specifically, an application latter explains what qualifies you for the position/study, and the cover letter goes into more detail as to what qualifies you and explains your interests in the position/study.

I hope this helps (and best wishes with your application and studies!)


What should I do if I submitted an article to a predatory journal?

If the paper has not yet been accepted for publication, you are free to withdraw the paper from consideration. Depending on the policies of the journal to which you submit the article, you may need to disclose the prior submission, and explain why you withdrew the publication from consideration.

Unfortunately, there's little you can do to stop the publishers of the first journal from doing something unsavory with your article. You will need to exercise vigilance in monitoring the work in this area to ensure that the paper isn't mishandled or worse. Be sure to maintain records of all of the correspondence you have had with the journal—and make sure of all it is documentable—phone calls won't suffice here.

However, if all the journal has is a PDF of your original article, it makes it a lot harder to do anything with it: it is tedious work to convert it into the template that most publishers use without significant effort. Thus, without the original graphics and text files, it will be difficult for them to "transmit" the paper elsewhere.


Co-supervisor comes to the office to help her students, which distracts me

I'm not sure if I would use the word "unprecedented" here - I have definitely had my supervisor come into my office to explain stuff (or just chat), and I have also done the same with my own students. I can't imagine that we are total outliers here.

That said, unless you have a particularly bad relationship to your fellow students and your co-supervisor, is there anything wrong with asking them to discuss in a meeting room (or their office) if these discussion are lengthy and/or happen very frequently? I certainly would not mind taking our discussion elsewhere if other people are bothered.

To directly address your proposals:

  shall I message her

Why not just ask her friendly when they are discussing next time if they would mind moving to a meeting room?

  mention her students

You can, but talking to both involved parties at the same time feels a little less passive-aggressive to me.

  mention the issue to a superior academic or change office.

That sounds like a massive overreaction, especially if you haven't even mentioned anything to her directly so far. Reporting your (co-)supervisor to some higher authority is a nuclear action of sorts, which you should definitely not do without exploring other options first. And even if you report this, I have a seriously hard time seeing anything coming out of it (aside from a pissed co-supervisor, that is).

The more fundamental issue here may be that your expectation of a "productive" workplace may be different from other students in the room. If you go over to Workplace.SE, there are plenty of questions of workers trying to convince their co-workers to hush up - but the fact of the matter remains that a dead-silent, only-strictly-required-talking workspace is simply not the preferred option for many people (I actually find it extremely uncomfortable if I sit in a shared office where nobody ever chats).

The only real practical solution to this problem is either to change office, or get / order noise cancellation headphones.


How to stop spam from ConfDriver of TU Wien?

The "Dexa Conference" was set up at the TU Wien using ConfDriver. The website notes that "In case of difficulties please contact confdriver@ifs.tuwien.ac.at". Maybe you should give that a try.

BTW, ironically one of the workshops was about "Defence against Spam in Electronic Communication".


How to read and take notes on research papers

This probably isn't an ideal solution; but I still find it to be the most effective in the long run:

I simply keep a log of what I read, and I specifically do this using tex. That way, you will have a searchable document for any words that you may be looking for in your notes. You can also use the makeidx package to add an index to your text document, which lets you "tag" sections of your documents with various keywords. I also make sure to cite what I read, even if it is for my own purposes. This is especially useful when you are writing a paper, since most of your references will be ready in bibtex format.

It took me a while to get used to, but I find it very nice to have a well organized research log.

Since requested in the comments, given below is what the log looks like. I don't want it to become a full latex document, but it should be sufficient enough to give you an idea. Note the index markers, which are basically "tags" that don't show up in the text.

\section{Paper #1 Name, Authors, Date, \cite{...}}
My summary of the motivation and findings of the paper, or whatever I find interesting/useful.
May be as short as a few sentences or as long as a page, depending on how relevant it is.
\index{an important word}

\section{Paper #2 Name, Authors, Date, \cite{...}}
Same thing here.. \index{another important word or two}

\section{Paper #3 Name, Authors, Date, \cite{...}}
and so on..

\printindex

Then you can look up your page numbers in the index, which is included at the end of the document. For more information about the package, see CTAN and Wiki.


objective, quantitative measure of student learning

This is impossible today and probably always will be.  "Learning" is too broad for a single metric.  Form a specific hypothesis, then test it using a pre-test and post-test.  Ideally, you should use two groups of students, one of which receives an intervention.  The other group is a control.

You can get free training courses here: https://www.cirtl.net/p/cirtl-programming#Courses (see "Teaching-as-Research")

Do not forget to include qualitative information and feedback from peer faculty.


A "cold" request sent to a faculty member—sent when there is either no announced opening for a position or no established cycle for admissions—is unlikely to generate a response. This is because of the sheer amount of email that German professors can receive, particularly if they run large research groups. (In many cases, the public email address may not be directly handled by the professor but be filtered by an administrative assistant.) In that case, there's not much you can do.

Your best bet is to look for groups that have announcements for open positions and apply to those. In such cases, you may get a response, but even then there is a possibility you might not hear anything back. It's basically saying "no" without sending a rejection email.


Do I own the copyright to my Master's thesis? or does it belong to my university?

In Germany, the student is typically owner of the copyright (including Verwertungsrechte) their thesis.
These theses are parts of exams (Prüfungsleistung). Such work must be solely produced by the student, and the thesis typically also contains a declaration specifying this. This implies that the work is owned by the student.

You can read through the forms you signed and the exam regulations (Prüfungsordnung): if no exclusive transfer of rights is mentioned, they are yours for sure. If an exclusive transfer is mentioned it is probably void according to the source I link below.

Exam regulations forbid that the professor (who's considered a public official person for the exams) or the university accept anything from the student that is not specified by the exam regulations. IP rights are not in that list. The university can and does ask for a certain number of copies of the thesis (in paper and/or electronically), this comes with a license to use these copies, e.g. to put then into their archive and to make them available in the university library (the same kind of license you get when buying a book). However, I have not yet seen an exclusive transfer of rights in that context. AFAIK the Prüfungsordnung can also specify that the thesis has to be published, though I have met that requirement only for PhD theses.

Students are typically not employees at the university. Often the exam rules explicitly forbid that students can be paid/hired by the university for the thesis. Thus, IP rights could only be transferred to the university by an explicit contract. However, contracts saying that "all transferable rights on the thesis go to university otherwise you cannot do your thesis here" are void because they are considered to be established under undue pressure to the student, and are considered acceptance of benefits by a public official (Vorteilsannahme). There seem to be ways of having a valid contract before the exam that transfers the IP to university, but I gather this is rather complicated to get right.
After the exam is finished and the student has  grades and certificates, valid contracts to transfer rights to the university can be negotiated.

Source and highly relevant reading (in German) Helmut Messer: Rechtsgrundsäte zu Diplomarbeiten.


is it possible to complete a PhD in Industrial Engineering without any coursework? (US/Europe)

In Europe it is quite common to do a PhD without course requirements. You will generally have to have a Master's degree though, before you can start. This answer is about the situation in Europe (or at least, the Netherlands).

To do a PhD while working for a company can be possible, if you can find a professor that is willing to supervise you. It will be hard though if you are not in regular contact with the advisor. The most realistic option would be to do research on a joint project with academia and industry. I don't think though that this would be feasible if you work in the US, and the university is in Europe.


What are the most important criteria to consider when hiring postdocs for a research group?

My answer, item by item:

I think that there is a difference if this is yet another postdoc or your only postdoc. But most important, we should pay attention to the ratio postdoc/permanent researchers. If the ratio is low (few postdoc, lot of permanent researchers), you can choose to work with "junior" postdoc (=someone not completely capable for working alone), while if the ratio is high, you need postdoc that are in fact already at the level of an assistant prof.
But at some point I think we must ask ourselves if we always need one more postdoc. I guess this will depend on the field. In theoretical fields, when we hire a postdoc, this is to work with him. In some more practical fields, we tend to hire postdoc to make them working for us. The two cases are different : in the first case we need someone that will have ultimately an academic position, in the latter we need someone for coding, experimenting, etc.
Personally, I am not interested in the letters. I ask for references and I take my phone to know more about the candidate. Letters are always telling that the candidate is great, even if this is not completely true.
I ask the candidate his/her papers, even those unpublished, and I read them. Then I contact some of the other authors to know more about who done what.
Clearly yes. A postdoc is a researcher, I think that the way of working is very different : you can spend a lot of time without being "productive" when you are a postdoc, which is not the case in industry. This can be depressing, so we have to make sure that a postdoc (which has less guidance than a PhD student) can handle that.


Does an admissions committee check if a student retook a class

If the class shows up twice on your transcript, the committee will know you retook it.  But they probably won't care.

If it doesn't, it won't even occur to them to ask.  (At least in my experience.)


What is the best career choice for a social psychology graduate?

In general I would counsel against further study. I have seen many people finish an undergraduate degree, look for a job they like/a job, and when they have no luck go back to study. This has almost always ended badly. In most cases they have no understanding of how a further degree will allow them to get the jobs they are interested in, and are merely spending a lot of money to prolong (or make worse) the problem.

If you are incredibly passionate in an area go for it. However the fact that you are posting this/reading this suggests that you are not.


I would avoid giving food-- especially a full meal-- to a professor, unless you know them very well. This is because you may not know their tastes or dietary requirements; for instance, unwittingly giving them a dish with nuts in if they have a severe allergy is definitely not a good idea.

It's also a bit strange to deliver such a meal to their office. They probably want to go home and eat their dinner there, rather than sit in the office and eat your gift.

While you are understandably grateful for the reference letters, the professor probably just considers this part of their job. If you really want, a nice handwritten card saying thank you would certainly suffice.


how to indicate citations from the same, long document at different pages

When citing a specific page or pages of a longer document (not generally necessary for published journal articles although that may also be mandatory in some fields) one adds the page number to the reference. In the Harvard system one would write "Smith (1969, p. 24)" or "(Smith, 1969, p. 25)". There are as far as I know no hard rules when such references should be made but an author should consider the readers of the work they produce and facilitate finding the information cited as well as possible. In a short article of 10-15 pages this would not be difficult but in longer works one should consider providing pages. The point of references is after all to provide sources for information used in the article and one should not have to read an entire book to find it.

If I understand the second question correctly, citing different pages in a specific document is done as above and the reference in the reference list will be just the document itself; no need to refer to page numbers there. The reference list provides the litterature to find and the in-text referenes will provide information on where in the literature you need to look.


How to motivate speakers to give less specialized talks at a "colloquium?"

One important thing to do is to be more choosey about inviting speakers who you know are capable of presenting to a broad audience.  Some people will never give an accessible talk, no matter what you do.  Others are good at speaking to a broad audience.  Some good ways to find such speakers:

People who do cross-disciplinary work are often really good at this, since they are generally used to speaking to non-specialists (i.e., people who are specialists in the other disciplines that they work with).
Look for people who have recent survey publications which are broadly accessible, or who have had recent articles or other publications in the popular media.
If you go to conferences and workshops, look for people who give accessible talks, even to a specialist audience.  The best speakers will always frame their work accessibly, even when the meat of it is extremely specialized.

Once you have invited a speaker, make the speaker give you a full abstract, as well as a title.  If the abstract is getting too technical, it's a bad sign for the talk.  Send it back with request for revision to attract a broader audience.  This can help people adjust expectations, though you can never prevent a speaker from speaking badly once they've begun.

If you feel brave, you might even explicitly challenge your speakers more in the information that you send them.  My favorite series that I have ever been involved in organizing was the "Seminar on Dangerous Ideas" that I helped create when I was a graduate student, and which ran for about five years.  This seminar was really trying to push people outside the box, and one of the ways we did it was to ask the speakers to address "the five questions",  which included things like "Why should I fear your research?" and "What should I tell my mom about it?"  Many of the best talks that I have ever heard were in this series, because the challenges that we gave were able to create an atmosphere in which academics felt safe to say things they otherwise would not.

You'll also need to work to revive your existing seminar series.  A good way to do that is to line up several speakers in a row who you are certain will have broad appeal and be able to give a good talk.


Why do people publish on arXiv instead of other places?

The major use case of arXiv is for disseminating manuscripts that you also publish in a journal or conference. By posting a preprint on arXiv, people can find your research, build on it, cite it, and give you feedback on it immediately, while at the same time the same work goes through the (sometimes slow) peer review process. Some of these papers will fall out of the peer review pipeline at some point, and only appear on arXiv, but that doesn't necessarily mean that  they are less useful, important, or sound.

To give a specific example, in the last year or so I have been working in an area so new that most of the relevant research is still only available on arXiv.  I expect these papers will eventually appear in journals too, but the slow peer review process means that the latest journal issues do not represent the state of the art for this particular topic. Conferences have a quicker peer review cycle and are more current, but most only publish relatively short papers.

arXiv is also useful for work that is in a format not suited for a conference or journal (e.g. a thesis), or for extended versions of papers that are published somewhere else.

I would caution against rules like "I should not cite materials on arXiv because they are not peer reviewed." Peer review does not guarantee sound, high quality research, nor is the inverse true.  You should critically evaluate each paper, peer reviewed or not, on its individual merits. (Also see this related question on Math Overflow.)


For MathJobs does it matter what you put down for Primary Interest?

When I, as a faculty member, go to MathJobs to evaluate postdoc applications, the first thing I do is to click a link that sorts the applications by research area. That way, I can efficiently go through the applications in my field without having to scroll through the whole database. As far as I can tell, the sorting is done on the basis of the applicant's primary interest. So the answer to your title is yes, your choice of primary interest definitely matters.


How to start writing a literature review?

Since you don't say what field you are in, this may not work for you - but I'll describe how I do a literature review in the biomedical sciences. I've tried to be general, so it could apply to other fields, but if you're not in science at all it might not work for you.

The first step to writing a literature review is defining your topic. What is the key question/ concept you are trying to explain or summarize? This can be difficult if you are really starting from zero on a topic, and will probably need to be refined as you work on your review. But it's important to define this at least in draft form before you start.

The second step is coming up with search terms. Begin by searching your question/ concept on Google Scholar or another large database - if it's a biomedical topic, Cochrane Reviews is a good place to start. I'm not sure if there are similar review databases for other fields. Look for a few key papers in the area, read those, and look at their reference lists. Also, record their 'key terms' (usually below the abstract) - these will help you define search terms. Pull relevant papers from their reference lists and repeat. Once you've gone through ~ 10 papers you will probably have a good sense of the type of key words that are important for your topic. Use these terms to build an improved literature search.

Third, you need to actually do the literature search. Your field probably has a database of journals - use this and your search terms to identify all relevant papers over whatever time frame you are interested. You'll probably need to refine as you go, so you don't get swamped with papers. I prefer to go use a systematic search strategy, even if I'm not doing a systematic review, since this removes some subjectivity. This means going through all results, and reading any papers which have titles or abstracts that suggest they may be relevant to your question.

Fourth, you need to read and take notes. Make sure your notes are indexed by paper, so that you always have the citation of the original paper with whatever facts you note down. I find OneNote is a great way to do this, but there are other tools I'm sure.

For me, once I've read 20 or so papers, I usually have a pretty good idea of what the answer to my question/topic is, and what the nuances are. Then it's just a matter of organizing the notes that I've already taken into a rough outline of what I want to say (remembering to keep label all the facts/opinions with their citations). After that, you're ready to start writing, and it's not too difficult since you've already got a good sense of what to write as well as a rough draft in the form of notes.

One important caveat is that you should always re-write all your notes in your own words as you go through the outline converting it into a paper. This way, if you occasionally just copied the original author's text when taking notes, you won't end up with their words in your paper (which would be plagiarizing).


Should I mention my university name when publishing a paper if I'm tenured teacher but not researcher?

The fact that this research isn't part of your job shouldn't prevent you from giving your employer as your affiliation. A paper by David Pincus about certain weak forms of the axiom of choice in set theory (J. Symbolic Logic 67 (1997) 438-456) lists his affiliations as "Department of Anesthesia, Harvard Medical School, Massachusetts General Hospital, Cambridge City Hospital". I can assure you that none of these anesthesiology departments paid David to prove theorems in set theory; he did this work in his free time.


Do researchers actually read all of the papers they cite?

There are a couple of background issues worth addressing before actually answering your main question.  Also what I say is I think fairly typical for math and theoretical CS; I guess some but not all is similar for other fields.

You’ll get faster at reading papers as you gain experience.  Much, much faster.  I remember in my first couple of years of grad school feeling similarly to you: reading a paper was a big undertaking — it could take weeks of work to get through a particular paper.  Now that’s very rare —  even a pretty thorough read of a paper (e.g. for a review) is typically under a day’s work.  Longer than that comes only occasionally, if I need to really thoroughly understand an unusually substantial and novel paper.  Mostly, it’s just being more familiar with the landscape the papers are working in, and the techniques used.  Also, partly, reading papers is itself a learned skill.

You’ll learn how to read a paper in less than full detail (and when that’s  appropriate).  Again, I remember first reading papers, I would go through them line by line and make sure I absolutely understood every step.  Now, I usually don’t need to, for multiple reasons.  One is that I no longer need all the details in order to follow the general outline, because I understand the big picture better.  Another is that I’m better at judging in advance which details I will or won’t need to know: e.g. if it looks like some proof is a routine calculation, then I’ll skip it, knowing that I can come back to it later if I ever need a similar calculation and have trouble doing it myself.  Another is that I may be able to see in advance (e.g. from the introduction) that some sections will be more relevant to my work than others.  And, of course, I can skip or skim parts that recall background material that I already know.

So, coming back now to answer your main question: The actual proportions will vary greatly, but typically, authors will have read all the cited papers at least in part, but will not have read most of them in full detail.  That said, reading 12–15 papers thoroughly isn’t infeasible by any means.

Looking at the bibliography a recent 2-author paper of mine with about 30 references in the bibliography, they break down very roughly as:

30%: I’ve read these papers/books carefully in their entirety at some point in the past.
40%: I’ve read parts of these papers/books thoroughly (including the parts relevant to what we’re citing them for), and at least skimmed all or most of the rest.
20%: I’ve just dipped into these papers/books for specific results we needed to cite (plus relevant background); I’ve not read most of the rest.
10%: I’ve not looked seriously at these ones at all; my co-author is responsible for the citations to them.

This is I think fairly typical for me; but I also know some authors for whom I suspect those numbers would typically look more like 10-30-40-20, and others for whom they’d be more like 80–20–0–0.


How to deal with alma mater pushing crack science?

Do not intervene.  It won't work, and may damage you.

Political and ecological matters can be highly divisive.  No project has zero impact, so even if everybody agrees about the facts, strong disagreements in the balancing of pros and cons are likely to remain.  Therefore, the most likely outcome of trying to intervene is that you make enemies, without being one step closer to your desired outcome.  It is very unlikely that you will be able to convince students and faculty that they should change their opinion or actions on this.


As in many situations, more novelty creates greater cognitive load, while non-novelty creates essentially no load. A teensy bit of interesting novelty is little cognitive load, but/and can be quite provocative, depending.

Since relatively experienced people have ... experienced many things... few seminar talks would present much that is radically new, even if it is new to novices. So, even if it is not somehow made explicit by the speaker or by the senior members of the audience, 90% or more of any talk will be a recapitulation of known things... Yes, it is understood that this is mostly necessary, to set a common context for discussion, and that there is not any genuine novelty there.

Also, there is a self-referential aspect to the premises of the question. Namely, the people one sees multi-tasking happily are the ones who can do it. Those who prefer mono-tasking will not be seen multi-tasking. So there's a "selection bias", as well.

And, for me, as for many relatively senior people, I/we have seen many things, and even superficially novel aspects of a seminar presentation may be echoes of things we thought about 30 years ago, etc. Not that there's not progress, but that there are questions that have been pending for decades, and preying on our minds, so (hoping that our minds are still working well) it is not burdensome to hear contemporary progress, but, rather, a happy event. But, in contrast, novices of course have no reference to related technicalities they reflected upon 30 years ago, etc.

And, apart from a greater accumulated experience of ideas and facts, I imagine that a vastly greater experience of coping with novelty and confusion gives a great advantage. E.g., if a smart kid has never in their life before been seriously confused, it is a disturbing experience. And this is a serious issue for very-smart kids in most environments. Similarly for very-smart kids in most undergrad environments. Even up to a point in graduate programs... but/and all the worse to soooo belatedly (after establishing habits that cannot accommodate for this) discover that high-level science (etc.) involves a constant rain of confusion and exceeding-parameters. (For me, this is entertaining, yes, but for those who think that people can control/understand everything easily, and not be confused, it is often deeply disquieting, I gather.)

Practice makes perfect.


How to distribute credit in this situation?

As noted in the comments, it would be best if Alice and Bob didn't try to get either of their names on the object. That smacks of both egotism and insecurity, and is a recipe more designed to create bitterness than scientific progress.

Instead, this type of complexity is exactly what related work sections are for, in which you can say something like:

  Homogeoisopolymorpholisms were first identified in [1,2], then generalized in [3].

and let credit be distributed over time by citation and by ongoing work.  Alice and Bob, as current leaders in this subfield, are in a good position to set a descriptive name, and if they do so and insist that others use it rather than using people's names, then they are likely to have a strong influence on the name that does get adopted.

In contrast, fighting over which person's names are on the object seems likely to damage what appears to be a productive collaboration, and to prevent Alice and Bob from publishing a future set of high impact papers together.


How can we differentiate a "completed working paper" from "incomplete working paper"?

In practice it is very hard to determine when a paper is done. So there is no easy answer other than read the paper, and make up your own mind whether you consider it complete.


Contributing to the cause of biology (beyond research)

Wikipedia has a dedicated portal called Biotechnology, which has some promising content right now. A formal categorization of topics is available, also major keywords have a longer description. The problem is, that many specialized articles are missing right now. They are only available in a dedicated research encyclopedia which is sold as a commercial product for 2000 US$. That means, there is a knowledge gap between the content in Wikipedia and the content in encyclopedias used by researchers. So if somebody has too much time he can try to transfer the knowledge from Academia into the public domain and create some Wikipedia stubs. This would help to bring Open Science forward.


Can I submit a paper under an alias so as to avoid trouble in my country?

This is a highly sensitive topic, see Brian Borchers' comment:

  As a practical matter, even if the publishers of the conference proceeding were willing to keep your identity secret it would probably be relatively easy for officials from your country to determine your identity. It's likely that the publisher will want to avoid having any responsibility for keeping your identity private.

My advice: Talk to people from your university what to do. Ask trusted colleagues (which work on the same topic), university lawyers etc.

This question is too complicated to be handled by you on your own.


How to ask a professor if s/he is interested in being a coauthor on a paper?

Should I just ask him at the next meeting, "Would you be interested in being a coauthor?" Is that the typical way this conversation goes?

In short, yes. "I think you contributed valuable ideas to the paper. Would you like to be a coauthor?" would also do. If he rejects, you can insist, say, two more times for politeness reasons, and if he still rejects, go on without him. But also be prepared for an answer "it is too early to speak about my contribution; I did not do too much yet". The deal is: you would be trying to make him work on a paper (via writing, discussions, or by providing ideas) and would offer him a place among the coauthors commensurate with the contribution.


Licence that converts to GPL after publication but is copyrighted prior to publication

Honestly, I doubt that copyright protection is of any use. The copyright on the code itself does not* extend to data produced using the code. Similarly, the copyright you would hold on the paper submission covers* that particular presentation of the data, but not the data itself. So as long as someone is physically able to view your data, I believe there is no legal avenue to prohibit them from doing their own analysis on their data.

However, for another researcher to take the output of your code and perform their own analysis in an attempt to scoop you, when they know you have your own paper doing the same analysis pending, is ethically very questionable. If it came to light that something like this happened, I think the academic community would strongly frown on it. That's a very strong incentive for any other researcher not to do this, and so I personally wouldn't worry about it.

Besides, if it does happen, the other researcher will have to cite your code anyway so you still get credit. This can actually be a good thing. I would recommend including in your code a notice of the form

  Please cite the following reference if you use the results of this code in a publication:

  [reference to paper or code]

(see this example from my own publication history) If you're worried about someone else abandoning all pretense of ethics and just using your results without citing them, rest assured that it is very difficult to pull that off, and it constitutes academic fraud, which is a career-ender if it's discovered.

And finally, as a practical matter, you have a very large head start on anyone else who might want to publish an analysis of the outcome of your code. Don't underestimate the time and effort it takes for someone else to go through your code in enough detail to learn what it does and figure out how to use it enough to generate original results, and then to write and submit a paper and have it reviewed, typeset, and published.

One more point worth mentioning:

  So I'd be interested also in what is considered good practice when you are in the situation of wanting to share data and code while an article is being peer reviewed, but not wanting to lose your right of first publication.

You don't have a right of first publication. Not legally, anyway. If you want to ensure that you are the first one to have an opportunity to publish a paper based on some result, the standard practice is to keep the result private until you are close to publishing the paper yourself. But keep in mind that "publishing" in this context doesn't have to be peer reviewed. For instance, in physics it's very common to put a paper on arXiv before submitting it to a journal. That establishes the authors' claim to the result before it enters the peer review process.

*informed layperson speculation; see a lawyer for a definitive statement


How do I keep my tenure track job search confidential?

You should tell your references that you would like to keep your application confidential. The problem is that while the job search process is nominally confidential, leaks happen all over the place. For example, people call colleagues asking for informal assessments of applicants. They may not say the person is applying, but when you get a phone call like that, it is pretty obvious. Another example is that sometimes applicants give job talks during a normally scheduled departmental seminar. These are often "advertised" on the web. Again, even if it doesn't say job talk, it can be pretty obvious. At some point you are going to visit the school (if you make it that far) and meet tons of people. Asking/expecting the search committee to keep things quiet is one thing, expecting the entire faculty is another, expecting grad students and post docs is another.


What constitutes a unique research paper?

The following is general guidelines under the assumption that you're looking at this as a computer science project. If you specify the field, I can modify this advice accordingly. For advice about a particular project, you'll have to share the details of your project with someone with experience publishing in CS or whatever field you're working in.

The bar is, roughly, "is this something people would want to read." When you try to present new work to an audience, your job is pretty much to sell the arbiter (be it dissertation adviser, journal referee, or conference organizer) that the work that you did is something people would be interested in reading and using.

The most important question is: have other people used this algorithm, on any data set, before? If the answer is "no" than your work is almost certainly publishable, especially as it sounds like your algorithm preforms comparably well to other algorithms that preform the same or similar task. Your paper should explicitly analyze this and seek to give examples of data sets or contexts in which your algorithm out-preforms known algorithms.

If the answer is "yes," then your work may or may not be publishable. Applying a well-known algorithm like the Gale-Shipley Algorithm or Diijkstra's Algorithm to some random data set isn't generally going to be considered interesting because any researcher who is interested in this data set could do that, and the fact that no one has indicates that people don't currently care to. However, if you use a known algorithm to find an unexpected or surprising result then your project might still be publishable, and the more surprising or interesting the conclusions you can draw are, the more publishable the algorithm is. Here the strength of your paper is going to be determined by the data analysis you do, and how you show that your work is connected to work people are already interested in.

For example, I do a lot of research on social networks, and one hot topic in social network analysis is the detecting of communities inside of a broader social network. For the second approach, if you create a new algorithm for community detection, you can write a paper about your new algorithm comparing it to old algorithms and pointing out data sets where your algorithm is preferred. If you take a known community detection algorithm and use it to show that communities in certain types of graphs have an interesting property, that would be publishable. Additionally, you can somewhat blend these two cases if you were to take a known algorithm and show how it can be used for community detection, while everyone else is using it for some other purpose.


Peer-review in ‘fully peer-review journals’

I think most of this question should be closed as a duplicate, and I would strongly recommend the OP read all of the highly upvoted answers here before commenting further:

I believe I have solved a famous open problem. How do I convince people in the field that I am not a crank?

However perhaps the last part of the question can still be answered:

  How can the author get an honest, unbiased assessment of his work in this situation?

Have your work reviewed by a close colleague who knows you better than the strangers your work goes to through peer review. Ideally, this is what an academic advisor is for, but other people can act as surrogates in some situations. The person should be someone close to you, who is willing to spend some time reviewing your work because of that relationship, but who has the academic abilities, rigor, and qualifications to review your work.

Impress upon this person that you fear your work has some error, because otherwise it is a very important finding, and ask for their assistance in finding the error. Make it clear that you are not looking for praise or affirmation, but want to find the error. Don't tell them how long you have worked on it or say anything else that makes it seem like you have some personal need to feel good about this work: you only want to find the error.

If together you actually find no errors, and given you have followed my advice about finding someone qualified, then, given the importance of your finding, I would expect this person to make every effort to help you with explaining the work to others.


Copying the format of a past journal article as a model

It can  be done in an acceptable way. I would frame such an article as a replication: This is what XX and YY found in India. This is what I know about Kenya. So this is how I expect the findings to be different (or the same) in Kenya. Now lets look.

Beware of plagiarism though. Your article will be close to the original, so make sure you don't (unconciously) copy phrases, and cite every time you use ideas from the original article.


Reply with "Hi" and his first name. If he's using this format to address you, that's a sign that you don't need to be so formal anymore.


When applying to a PhD program whose strength is not my concentration field, should I adjust my statement of purpose to match their area of strength?

It seems you are looking at this from the wrong angle.

You should not (primarily) tune your SOP to whatever increases your chances of acceptance, but to your interests. If you are "a big Macro guy", then what good does it do you to pretend like you are really into Game Theory? Do you want to do your PhD in Game Theory, even if you are not passionate about it (hint: you really shouldn't)?

Further, is it possible that you are actually not applying to the right school, if they have close to no faculty in your speciality? Why do you think this school is a good fit? If this question has a good (academic) answer, this is what you write in the SOP. If the answer is non-academic ("I like their sports team!"), I suggest you should reconsider applying to this school altogether. As you can see from browsing various questions on this site, being in the "wrong" grad school can be a terrible experience.


Using present tense in the evaluation section of a paper

There are several reasons to use present tense.

1) It is present time for the reader. But everyone understands the work was done before.

2) There are several versions of past tense. It simpler not to have to choose among them by putting everything into present tense.

2) English has become the international language of science. For most non-native speakers, present tense is simpler to read. In a prior era when many must-read papers in my field were written in French and German, I was always glad present tense was standard for scientific papers in those languages.


Searching for remotely working industrial Scholarship For university department Students

@moha_alpha-web.net,
Do you mean Remote base work for Student, like an Intern? Right.
If so, I will like to recommend some website to you whereby you can get a different type of remote job;
Like:
Remotely.com,
outreachy.com,
Landingjob.com,
vanhack.com,

I will like to know if you find any help with this.


Since you have tagged it exams, let me offer some hints. I don't know what subject, so I'll assume something like math or CS.

The best way to study for exams is not to have to do it at all. That is to say, make sure that you know the answers to most of the questions likely to come up in an exam long before the date of the exam.

In order to learn something deeply, you need to use repetition and feedback. The repetition means doing exercises, working problems, writing programs, etc. In other fields it might mean writing on topics of the course. The feedback part means that you have to get someone to comment on your work on the exercises. Normally that is the professor grading your work, but you can also use study groups to get feedback from peers (and give it to them as well). For some things you can use some form of automation to get feedback.

But if your main technique is memorization it will likely be ineffective. It will be ineffective for most people, at least. It would be possible to memorize something like the complete text of a calculus book, for example, while actually understanding almost nothing and also not being able to solve anything beyond the easiest problems. Practice - reinforcement - and feedback.

And you also want to give you brain a rest. You aren't a machine that works efficiently as long as it has fuel. Your brain needs periods of rest to actually allow it to synthesize the ideas that you are trying to learn. Pushing it constantly leads to less and less efficient working. Take a nap, or use physical activity to recharge.


Leaving an Area of Specialization (AOS) off of my CV?

This seems like an obvious opportunity to briefly explain yourself on your CV by listing the formal names but then stating what that actually means in parentheses. As an example:

PhD, Some Named Institution (2007-Present)
Areas of Concentration:
 - Science thing 1
 - Science thing 2
 - Crystal healing sounding thing (Chemical Engineering)


Prof's neurological health is declining rapidly. What can I (TA) do?

Let the department head know what you've observed. You can write an anonymous letter if you feel uncomfortable or are worried about burning bridges.

(I've been in this situation, as a student. We - the students in the class - wrote a collective letter to the department head. He was able to arrange extra TA support for the professor for the rest of that semester. He also arranged things so that this professor had other duties in the department going forward, but no more teaching.)


Does publishing in a journal and getting cited constitute a "contribution to knowledge"?

What journal?

In principle, regardless of citations, anything accepted to be published in a journal should be a contribution of knowledge. There are some exceptions to this, like survey papers, but for the most part publications should have a novel contribution.

The citations help measure the impact of the contribution i.e. how relevant or useful it is in the field. But an uncited, published paper should still contribute knowledge.

And, of course, if it was published in a predatory journal, it may not contain a knowledge contribution. Citations make this less likely, unless the citing papers themselves are also in predato journals.


Why were faculty allowed to vote on deciding their own tenure? Presumably the dean didn't sanction the vote, which is why they are denying requests. I don't understand why any university would invite faculty to award themselves tenure. Tenure is a form of promotion, granted by universities, not by faculty.


When should I tell a potential employer about a spousal accommodation?

I don't believe there's a universal right answer for this question. I think it depends on the level of accommodation required, as well as the particulars of your own situation. In general, if you're not being considered for a tenure-track or permanent-level position, there often isn't a lot you can do in terms of getting spousal accommodations, unless you have a very generous employer. In that case, I wouldn't think there's ever a good time to bring up the matter, because there won't be much in the way of possibilities.

For a tenure-track or equivalent position, on the other hand, I think that I would wait at least until the level of having secured an interview before bringing up these issues. Any earlier, and some employers may (perhaps illegally, depending on jurisdiction) wash their hands of the issue by skipping you in making the list of finalists. Once you've gotten the interview, though, that's no longer a concern.

Whether to mention it during or after the interview depends on the ability of the school to do something about it. I would lean towards mentioning at the interview, and particularly so f the school has a "dual-career" office in place. If you wait, then you may spend your time negotiating and having to accept or decline the offer without a firm commitment of help in hand at the time.


How do I deal with an advisor who's biased and doesn't give you time?

As Patricia comments, you should discuss this with your primary advisor.  However, you should try to do this in a diplomatic, non-accusatory way.  It this case, there are a couple of concrete points you can make

You have trouble arranging meetings with your pro tem advisor.
He does not give (or rarely gives?) you satisfactory answers to your questions.

And if there is anything useful he is doing, give him credit for that.

Incidentally, what is he supposed to be doing?  Directing you in some reading?  Giving you advice on your research?  Were there clear expectations laid out in advance?


is freely printing a fundamental right for PhD students?

A fundamental right? No. But charging for printing borders on the ridiculous. – Printing is a necessity, not a right.

Think of it in economic terms. A PhD is a job (there are a few peculiarities, and it’s also part of a student’s education, but nevertheless you ultimately are doing a job, which consists of doing research). If preventing you from printing makes your job harder, the institute has a financial interest in removing that obstacle.

What company charges employees for office supplies? The concept is ludicrous. Why not charge them rent for their cubicles as well? Printing publications, drafts and reports for reading is simply a fundamental part of doing research – unless your institute sponsors ebook readers; and even then your PhD will probably involve filling out forms for HR etc.

If your institute suspects that printing is predominantly used for non job related purposes then that may be a problem that needs addressing (and the same goes if the institute suspects that printing could be reduced without impacting performance – lots of companies have tried paper-free offices but so far I haven’t heard of any resounding success, at least not in science). But charging students for printing is still unacceptable since it obstructs them from doing their jobs.


You need to cite the paper only if you use it or depend on it in your research in some way. However, if you have a section on "Similar Research" then you should probably mention it there. You don't forfeit anything if your work was independent. For purposes of your degree, your supervisor will decide if you have made a proper contribution. For purposes of publishing, the editors and reviewers will decide on priority. Just because you don't cite it doesn't mean that it isn't known.

Independent research on a topic goes on constantly in the real world.

The worst case for you is that if you don't cite it and someone thinks you have plagiarized. But the real world situation is as it is. You can't change that.


what would be the level of novelty of an undergraduate thesis?

Requiring a new contribution to the field seems like an absurd bar to set for undergraduate students.  Not that it's impossible for an undergraduate to do so, but it shouldn't be the minimum standard you expect.

Of course it's possible that computer science is entirely different from my own field (economics), but I find it hard to believe it's that far off.  At the undergraduate level you're learning broad foundational material and techniques; at the master's level you're gaining a deep mastery of the material, possibly even focusing in a more specialized subset.  Then when completing a full PhD the student takes literally years to produce research that expands human knowledge within the field.

Requiring that a student meets PhD-like qualifications in their undergraduate work seems like it's setting them up for frustration, bad methods, or outright failure.  Maybe a truly exceptional student could do it anyway, with the limited time and resources available to them as an undergraduate, and more power to them obviously.  But that shouldn't be the requirement set for graduating.


Is it bad form to use the word exciting in a paper, when discussing other people's results?

An established rule on proper writing demands to "show, don't tell". This does not mean that your results can be left to "speak for themselves", but it suggests that rather than simply claiming that your results are exciting, you should demonstrate and argue why they are. The onus is on your interpretation.

Moreover, the attribute "exciting", just as "interesting", is particularly trite because it is over-used and terribly vague. It begs the question as to what it is that is so exciting.


Two students having separate topics chose to use the same paper format

No.
If using the same format were plagiarism, then almost every article published in a journal is plagiarizing, since they all have the same format. Plagiarism happens when some kind of intellectual idea is involved, and the format used is not an intellectual idea.


How can I politely tell a professor that I'm too busy to do research with him this term?

Just say so directly! He will value your directness and honesty – 'beating around the bush' gets rather tiresome. There's enough of that from management...

  I'm sorry that I don't have time to work with you this term, as I have now started on a research project with Prof A that I am committed to finishing. However, I would still really like to work with you in the future. Since I aim to finish my current project in a few months, around the end of June, would you mind if I contact you again then?


What is the difference between doing a PhD in a small university versus a big reputed university in Germany?

Does the size of a university play any role in someone's PhD research experience in Germany?

First of all, I am assuming that your PhD does not contain any course components, because that’s the norm in Germany. Otherwise, it gets complicated and strongly depends on the PhD programme in question.

When doing a PhD, the vast majority happens within your group. The money and facilities you have available here mostly depend on what funding, facilities, etc. the professor managed to acquire. This might slightly correlate with the power of the university, but the fluctuations between groups are much higher. It makes for more sense to judge the group in this respect.

Aspects of the location that affect your PhD from outside your group will be:

Are there more groups in your general field? If yes, there will be more opportunities to interact with visiting researchers, get quick feedback on certain aspects, have a secondary supervisor who at least somewhat knows what you are doing, etc. It is a small drawback if your group is isolated at your university. (Note that you sometimes have to take neighbouring universities into account here. There are not few cases, where parts of the next university are easier to reach than other parts of the same university.)
Does the university have all the facilities that go beyond what a single group usually has, like a workshop to create special devices, analysing facilities, a supercomputer, etc.
Will you have any teaching duties and if yes, what are they? You probably want to gather some relevant teaching experience, but not spend too much time on this.
Are there enough students for your group to regularly have bachelor and master students doing there thesis? This may give you the opportunity to gather advising experience and benefit from the research output of delegated side projects. Depending on your field, however, this may also be just a huge time sink.
Many if not all universities offer workshops or similar for PhD students about teaching, scientific writing, searching for postdoc jobs, writing grants, etc.

You will get more reliable information on most of the above when you directly ask the professor you are applying to. Moreover, most of this depends on your department or faculty, and not on the university. For example, if you are doing your PhD in computer science, it does not matter whether your university hosts faculties or departments of social sciences, engineering, law, medicine, agriculture, biology, etc. (unless, of course, you are doing research about direct application to those fields). In particular some faculties have run pretty much independently over centuries; they just share a common administrative backbone, location, and name and sometimes some of their researchers collaborate with each other.

At least in Germany, the variability between individual groups within a department is higher that the variability between individual departments and faculties within a university, which in turn is higher than the variability between universities.
The main thing you probably need to consider will be whether your future potential employers are aware of this, but that really depends on what you want to do with your degree and where:
Some people just like easy categorisations like having high- and low-quality universities, even though these are completely oversimplifying things.


Students not engaged at all - despite the efforts of their instructor

I can't really answer the question, which seems to assume (and presents as the major issue) that you get bad feedback which may not be true (the students still have what the other lecturers do to compare, so I wouldn't assume they use your specific feedback to complain about the general situation).
I wonder if you had to do pre-recorded lectures. We do (and record) lectures in real time with students present online, which has the advantage that students can ask specific questions on issues that may affect their understanding of what follows when they arise. (I do realise that this could be problematic with 320 students, however it may work in your favour that only a small number of them appear to be willing to interact.) Surely it makes things somewhat more lively.
One thing you could do is to have online surveys about their satisfaction, how they perceive the course, what they like, and what can be improved. You don't seem to have a clear idea on how students use and perceive your course, and you could do something to improve your knowledge on this.
To some extent online teaching encourages students to hide and not participate and do things last minute. However I'd think something more can be done to encourage interaction. I also have a written questions and comments forum, which is well used (if mostly of course by a minority of active students, but that's how these things always are and were before the age of Covid) on top of being available for online Q&A.


Should I write a rebuttal for all for the reviewers or just the rejecting reviewers?

You should address comments from all the reviewers, but focus on responding to the negative reviews.

Also, it's always good to say something generic like "we thank all four reviewers for their time and thoughtful comments".

If the reviews include questions, definitely respond to those questions. If the reviews include helpful suggestions, acknowledge them and say that you will implement them in the final version.

When responding to the negative reviews, acknowledge what they have said and then explain why you think differently. Avoid sounding combative.


Is it necessary for a letter of recommendation to include the full name of the candidate?

Letters of recommendation are proper documents, and as such they must include candidate's full name at least once. It is often included in the first sentence, e.g.

  It is my pleasure to write this letter of reference in support of Mr Ice Dune's application to the College of Crafts and Wizardry.

The following text can refer to the Candidate by the first name.


How bad is it to accept a competitive Fellowship, then reject it BEFORE April 15

Let your ‘Yes’ be ‘Yes,’ and your ‘No,’ ‘No.’

It may be legal to accept and then reject the fellowship, but it does not make it right (in my opinion). Academia is still very much built on trust and goodwill. People who choose to scheme their way through loopholes in the regulations may benefit in a short term. But people who stand behind their word deserve ongoing respect and make for leaders of very strong academic teams.

Don't do anything to people that you wound not enjoy done to yourself. If you are having second thoughts about this option, leave it and wait for something else which may be going your way.


I'm not comfortable with paying for a practicum that involves doing work for a company, that also pays the school. How to handle this?

I doubt you will have much luck convincing the faculty to change their curriculum, which is subject to institutional vetting on dimensions that even graduate students may never hear about. However, they might be sympathetic enough to your concerns (expressed politely) to grant you the chance to work on a non-corporate problem. If not, expect to grin and bear it -- and do good enough work to put the experience on your resume/CV.


What's behind the teen prodigies inventing things?

I actually disagree with the answer given, and having judged a fair number of high-end science fairs myself (not Intel, granted, but the all-Chicago science fair, which is essentially an Intel qualifier), took something different away from it. I am also close friends with a number of Intel finalists, and have discussed their experiences in depth.

While most of the high schoolers at this level of science fair are extremely intelligent and will eventually become great, independent drivers of research, at this level they typically are not there yet. Their projects, for the most part, are designed by a faculty member or senior grad student/post doc, and the student is guided through the many experimental steps involved until they find something, at which case, because the research was done in a university lab and it is already better than 98% of other science fair projects (which are usually done at home with minimal resources), they typically do very well in science fairs.

Occasionally, one of the students is truly head and shoulders above everyone else, and can operate somewhat autonomously in a lab setting and can ask and answer their own questions - essentially at the level of an older graduate student. But, like a graduate student, they typically still need the oversight of a senior person who "gets" research.

I realize that this response is mostly to the answer given above, and not the the main question, but I felt strongly that the answer needed to be addressed.

As for prodigies:

In the sciences, which require tons of background knowledge to even know what's going on (see: cancer), I have never, ever, heard of a true prodigy who could, for example, be running a 15 person cancer research lab, writing papers, etc. You don't just "understand" cancer the way some people "understand" math, innately.
In math, the story is much different. There are always math prodigies, and they typically get tenure in their early twenties (see: Manjul Bhargava, Charles Fefferman, etc.)
There are, of course, CS "prodigies" who are good at coding and creative enough to think of something that hasn't been done. But this isn't really what you are talking about.

tl;dr: there are no true "prodigies" in science. There are in math, though.


Does a low acceptance rate imply quality?

Low acceptance rate does not necessarily imply quality, but it is correlated.  Crappy conferences often have high acceptance rates because they don't care.  Broad-community high quality conferences often have low acceptance rates because lots of people are trying to get their material into the same conference.

These are just correlations, however, and not causal in nature.  For example, some very good conference have high acceptance rates because they serve a highly specific community; thus they tend to draw high-quality submissions from within that community and few submissions from outside.

Complementarily, I know of at least one conference that games its acceptance rate by artificially regulating the number of papers accepted.  They decide in advance how selective the conference will be, and set the cutoff not in terms of quality but in terms of their judgement of "good conference" acceptance rate.

Finally, having too high a selectivity may be bad for a conference.  A colleague of mine who is an insider at one of the extremely selective CS conference told me that they were worried that their acceptance rate was too low, and that therefore they weren't getting very interesting work any more: a single dubious reviewer was enough to sink a paper, so only conservative and incremental work was making it in.

Thus, acceptance rate is not a very good metric.  It's much better to look at who the people are who go to the conference, what they've been publishing there, and whether you want to be associated with those people and that type of work.


What are unique job titles in academia called?

In the United States, these types of "one-off" titles are typically given as a stage of promotion beyond full professorship.  The typical generic name would be "chaired professor," "distinguished professor," or "titled professor."  This is a rank that many faculty never reach, and typically the highest rank that a professor can achieve in the university as a professor---any further "promotion" is actually a change of position into management, e.g., dean, provost, president.

Such positions often come with a set of funds dedicated to support them, giving the faculty promoted to the position additional freedom of operation.  Often the exact title is set by the person or organization that endows support for the position.  For example, my thesis advisor is the "Panasonic Professor of Electrical Engineering" at MIT, meaning that his particular "one-off" position was endowed by the Panasonic corporation.  Such ties, however, typically mean little besides the name.


I suggest a middle ground. Even granting that the facts are exactly as you stated, it seems to me that you don't know for sure what communication there was between A and B. A may have provided some sample code, intending that B would at least rewrite it. And, unlikely as it seems, B may have studied the code and rewritten it. So this could be a borderline case. Even if A complained to you that they had to "write B's assignment for them", that may have been an exaggeration.

So I suggest that you go to the professor and explain that you think that B had an excessive amount of help. Explain that someone was tutoring B, and may have crossed a line without intending to. I don't think you need to name A even if you are asked. And if the professor does find out who A is, well, professors are people too, and will probably exercise some judgement.

Of course, I'm not excusing what A or B did. I'm just pointing out that you don't know exactly what happened (even if you're sure you have the facts straight), so report what you know, but be careful not to overstate it.


Sources of Income for US Engineering Faculties

In my experience, here are the common sources of additional income for faculty in the US.  Some of this can be done only in the summer, while other things can be done throughout the year.

Summer salary from research grants.  This is paid by the university to the faculty member as salary at the same monthly rate as during the academic year.  This summer salary must have written into the budget of the grant proposal, and it's not possible to simply take arbitrary amounts of cash out of the grant.  This goes to your question about "paying yourself from non-industrial projects."
Summer salary from teaching.  A professor may be paid to teach one or more summer school courses.  The pay rate might vary, but a typical policy is that a faculty member receives one month of summer salary for teaching a course during the summer.  At our institution summer school courses meet for one hour a day, 5 days a week, for 8 weeks (about the same number of hours as meeting for one hour, three days per week, during a 14 week semester.)  We get paid one month of summer salary per course and sometimes have the opportunity to teach two courses.
Consulting income.  Most universities have policies that allow faculty to work for companies outside of the university, typically with a limit on how much time a faculty member can spend on consulting (e.g. no more than 1 day every two weeks, or perhaps 1 day per week during the academic year.)  Consulting rates are negotiated between faculty and their clients and vary widely, but it's not at all uncommon to charge hundreds of dollars per hour.  This can be very lucrative if you can find enough consulting work to keep busy.
Patents and other "intellectual property."  Most universities have policies that allow the faculty member to receive a share of the profits the university earns from the faculty member's inventions.  This typically also applies to profits from software that is protected by licensing and copyright.  Some patents can generate millions of dollars, but most never make any money.
Royalties from books.  This is different from (4) in that most universities allow faculty to receive 100% of the royalties from books that they write.  Research monographs and textbooks for upper division and graduate level courses seldom sell more than a few thousand copies, and the royalties per book are typically less than $5, so it is hard to make any significant income in this way.  Popular textbooks for lower division gen ed courses (Intro Economics, Calculus, etc.) can generate a lot more in royalties.
Starting a company.  A faculty member can use his/her expertise (and perhaps patents from point 4 above) to start a company.  Most startups fail, but a few have become very successful.

In terms of "caps", the most important one is that you can only earn up to three months of summer salary paid from grants and summer teaching.  There's no cap on how much you can earn from consulting, patents, book royalties, or your own company.   There is also typically a limit on how much time you can spend on consulting during the academic year.


Should I let my recommendation letter writers know that I didn't submit my application in the end?

This really depends on the situation. If you only planned to apply to the one school, and ended up not applying, then you've wasted the time of your references, as they did not need to write the letter at all, and could have used the time for other projects.

On the other hand, if this is just one out of some number of schools, then the issue is not as severe. The extra investment to write the "last" letter is not that great. While it is unfortunate that you might not apply, such things happen.

In either event, though, it may be worthwhile to let them know you didn't submit the application—they may ask the school directly if they have contacts, and it wouldn't be useful to find out from the school that you didn't apply, rather than from you personally.


Masters thesis if course credits have expired

Could you challenge the exam in all of these courses? If not, then you might have to retake the courses. To answer your question about ways to work with someone to do research without being enrolled in a university you can approach the department asking if you could be a research assistant. Its not too common so you might have to try multiple times, but my department has one researcher who has never been enrolled at my university.


Usually a PI would have tons of students asking for recommendation letters

...which is why the experienced ones will say no to anyone they don't think they can honestly give a strong recommendation.

  it's still a big favor.

No, it's not.  It's their job.

  How is a great letter composed?

Most successful reference letters follow the same general outline:

A short blurb describing how long the writer has known you, and in what capacity (student in class, independent study, senior thesis, lab slave, coauthor, squash partner, etc.)
A detailed description of why (not just whether) the writer thinks you are a strong candidate for PhD admission, and in particular your potential for independent research in direct, personal, technical, and credible detail.  This part is different for every letter.
Direct comparisons, by name, with other students the writer has worked with and/or recommended in the past.
A short blurb describing the writer's credentials and experience.

  Are the writers really aware of what they have to write?

In general, yes—after all, they read recommendation letters themselves (or they're the wrong people to ask)—but the only way to really be sure is to ask them directly.  If they are anything but confident about their ability to write you a strong and effective letter, ask someone else.

  is the same letter suitable for two PhD programs?

At least within the US, yes, definitely.

  What if they're in different countries?

Ask your references directly whether they understand the cultural expectations in those countries.  But in my experience (in computer science), these differences are shrinking rapidly.

  Then, should a pre-PhD student work in both continents first and then apply?

Nobody can tell you what you "should" do.  There's an obvious tradeoff between breadth and depth in your pre-PhD research experience.  The choice depends on which is more likely to provide evidence of your potential as an independent researcher.

  How to deal with the fact that the PIs may be unknown?

There is no such thing as an unknown PI; everyone has a professional web page, and everyone can use Google.  (Corollary: If someone doesn't have a professional web page, do not under any circumstances ask them for a letter.)  But more junior writers do need to provide more narrative detail in their letters, to make up for being less known and less experienced.

  How to deal with the fact that you need many different PIs writing you many different letters?

What is there to "deal with"?  With rare exceptions, you need three our four PIs to write one letter each, possibly with some very minor customization.  Ask them if they are willing to write you a strong letter.  (Use the word "strong" when you ask.)  If they say yes, give them everything they need to write a strong letter, including time, and then get out of the way.

  How to ask your PI a recommendation letter to "leave" him/her?

Directly—just as if the PI were actually a responsible, mature, adult human being—and far enough in advance that they can plan for your departure.  Anything else would be incredibly disrespectful.

(If they get huffy about the idea that you might pursue opportunities elsewhere, then be very happy you asked—you really don't want to work for them.)


Does a bad paper get rejected very fast and if a paper is under review for long time, should one expect at least reasonable review?

No.  There are tremendous differences across journals.  A "bad" paper can get rejected within hours after submission, or 6 months after submission.  Good papers can also get rejected within the same timeframe.  Some reviewers are very conscientious and complete the reviews quickly, but the paper can still sit with the editor for a long time.  Or, more often than not, you have multiple reviewers on much different time schedules.  Some journals do a very good job of triaging papers, so a rejection of a bad paper may happen quickly.  But you will learn that "bad" is a very subjective viewpoint.  I suggest that you do not associate the quality of the paper (i.e., good vs. bad) with the time under review.


Slides are different beasts from papers and the style should match the medium. For example, we usually enumerate equations in papers, but shall we do it on slides? Clearly, readers can not go back until the presenter himself does it, so why wasting space on numbers in the first place?

Applying it to your example: why would you need [1]? Simply put reference if you feel it's needed. Or symbolise, [Kingma et al 2015].


What if a faculty member is not successful in obtaining the summer salary from a funding agency?

In the US, salaries for tenure-track positions are usually for the academic year; one might get the summer salary thrown in as part of the startup package for the first year or two.  So your academic-year (9-month) salary of $70K would translate to a full-year salary of $70*12/9 = around $93K.  The expectation would be that you would use those first two years to establish a research program, write grant proposals, etc., so as to be able to fend for yourself after that.

While it's true that grants are getting harder to get, remember that single-investigator grants are not your only option: you can also participate in larger multi-PI and collaborative proposals.  For example, you may be able to put together a collaborative proposal with your dissertation advisor while at the same time striking out on your own -- his greater seniority and track record may make it easier to land such a grant.

Finally, I would counsel against spending a lot of time teaching during the summer --- IMHO you'd be better off spending the time moving your research forward (remember why your initial summer salary was included in your startup package).  One reason (not the only one) is that having a solid record of peer-reviewed external funding greatly strengthens your case when you go up for tenure.